diff --git a/.github/codeql/codeql-config.yml b/.github/codeql/codeql-config.yml
index 80657da5dd7..d2a6507d76b 100644
--- a/.github/codeql/codeql-config.yml
+++ b/.github/codeql/codeql-config.yml
@@ -8,6 +8,8 @@ queries:
     uses: ./.github/codeql/queries
 paths:
   - ./extensions/ql-vscode
+  - ./.github/workflows
+  - ./.github/actions
 paths-ignore:
   - '**/node_modules'
   - '**/build'
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
index 45789f2055a..901fb8ab76f 100644
--- a/.github/dependabot.yml
+++ b/.github/dependabot.yml
@@ -38,7 +38,7 @@ updates:
     labels:
       - "Update dependencies"
   - package-ecosystem: docker
-    directory: "extensions/ql-vscode/test/e2e"
+    directory: "extensions/ql-vscode/test/e2e/docker"
     schedule:
       interval: "weekly"
       day: "thursday" # Thursday is arbitrary
diff --git a/.github/workflows/build-storybook.yml b/.github/workflows/build-storybook.yml
new file mode 100644
index 00000000000..5634b5580f6
--- /dev/null
+++ b/.github/workflows/build-storybook.yml
@@ -0,0 +1,57 @@
+name: Build Storybook
+
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+  push:
+    branches:
+      - main
+
+permissions: {}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - uses: actions/setup-node@v5
+        with:
+          node-version-file: extensions/ql-vscode/.nvmrc
+
+      - name: Install dependencies
+        run: |
+          cd extensions/ql-vscode
+          npm ci
+        shell: bash
+
+      - name: Build Storybook
+        run: |
+          cd extensions/ql-vscode
+          npm run build-storybook
+        shell: bash
+
+      - name: Upload to GitHub Pages
+        id: deployment
+        uses: actions/upload-pages-artifact@v4
+        with:
+          path: extensions/ql-vscode/storybook-static
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+      pages: write
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/bump-cli.yml b/.github/workflows/bump-cli.yml
index e5bc038de1b..c79fb04696c 100644
--- a/.github/workflows/bump-cli.yml
+++ b/.github/workflows/bump-cli.yml
@@ -1,25 +1,12 @@
 name: Bump CLI version
 on:
   workflow_dispatch:
-    inputs:
-      option:
-        description: "Option"
-        required: true
-        default: 'replace'
-        type: choice
-        options:
-          - prepend
-          - replace
-      version:
-        description: |
-          The version to prepend to the supported versions file. This should be in the form: `vA.B.C`.
-        required: false
-        type: string
   pull_request:
     branches: [main]
     paths:
       - .github/actions/create-pr/action.yml
       - .github/workflows/bump-cli.yml
+      - extensions/ql-vscode/scripts/bump-supported-cli-versions.ts
   schedule:
   - cron: 0 0 */14 * * # run every 14 days
 
@@ -33,29 +20,32 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
+      - uses: actions/setup-node@v5
         with:
-          fetch-depth: 1
+          node-version-file: extensions/ql-vscode/.nvmrc
+          cache: 'npm'
+          cache-dependency-path: extensions/ql-vscode/package-lock.json
+      - name: Install dependencies
+        working-directory: extensions/ql-vscode
+        run: |
+          npm ci
+        shell: bash
       - name: Bump CLI
-        if: ${{ inputs.option == 'replace' }}
+        working-directory: extensions/ql-vscode
+        id: bump-cli
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          scripts/replace-cli-version.sh
-      - name: Prepend another version
-        if: ${{ inputs.option == 'prepend' }}
-        run: |
-          cat extensions/ql-vscode/supported_cli_versions.json | jq '. |= ["${{ inputs.version }}"] + .' > supported_cli_versions_temp.json
-          mv supported_cli_versions_temp.json extensions/ql-vscode/supported_cli_versions.json
-          echo "LATEST_VERSION=${{ inputs.version }}" >> $GITHUB_ENV
-          echo "PREVIOUS_VERSION=`jq -r '.[1]' extensions/ql-vscode/supported_cli_versions.json`" >> $GITHUB_ENV
+          npx vite-node scripts/bump-supported-cli-versions.ts
+        shell: bash
       - name: Commit, Push and Open a PR
         uses: ./.github/actions/create-pr
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           base-branch: main
           head-branch: github-action/bump-cli
-          commit-message: Bump CLI version from ${{ env.PREVIOUS_VERSION }} to ${{ env.LATEST_VERSION }} for integration tests
-          title: Bump CLI Version to ${{ env.LATEST_VERSION }} for integration tests
+          commit-message: Bump CLI version from ${{ steps.bump-cli.outputs.PREVIOUS_VERSION }} to ${{ steps.bump-cli.outputs.LATEST_VERSION }} for integration tests
+          title: Bump CLI Version to ${{ steps.bump-cli.outputs.LATEST_VERSION }} for integration tests
           body: >
-            Bumps CLI version from ${{ env.PREVIOUS_VERSION }} to ${{ env.LATEST_VERSION }}
+            Bumps CLI version from ${{ steps.bump-cli.outputs.PREVIOUS_VERSION }} to ${{ steps.bump-cli.outputs.LATEST_VERSION }}
diff --git a/.github/workflows/cli-test.yml b/.github/workflows/cli-test.yml
index 5e2463d00e1..c6af5dffe96 100644
--- a/.github/workflows/cli-test.yml
+++ b/.github/workflows/cli-test.yml
@@ -17,6 +17,8 @@ jobs:
   find-nightly:
     name: Find Nightly Release
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     outputs:
       url: ${{ steps.get-url.outputs.nightly-url }}
     steps:
@@ -33,9 +35,11 @@ jobs:
   set-matrix:
     name: Set Matrix for cli-test
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Set the variables
         id: set-variables
         run: echo "cli-versions=$(cat ./extensions/ql-vscode/supported_cli_versions.json | jq -rc)" >> $GITHUB_OUTPUT
@@ -47,6 +51,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     needs: [find-nightly, set-matrix]
     timeout-minutes: 30
+    permissions:
+      contents: read
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
@@ -59,9 +65,9 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -92,7 +98,7 @@ jobs:
           echo "ref=$REF" >> "$GITHUB_OUTPUT"
 
       - name: Checkout QL
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           repository: github/codeql
           ref: ${{ steps.choose-ref.outputs.ref }}
diff --git a/.github/workflows/codeql.yml b/.github/workflows/codeql.yml
index c529a772619..669b1cc46a4 100644
--- a/.github/workflows/codeql.yml
+++ b/.github/workflows/codeql.yml
@@ -11,6 +11,12 @@ on:
 jobs:
   codeql:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        language:
+          - javascript
+          - actions
+      fail-fast: false
 
     permissions:
       contents: read
@@ -19,14 +25,14 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Initialize CodeQL
         uses: github/codeql-action/init@main
         with:
-            languages: javascript
+            languages: ${{ matrix.language }}
             config-file: ./.github/codeql/codeql-config.yml
-            tools: latest
+            tools: nightly
 
       - name: Perform CodeQL Analysis
         uses: github/codeql-action/analyze@main
diff --git a/.github/workflows/dependency-review.yml b/.github/workflows/dependency-review.yml
index 47d874e86a9..57223af28ca 100644
--- a/.github/workflows/dependency-review.yml
+++ b/.github/workflows/dependency-review.yml
@@ -11,6 +11,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout Repository'
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: 'Dependency Review'
         uses: actions/dependency-review-action@v4
diff --git a/.github/workflows/e2e-tests.yml b/.github/workflows/e2e-tests.yml
index 34be85e8fdf..8771b0139d3 100644
--- a/.github/workflows/e2e-tests.yml
+++ b/.github/workflows/e2e-tests.yml
@@ -1,9 +1,14 @@
 name: Run E2E Playwright tests
 on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
+  workflow_dispatch:
+# Temporarily disable running tests until they're fixed
+#   push:
+#     branches: [main]
+#   pull_request:
+#     branches: [main]
+
+permissions:
+  contents: read
 
 jobs:
   e2e-test:
@@ -12,9 +17,9 @@ jobs:
     timeout-minutes: 30
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
diff --git a/.github/workflows/label-issue.yml b/.github/workflows/label-issue.yml
index e4a51b71b13..ac7bbeb704c 100644
--- a/.github/workflows/label-issue.yml
+++ b/.github/workflows/label-issue.yml
@@ -3,6 +3,9 @@ on:
   issues:
     types: [opened]
 
+permissions:
+  issues: write
+
 jobs:
   label:
     name: Label issue
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e36bc9c2b50..b42802099f6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -7,6 +7,9 @@ on:
     branches:
       - main
 
+permissions:
+  contents: read
+
 jobs:
   build:
     name: Build
@@ -16,11 +19,11 @@ jobs:
         os: [ubuntu-latest, windows-latest]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -56,13 +59,16 @@ jobs:
   lint:
     name: Lint
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      security-events: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -79,13 +85,6 @@ jobs:
         run: |
           npm run check-types
 
-      - name: Lint
-        working-directory: extensions/ql-vscode
-        env:
-          NODE_OPTIONS: '--max-old-space-size=4096'
-        run: |
-          npm run lint
-
       - name: Lint Markdown
         working-directory: extensions/ql-vscode
         run: |
@@ -101,16 +100,31 @@ jobs:
         run: |
           npm run find-deadcode
 
+      - name: Lint
+        if: "${{ !cancelled() }}"
+        working-directory: extensions/ql-vscode
+        env:
+          NODE_OPTIONS: '--max-old-space-size=4096'
+        run: |
+          npm run lint-ci
+
+      - name: Upload ESLint results to Code Scanning
+        if: "${{ !cancelled() && !startsWith(github.head_ref, 'dependabot/')}}"
+        uses: github/codeql-action/upload-sarif@main
+        with:
+          sarif_file: extensions/ql-vscode/build/eslint.sarif
+          category: eslint
+
   generated:
     name: Check generated code
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -158,11 +172,11 @@ jobs:
           }
 
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -192,11 +206,11 @@ jobs:
         os: [ubuntu-latest, windows-latest]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -238,7 +252,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
       - name: Set the variable
         id: set-variable
         run: |
@@ -262,9 +276,9 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -283,7 +297,7 @@ jobs:
         shell: bash
 
       - name: Checkout QL
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           repository: github/codeql
           ref: 'codeql-cli/${{ needs.get-latest-cli-version.outputs.cli-version }}'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 4eb21da1117..6c85563dd73 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -12,15 +12,21 @@ on:
     tags:
       - 'v[0-9]+.[0-9]+.[0-9]+*'
 
+permissions:
+  contents: read
+
 jobs:
   build:
     name: Release
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
-      - uses: actions/setup-node@v4
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
 
@@ -124,28 +130,52 @@ jobs:
     needs: build
     environment: publish-vscode-marketplace
     runs-on: ubuntu-latest
-    env:
-      VSCE_TOKEN: ${{ secrets.VSCE_TOKEN }}
+    permissions:
+      contents: read
+      id-token: write
     steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - uses: actions/setup-node@v5
+        with:
+          node-version-file: extensions/ql-vscode/.nvmrc
+
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: vscode-codeql-extension
 
+      - name: Azure User-assigned managed identity login
+        uses: azure/login@a457da9ea143d694b1b9c7c869ebb04ebe844ef5 # v2.3.0
+        with:
+          client-id: ${{ secrets.AZURE_CLIENT_ID }}
+          tenant-id: ${{ secrets.AZURE_TENANT_ID }}
+          allow-no-subscriptions: true
+          enable-AzPSSession: true
+
       - name: Publish to Registry
-        run: |
-          npx @vscode/vsce publish -p $VSCE_TOKEN --packagePath *.vsix
+        run: npx @vscode/vsce publish --azure-credential --packagePath *.vsix
 
   open-vsx-publish:
     name: Publish to Open VSX Registry
     needs: build
     environment: publish-open-vsx
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     env:
       OPEN_VSX_TOKEN: ${{ secrets.OPEN_VSX_TOKEN }}
     steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - uses: actions/setup-node@v5
+        with:
+          node-version-file: extensions/ql-vscode/.nvmrc
+
       - name: Download artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v5
         with:
           name: vscode-codeql-extension
 
diff --git a/.github/workflows/update-node-version.yml b/.github/workflows/update-node-version.yml
index 800a34f38aa..a4b8ef7d0b1 100644
--- a/.github/workflows/update-node-version.yml
+++ b/.github/workflows/update-node-version.yml
@@ -14,8 +14,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
-      - uses: actions/setup-node@v4
+        uses: actions/checkout@v5
+      - uses: actions/setup-node@v5
         with:
           node-version-file: extensions/ql-vscode/.nvmrc
           cache: 'npm'
@@ -34,7 +34,7 @@ jobs:
       - name: Update Node version
         working-directory: extensions/ql-vscode
         run: |
-          npx ts-node scripts/update-node-version.ts
+          npx vite-node scripts/update-node-version.ts
         shell: bash
       - name: Get current Node version
         working-directory: extensions/ql-vscode
diff --git a/.gitignore b/.gitignore
index 4784b9ab81d..332b925b9fc 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,4 +22,7 @@ artifacts/
 
 # E2E Reports
 **/playwright-report/**
-**/test-results/**
\ No newline at end of file
+**/test-results/**
+
+# Storybook artifacts
+**/storybook-static/**
diff --git a/.husky/pre-commit b/.husky/pre-commit
index 5dc94bf999d..abc5efe4456 100755
--- a/.husky/pre-commit
+++ b/.husky/pre-commit
@@ -1,4 +1 @@
-#!/usr/bin/env sh
-. "$(dirname -- "$0")/_/husky.sh"
-
 cd extensions/ql-vscode && npm run format-staged
diff --git a/.husky/pre-push b/.husky/pre-push
index dc6c09fd782..f3f1a028d7e 100755
--- a/.husky/pre-push
+++ b/.husky/pre-push
@@ -1,4 +1 @@
-#!/usr/bin/env sh
-. "$(dirname -- "$0")/_/husky.sh"
-
 cd extensions/ql-vscode && ./scripts/forbid-test-only
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 715aa1a5fd4..879b85bb9ca 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -78,7 +78,7 @@ $ vscode/scripts/code-cli.sh --install-extension dist/vscode-codeql-*.vsix # if
 
 ### Debugging
 
-You can use VS Code to debug the extension without explicitly installing it. Just open this directory as a workspace in VS Code, and hit `F5` to start a debugging session.
+You can use VS Code to debug the extension without explicitly installing it. Just open this repository's root directory as a workspace in VS Code, and hit `F5` to start a debugging session.
 
 ### Storybook
 
diff --git a/README.md b/README.md
index 03b564f5ace..cf7c48dddf9 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,7 @@ The extension is released. You can download it from the [Visual Studio Marketpla
 
 To see what has changed in the last few versions of the extension, see the [Changelog](https://github.com/github/vscode-codeql/blob/main/extensions/ql-vscode/CHANGELOG.md).
 
-[![CI status badge](https://github.com/github/vscode-codeql/workflows/Build%20Extension/badge.svg)](https://github.com/github/vscode-codeql/actions?query=workflow%3A%22Build+Extension%22+branch%3Amain)
+[![CI status badge](https://github.com/github/vscode-codeql/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/github/vscode-codeql/actions?query=workflow%3A%22Build+Extension%22+branch%3Amain)
 [![VS Marketplace badge](https://vsmarketplacebadges.dev/version/github.vscode-codeql.svg)](https://marketplace.visualstudio.com/items?itemName=github.vscode-codeql)
 
 ## Features
diff --git a/docs/releasing.md b/docs/releasing.md
index 8a2441d17bd..2d1495c5dc6 100644
--- a/docs/releasing.md
+++ b/docs/releasing.md
@@ -1,6 +1,5 @@
 # Releasing (write access required)
 
-1. Make sure the needed authentication keys are valid. Most likely the Azure DevOps PAT needs to be regenerated. See below.
 1. Determine the new version number. We default to increasing the patch version number, but make our own judgement about whether a change is big enough to warrant a minor version bump. Common reasons for a minor bump could include:
     - Making substantial new features available to all users. This can include lifting a feature flag.
     - Breakage in compatibility with recent versions of the CLI.
@@ -61,7 +60,7 @@
 
 ## Secrets and authentication for publishing
 
-Repository administrators, will need to manage the authentication keys for publishing to the VS Code marketplace and Open VSX. Each requires an authentication token.
+Repository administrators will need to manage the authentication keys for publishing to the VS Code marketplace and Open VSX. Each requires an authentication token.
 
 To regenerate the Open VSX token:
 
@@ -70,4 +69,4 @@ To regenerate the Open VSX token:
 1. Go to the [Access Tokens](https://open-vsx.org/user-settings/tokens) page and generate a new token.
 1. Update the secret in the `publish-open-vsx` environment in the project settings.
 
-To regenerate the VSCode Marketplace token, please see our internal documentation. Note that Azure DevOps PATs expire every 7 days and must be regenerated.
+Publishing to the VS Code Marketplace is done using a user-assigned managed identity and should not require the token to be manually updated.
diff --git a/docs/test-plan.md b/docs/test-plan.md
index b5441f60b54..90fe3cc2abf 100644
--- a/docs/test-plan.md
+++ b/docs/test-plan.md
@@ -45,7 +45,7 @@ choose to go through some of the Optional Test Cases.
 #### Test case 2: Running a problem query and viewing results
 
 1. Open the [javascript ReDoS query](https://github.com/github/codeql/blob/main/javascript/ql/src/Performance/ReDoS.ql).
-2. Select the `babel/babel` database (or download it if you don't have one already)
+2. Select the `angular-cn/ng-nice` database (or download it if you don't have one already)
 3. Run a local query.
 4. Once the query completes:
    - Check that the result messages are rendered
@@ -490,7 +490,7 @@ This requires running a MRVA query and seeing the results view.
 1. Make changes via config file (ensure JSON schema is helping out)
 1. Close and re-open VS Code (ensure lists are there)
 1. Collapse/expand tree nodes
-1. Create a new list, right click and select "Add repositories with GitHub Code Search". Enter the language 'python' and the query "UserMixin". This should show a rate limiting notification after a while but eventually populate the list with roughly 770 items.
+1. Create a new list, right click and select "Add repositories with GitHub Code Search". Enter the language 'python' and the query "UserMixin". This might result in an HttpError when it is run for the first time. If so, try again. When run for the second time it might show a rate limiting notification after a while or directly populate the list with roughly 900 repositories.
 
 Error cases that trigger an error notification:
 
diff --git a/extensions/ql-vscode/.eslintignore b/extensions/ql-vscode/.eslintignore
deleted file mode 100644
index 73702ce5402..00000000000
--- a/extensions/ql-vscode/.eslintignore
+++ /dev/null
@@ -1,7 +0,0 @@
-.vscode-test/
-node_modules/
-out/
-build/
-
-# Include the Storybook config
-!.storybook
diff --git a/extensions/ql-vscode/.eslintrc.js b/extensions/ql-vscode/.eslintrc.js
deleted file mode 100644
index a6a4d56b694..00000000000
--- a/extensions/ql-vscode/.eslintrc.js
+++ /dev/null
@@ -1,195 +0,0 @@
-const { resolve } = require("path");
-
-const baseConfig = {
-  parser: "@typescript-eslint/parser",
-  parserOptions: {
-    ecmaVersion: 2018,
-    sourceType: "module",
-    project: [
-      resolve(__dirname, "tsconfig.lint.json"),
-      resolve(__dirname, "src/**/tsconfig.json"),
-      resolve(__dirname, "test/**/tsconfig.json"),
-      resolve(__dirname, "gulpfile.ts/tsconfig.json"),
-      resolve(__dirname, "scripts/tsconfig.json"),
-      resolve(__dirname, ".storybook/tsconfig.json"),
-    ],
-  },
-  plugins: ["github", "@typescript-eslint", "etc"],
-  env: {
-    node: true,
-    es6: true,
-  },
-  extends: [
-    "eslint:recommended",
-    "plugin:github/recommended",
-    "plugin:github/typescript",
-    "plugin:jest-dom/recommended",
-    "plugin:prettier/recommended",
-    "plugin:@typescript-eslint/recommended",
-    "plugin:import/recommended",
-    "plugin:import/typescript",
-    "plugin:deprecation/recommended",
-  ],
-  rules: {
-    "@typescript-eslint/await-thenable": "error",
-    "@typescript-eslint/no-unused-vars": [
-      "warn",
-      {
-        vars: "all",
-        args: "none",
-        ignoreRestSiblings: false,
-      },
-    ],
-    "@typescript-eslint/no-explicit-any": "error",
-    "@typescript-eslint/no-floating-promises": ["error", { ignoreVoid: true }],
-    "@typescript-eslint/no-invalid-this": "off",
-    "@typescript-eslint/no-shadow": "off",
-    "prefer-const": ["warn", { destructuring: "all" }],
-    "@typescript-eslint/no-throw-literal": "error",
-    "@typescript-eslint/consistent-type-imports": "error",
-    "import/consistent-type-specifier-style": ["error", "prefer-top-level"],
-    curly: ["error", "all"],
-    "escompat/no-regexp-lookbehind": "off",
-    "etc/no-implicit-any-catch": "error",
-    "filenames/match-regex": "off",
-    "i18n-text/no-en": "off",
-    "no-invalid-this": "off",
-    "no-console": "off",
-    "no-shadow": "off",
-    "github/array-foreach": "off",
-    "github/no-then": "off",
-    "react/jsx-key": ["error", { checkFragmentShorthand: true }],
-    "import/no-cycle": "error",
-    // Never allow extensions in import paths, except for JSON files where they are required.
-    "import/extensions": ["error", "never", { json: "always" }],
-  },
-  settings: {
-    "import/resolver": {
-      typescript: true,
-      node: true,
-    },
-    "import/extensions": [".js", ".jsx", ".ts", ".tsx", ".json"],
-    // vscode and sarif don't exist on-disk, but only provide types.
-    "import/core-modules": ["vscode", "sarif"],
-  },
-};
-
-module.exports = {
-  root: true,
-  ...baseConfig,
-  overrides: [
-    {
-      files: ["src/stories/**/*"],
-      parserOptions: {
-        project: resolve(__dirname, "src/stories/tsconfig.json"),
-      },
-      extends: [
-        ...baseConfig.extends,
-        "plugin:react/recommended",
-        "plugin:react/jsx-runtime",
-        "plugin:react-hooks/recommended",
-        "plugin:storybook/recommended",
-        "plugin:github/react",
-      ],
-      rules: {
-        ...baseConfig.rules,
-      },
-      settings: {
-        react: {
-          version: "detect",
-        },
-      },
-    },
-    {
-      files: ["src/view/**/*"],
-      parserOptions: {
-        project: resolve(__dirname, "src/view/tsconfig.json"),
-      },
-      extends: [
-        ...baseConfig.extends,
-        "plugin:react/recommended",
-        "plugin:react/jsx-runtime",
-        "plugin:react-hooks/recommended",
-        "plugin:github/react",
-      ],
-      rules: {
-        ...baseConfig.rules,
-      },
-      settings: {
-        react: {
-          version: "detect",
-        },
-      },
-    },
-    {
-      files: ["test/vscode-tests/**/*"],
-      parserOptions: {
-        project: resolve(__dirname, "test/tsconfig.json"),
-      },
-      env: {
-        jest: true,
-      },
-      rules: {
-        ...baseConfig.rules,
-        // We want to allow mocking of functions in modules, so we need to allow namespace imports.
-        "import/no-namespace": "off",
-        "@typescript-eslint/ban-types": [
-          "error",
-          {
-            // For a full list of the default banned types, see:
-            // https://github.com/typescript-eslint/typescript-eslint/blob/master/packages/eslint-plugin/docs/rules/ban-types.md
-            extendDefaults: true,
-            types: {
-              // Don't complain about the `Function` type in test files. (Default is `true`.)
-              Function: false,
-            },
-          },
-        ],
-      },
-    },
-    {
-      files: ["test/**/*"],
-      parserOptions: {
-        project: resolve(__dirname, "test/tsconfig.json"),
-      },
-      env: {
-        jest: true,
-      },
-      rules: {
-        "@typescript-eslint/no-explicit-any": "off",
-      },
-    },
-    {
-      files: [
-        ".eslintrc.js",
-        "test/**/jest-runner-vscode.config.js",
-        "test/**/jest-runner-vscode.config.base.js",
-      ],
-      parser: undefined,
-      plugins: ["github"],
-      extends: [
-        "eslint:recommended",
-        "plugin:github/recommended",
-        "plugin:prettier/recommended",
-      ],
-      rules: {
-        "import/no-commonjs": "off",
-        "prefer-template": "off",
-        "filenames/match-regex": "off",
-        "@typescript-eslint/no-var-requires": "off",
-      },
-    },
-    {
-      files: [".storybook/**/*.tsx"],
-      parserOptions: {
-        project: resolve(__dirname, ".storybook/tsconfig.json"),
-      },
-      rules: {
-        ...baseConfig.rules,
-        // Storybook doesn't use the automatic JSX runtime in the addon yet, so we need to allow
-        // `React` to be imported.
-        "import/no-namespace": ["error", { ignore: ["react"] }],
-      },
-    },
-  ],
-};
diff --git a/extensions/ql-vscode/.nvmrc b/extensions/ql-vscode/.nvmrc
index 42e31a00cf2..6edc5a20f3f 100644
--- a/extensions/ql-vscode/.nvmrc
+++ b/extensions/ql-vscode/.nvmrc
@@ -1 +1 @@
-v20.14.0
+v22.17.0
diff --git a/extensions/ql-vscode/.storybook/tsconfig.json b/extensions/ql-vscode/.storybook/tsconfig.json
index c3a8a6ce092..defe43edce5 100644
--- a/extensions/ql-vscode/.storybook/tsconfig.json
+++ b/extensions/ql-vscode/.storybook/tsconfig.json
@@ -2,7 +2,7 @@
   "compilerOptions": {
     "module": "esnext",
     "moduleResolution": "node",
-    "target": "es6",
+    "target": "es2021",
     "outDir": "out",
     "lib": ["ES2021", "dom"],
     "jsx": "react",
diff --git a/extensions/ql-vscode/.vscodeignore b/extensions/ql-vscode/.vscodeignore
index 313df6c9531..4e9f0d9300a 100644
--- a/extensions/ql-vscode/.vscodeignore
+++ b/extensions/ql-vscode/.vscodeignore
@@ -1,17 +1 @@
-.vs/**
-.vscode/**
-.vscode-test/**
-typings/**
-out/test/**
-out/vscode-tests/**
-**/@types/**
-**/*.ts
-test/**
-src/**
 **/*.map
-.gitignore
-gulpfile.js/**
-tsconfig.json
-.prettierrc
-vsc-extension-quickstart.md
-node_modules/**
diff --git a/extensions/ql-vscode/CHANGELOG.md b/extensions/ql-vscode/CHANGELOG.md
index d638979fb89..7db975b552d 100644
--- a/extensions/ql-vscode/CHANGELOG.md
+++ b/extensions/ql-vscode/CHANGELOG.md
@@ -2,6 +2,54 @@
 
 ## [UNRELEASED]
 
+- Remove support for CodeQL CLI versions older than 2.20.7. [#4159](https://github.com/github/vscode-codeql/pull/4159)
+
+## 1.17.5 - 02 October 2025
+
+- Add new command "CodeQL: Trim Overlay Base Cache" that returns a database to the state prior to overlay evaluation, leaving only base predicates and types that may later be referenced during overlay evaluation. [#4082](https://github.com/github/vscode-codeql/pull/4082)
+- Remove support for CodeQL CLI versions older than 2.19.4. [#4108](https://github.com/github/vscode-codeql/pull/4108)
+- Fix a bug where quick evaluation within a `.ql` file could cause spurious errors about processing query metadata. [#4141](https://github.com/github/vscode-codeql/pull/4141)
+
+## 1.17.4 - 10 July 2025
+
+- Fix variant analysis pack creation on some Windows systems [#4068](https://github.com/github/vscode-codeql/pull/4068)
+
+## 1.17.3 - 3 June 2025
+
+- Fix reporting of bad join orders in recursive predicates. [#4019](https://github.com/github/vscode-codeql/pull/4019)
+
+## 1.17.2 - 27 March 2025
+
+- Always authenticate when downloading databases from GitHub, instead of only when in canary mode. [#3941](https://github.com/github/vscode-codeql/pull/3941)
+
+## 1.17.1 - 23 January 2025
+
+- Remove support for CodeQL CLI versions older than 2.18.4. [#3895](https://github.com/github/vscode-codeql/pull/3895)
+- Fix regex in CodeQL TextMate grammar that was silently failing. [#3903](https://github.com/github/vscode-codeql/pull/3903)
+
+## 1.17.0 - 20 December 2024
+
+- Add a palette command that allows importing all databases directly inside of a parent folder. [#3797](https://github.com/github/vscode-codeql/pull/3797)
+- Only use VS Code telemetry settings instead of using `codeQL.telemetry.enableTelemetry` [#3853](https://github.com/github/vscode-codeql/pull/3853)
+- Improve the performance of the results view with large numbers of results. [#3862](https://github.com/github/vscode-codeql/pull/3862)
+
+## 1.16.1 - 6 November 2024
+
+- Support result columns of type `QlBuiltins::BigInt` in quick evaluations. [#3647](https://github.com/github/vscode-codeql/pull/3647)
+- Fix a bug where the CodeQL CLI would be re-downloaded if you switched to a different filesystem (for example Codespaces or a remote SSH host). [#3762](https://github.com/github/vscode-codeql/pull/3762)
+- Clean up old extension-managed CodeQL CLI distributions. [#3763](https://github.com/github/vscode-codeql/pull/3763)
+- Only compare the source and sink of a path when comparing alerts of local queries. [#3772](https://github.com/github/vscode-codeql/pull/3772)
+
+## 1.16.0 - 10 October 2024
+
+- Increase the required version of VS Code to 1.90.0. [#3737](https://github.com/github/vscode-codeql/pull/3737)
+- Fix a bug where some variant analysis results failed to download. [#3750](https://github.com/github/vscode-codeql/pull/3750)
+
+## 1.15.0 - 26 September 2024
+
+- Update results view to display the length of the shortest path for path queries. [#3687](https://github.com/github/vscode-codeql/pull/3687)
+- Remove support for CodeQL CLI versions older than 2.16.6. [#3728](https://github.com/github/vscode-codeql/pull/3728)
+
 ## 1.14.0 - 7 August 2024
 
 - Add Python support to the CodeQL Model Editor. [#3676](https://github.com/github/vscode-codeql/pull/3676)
diff --git a/extensions/ql-vscode/eslint.config.mjs b/extensions/ql-vscode/eslint.config.mjs
new file mode 100644
index 00000000000..e453a1f9838
--- /dev/null
+++ b/extensions/ql-vscode/eslint.config.mjs
@@ -0,0 +1,200 @@
+import { resolve, dirname } from "path";
+import { fileURLToPath } from "url";
+import eslint from "@eslint/js";
+import { globalIgnores } from "eslint/config";
+import github from "eslint-plugin-github";
+import tseslint from "typescript-eslint";
+import eslintPrettierRecommended from 'eslint-plugin-prettier/recommended';
+import * as jestDom from "eslint-plugin-jest-dom";
+import * as typescriptESLintParser from "@typescript-eslint/parser";
+import react from "eslint-plugin-react";
+import reactHooks from "eslint-plugin-react-hooks";
+import storybook from "eslint-plugin-storybook";
+
+const __dirname = dirname(fileURLToPath(import.meta.url));
+
+export default tseslint.config(
+  globalIgnores([
+    ".vscode-test/",
+    "node_modules/",
+    "out/",
+    "build/",
+    "scripts/",
+    "**/jest.config.ts",
+    "**/jest.config.js",
+    "**/jest-runner-vscode.config.js",
+    "**/jest-runner-vscode.config.base.js",
+    ".markdownlint-cli2.cjs",
+    "eslint.config.mjs",
+    "!.storybook",
+  ]),
+  github.getFlatConfigs().recommended,
+  ...github.getFlatConfigs().typescript,
+  tseslint.configs.recommendedTypeChecked,
+  eslint.configs.recommended,
+  tseslint.configs.recommended,
+  jestDom.configs["flat/recommended"],
+  {
+    rules: {
+      "@typescript-eslint/await-thenable": "error",
+      "@typescript-eslint/no-unused-vars": [
+        "warn",
+        {
+          vars: "all",
+          args: "none",
+          ignoreRestSiblings: false,
+        },
+      ],
+      "@typescript-eslint/no-explicit-any": "error",
+      "@typescript-eslint/no-floating-promises": ["error", { ignoreVoid: true }],
+      "@typescript-eslint/no-invalid-this": "off",
+      "@typescript-eslint/no-shadow": "off",
+      "prefer-const": ["warn", { destructuring: "all" }],
+      "@typescript-eslint/only-throw-error": "error",
+      "@typescript-eslint/consistent-type-imports": "error",
+      "import/consistent-type-specifier-style": ["error", "prefer-top-level"],
+      curly: ["error", "all"],
+      "escompat/no-regexp-lookbehind": "off",
+      "filenames/match-regex": "off",
+      "i18n-text/no-en": "off",
+      "no-invalid-this": "off",
+      "no-console": "off",
+      "no-shadow": "off",
+      "github/array-foreach": "off",
+      "github/no-then": "off",
+      // "react/jsx-key": ["error", { checkFragmentShorthand: true }],
+      "import/no-cycle": "error",
+      // Never allow extensions in import paths, except for JSON files where they are required.
+      "import/extensions": ["error", "never", { json: "always" }],
+
+      // Rules disabled during eslint 9 migration
+      "github/filenames-match-regex": "off",
+      "@typescript-eslint/no-unsafe-assignment": "off",
+      "@typescript-eslint/no-unsafe-argument": "off",
+      "@typescript-eslint/no-unsafe-member-access": "off",
+      "@typescript-eslint/no-unsafe-call": "off",
+      "@typescript-eslint/restrict-plus-operands": "off",
+      "@typescript-eslint/unbound-method": "off",
+      "@typescript-eslint/require-await": "off",
+      "@typescript-eslint/no-misused-promises": "off",
+      "@typescript-eslint/no-base-to-string": "off",
+      "@typescript-eslint/no-array-delete": "off",
+    },
+    settings: {
+      "import/parsers": {
+        "@typescript-eslint/parser": [".ts", ".tsx"]
+      },
+      "import/resolver": {
+        typescript: true,
+        node: true,
+      },
+      "import/extensions": [".js", ".jsx", ".ts", ".tsx", ".json"],
+      // vscode and sarif don't exist on-disk, but only provide types.
+      "import/core-modules": ["vscode", "sarif"],
+    },
+    languageOptions: {
+      parser: typescriptESLintParser,
+      parserOptions: {
+        ecmaVersion: 2018,
+        sourceType: "module",
+        projectService: true,
+        tsconfigRootDir: import.meta.dirname,
+        project: resolve(__dirname, "tsconfig.lint.json"),
+      },
+    },
+  },
+  {
+    files: ["src/stories/**/*"],
+    languageOptions: {
+      parserOptions: {
+        project: resolve(__dirname, "src/stories/tsconfig.json"),
+      },
+    },
+    extends: [
+      react.configs.flat.recommended,
+      react.configs.flat['jsx-runtime'],
+      reactHooks.configs['recommended-latest'],
+      storybook.configs['flat/recommended'],
+      github.getFlatConfigs().react,
+    ],
+    settings: {
+      react: {
+        version: "detect",
+      },
+    },
+  },
+  {
+    files: ["src/view/**/*"],
+    languageOptions: {
+      parserOptions: {
+        project: resolve(__dirname, "src/view/tsconfig.json"),
+      },
+    },
+    extends: [
+      react.configs.flat.recommended,
+      react.configs.flat['jsx-runtime'],
+      reactHooks.configs['recommended-latest'],
+      github.getFlatConfigs().react,
+    ],
+    settings: {
+      react: {
+        version: "detect",
+      },
+    },
+  },
+  {
+    files: ["test/vscode-tests/**/*"],
+    languageOptions: {
+      parserOptions: {
+        project: resolve(__dirname, "test/tsconfig.json"),
+      },
+      globals: {
+        jest: true,
+      },
+    },
+    rules: {
+      // We want to allow mocking of functions in modules, so we need to allow namespace imports.
+      "import/no-namespace": "off",
+      "@typescript-eslint/no-unsafe-function-type": "off",
+    },
+  },
+  {
+    files: ["test/**/*"],
+    languageOptions: {
+      parserOptions: {
+        project: resolve(__dirname, "test/tsconfig.json"),
+      },
+      globals: {
+        jest: true,
+      },
+    },
+    rules: {
+      "@typescript-eslint/no-explicit-any": "off",
+
+      // Rules disabled during eslint 9 migration
+      "@typescript-eslint/no-unsafe-assignment": "off",
+      "@typescript-eslint/no-unsafe-member-access": "off",
+      "@typescript-eslint/no-unsafe-call": "off",
+      "@typescript-eslint/unbound-method": "off",
+    },
+  },
+  {
+    files: [".storybook/**/*", "src/stories/**/*"],
+    languageOptions: {
+      parserOptions: {
+        project: resolve(__dirname, ".storybook/tsconfig.json"),
+      },
+    },
+    rules: {
+      // Storybook doesn't use the automatic JSX runtime in the addon yet, so we need to allow
+      // `React` to be imported.
+      "import/no-namespace": ["error", { ignore: ["react"] }],
+
+      // Rules disabled during eslint 9 migration
+      "@typescript-eslint/no-unsafe-argument": "off",
+      "storybook/no-renderer-packages": "off",
+      "storybook/story-exports": "off",
+    },
+  },
+  eslintPrettierRecommended,
+);
diff --git a/extensions/ql-vscode/gulpfile.ts/appInsights.ts b/extensions/ql-vscode/gulpfile.ts/appInsights.ts
index 8e96f286675..86d36aae4fe 100644
--- a/extensions/ql-vscode/gulpfile.ts/appInsights.ts
+++ b/extensions/ql-vscode/gulpfile.ts/appInsights.ts
@@ -1,6 +1,5 @@
 import { src, dest } from "gulp";
-// eslint-disable-next-line @typescript-eslint/no-var-requires,import/no-commonjs
-const replace = require("gulp-replace");
+import replace from "gulp-replace";
 
 /** Inject the application insights key into the telemetry file */
 export function injectAppInsightsKey() {
diff --git a/extensions/ql-vscode/gulpfile.ts/chromium-version.json b/extensions/ql-vscode/gulpfile.ts/chromium-version.json
index e3f8f015fed..e2433ceb1f9 100644
--- a/extensions/ql-vscode/gulpfile.ts/chromium-version.json
+++ b/extensions/ql-vscode/gulpfile.ts/chromium-version.json
@@ -1,4 +1,4 @@
 {
-  "chromiumVersion": "114",
-  "electronVersion": "25.8.0"
+  "chromiumVersion": "122",
+  "electronVersion": "29.4.0"
 }
diff --git a/extensions/ql-vscode/gulpfile.ts/deploy.ts b/extensions/ql-vscode/gulpfile.ts/deploy.ts
index da02b9fd494..7b98600815b 100644
--- a/extensions/ql-vscode/gulpfile.ts/deploy.ts
+++ b/extensions/ql-vscode/gulpfile.ts/deploy.ts
@@ -4,6 +4,7 @@ import {
   mkdirs,
   readdir,
   unlinkSync,
+  rename,
   remove,
   writeFile,
 } from "fs-extra";
@@ -45,6 +46,10 @@ async function copyPackage(
       copyDirectory(resolve(sourcePath, file), resolve(destPath, file)),
     ),
   );
+
+  // The koffi directory needs to be located at the root of the package to ensure
+  // that the koffi package can find its native modules.
+  await rename(resolve(destPath, "out", "koffi"), resolve(destPath, "koffi"));
 }
 
 export async function deployPackage(): Promise<DeployedPackage> {
diff --git a/extensions/ql-vscode/gulpfile.ts/index.ts b/extensions/ql-vscode/gulpfile.ts/index.ts
index d3084561cea..3c20b838c09 100644
--- a/extensions/ql-vscode/gulpfile.ts/index.ts
+++ b/extensions/ql-vscode/gulpfile.ts/index.ts
@@ -5,7 +5,7 @@ import {
   checkTypeScript,
   watchCheckTypeScript,
   cleanOutput,
-  copyWasmFiles,
+  copyModules,
 } from "./typescript";
 import { compileTextMateGrammar } from "./textmate";
 import { packageExtension } from "./package";
@@ -21,7 +21,7 @@ export const buildWithoutPackage = series(
   cleanOutput,
   parallel(
     compileEsbuild,
-    copyWasmFiles,
+    copyModules,
     checkTypeScript,
     compileTextMateGrammar,
     compileViewEsbuild,
@@ -46,7 +46,7 @@ export {
   watchCheckTypeScript,
   watchViewEsbuild,
   compileEsbuild,
-  copyWasmFiles,
+  copyModules,
   checkTypeScript,
   injectAppInsightsKey,
   compileViewEsbuild,
diff --git a/extensions/ql-vscode/gulpfile.ts/package.ts b/extensions/ql-vscode/gulpfile.ts/package.ts
index 4675a130718..9f33938195e 100644
--- a/extensions/ql-vscode/gulpfile.ts/package.ts
+++ b/extensions/ql-vscode/gulpfile.ts/package.ts
@@ -1,6 +1,6 @@
 import { resolve } from "path";
 import { deployPackage } from "./deploy";
-import { spawn } from "child-process-promise";
+import { spawn } from "cross-spawn";
 
 export async function packageExtension(): Promise<void> {
   const deployedPackage = await deployPackage();
@@ -16,16 +16,22 @@ export async function packageExtension(): Promise<void> {
       `${deployedPackage.name}-${deployedPackage.version}.vsix`,
     ),
     "--no-dependencies",
+    "--skip-license",
   ];
   const proc = spawn(resolve(__dirname, "../node_modules/.bin/vsce"), args, {
     cwd: deployedPackage.distPath,
-  });
-  proc.childProcess.stdout!.on("data", (data) => {
-    console.log(data.toString());
-  });
-  proc.childProcess.stderr!.on("data", (data) => {
-    console.error(data.toString());
+    stdio: ["ignore", "inherit", "inherit"],
   });
 
-  await proc;
+  await new Promise((resolve, reject) => {
+    proc.on("error", reject);
+
+    proc.on("close", (code) => {
+      if (code === 0) {
+        resolve(undefined);
+      } else {
+        reject(new Error(`Failed to package extension with code ${code}`));
+      }
+    });
+  });
 }
diff --git a/extensions/ql-vscode/gulpfile.ts/textmate.ts b/extensions/ql-vscode/gulpfile.ts/textmate.ts
index 0b7d2b88fac..a2ed4db083b 100644
--- a/extensions/ql-vscode/gulpfile.ts/textmate.ts
+++ b/extensions/ql-vscode/gulpfile.ts/textmate.ts
@@ -9,6 +9,7 @@ import type {
   Pattern,
   TextmateGrammar,
 } from "./textmate-grammar";
+import { pipeline } from "stream/promises";
 
 /**
  * Replaces all rule references with the match pattern of the referenced rule.
@@ -22,7 +23,6 @@ function replaceReferencesWithStrings(
   replacements: Map<string, string>,
 ): string {
   let result = value;
-  // eslint-disable-next-line no-constant-condition
   while (true) {
     const original = result;
     for (const key of Array.from(replacements.keys())) {
@@ -66,8 +66,7 @@ function getNodeMatchText(rule: Pattern): string {
   } else if (rule.patterns !== undefined) {
     const patterns: string[] = [];
     // For a list of patterns, use the disjunction of those patterns.
-    for (const patternIndex in rule.patterns) {
-      const pattern = rule.patterns[patternIndex];
+    for (const pattern of rule.patterns) {
       if (pattern.include !== null) {
         patterns.push(`(?${pattern.include})`);
       }
@@ -180,11 +179,11 @@ function expandPatternMatchProperties<T>(
     const patterns: string[] = Array.isArray(pattern) ? pattern : [pattern];
     rule[key] = patterns.map((p) => `((?${p}))`).join("|") as T;
     const captures: Pattern["captures"] = {};
-    for (const patternIndex in patterns) {
-      captures[(Number(patternIndex) + 1).toString()] = {
+    for (const [captureIndex, capture] of patterns.entries()) {
+      captures[(Number(captureIndex) + 1).toString()] = {
         patterns: [
           {
-            include: patterns[patternIndex],
+            include: capture,
           },
         ],
       };
@@ -276,7 +275,9 @@ export function transpileTextMateGrammar() {
 }
 
 export function compileTextMateGrammar() {
-  return src("syntaxes/*.tmLanguage.yml")
-    .pipe(transpileTextMateGrammar())
-    .pipe(dest("out/syntaxes"));
+  return pipeline(
+    src("syntaxes/*.tmLanguage.yml"),
+    transpileTextMateGrammar(),
+    dest("out/syntaxes"),
+  );
 }
diff --git a/extensions/ql-vscode/gulpfile.ts/typescript.ts b/extensions/ql-vscode/gulpfile.ts/typescript.ts
index c7f12785507..9d49b56821e 100644
--- a/extensions/ql-vscode/gulpfile.ts/typescript.ts
+++ b/extensions/ql-vscode/gulpfile.ts/typescript.ts
@@ -1,9 +1,10 @@
 import { gray, red } from "ansi-colors";
-import { dest, src, watch } from "gulp";
+import { dest, parallel, src, watch } from "gulp";
 import esbuild from "gulp-esbuild";
 import type { reporter } from "gulp-typescript";
 import { createProject } from "gulp-typescript";
 import del from "del";
+import { pipeline } from "stream/promises";
 
 export function goodReporter(): reporter.Reporter {
   return {
@@ -37,23 +38,23 @@ export function cleanOutput() {
 }
 
 export function compileEsbuild() {
-  return src("./src/extension.ts")
-    .pipe(
-      esbuild({
-        outfile: "extension.js",
-        bundle: true,
-        external: ["vscode", "fsevents"],
-        format: "cjs",
-        platform: "node",
-        target: "es2020",
-        sourcemap: "linked",
-        sourceRoot: "..",
-        loader: {
-          ".node": "copy",
-        },
-      }),
-    )
-    .pipe(dest("out"));
+  return pipeline(
+    src("./src/extension.ts"),
+    esbuild({
+      outfile: "extension.js",
+      bundle: true,
+      external: ["vscode", "fsevents"],
+      format: "cjs",
+      platform: "node",
+      target: "es2020",
+      sourcemap: "linked",
+      sourceRoot: "..",
+      loader: {
+        ".node": "copy",
+      },
+    }),
+    dest("out"),
+  );
 }
 
 export function watchEsbuild() {
@@ -70,7 +71,7 @@ export function watchCheckTypeScript() {
   watch(["src/**/*.ts", "!src/view/**/*.ts"], checkTypeScript);
 }
 
-export function copyWasmFiles() {
+function copyWasmFiles() {
   // We need to copy this file for the source-map package to work. Without this fie, the source-map
   // package is not able to load the WASM file because we are not including the full node_modules
   // directory. In version 0.7.4, it is not possible to call SourceMapConsumer.initialize in Node environments
@@ -82,3 +83,18 @@ export function copyWasmFiles() {
     encoding: false,
   }).pipe(dest("out"));
 }
+
+function copyNativeAddonFiles() {
+  // We need to copy these files manually because we only want to include Windows x64 to limit
+  // the size of the extension. Windows x64 is the most common platform that requires short path
+  // expansion, so we only include this platform.
+  // See src/common/short-paths.ts
+  return pipeline(
+    src("node_modules/koffi/build/koffi/win32_x64/*.node", {
+      encoding: false,
+    }),
+    dest("out/koffi/win32_x64"),
+  );
+}
+
+export const copyModules = parallel(copyWasmFiles, copyNativeAddonFiles);
diff --git a/extensions/ql-vscode/gulpfile.ts/view.ts b/extensions/ql-vscode/gulpfile.ts/view.ts
index fea09031d70..698f39c113e 100644
--- a/extensions/ql-vscode/gulpfile.ts/view.ts
+++ b/extensions/ql-vscode/gulpfile.ts/view.ts
@@ -3,28 +3,29 @@ import esbuild from "gulp-esbuild";
 import { createProject } from "gulp-typescript";
 import { goodReporter } from "./typescript";
 
+import { pipeline } from "stream/promises";
 import chromiumVersion from "./chromium-version.json";
 
 const tsProject = createProject("src/view/tsconfig.json");
 
 export function compileViewEsbuild() {
-  return src("./src/view/webview.tsx")
-    .pipe(
-      esbuild({
-        outfile: "webview.js",
-        bundle: true,
-        format: "iife",
-        platform: "browser",
-        target: `chrome${chromiumVersion.chromiumVersion}`,
-        jsx: "automatic",
-        sourcemap: "linked",
-        sourceRoot: "..",
-        loader: {
-          ".ttf": "file",
-        },
-      }),
-    )
-    .pipe(dest("out"));
+  return pipeline(
+    src("./src/view/webview.tsx"),
+    esbuild({
+      outfile: "webview.js",
+      bundle: true,
+      format: "iife",
+      platform: "browser",
+      target: `chrome${chromiumVersion.chromiumVersion}`,
+      jsx: "automatic",
+      sourcemap: "linked",
+      sourceRoot: "..",
+      loader: {
+        ".ttf": "file",
+      },
+    }),
+    dest("out"),
+  );
 }
 
 export function watchViewEsbuild() {
diff --git a/extensions/ql-vscode/package-lock.json b/extensions/ql-vscode/package-lock.json
index c3c1e168584..7b602d054f9 100644
--- a/extensions/ql-vscode/package-lock.json
+++ b/extensions/ql-vscode/package-lock.json
@@ -1,42 +1,42 @@
 {
   "name": "vscode-codeql",
-  "version": "1.14.1",
+  "version": "1.17.6",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "vscode-codeql",
-      "version": "1.14.1",
+      "version": "1.17.6",
       "hasInstallScript": true,
       "license": "MIT",
       "dependencies": {
-        "@floating-ui/react": "^0.26.12",
-        "@octokit/plugin-retry": "^6.0.1",
-        "@octokit/plugin-throttling": "^8.0.0",
-        "@octokit/rest": "^20.0.2",
+        "@floating-ui/react": "^0.27.0",
+        "@octokit/plugin-retry": "^7.2.0",
+        "@octokit/plugin-throttling": "^9.6.0",
+        "@octokit/rest": "^22.0.0",
+        "@vscode-elements/react-elements": "^0.9.0",
         "@vscode/codicons": "^0.0.36",
         "@vscode/debugadapter": "^1.59.0",
-        "@vscode/debugprotocol": "^1.65.0",
-        "@vscode/webview-ui-toolkit": "^1.0.1",
+        "@vscode/debugprotocol": "^1.68.0",
         "ajv": "^8.11.0",
-        "child-process-promise": "^2.2.1",
         "chokidar": "^3.6.0",
         "d3": "^7.9.0",
         "d3-graphviz": "^5.0.2",
         "fs-extra": "^11.1.1",
         "js-yaml": "^4.1.0",
-        "msw": "^2.2.13",
+        "koffi": "^2.12.0",
+        "msw": "^2.7.4",
         "nanoid": "^5.0.7",
-        "node-fetch": "^2.6.7",
         "p-queue": "^8.0.1",
+        "proper-lockfile": "^4.1.2",
         "react": "^18.3.1",
         "react-dom": "^18.3.1",
         "semver": "^7.6.2",
-        "source-map": "^0.7.4",
+        "source-map": "^0.7.6",
         "source-map-support": "^0.5.21",
         "stream-json": "^1.7.3",
-        "styled-components": "^6.1.9",
-        "tmp": "^0.2.1",
+        "styled-components": "^6.1.13",
+        "tmp": "^0.2.5",
         "tmp-promise": "^3.0.2",
         "tree-kill": "^1.2.2",
         "vscode-extension-telemetry": "^0.1.6",
@@ -46,32 +46,36 @@
         "zip-a-folder": "^3.1.6"
       },
       "devDependencies": {
-        "@babel/core": "^7.24.6",
-        "@babel/plugin-transform-modules-commonjs": "^7.24.7",
+        "@babel/core": "^7.28.3",
+        "@babel/plugin-transform-modules-commonjs": "^7.26.3",
         "@babel/preset-env": "^7.24.4",
-        "@babel/preset-react": "^7.24.1",
-        "@babel/preset-typescript": "^7.21.4",
-        "@faker-js/faker": "^8.4.1",
-        "@github/markdownlint-github": "^0.6.2",
-        "@playwright/test": "^1.40.1",
-        "@storybook/addon-a11y": "^8.2.8",
-        "@storybook/addon-actions": "^8.2.8",
-        "@storybook/addon-essentials": "^8.2.8",
-        "@storybook/addon-interactions": "^8.2.8",
-        "@storybook/addon-links": "^8.2.8",
-        "@storybook/blocks": "^8.0.2",
-        "@storybook/components": "^8.2.8",
-        "@storybook/csf": "^0.1.11",
-        "@storybook/icons": "^1.2.10",
-        "@storybook/manager-api": "^8.2.8",
-        "@storybook/react": "^8.2.8",
-        "@storybook/react-vite": "^8.2.8",
-        "@storybook/theming": "^8.2.4",
-        "@testing-library/dom": "^10.4.0",
-        "@testing-library/jest-dom": "^6.4.8",
-        "@testing-library/react": "^16.0.0",
-        "@testing-library/user-event": "^14.5.2",
-        "@types/child-process-promise": "^2.2.1",
+        "@babel/preset-react": "^7.27.1",
+        "@babel/preset-typescript": "^7.26.0",
+        "@eslint/js": "^9.28.0",
+        "@faker-js/faker": "^9.0.3",
+        "@github/markdownlint-github": "^0.8.0",
+        "@jest/environment": "^30.0.0-alpha.7",
+        "@jest/environment-jsdom-abstract": "^30.0.0-alpha.7",
+        "@microsoft/eslint-formatter-sarif": "^3.1.0",
+        "@playwright/test": "^1.50.1",
+        "@storybook/addon-a11y": "^8.6.14",
+        "@storybook/addon-actions": "^8.6.14",
+        "@storybook/addon-essentials": "^8.6.14",
+        "@storybook/addon-interactions": "^8.6.14",
+        "@storybook/addon-links": "^8.6.14",
+        "@storybook/blocks": "^8.6.0",
+        "@storybook/components": "^8.6.14",
+        "@storybook/csf": "^0.1.13",
+        "@storybook/icons": "^1.4.0",
+        "@storybook/manager-api": "^8.6.14",
+        "@storybook/react": "^8.6.14",
+        "@storybook/react-vite": "^8.6.14",
+        "@storybook/theming": "^8.6.14",
+        "@testing-library/dom": "^10.4.1",
+        "@testing-library/jest-dom": "^6.9.1",
+        "@testing-library/react": "^16.3.0",
+        "@testing-library/user-event": "^14.6.1",
+        "@types/cross-spawn": "^6.0.6",
         "@types/d3": "^7.4.0",
         "@types/d3-graphviz": "^2.6.6",
         "@types/del": "^4.0.0",
@@ -80,11 +84,10 @@
         "@types/gulp-replace": "^1.1.0",
         "@types/jest": "^29.5.12",
         "@types/js-yaml": "^4.0.6",
-        "@types/nanoid": "^3.0.0",
-        "@types/node": "20.14.*",
-        "@types/node-fetch": "^2.5.2",
-        "@types/react": "^18.3.1",
-        "@types/react-dom": "^18.3.0",
+        "@types/node": "22.17.*",
+        "@types/proper-lockfile": "^4.1.4",
+        "@types/react": "^18.3.12",
+        "@types/react-dom": "^18.3.1",
         "@types/sarif": "^2.1.2",
         "@types/semver": "^7.5.8",
         "@types/stream-json": "^1.7.1",
@@ -92,59 +95,59 @@
         "@types/tar-stream": "^3.1.3",
         "@types/through2": "^2.0.36",
         "@types/tmp": "^0.2.6",
-        "@types/vscode": "^1.82.0",
+        "@types/vscode": "1.90.0",
         "@types/yauzl": "^2.10.3",
-        "@typescript-eslint/eslint-plugin": "^7.5.0",
-        "@typescript-eslint/parser": "^7.5.0",
+        "@typescript-eslint/eslint-plugin": "^8.45.0",
+        "@typescript-eslint/parser": "^8.45.0",
         "@vscode/test-electron": "^2.3.9",
-        "@vscode/vsce": "^2.24.0",
+        "@vscode/vsce": "^3.2.1",
         "ansi-colors": "^4.1.1",
         "applicationinsights": "^2.9.5",
         "cosmiconfig": "^9.0.0",
         "cross-env": "^7.0.3",
+        "cross-spawn": "^7.0.6",
         "del": "^6.0.0",
-        "eslint": "^8.56.0",
+        "eslint": "^9.28.0",
         "eslint-config-prettier": "^9.0.0",
-        "eslint-import-resolver-typescript": "^3.6.1",
-        "eslint-plugin-deprecation": "^2.0.0",
+        "eslint-import-resolver-typescript": "^3.6.3",
         "eslint-plugin-etc": "^2.0.2",
-        "eslint-plugin-github": "^4.10.2",
-        "eslint-plugin-import": "^2.29.1",
-        "eslint-plugin-jest-dom": "^5.2.0",
-        "eslint-plugin-prettier": "^5.1.3",
-        "eslint-plugin-react": "^7.34.1",
-        "eslint-plugin-react-hooks": "^4.6.2",
-        "eslint-plugin-storybook": "^0.8.0",
-        "glob": "^10.0.0",
+        "eslint-plugin-github": "^6.0.0",
+        "eslint-plugin-jest-dom": "^5.5.0",
+        "eslint-plugin-prettier": "^5.2.6",
+        "eslint-plugin-react": "^7.37.5",
+        "eslint-plugin-react-hooks": "^5.2.0",
+        "eslint-plugin-storybook": "^9.0.12",
+        "glob": "^11.0.1",
         "gulp": "^5.0.0",
-        "gulp-esbuild": "^0.12.0",
+        "gulp-esbuild": "^0.14.0",
         "gulp-replace": "^1.1.3",
         "gulp-typescript": "^5.0.1",
-        "husky": "^9.0.11",
-        "jest": "^29.0.3",
-        "jest-environment-jsdom": "^29.0.3",
+        "husky": "^9.1.7",
+        "jest": "^30.0.0-alpha.7",
         "jest-runner-vscode": "^3.0.1",
-        "lint-staged": "^15.2.2",
-        "markdownlint-cli2": "^0.13.0",
-        "markdownlint-cli2-formatter-pretty": "^0.0.6",
+        "jsdom": "^26.1.0",
+        "lint-staged": "^15.3.0",
+        "markdownlint-cli2": "^0.17.0",
+        "markdownlint-cli2-formatter-pretty": "^0.0.7",
         "npm-run-all": "^4.1.5",
         "patch-package": "^8.0.0",
-        "prettier": "^3.2.5",
-        "storybook": "^8.2.8",
+        "prettier": "^3.6.1",
+        "storybook": "^8.6.14",
         "tar-stream": "^3.1.7",
         "through2": "^4.0.2",
-        "ts-jest": "^29.1.4",
-        "ts-json-schema-generator": "^2.1.1",
+        "ts-jest": "^29.3.2",
+        "ts-json-schema-generator": "^2.3.0",
         "ts-node": "^10.9.2",
         "ts-unused-exports": "^10.1.0",
-        "typescript": "^5.0.2",
-        "vite": "^5.2.11",
-        "vite-node": "^1.5.3"
+        "typescript": "^5.6.2",
+        "typescript-plugin-css-modules": "^5.1.0",
+        "vite": "^7.1.5",
+        "vite-node": "^3.0.7"
       },
       "engines": {
-        "node": "^20.14.0",
+        "node": "^22.17.0",
         "npm": ">=7.20.6",
-        "vscode": "^1.82.0"
+        "vscode": "^1.90.0"
       }
     },
     "node_modules/@aashutoshrathi/word-wrap": {
@@ -157,17 +160,18 @@
       }
     },
     "node_modules/@achrinza/node-ipc": {
-      "version": "9.2.8",
-      "resolved": "https://registry.npmjs.org/@achrinza/node-ipc/-/node-ipc-9.2.8.tgz",
-      "integrity": "sha512-DSzEEkbMYbAUVlhy7fg+BzccoRuSQzqHbIPGxGv19OJ2WKwS3/9ChAnQcII4g+GujcHhyJ8BUuOVAx/S5uAfQg==",
+      "version": "9.2.9",
+      "resolved": "https://registry.npmjs.org/@achrinza/node-ipc/-/node-ipc-9.2.9.tgz",
+      "integrity": "sha512-7s0VcTwiK/0tNOVdSX9FWMeFdOEcsAOz9HesBldXxFMaGvIak7KC2z9tV9EgsQXn6KUsWsfIkViMNuIo0GoZDQ==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
         "@node-ipc/js-queue": "2.0.3",
         "event-pubsub": "4.3.0",
         "js-message": "1.0.7"
       },
       "engines": {
-        "node": "8 || 9 || 10 || 11 || 12 || 13 || 14 || 15 || 16 || 17 || 18 || 19 || 20 || 21"
+        "node": "8 || 9 || 10 || 11 || 12 || 13 || 14 || 15 || 16 || 17 || 18 || 19 || 20 || 21 || 22"
       }
     },
     "node_modules/@adobe/css-tools": {
@@ -189,6 +193,27 @@
         "node": ">=6.0.0"
       }
     },
+    "node_modules/@asamuzakjp/css-color": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/@asamuzakjp/css-color/-/css-color-3.1.1.tgz",
+      "integrity": "sha512-hpRD68SV2OMcZCsrbdkccTw5FXjNDLo5OuqSHyHZfwweGsDWZwDJ2+gONyNAbazZclobMirACLw0lk8WVxIqxA==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "@csstools/css-calc": "^2.1.2",
+        "@csstools/css-color-parser": "^3.0.8",
+        "@csstools/css-parser-algorithms": "^3.0.4",
+        "@csstools/css-tokenizer": "^3.0.3",
+        "lru-cache": "^10.4.3"
+      }
+    },
+    "node_modules/@asamuzakjp/css-color/node_modules/lru-cache": {
+      "version": "10.4.3",
+      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-10.4.3.tgz",
+      "integrity": "sha512-JNAzZcXrCt42VGLuYz0zfAzDfAvJWW6AfYlDBQyDV5DClI2m5sAmK+OIO7s59XfsRsWHp02jAJrRadPRGTt6SQ==",
+      "dev": true,
+      "license": "ISC"
+    },
     "node_modules/@azure/abort-controller": {
       "version": "1.1.0",
       "resolved": "https://registry.npmjs.org/@azure/abort-controller/-/abort-controller-1.1.0.tgz",
@@ -202,17 +227,91 @@
       }
     },
     "node_modules/@azure/core-auth": {
-      "version": "1.5.0",
-      "resolved": "https://registry.npmjs.org/@azure/core-auth/-/core-auth-1.5.0.tgz",
-      "integrity": "sha512-udzoBuYG1VBoHVohDTrvKjyzel34zt77Bhp7dQntVGGD0ehVq48owENbBG8fIgkHRNUBQH5k1r0hpoMu5L8+kw==",
+      "version": "1.9.0",
+      "resolved": "https://registry.npmjs.org/@azure/core-auth/-/core-auth-1.9.0.tgz",
+      "integrity": "sha512-FPwHpZywuyasDSLMqJ6fhbOK3TqUdviZNF8OqRGA4W5Ewib2lEEZ+pBsYcBa88B2NGO/SEnYPGhyBqNlE8ilSw==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
-        "@azure/abort-controller": "^1.0.0",
-        "@azure/core-util": "^1.1.0",
-        "tslib": "^2.2.0"
+        "@azure/abort-controller": "^2.0.0",
+        "@azure/core-util": "^1.11.0",
+        "tslib": "^2.6.2"
       },
       "engines": {
-        "node": ">=14.0.0"
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-        "tr46": "^3.0.0",
+        "tr46": "^5.1.0",
         "webidl-conversions": "^7.0.0"
       },
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-        "node": ">=12"
+        "node": ">=18"
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@@ -25273,39 +27555,45 @@
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+      "resolved": "https://registry.npmjs.org/which-boxed-primitive/-/which-boxed-primitive-1.1.1.tgz",
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+      "license": "MIT",
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-        "is-bigint": "^1.0.1",
-        "is-boolean-object": "^1.1.0",
-        "is-number-object": "^1.0.4",
-        "is-string": "^1.0.5",
-        "is-symbol": "^1.0.3"
+        "is-bigint": "^1.1.0",
+        "is-boolean-object": "^1.2.1",
+        "is-number-object": "^1.1.1",
+        "is-string": "^1.1.1",
+        "is-symbol": "^1.1.1"
+      },
+      "engines": {
+        "node": ">= 0.4"
       },
       "funding": {
         "url": "https://github.com/sponsors/ljharb"
       }
     },
     "node_modules/which-builtin-type": {
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+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/which-builtin-type/-/which-builtin-type-1.2.1.tgz",
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       "dev": true,
+      "license": "MIT",
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-        "function.prototype.name": "^1.1.5",
-        "has-tostringtag": "^1.0.0",
+        "call-bound": "^1.0.2",
+        "function.prototype.name": "^1.1.6",
+        "has-tostringtag": "^1.0.2",
         "is-async-function": "^2.0.0",
-        "is-date-object": "^1.0.5",
-        "is-finalizationregistry": "^1.0.2",
+        "is-date-object": "^1.1.0",
+        "is-finalizationregistry": "^1.1.0",
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-        "is-regex": "^1.1.4",
+        "is-regex": "^1.2.1",
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-        "which-boxed-primitive": "^1.0.2",
-        "which-collection": "^1.0.1",
-        "which-typed-array": "^1.1.9"
+        "which-boxed-primitive": "^1.1.0",
+        "which-collection": "^1.0.2",
+        "which-typed-array": "^1.1.16"
       },
       "engines": {
         "node": ">= 0.4"
@@ -25315,30 +27603,37 @@
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     "node_modules/which-collection": {
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-      "resolved": "https://registry.npmjs.org/which-collection/-/which-collection-1.0.1.tgz",
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+      "version": "1.0.2",
+      "resolved": "https://registry.npmjs.org/which-collection/-/which-collection-1.0.2.tgz",
+      "integrity": "sha512-K4jVyjnBdgvc86Y6BkaLZEN933SwYOuBFkdmBu9ZfkcAbdVbpITnDmjvZ/aQjRXQrv5EPkTnD1s39GiiqbngCw==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
-        "is-map": "^2.0.1",
-        "is-set": "^2.0.1",
-        "is-weakmap": "^2.0.1",
-        "is-weakset": "^2.0.1"
+        "is-map": "^2.0.3",
+        "is-set": "^2.0.3",
+        "is-weakmap": "^2.0.2",
+        "is-weakset": "^2.0.3"
+      },
+      "engines": {
+        "node": ">= 0.4"
       },
       "funding": {
         "url": "https://github.com/sponsors/ljharb"
       }
     },
     "node_modules/which-typed-array": {
-      "version": "1.1.15",
-      "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.15.tgz",
-      "integrity": "sha512-oV0jmFtUky6CXfkqehVvBP/LSWJ2sy4vWMioiENyJLePrBO/yKyV9OyJySfAKosh+RYkIl5zJCNZ8/4JncrpdA==",
+      "version": "1.1.19",
+      "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.19.tgz",
+      "integrity": "sha512-rEvr90Bck4WZt9HHFC4DJMsjvu7x+r6bImz0/BrbWb7A2djJ8hnZMrWnHo9F8ssv0OMErasDhftrfROTyqSDrw==",
       "dev": true,
+      "license": "MIT",
       "dependencies": {
         "available-typed-arrays": "^1.0.7",
-        "call-bind": "^1.0.7",
-        "for-each": "^0.3.3",
-        "gopd": "^1.0.1",
+        "call-bind": "^1.0.8",
+        "call-bound": "^1.0.4",
+        "for-each": "^0.3.5",
+        "get-proto": "^1.0.1",
+        "gopd": "^1.2.0",
         "has-tostringtag": "^1.0.2"
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@@ -25422,9 +27717,9 @@
       }
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     "node_modules/wrap-ansi/node_modules/ansi-regex": {
-      "version": "6.0.1",
-      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.0.1.tgz",
-      "integrity": "sha512-n5M855fKb2SsfMIiFFoVrABHJC8QtHwVx+mHWP3QcEqBHYienj5dHSgjbxtC0WEZXYt4wcD6zrQElDPhFuZgfA==",
+      "version": "6.1.0",
+      "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.1.0.tgz",
+      "integrity": "sha512-7HSX4QQb4CspciLpVFwyRe79O3xsIZDDLER21kERQ71oaPodF8jL725AgJMFAYbooIqolJoRLuM81SpeUkpkvA==",
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         "node": ">=12"
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@@ -25482,10 +27777,11 @@
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-      "resolved": "https://registry.npmjs.org/ws/-/ws-8.17.1.tgz",
-      "integrity": "sha512-6XQFvXTkbfUOZOKKILFG1PDK2NDQs4azKQl26T0YS5CxqWLgXajbPZ+h4gZekJyRqFU8pvnbAbbs/3TgRPy+GQ==",
+      "version": "8.18.1",
+      "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.1.tgz",
+      "integrity": "sha512-RKW2aJZMXeMxVpnZ6bck+RswznaxmzdULiBr6KY7XkTnW8uvt0iT9H5DkHUChXrc+uurzwa0rVI16n/Xzjdz1w==",
       "dev": true,
+      "license": "MIT",
       "engines": {
         "node": ">=10.0.0"
       },
@@ -25503,12 +27799,13 @@
       }
     },
     "node_modules/xml-name-validator": {
-      "version": "4.0.0",
-      "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz",
-      "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==",
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-5.0.0.tgz",
+      "integrity": "sha512-EvGK8EJ3DhaHfbRlETOWAS5pO9MZITeauHKJyb8wyajUfQUenkIg2MvLDTZ4T/TgIcm3HU0TFBgWWboAZ30UHg==",
       "dev": true,
+      "license": "Apache-2.0",
       "engines": {
-        "node": ">=12"
+        "node": ">=18"
       }
     },
     "node_modules/xml2js": {
@@ -25563,10 +27860,14 @@
       "dev": true
     },
     "node_modules/yaml": {
-      "version": "2.3.4",
-      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.3.4.tgz",
-      "integrity": "sha512-8aAvwVUSHpfEqTQ4w/KMlf3HcRdt50E5ODIQJBw1fQ5RL34xabzxtUlzTXVqc4rkZsPbvrXKWnABCD7kWSmocA==",
+      "version": "2.6.1",
+      "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.6.1.tgz",
+      "integrity": "sha512-7r0XPzioN/Q9kXBro/XPnA6kznR73DHq+GXh5ON7ZozRO6aMjbmiBuKste2wslTFkC5d1dw0GooOCepZXJ2SAg==",
       "dev": true,
+      "license": "ISC",
+      "bin": {
+        "yaml": "bin.mjs"
+      },
       "engines": {
         "node": ">= 14"
       }
@@ -25661,6 +27962,18 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/yoctocolors-cjs": {
+      "version": "2.1.2",
+      "resolved": "https://registry.npmjs.org/yoctocolors-cjs/-/yoctocolors-cjs-2.1.2.tgz",
+      "integrity": "sha512-cYVsTjKl8b+FrnidjibDWskAv7UKOfcwaVZdp/it9n1s9fU3IkgDbhdIRKCW4JDsAlECJY0ytoVPT3sK6kideA==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/zip-a-folder": {
       "version": "3.1.6",
       "resolved": "https://registry.npmjs.org/zip-a-folder/-/zip-a-folder-3.1.6.tgz",
@@ -25671,6 +27984,82 @@
         "is-glob": "^4.0.3"
       }
     },
+    "node_modules/zip-a-folder/node_modules/brace-expansion": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
+      "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
+      "license": "MIT",
+      "dependencies": {
+        "balanced-match": "^1.0.0"
+      }
+    },
+    "node_modules/zip-a-folder/node_modules/glob": {
+      "version": "10.4.5",
+      "resolved": "https://registry.npmjs.org/glob/-/glob-10.4.5.tgz",
+      "integrity": "sha512-7Bv8RF0k6xjo7d4A/PxYLbUCfb6c+Vpd2/mB2yRDlew7Jb5hEXiCD9ibfO7wpk8i4sevK6DFny9h7EYbM3/sHg==",
+      "dependencies": {
+        "foreground-child": "^3.1.0",
+        "jackspeak": "^3.1.2",
+        "minimatch": "^9.0.4",
+        "minipass": "^7.1.2",
+        "package-json-from-dist": "^1.0.0",
+        "path-scurry": "^1.11.1"
+      },
+      "bin": {
+        "glob": "dist/esm/bin.mjs"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
+      }
+    },
+    "node_modules/zip-a-folder/node_modules/jackspeak": {
+      "version": "3.4.3",
+      "resolved": "https://registry.npmjs.org/jackspeak/-/jackspeak-3.4.3.tgz",
+      "integrity": "sha512-OGlZQpz2yfahA/Rd1Y8Cd9SIEsqvXkLVoSw/cgwhnhFMDbsQFeZYoJJ7bIZBS9BcamUW96asq/npPWugM+RQBw==",
+      "dependencies": {
+        "@isaacs/cliui": "^8.0.2"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
+      },
+      "optionalDependencies": {
+        "@pkgjs/parseargs": "^0.11.0"
+      }
+    },
+    "node_modules/zip-a-folder/node_modules/lru-cache": {
+      "version": "10.4.3",
+      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-10.4.3.tgz",
+      "integrity": "sha512-JNAzZcXrCt42VGLuYz0zfAzDfAvJWW6AfYlDBQyDV5DClI2m5sAmK+OIO7s59XfsRsWHp02jAJrRadPRGTt6SQ=="
+    },
+    "node_modules/zip-a-folder/node_modules/minimatch": {
+      "version": "9.0.5",
+      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.5.tgz",
+      "integrity": "sha512-G6T0ZX48xgozx7587koeX9Ys2NYy6Gmv//P89sEte9V9whIapMNF4idKxnW2QtCcLiTWlb/wfCabAtAFWhhBow==",
+      "dependencies": {
+        "brace-expansion": "^2.0.1"
+      },
+      "engines": {
+        "node": ">=16 || 14 >=14.17"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
+      }
+    },
+    "node_modules/zip-a-folder/node_modules/path-scurry": {
+      "version": "1.11.1",
+      "resolved": "https://registry.npmjs.org/path-scurry/-/path-scurry-1.11.1.tgz",
+      "integrity": "sha512-Xa4Nw17FS9ApQFJ9umLiJS4orGjm7ZzwUrwamcGQuHSzDyth9boKDaycYdDcZDuqYATXw4HFXgaqWTctW/v1HA==",
+      "dependencies": {
+        "lru-cache": "^10.2.0",
+        "minipass": "^5.0.0 || ^6.0.2 || ^7.0.0"
+      },
+      "engines": {
+        "node": ">=16 || 14 >=14.18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/isaacs"
+      }
+    },
     "node_modules/zip-stream": {
       "version": "5.0.1",
       "resolved": "https://registry.npmjs.org/zip-stream/-/zip-stream-5.0.1.tgz",
diff --git a/extensions/ql-vscode/package.json b/extensions/ql-vscode/package.json
index 3283a9ac84a..9f8d3ab41b3 100644
--- a/extensions/ql-vscode/package.json
+++ b/extensions/ql-vscode/package.json
@@ -4,7 +4,7 @@
   "description": "CodeQL for Visual Studio Code",
   "author": "GitHub",
   "private": true,
-  "version": "1.14.1",
+  "version": "1.17.6",
   "publisher": "GitHub",
   "license": "MIT",
   "icon": "media/VS-marketplace-CodeQL-icon.png",
@@ -13,8 +13,8 @@
     "url": "https://github.com/github/vscode-codeql"
   },
   "engines": {
-    "vscode": "^1.82.0",
-    "node": "^20.14.0",
+    "vscode": "^1.90.0",
+    "node": "^22.17.0",
     "npm": ">=7.20.6"
   },
   "categories": [
@@ -42,13 +42,6 @@
     "workspaceContains:.git"
   ],
   "main": "./out/extension",
-  "files": [
-    "gen/*.js",
-    "media/**",
-    "out/**",
-    "package.json",
-    "language-configuration.json"
-  ],
   "contributes": {
     "configurationDefaults": {
       "[ql]": {
@@ -302,8 +295,8 @@
         "properties": {
           "codeQL.queryHistory.format": {
             "type": "string",
-            "default": "%q on %d - %s %r [%t]",
-            "markdownDescription": "Default string for how to label query history items.\n* %t is the time of the query\n* %q is the human-readable query name\n* %f is the query file name\n* %d is the database name\n* %r is the number of results\n* %s is a status string"
+            "default": "${queryName} on ${databaseName} - ${status} ${resultCount} [${startTime}]",
+            "markdownDescription": "Default string for how to label query history items.\n\nThe following variables are supported:\n* **${startTime}** - the time of the query\n* **${queryName}** - the human-readable query name\n* **${queryFileBasename}** - the query file's base name\n* **${queryLanguage}** - the query language\n* **${databaseName}** - the database name\n* **${resultCount}** - the number of results\n* **${status}** - a status string"
           },
           "codeQL.queryHistory.ttl": {
             "type": "number",
@@ -497,16 +490,6 @@
         "title": "Telemetry",
         "order": 11,
         "properties": {
-          "codeQL.telemetry.enableTelemetry": {
-            "type": "boolean",
-            "default": false,
-            "scope": "application",
-            "markdownDescription": "Specifies whether to send CodeQL usage telemetry. This setting AND the one of the global telemetry settings (`#telemetry.enableTelemetry#` or `#telemetry.telemetryLevel#`) must be enabled for telemetry to be sent to GitHub. For more information, see the [telemetry documentation](https://codeql.github.com/docs/codeql-for-visual-studio-code/about-telemetry-in-codeql-for-visual-studio-code)",
-            "tags": [
-              "telemetry",
-              "usesOnlineServices"
-            ]
-          },
           "codeQL.telemetry.logTelemetry": {
             "type": "boolean",
             "default": false,
@@ -588,6 +571,10 @@
         "command": "codeQL.runQueries",
         "title": "CodeQL: Run Queries in Selected Files"
       },
+      {
+        "command": "codeQL.runQuerySuite",
+        "title": "CodeQL: Run Selected Query Suite"
+      },
       {
         "command": "codeQL.quickEval",
         "title": "CodeQL: Quick Evaluation"
@@ -803,6 +790,10 @@
         "command": "codeQL.trimCache",
         "title": "CodeQL: Trim Cache"
       },
+      {
+        "command": "codeQL.trimOverlayBaseCache",
+        "title": "CodeQL: Trim Overlay Base Cache"
+      },
       {
         "command": "codeQL.installPackDependencies",
         "title": "CodeQL: Install Pack Dependencies"
@@ -839,6 +830,10 @@
         "command": "codeQL.chooseDatabaseFolder",
         "title": "CodeQL: Choose Database from Folder"
       },
+      {
+        "command": "codeQL.chooseDatabaseFoldersParent",
+        "title": "CodeQL: Import All Databases Directly Contained in a Parent Folder"
+      },
       {
         "command": "codeQL.chooseDatabaseArchive",
         "title": "CodeQL: Choose Database from Archive"
@@ -955,6 +950,10 @@
         "command": "codeQLQueryHistory.compareWith",
         "title": "Compare Results"
       },
+      {
+        "command": "codeQLQueryHistory.comparePerformanceWith",
+        "title": "Compare Performance"
+      },
       {
         "command": "codeQLQueryHistory.openOnGithub",
         "title": "View Logs"
@@ -963,6 +962,10 @@
         "command": "codeQLQueryHistory.copyRepoList",
         "title": "Copy Repository List"
       },
+      {
+        "command": "codeQLQueryHistory.viewAutofixes",
+        "title": "View Autofixes"
+      },
       {
         "command": "codeQLQueryResults.down",
         "title": "CodeQL: Navigate Down in Local Result Viewer"
@@ -1226,6 +1229,11 @@
           "group": "3_queryHistory@0",
           "when": "viewItem == rawResultsItem || viewItem == interpretedResultsItem"
         },
+        {
+          "command": "codeQLQueryHistory.comparePerformanceWith",
+          "group": "3_queryHistory@1",
+          "when": "viewItem == rawResultsItem && config.codeQL.canary || viewItem == interpretedResultsItem && config.codeQL.canary"
+        },
         {
           "command": "codeQLQueryHistory.showQueryLog",
           "group": "4_queryHistory@4",
@@ -1296,6 +1304,11 @@
           "group": "1_queryHistory@1",
           "when": "viewItem == remoteResultsItem"
         },
+        {
+          "command": "codeQLQueryHistory.viewAutofixes",
+          "group": "1_queryHistory@2",
+          "when": "viewItem == remoteResultsItem && config.codeQL.canary"
+        },
         {
           "command": "codeQLQueries.runLocalQueryFromQueriesPanel",
           "group": "inline",
@@ -1365,6 +1378,11 @@
           "group": "9_qlCommands",
           "when": "resourceScheme != codeql-zip-archive"
         },
+        {
+          "command": "codeQL.runQuerySuite",
+          "group": "9_qlCommands",
+          "when": "resourceScheme != codeql-zip-archive && resourceExtname == .qls && !explorerResourceIsFolder && !listMultiSelection && config.codeQL.canary"
+        },
         {
           "command": "codeQL.runVariantAnalysisContextExplorer",
           "group": "9_qlCommands",
@@ -1462,6 +1480,10 @@
           "command": "codeQL.runQueries",
           "when": "false"
         },
+        {
+          "command": "codeQL.runQuerySuite",
+          "when": "false"
+        },
         {
           "command": "codeQL.quickEval",
           "when": "editorLangId == ql"
@@ -1697,6 +1719,10 @@
           "command": "codeQLQueryHistory.copyRepoList",
           "when": "false"
         },
+        {
+          "command": "codeQLQueryHistory.viewAutofixes",
+          "when": "false"
+        },
         {
           "command": "codeQLQueryHistory.showQueryText",
           "when": "false"
@@ -1729,6 +1755,10 @@
           "command": "codeQLQueryHistory.compareWith",
           "when": "false"
         },
+        {
+          "command": "codeQLQueryHistory.comparePerformanceWith",
+          "when": "false"
+        },
         {
           "command": "codeQLQueryHistory.sortByName",
           "when": "false"
@@ -1791,6 +1821,10 @@
         },
         {
           "command": "codeQL.trimCache"
+        },
+        {
+          "command": "codeQL.trimOverlayBaseCache",
+          "when": "codeQL.cliFeatures.queryServerTrimCacheWithMode"
         }
       ],
       "editor/context": [
@@ -1951,8 +1985,9 @@
     "test:cli-integration": "jest --projects test/vscode-tests/cli-integration --verbose",
     "clean-test-dir": "find . -type d -name .vscode-test -exec rm -r {} +",
     "update-vscode": "node ./node_modules/vscode/bin/install",
-    "format": "prettier --write **/*.{ts,tsx} && eslint . --ext .ts,.tsx --fix",
-    "lint": "eslint . --ext .js,.ts,.tsx --max-warnings=0",
+    "format": "prettier --write **/*.{ts,tsx} && eslint . --fix",
+    "lint": "eslint . --max-warnings=0",
+    "lint-ci": "SARIF_ESLINT_IGNORE_SUPPRESSED=true eslint . --max-warnings=0 --format @microsoft/eslint-formatter-sarif --output-file=build/eslint.sarif",
     "lint:markdown": "markdownlint-cli2 \"../../**/*.{md,mdx}\" \"!**/node_modules/**\" \"!**/.vscode-test/**\" \"!**/build/cli/v*/**\"",
     "find-deadcode": "vite-node scripts/find-deadcode.ts",
     "format-staged": "lint-staged",
@@ -1962,38 +1997,38 @@
     "generate": "npm-run-all -p generate:*",
     "generate:schemas": "vite-node scripts/generate-schemas.ts",
     "generate:chromium-version": "vite-node scripts/generate-chromium-version.ts",
-    "check-types": "find . -type f -name \"tsconfig.json\" -not -path \"./node_modules/*\" | sed -r 's|/[^/]+$||' | sort | uniq | xargs -I {} sh -c \"echo Checking types in {} && cd {} && npx tsc --noEmit\"",
+    "check-types": "find . -type f -name \"tsconfig.json\" -not -path \"./node_modules/*\" -not -path \"*/.vscode-test/*\" | sed -r 's|/[^/]+$||' | sort | uniq | xargs -I {} sh -c \"echo Checking types in {} && cd {} && npx tsc --noEmit\"",
     "postinstall": "patch-package",
-    "prepare": "cd ../.. && husky install"
+    "prepare": "cd ../.. && husky"
   },
   "dependencies": {
-    "@floating-ui/react": "^0.26.12",
-    "@octokit/plugin-retry": "^6.0.1",
-    "@octokit/plugin-throttling": "^8.0.0",
-    "@octokit/rest": "^20.0.2",
+    "@floating-ui/react": "^0.27.0",
+    "@octokit/plugin-retry": "^7.2.0",
+    "@octokit/plugin-throttling": "^9.6.0",
+    "@octokit/rest": "^22.0.0",
+    "@vscode-elements/react-elements": "^0.9.0",
     "@vscode/codicons": "^0.0.36",
     "@vscode/debugadapter": "^1.59.0",
-    "@vscode/debugprotocol": "^1.65.0",
-    "@vscode/webview-ui-toolkit": "^1.0.1",
+    "@vscode/debugprotocol": "^1.68.0",
     "ajv": "^8.11.0",
-    "child-process-promise": "^2.2.1",
     "chokidar": "^3.6.0",
     "d3": "^7.9.0",
     "d3-graphviz": "^5.0.2",
     "fs-extra": "^11.1.1",
     "js-yaml": "^4.1.0",
-    "msw": "^2.2.13",
+    "koffi": "^2.12.0",
+    "msw": "^2.7.4",
     "nanoid": "^5.0.7",
-    "node-fetch": "^2.6.7",
     "p-queue": "^8.0.1",
+    "proper-lockfile": "^4.1.2",
     "react": "^18.3.1",
     "react-dom": "^18.3.1",
     "semver": "^7.6.2",
-    "source-map": "^0.7.4",
+    "source-map": "^0.7.6",
     "source-map-support": "^0.5.21",
     "stream-json": "^1.7.3",
-    "styled-components": "^6.1.9",
-    "tmp": "^0.2.1",
+    "styled-components": "^6.1.13",
+    "tmp": "^0.2.5",
     "tmp-promise": "^3.0.2",
     "tree-kill": "^1.2.2",
     "vscode-extension-telemetry": "^0.1.6",
@@ -2003,32 +2038,36 @@
     "zip-a-folder": "^3.1.6"
   },
   "devDependencies": {
-    "@babel/core": "^7.24.6",
-    "@babel/plugin-transform-modules-commonjs": "^7.24.7",
+    "@babel/core": "^7.28.3",
+    "@babel/plugin-transform-modules-commonjs": "^7.26.3",
     "@babel/preset-env": "^7.24.4",
-    "@babel/preset-react": "^7.24.1",
-    "@babel/preset-typescript": "^7.21.4",
-    "@faker-js/faker": "^8.4.1",
-    "@github/markdownlint-github": "^0.6.2",
-    "@playwright/test": "^1.40.1",
-    "@storybook/addon-a11y": "^8.2.8",
-    "@storybook/addon-actions": "^8.2.8",
-    "@storybook/addon-essentials": "^8.2.8",
-    "@storybook/addon-interactions": "^8.2.8",
-    "@storybook/addon-links": "^8.2.8",
-    "@storybook/blocks": "^8.0.2",
-    "@storybook/components": "^8.2.8",
-    "@storybook/csf": "^0.1.11",
-    "@storybook/icons": "^1.2.10",
-    "@storybook/manager-api": "^8.2.8",
-    "@storybook/react": "^8.2.8",
-    "@storybook/react-vite": "^8.2.8",
-    "@storybook/theming": "^8.2.4",
-    "@testing-library/dom": "^10.4.0",
-    "@testing-library/jest-dom": "^6.4.8",
-    "@testing-library/react": "^16.0.0",
-    "@testing-library/user-event": "^14.5.2",
-    "@types/child-process-promise": "^2.2.1",
+    "@babel/preset-react": "^7.27.1",
+    "@babel/preset-typescript": "^7.26.0",
+    "@eslint/js": "^9.28.0",
+    "@faker-js/faker": "^9.0.3",
+    "@github/markdownlint-github": "^0.8.0",
+    "@jest/environment": "^30.0.0-alpha.7",
+    "@jest/environment-jsdom-abstract": "^30.0.0-alpha.7",
+    "@microsoft/eslint-formatter-sarif": "^3.1.0",
+    "@playwright/test": "^1.50.1",
+    "@storybook/addon-a11y": "^8.6.14",
+    "@storybook/addon-actions": "^8.6.14",
+    "@storybook/addon-essentials": "^8.6.14",
+    "@storybook/addon-interactions": "^8.6.14",
+    "@storybook/addon-links": "^8.6.14",
+    "@storybook/blocks": "^8.6.0",
+    "@storybook/components": "^8.6.14",
+    "@storybook/csf": "^0.1.13",
+    "@storybook/icons": "^1.4.0",
+    "@storybook/manager-api": "^8.6.14",
+    "@storybook/react": "^8.6.14",
+    "@storybook/react-vite": "^8.6.14",
+    "@storybook/theming": "^8.6.14",
+    "@testing-library/dom": "^10.4.1",
+    "@testing-library/jest-dom": "^6.9.1",
+    "@testing-library/react": "^16.3.0",
+    "@testing-library/user-event": "^14.6.1",
+    "@types/cross-spawn": "^6.0.6",
     "@types/d3": "^7.4.0",
     "@types/d3-graphviz": "^2.6.6",
     "@types/del": "^4.0.0",
@@ -2037,11 +2076,10 @@
     "@types/gulp-replace": "^1.1.0",
     "@types/jest": "^29.5.12",
     "@types/js-yaml": "^4.0.6",
-    "@types/nanoid": "^3.0.0",
-    "@types/node": "20.14.*",
-    "@types/node-fetch": "^2.5.2",
-    "@types/react": "^18.3.1",
-    "@types/react-dom": "^18.3.0",
+    "@types/node": "22.17.*",
+    "@types/proper-lockfile": "^4.1.4",
+    "@types/react": "^18.3.12",
+    "@types/react-dom": "^18.3.1",
     "@types/sarif": "^2.1.2",
     "@types/semver": "^7.5.8",
     "@types/stream-json": "^1.7.1",
@@ -2049,54 +2087,54 @@
     "@types/tar-stream": "^3.1.3",
     "@types/through2": "^2.0.36",
     "@types/tmp": "^0.2.6",
-    "@types/vscode": "^1.82.0",
+    "@types/vscode": "1.90.0",
     "@types/yauzl": "^2.10.3",
-    "@typescript-eslint/eslint-plugin": "^7.5.0",
-    "@typescript-eslint/parser": "^7.5.0",
+    "@typescript-eslint/eslint-plugin": "^8.45.0",
+    "@typescript-eslint/parser": "^8.45.0",
     "@vscode/test-electron": "^2.3.9",
-    "@vscode/vsce": "^2.24.0",
+    "@vscode/vsce": "^3.2.1",
     "ansi-colors": "^4.1.1",
     "applicationinsights": "^2.9.5",
     "cosmiconfig": "^9.0.0",
     "cross-env": "^7.0.3",
+    "cross-spawn": "^7.0.6",
     "del": "^6.0.0",
-    "eslint": "^8.56.0",
+    "eslint": "^9.28.0",
     "eslint-config-prettier": "^9.0.0",
-    "eslint-import-resolver-typescript": "^3.6.1",
-    "eslint-plugin-deprecation": "^2.0.0",
+    "eslint-import-resolver-typescript": "^3.6.3",
     "eslint-plugin-etc": "^2.0.2",
-    "eslint-plugin-github": "^4.10.2",
-    "eslint-plugin-import": "^2.29.1",
-    "eslint-plugin-jest-dom": "^5.2.0",
-    "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-react": "^7.34.1",
-    "eslint-plugin-react-hooks": "^4.6.2",
-    "eslint-plugin-storybook": "^0.8.0",
-    "glob": "^10.0.0",
+    "eslint-plugin-github": "^6.0.0",
+    "eslint-plugin-jest-dom": "^5.5.0",
+    "eslint-plugin-prettier": "^5.2.6",
+    "eslint-plugin-react": "^7.37.5",
+    "eslint-plugin-react-hooks": "^5.2.0",
+    "eslint-plugin-storybook": "^9.0.12",
+    "glob": "^11.0.1",
     "gulp": "^5.0.0",
-    "gulp-esbuild": "^0.12.0",
+    "gulp-esbuild": "^0.14.0",
     "gulp-replace": "^1.1.3",
     "gulp-typescript": "^5.0.1",
-    "husky": "^9.0.11",
-    "jest": "^29.0.3",
-    "jest-environment-jsdom": "^29.0.3",
+    "husky": "^9.1.7",
+    "jest": "^30.0.0-alpha.7",
     "jest-runner-vscode": "^3.0.1",
-    "lint-staged": "^15.2.2",
-    "markdownlint-cli2": "^0.13.0",
-    "markdownlint-cli2-formatter-pretty": "^0.0.6",
+    "jsdom": "^26.1.0",
+    "lint-staged": "^15.3.0",
+    "markdownlint-cli2": "^0.17.0",
+    "markdownlint-cli2-formatter-pretty": "^0.0.7",
     "npm-run-all": "^4.1.5",
     "patch-package": "^8.0.0",
-    "prettier": "^3.2.5",
-    "storybook": "^8.2.8",
+    "prettier": "^3.6.1",
+    "storybook": "^8.6.14",
     "tar-stream": "^3.1.7",
     "through2": "^4.0.2",
-    "ts-jest": "^29.1.4",
-    "ts-json-schema-generator": "^2.1.1",
+    "ts-jest": "^29.3.2",
+    "ts-json-schema-generator": "^2.3.0",
     "ts-node": "^10.9.2",
     "ts-unused-exports": "^10.1.0",
-    "typescript": "^5.0.2",
-    "vite": "^5.2.11",
-    "vite-node": "^1.5.3"
+    "typescript": "^5.6.2",
+    "typescript-plugin-css-modules": "^5.1.0",
+    "vite": "^7.1.5",
+    "vite-node": "^3.0.7"
   },
   "lint-staged": {
     "./**/*.{json,css,scss}": [
diff --git a/extensions/ql-vscode/patches/jest-runner-vscode+3.0.1.patch b/extensions/ql-vscode/patches/jest-runner-vscode+3.0.1.patch
index 155e00635b0..f71e37b268e 100644
--- a/extensions/ql-vscode/patches/jest-runner-vscode+3.0.1.patch
+++ b/extensions/ql-vscode/patches/jest-runner-vscode+3.0.1.patch
@@ -1,29 +1,3 @@
-diff --git a/node_modules/jest-runner-vscode/dist/child/environment.js b/node_modules/jest-runner-vscode/dist/child/environment.js
-index 1ac28d5..f91f216 100644
---- a/node_modules/jest-runner-vscode/dist/child/environment.js
-+++ b/node_modules/jest-runner-vscode/dist/child/environment.js
-@@ -10,6 +10,21 @@ const wrap_io_1 = __importDefault(require("./wrap-io"));
- const load_pnp_1 = __importDefault(require("./load-pnp"));
- const ipc = new ipc_client_1.default('env');
- class VSCodeEnvironment extends jest_environment_node_1.default {
-+    constructor(config, context) {
-+        super(config, context);
-+        // The _VSCODE_NODE_MODULES is a proxy which will require a module if any property
-+        // on it is accessed. This is a workaround for the fact that jest will call
-+        // _isMockFunction on the module, which will cause that function to be required.
-+        this.global._VSCODE_NODE_MODULES = new Proxy(this.global._VSCODE_NODE_MODULES, {
-+          get(target, prop) {
-+            if (prop === '_isMockFunction') {
-+              return undefined;
-+            }
-+            return target[prop];
-+          },
-+        });
-+    }
-+
-     async setup() {
-         await super.setup();
-         await (0, load_pnp_1.default)();
 diff --git a/node_modules/jest-runner-vscode/dist/child/runner.js b/node_modules/jest-runner-vscode/dist/child/runner.js
 index 0663c5c..bdf4a8b 100644
 --- a/node_modules/jest-runner-vscode/dist/child/runner.js
diff --git a/extensions/ql-vscode/scripts/bump-supported-cli-versions.ts b/extensions/ql-vscode/scripts/bump-supported-cli-versions.ts
new file mode 100644
index 00000000000..12985cf4bdb
--- /dev/null
+++ b/extensions/ql-vscode/scripts/bump-supported-cli-versions.ts
@@ -0,0 +1,95 @@
+import { spawnSync } from "child_process";
+import { resolve } from "path";
+import { appendFile, outputJson, readJson } from "fs-extra";
+import { SemVer } from "semver";
+
+const supportedCliVersionsPath = resolve(
+  __dirname,
+  "..",
+  "supported_cli_versions.json",
+);
+
+async function bumpSupportedCliVersions() {
+  const existingVersions = (await readJson(
+    supportedCliVersionsPath,
+  )) as string[];
+
+  const release = runGhJSON<Release>([
+    "release",
+    "view",
+    "--json",
+    "id,name",
+    "--repo",
+    "github/codeql-cli-binaries",
+  ]);
+
+  // There are two cases:
+  // - Replace the version if it's the same major and minor version
+  // - Prepend the version if it's a new major or minor version
+
+  const latestSupportedVersion = new SemVer(existingVersions[0]);
+  const latestReleaseVersion = new SemVer(release.name);
+
+  if (latestSupportedVersion.compare(latestReleaseVersion) === 0) {
+    console.log("No need to update supported CLI versions");
+    return;
+  }
+
+  if (process.env.GITHUB_OUTPUT) {
+    await appendFile(
+      process.env.GITHUB_OUTPUT,
+      `PREVIOUS_VERSION=${existingVersions[0]}\n`,
+      {
+        encoding: "utf-8",
+      },
+    );
+  }
+
+  if (
+    latestSupportedVersion.major === latestReleaseVersion.major &&
+    latestSupportedVersion.minor === latestReleaseVersion.minor
+  ) {
+    existingVersions[0] = release.name;
+    console.log(`Replaced latest supported CLI version with ${release.name}`);
+  } else {
+    existingVersions.unshift(release.name);
+    console.log(`Added latest supported CLI version ${release.name}`);
+  }
+
+  await outputJson(supportedCliVersionsPath, existingVersions, {
+    spaces: 2,
+    finalEOL: true,
+  });
+
+  if (process.env.GITHUB_OUTPUT) {
+    await appendFile(
+      process.env.GITHUB_OUTPUT,
+      `LATEST_VERSION=${existingVersions[0]}\n`,
+      {
+        encoding: "utf-8",
+      },
+    );
+  }
+}
+
+bumpSupportedCliVersions().catch((e: unknown) => {
+  console.error(e);
+  process.exit(2);
+});
+
+function runGh(args: readonly string[]): string {
+  const gh = spawnSync("gh", args);
+  if (gh.status !== 0) {
+    throw new Error(`Failed to run gh ${args.join(" ")}: ${gh.stderr}`);
+  }
+  return gh.stdout.toString("utf-8");
+}
+
+function runGhJSON<T>(args: readonly string[]): T {
+  return JSON.parse(runGh(args));
+}
+
+type Release = {
+  id: string;
+  name: string;
+};
diff --git a/extensions/ql-vscode/scripts/find-deadcode.ts b/extensions/ql-vscode/scripts/find-deadcode.ts
index 9e21286b4a5..14d9d44a1c1 100644
--- a/extensions/ql-vscode/scripts/find-deadcode.ts
+++ b/extensions/ql-vscode/scripts/find-deadcode.ts
@@ -12,6 +12,7 @@ function ignoreFile(file: string): boolean {
       join("test", "vscode-tests", "jest-runner-vscode-codeql-cli.ts"),
       file,
     ) ||
+    pathsEqual(join("src", "view", "jest-environment-jsdom.ts"), file) ||
     basename(file) === "jest.config.ts" ||
     basename(file) === "index.tsx" ||
     basename(file) === "index.ts" ||
diff --git a/extensions/ql-vscode/scripts/source-map.ts b/extensions/ql-vscode/scripts/source-map.ts
index 62ff6ca06cd..f0e6af88923 100644
--- a/extensions/ql-vscode/scripts/source-map.ts
+++ b/extensions/ql-vscode/scripts/source-map.ts
@@ -41,6 +41,7 @@ async function extractSourceMap() {
   const releaseAssetsDirectory = resolve(
     __dirname,
     "..",
+    "artifacts",
     "release-assets",
     versionNumber,
   );
@@ -64,7 +65,9 @@ async function extractSourceMap() {
     ]);
 
     const sourcemapAsset = release.assets.find(
-      (asset) => asset.name === `vscode-codeql-sourcemaps-${versionNumber}.zip`,
+      (asset) =>
+        asset.label === `vscode-codeql-sourcemaps-${versionNumber}.zip` ||
+        asset.name === "vscode-codeql-sourcemaps.zip",
     );
 
     if (sourcemapAsset) {
@@ -128,7 +131,7 @@ async function extractSourceMap() {
               resolve(sourceMapsDirectory, `${basename(file)}.map`),
             );
             rawSourceMaps.set(file, rawSourceMap);
-          } catch (e: unknown) {
+          } catch (e) {
             // If the file is not found, we will not decode it and not try reading this source map again
             if (e instanceof Error && "code" in e && e.code === "ENOENT") {
               rawSourceMaps.set(file, null);
@@ -213,9 +216,7 @@ extractSourceMap().catch((e: unknown) => {
 function runGh(args: readonly string[]): string {
   const gh = spawnSync("gh", args);
   if (gh.status !== 0) {
-    throw new Error(
-      `Failed to get the source map for ${versionNumber}: ${gh.stderr}`,
-    );
+    throw new Error(`Failed to run gh ${args.join(" ")}: ${gh.stderr}`);
   }
   return gh.stdout.toString("utf-8");
 }
@@ -227,6 +228,7 @@ function runGhJSON<T>(args: readonly string[]): T {
 type ReleaseAsset = {
   id: string;
   name: string;
+  label: string;
 };
 
 type Release = {
diff --git a/extensions/ql-vscode/scripts/update-node-version.ts b/extensions/ql-vscode/scripts/update-node-version.ts
index b07cfb88a3d..8f412a3a683 100644
--- a/extensions/ql-vscode/scripts/update-node-version.ts
+++ b/extensions/ql-vscode/scripts/update-node-version.ts
@@ -1,8 +1,9 @@
 import { join, resolve } from "path";
 import { execSync } from "child_process";
-import { outputFile, readFile, readJSON } from "fs-extra";
+import { outputFile, readJSON } from "fs-extra";
 import { getVersionInformation } from "./util/vscode-versions";
 import { fetchJson } from "./util/fetch";
+import { SemVer } from "semver";
 
 const extensionDirectory = resolve(__dirname, "..");
 
@@ -10,6 +11,29 @@ interface Release {
   tag_name: string;
 }
 
+interface NpmViewError {
+  error: {
+    code: string;
+    summary: string;
+    detail: string;
+  };
+}
+
+interface ExecError extends Error {
+  status: number;
+  stdout: string;
+}
+
+function isExecError(e: unknown): e is ExecError {
+  return (
+    e instanceof Error &&
+    "status" in e &&
+    typeof e.status === "number" &&
+    "stdout" in e &&
+    typeof e.stdout === "string"
+  );
+}
+
 async function updateNodeVersion() {
   const latestVsCodeRelease = await fetchJson<Release>(
     "https://api.github.com/repos/microsoft/vscode/releases/latest",
@@ -23,19 +47,7 @@ async function updateNodeVersion() {
     `VS Code ${versionInformation.vscodeVersion} uses Electron ${versionInformation.electronVersion} and Node ${versionInformation.nodeVersion}`,
   );
 
-  let currentNodeVersion = (
-    await readFile(join(extensionDirectory, ".nvmrc"), "utf8")
-  ).trim();
-  if (currentNodeVersion.startsWith("v")) {
-    currentNodeVersion = currentNodeVersion.slice(1);
-  }
-
-  if (currentNodeVersion === versionInformation.nodeVersion) {
-    console.log("Node version is already up to date");
-    return;
-  }
-
-  console.log("Node version needs to be updated, updating now");
+  console.log("Updating files related to the Node version");
 
   await outputFile(
     join(extensionDirectory, ".nvmrc"),
@@ -49,6 +61,8 @@ async function updateNodeVersion() {
     "utf8",
   );
 
+  const nodeVersion = new SemVer(versionInformation.nodeVersion);
+
   // The @types/node version needs to match the first two parts of the Node
   // version, e.g. if the Node version is 18.17.3, the @types/node version
   // should be 18.17.*. This corresponds with the documentation at
@@ -56,13 +70,56 @@ async function updateNodeVersion() {
   // "The patch version of the type declaration package is unrelated to the library patch version. This allows
   // Definitely Typed to safely update type declarations for the same major/minor version of a library."
   // 18.17.* is equivalent to >=18.17.0 <18.18.0
-  const typesNodeVersion = versionInformation.nodeVersion
-    .split(".")
-    .slice(0, 2)
-    .join(".");
+  // In some cases, the @types/node version matching the exact Node version may not exist, in which case we'll try
+  // the next lower minor version, and so on, until we find a version that exists.
+  const typesNodeSemver = new SemVer(nodeVersion);
+  typesNodeSemver.patch = 0;
+
+  // eslint-disable-next-line no-constant-condition
+  while (true) {
+    const typesNodeVersion = `${typesNodeSemver.major}.${typesNodeSemver.minor}.*`;
+
+    try {
+      // Check that this version actually exists
+      console.log(`Checking if @types/node@${typesNodeVersion} exists`);
+
+      execSync(`npm view --json "@types/node@${typesNodeVersion}"`, {
+        encoding: "utf-8",
+        stdio: "pipe",
+        maxBuffer: 10 * 1024 * 1024,
+      });
+
+      console.log(`@types/node@${typesNodeVersion} exists`);
+
+      // If it exists, we can break out of this loop
+      break;
+    } catch (e) {
+      if (!isExecError(e)) {
+        throw e;
+      }
+
+      const error = JSON.parse(e.stdout) as NpmViewError;
+      if (error.error.code !== "E404") {
+        throw new Error(error.error.detail);
+      }
+
+      console.log(
+        `@types/node package doesn't exist for ${typesNodeVersion}, trying a lower version (${error.error.summary})`,
+      );
+
+      // This means the version doesn't exist, so we'll try decrementing the minor version
+      typesNodeSemver.minor -= 1;
+      if (typesNodeSemver.minor < 0) {
+        throw new Error(
+          `Could not find a suitable @types/node version for Node ${nodeVersion.format()}`,
+        );
+      }
+    }
+  }
 
   packageJson.engines.node = `^${versionInformation.nodeVersion}`;
-  packageJson.devDependencies["@types/node"] = `${typesNodeVersion}.*`;
+  packageJson.devDependencies["@types/node"] =
+    `${typesNodeSemver.major}.${typesNodeSemver.minor}.*`;
 
   await outputFile(
     join(extensionDirectory, "package.json"),
diff --git a/extensions/ql-vscode/src/codeql-cli/cli-version.ts b/extensions/ql-vscode/src/codeql-cli/cli-version.ts
index 94f1169c30a..ebd30cbdb62 100644
--- a/extensions/ql-vscode/src/codeql-cli/cli-version.ts
+++ b/extensions/ql-vscode/src/codeql-cli/cli-version.ts
@@ -10,9 +10,7 @@ interface VersionResult {
 }
 
 export interface CliFeatures {
-  featuresInVersionResult?: boolean;
-  mrvaPackCreate?: boolean;
-  generateSummarySymbolMap?: boolean;
+  queryServerRunQueries?: boolean;
 }
 
 export interface VersionAndFeatures {
diff --git a/extensions/ql-vscode/src/codeql-cli/cli.ts b/extensions/ql-vscode/src/codeql-cli/cli.ts
index 9ccdd9362b7..6ead0b338fc 100644
--- a/extensions/ql-vscode/src/codeql-cli/cli.ts
+++ b/extensions/ql-vscode/src/codeql-cli/cli.ts
@@ -1,9 +1,9 @@
 import { EOL } from "os";
-import { spawn } from "child-process-promise";
+import { spawn } from "cross-spawn";
 import type { ChildProcessWithoutNullStreams } from "child_process";
 import { spawn as spawnChildProcess } from "child_process";
 import { readFile } from "fs-extra";
-import { delimiter, dirname, join } from "path";
+import { delimiter, join } from "path";
 import type { Log } from "sarif";
 import { SemVer } from "semver";
 import type { Readable } from "stream";
@@ -19,6 +19,7 @@ import type { CliConfig } from "../config";
 import type { DistributionProvider } from "./distribution";
 import { FindDistributionResultKind } from "./distribution";
 import {
+  asError,
   assertNever,
   getErrorMessage,
   getErrorStack,
@@ -37,6 +38,7 @@ import { LOGGING_FLAGS } from "./cli-command";
 import type { CliFeatures, VersionAndFeatures } from "./cli-version";
 import { ExitCodeError, getCliError } from "./cli-errors";
 import { UserCancellationException } from "../common/vscode/progress";
+import type { LanguageClient } from "vscode-languageclient/node";
 
 /**
  * The version of the SARIF format that we are using.
@@ -91,15 +93,6 @@ export type QlpacksInfo = { [name: string]: string[] };
  */
 type LanguagesInfo = { [name: string]: string[] };
 
-/** Information about an ML model, as resolved by `codeql resolve ml-models`. */
-type MlModelInfo = {
-  checksum: string;
-  path: string;
-};
-
-/** The expected output of `codeql resolve ml-models`. */
-type MlModelsInfo = { models: MlModelInfo[] };
-
 /** Information about a data extension predicate, as resolved by `codeql resolve extensions`. */
 type DataExtensionResult = {
   predicate: string;
@@ -109,7 +102,6 @@ type DataExtensionResult = {
 
 /** The expected output of `codeql resolve extensions`. */
 type ResolveExtensionsResult = {
-  models: MlModelInfo[];
   data: {
     [path: string]: DataExtensionResult[];
   };
@@ -287,6 +279,7 @@ export class CodeQLCliServer implements Disposable {
 
   constructor(
     private readonly app: App,
+    private readonly languageClient: LanguageClient,
     private distributionProvider: DistributionProvider,
     private cliConfig: CliConfig,
     public readonly logger: Logger,
@@ -321,7 +314,7 @@ export class CodeQLCliServer implements Disposable {
       } catch (e) {
         // We are probably fine here, the process has already closed stdin.
         void this.logger.log(
-          `Shutdown request failed: process stdin may have already closed. The error was ${e}`,
+          `Shutdown request failed: process stdin may have already closed. The error was ${getErrorMessage(e)}`,
         );
         void this.logger.log("Stopping the process anyway.");
       }
@@ -726,13 +719,7 @@ export class CodeQLCliServer implements Disposable {
 
     // Spawn the CodeQL process
     const codeqlPath = await this.getCodeQlPath();
-    const childPromise = spawn(codeqlPath, args);
-    // Avoid a runtime message about unhandled rejection.
-    childPromise.catch(() => {
-      /**/
-    });
-
-    const child = childPromise.childProcess;
+    const child = spawn(codeqlPath, args);
 
     let cancellationRegistration: Disposable | undefined = undefined;
     try {
@@ -745,16 +732,28 @@ export class CodeQLCliServer implements Disposable {
       }
       if (logger !== undefined) {
         // The human-readable output goes to stderr.
-        void logStream(child.stderr!, logger);
+        void logStream(child.stderr, logger);
       }
 
-      for await (const event of splitStreamAtSeparators(child.stdout!, [
-        "\0",
-      ])) {
+      for await (const event of splitStreamAtSeparators(child.stdout, ["\0"])) {
         yield event;
       }
 
-      await childPromise;
+      await new Promise((resolve, reject) => {
+        child.on("error", reject);
+
+        child.on("close", (code) => {
+          if (code === 0) {
+            resolve(undefined);
+          } else {
+            reject(
+              new Error(
+                `${command.join(" ")} ${commandArgs.join(" ")} failed with code ${code}`,
+              ),
+            );
+          }
+        });
+      });
     } finally {
       if (cancellationRegistration !== undefined) {
         cancellationRegistration.dispose();
@@ -853,7 +852,7 @@ export class CodeQLCliServer implements Disposable {
             silent,
           ).then(resolve, reject);
         } catch (err) {
-          reject(err);
+          reject(asError(err));
         }
       };
       // If the server is not running a command, then run the given command immediately,
@@ -943,7 +942,7 @@ export class CodeQLCliServer implements Disposable {
           if (line.startsWith("Enter value for --github-auth-stdin")) {
             try {
               return await this.app.credentials.getAccessToken();
-            } catch (e) {
+            } catch {
               // If the user cancels the authentication prompt, we still need to give a value to the CLI.
               // By giving a potentially invalid value, the user will just get a 401/403 when they try to access a
               // private package and the access token is invalid.
@@ -980,7 +979,7 @@ export class CodeQLCliServer implements Disposable {
         subcommandArgs,
         "Resolving query by language",
       ),
-    );
+    ) as QueryInfoByLanguage;
   }
 
   /**
@@ -1097,24 +1096,6 @@ export class CodeQLCliServer implements Disposable {
     );
   }
 
-  /** Resolves the ML models that should be available when evaluating a query. */
-  async resolveMlModels(
-    additionalPacks: string[],
-    queryPath: string,
-  ): Promise<MlModelsInfo> {
-    const args =
-      // use the dirname of the path so that we can handle query libraries
-      [...this.getAdditionalPacksArg(additionalPacks), dirname(queryPath)];
-    return await this.runJsonCodeQlCliCommand<MlModelsInfo>(
-      ["resolve", "ml-models"],
-      args,
-      "Resolving ML models",
-      {
-        addFormat: false,
-      },
-    );
-  }
-
   /**
    * Gets the RAM setting for the query server.
    * @param queryMemoryMb The maximum amount of RAM to use, in MB.
@@ -1211,15 +1192,12 @@ export class CodeQLCliServer implements Disposable {
     outputPath: string,
     endSummaryPath: string,
   ): Promise<string> {
-    const supportsGenerateSummarySymbolMap =
-      await this.cliConstraints.supportsGenerateSummarySymbolMap();
     const subcommandArgs = [
       "--format=text",
       `--end-summary=${endSummaryPath}`,
       "--sourcemap",
-      ...(supportsGenerateSummarySymbolMap
-        ? ["--summary-symbol-map", "--minify-output"]
-        : []),
+      "--summary-symbol-map",
+      "--minify-output",
       inputPath,
       outputPath,
     ];
@@ -1606,11 +1584,13 @@ export class CodeQLCliServer implements Disposable {
   async packAdd(dir: string, queryLanguage: QueryLanguage) {
     const args = ["--dir", dir];
     args.push(`codeql/${queryLanguage}-all`);
-    return this.runCodeQlCliCommand(
+    const ret = await this.runCodeQlCliCommand(
       ["pack", "add"],
       args,
       `Adding and installing ${queryLanguage} pack dependency.`,
     );
+    await this.notifyPackInstalled();
+    return ret;
   }
 
   /**
@@ -1645,16 +1625,18 @@ export class CodeQLCliServer implements Disposable {
       args.push(
         // Allow prerelease packs from the ql submodule.
         "--allow-prerelease",
-        // Allow the use of --additional-packs argument without issueing a warning
+        // Allow the use of --additional-packs argument without issuing a warning
         "--no-strict-mode",
         ...this.getAdditionalPacksArg(workspaceFolders),
       );
     }
-    return this.runJsonCodeQlCliCommandWithAuthentication(
+    const ret = await this.runJsonCodeQlCliCommandWithAuthentication(
       ["pack", "install"],
       args,
       "Installing pack dependencies",
     );
+    await this.notifyPackInstalled();
+    return ret;
   }
 
   /**
@@ -1772,6 +1754,17 @@ export class CodeQLCliServer implements Disposable {
     this._versionChangedListeners.push(listener);
   }
 
+  /**
+   * This method should be called after a pack has been installed.
+   *
+   * This restarts the language client. Restarting the language client has the
+   * effect of removing compilation errors in open ql/qll files that are caused
+   * by the pack not having been installed previously.
+   */
+  private async notifyPackInstalled() {
+    await this.languageClient.restart();
+  }
+
   private async refreshVersion(): Promise<VersionAndFeatures> {
     const distribution = await this.distributionProvider.getDistribution();
     switch (distribution.kind) {
@@ -1842,7 +1835,7 @@ export function spawnServer(
   }
 
   let lastStdout: string | Buffer | undefined = undefined;
-  child.stdout!.on("data", (data) => {
+  child.stdout.on("data", (data) => {
     lastStdout = data;
   });
   // Set up event listeners.
@@ -1861,9 +1854,9 @@ export function spawnServer(
       void logger.log(`Last stdout was "${lastStdout.toString()}"`);
     }
   });
-  child.stderr!.on("data", stderrListener);
+  child.stderr.on("data", stderrListener);
   if (stdoutListener !== undefined) {
-    child.stdout!.on("data", stdoutListener);
+    child.stdout.on("data", stdoutListener);
   }
 
   if (progressReporter !== undefined) {
@@ -1909,43 +1902,13 @@ function shouldDebugCliServer() {
 export class CliVersionConstraint {
   // The oldest version of the CLI that we support. This is used to determine
   // whether to show a warning about the CLI being too old on startup.
-  public static OLDEST_SUPPORTED_CLI_VERSION = new SemVer("v2.15.5");
-
-  public static CLI_VERSION_WITHOUT_MRVA_EXTENSIBLE_PREDICATE_HACK = new SemVer(
-    "2.16.1",
-  );
-
-  /**
-   * CLI version where there is support for multiple queries on the pack create command.
-   */
-  public static CLI_VERSION_WITH_MULTI_QUERY_PACK_CREATE = new SemVer("2.16.1");
+  public static OLDEST_SUPPORTED_CLI_VERSION = new SemVer("2.20.7");
 
   constructor(private readonly cli: CodeQLCliServer) {
     /**/
   }
 
-  private async isVersionAtLeast(v: SemVer) {
-    return (await this.cli.getVersion()).compare(v) >= 0;
-  }
-
-  async preservesExtensiblePredicatesInMrvaPack() {
-    // Negated, because we _stopped_ preserving these in 2.16.1.
-    return !(await this.isVersionAtLeast(
-      CliVersionConstraint.CLI_VERSION_WITHOUT_MRVA_EXTENSIBLE_PREDICATE_HACK,
-    ));
-  }
-
-  async supportsPackCreateWithMultipleQueries() {
-    return this.isVersionAtLeast(
-      CliVersionConstraint.CLI_VERSION_WITH_MULTI_QUERY_PACK_CREATE,
-    );
-  }
-
-  async supportsMrvaPackCreate(): Promise<boolean> {
-    return (await this.cli.getFeatures()).mrvaPackCreate === true;
-  }
-
-  async supportsGenerateSummarySymbolMap(): Promise<boolean> {
-    return (await this.cli.getFeatures()).generateSummarySymbolMap === true;
+  async supportsQueryServerRunQueries(): Promise<boolean> {
+    return (await this.cli.getFeatures()).queryServerRunQueries === true;
   }
 }
diff --git a/extensions/ql-vscode/src/codeql-cli/distribution.ts b/extensions/ql-vscode/src/codeql-cli/distribution.ts
index 223bf5fe50a..35bbb7acf16 100644
--- a/extensions/ql-vscode/src/codeql-cli/distribution.ts
+++ b/extensions/ql-vscode/src/codeql-cli/distribution.ts
@@ -1,5 +1,12 @@
 import type { WriteStream } from "fs";
-import { createWriteStream, mkdtemp, pathExists, remove } from "fs-extra";
+import {
+  createWriteStream,
+  mkdtemp,
+  outputJson,
+  pathExists,
+  readJson,
+  remove,
+} from "fs-extra";
 import { tmpdir } from "os";
 import { delimiter, dirname, join } from "path";
 import { Range, satisfies } from "semver";
@@ -19,7 +26,9 @@ import {
   InvocationRateLimiter,
   InvocationRateLimiterResultKind,
 } from "../common/invocation-rate-limiter";
+import type { NotificationLogger } from "../common/logging";
 import {
+  showAndLogExceptionWithTelemetry,
   showAndLogErrorMessage,
   showAndLogWarningMessage,
 } from "../common/logging";
@@ -28,7 +37,12 @@ import { reportUnzipProgress } from "../common/vscode/unzip-progress";
 import type { Release } from "./distribution/release";
 import { ReleasesApiConsumer } from "./distribution/releases-api-consumer";
 import { createTimeoutSignal } from "../common/fetch-stream";
-import { AbortError } from "node-fetch";
+import { withDistributionUpdateLock } from "./lock";
+import { asError, getErrorMessage } from "../common/helpers-pure";
+import { isIOError } from "../common/files";
+import { telemetryListener } from "../common/vscode/telemetry";
+import { redactableError } from "../common/errors";
+import { ExtensionManagedDistributionCleaner } from "./distribution/cleaner";
 
 /**
  * distribution.ts
@@ -54,6 +68,11 @@ const NIGHTLY_DISTRIBUTION_REPOSITORY_NWO = "dsp-testing/codeql-cli-nightlies";
  */
 export const DEFAULT_DISTRIBUTION_VERSION_RANGE: Range = new Range("2.x");
 
+export interface DistributionState {
+  folderIndex: number;
+  release: Release | null;
+}
+
 export interface DistributionProvider {
   getCodeQlPathWithoutVersionCheck(): Promise<string | undefined>;
   onDidChangeDistribution?: Event<void>;
@@ -65,6 +84,7 @@ export class DistributionManager implements DistributionProvider {
     public readonly config: DistributionConfig,
     private readonly versionRange: Range,
     extensionContext: ExtensionContext,
+    logger: NotificationLogger,
   ) {
     this._onDidChangeDistribution = config.onDidChangeConfiguration;
     this.extensionSpecificDistributionManager =
@@ -72,6 +92,7 @@ export class DistributionManager implements DistributionProvider {
         config,
         versionRange,
         extensionContext,
+        logger,
       );
     this.updateCheckRateLimiter = new InvocationRateLimiter(
       extensionContext.globalState,
@@ -79,6 +100,16 @@ export class DistributionManager implements DistributionProvider {
       () =>
         this.extensionSpecificDistributionManager.checkForUpdatesToDistribution(),
     );
+    this.extensionManagedDistributionCleaner =
+      new ExtensionManagedDistributionCleaner(
+        extensionContext,
+        logger,
+        this.extensionSpecificDistributionManager,
+      );
+  }
+
+  public async initialize(): Promise<void> {
+    await this.extensionSpecificDistributionManager.initialize();
   }
 
   /**
@@ -256,6 +287,10 @@ export class DistributionManager implements DistributionProvider {
     );
   }
 
+  public startCleanup() {
+    this.extensionManagedDistributionCleaner.start();
+  }
+
   public get onDidChangeDistribution(): Event<void> | undefined {
     return this._onDidChangeDistribution;
   }
@@ -277,18 +312,63 @@ export class DistributionManager implements DistributionProvider {
 
   private readonly extensionSpecificDistributionManager: ExtensionSpecificDistributionManager;
   private readonly updateCheckRateLimiter: InvocationRateLimiter<DistributionUpdateCheckResult>;
+  private readonly extensionManagedDistributionCleaner: ExtensionManagedDistributionCleaner;
   private readonly _onDidChangeDistribution: Event<void> | undefined;
 }
 
 class ExtensionSpecificDistributionManager {
+  private distributionState: DistributionState | undefined;
+
   constructor(
     private readonly config: DistributionConfig,
     private readonly versionRange: Range,
     private readonly extensionContext: ExtensionContext,
+    private readonly logger: NotificationLogger,
   ) {
     /**/
   }
 
+  public async initialize() {
+    await this.ensureDistributionStateExists();
+  }
+
+  private async ensureDistributionStateExists() {
+    const distributionStatePath = this.getDistributionStatePath();
+    try {
+      this.distributionState = await readJson(distributionStatePath);
+    } catch (e) {
+      if (isIOError(e) && e.code === "ENOENT") {
+        // If the file doesn't exist, that just means we need to create it
+
+        this.distributionState = {
+          folderIndex:
+            this.extensionContext.globalState.get(
+              "distributionFolderIndex",
+              0,
+            ) ?? 0,
+          release:
+            this.extensionContext.globalState.get("distributionRelease") ??
+            null,
+        };
+
+        // This may result in a race condition, but when this happens both processes should write the same file.
+        await outputJson(distributionStatePath, this.distributionState);
+      } else {
+        void showAndLogExceptionWithTelemetry(
+          this.logger,
+          telemetryListener,
+          redactableError(
+            asError(e),
+          )`Failed to read distribution state from ${distributionStatePath}: ${getErrorMessage(e)}`,
+        );
+        this.distributionState = {
+          folderIndex: 0,
+          release: null,
+        };
+      }
+    }
+  }
+
   public async getCodeQlPathWithoutVersionCheck(): Promise<string | undefined> {
     if (this.getInstalledRelease() !== undefined) {
       // An extension specific distribution has been installed.
@@ -305,7 +385,7 @@ class ExtensionSpecificDistributionManager {
       } catch (e) {
         void extLogger.log(
           "WARNING: Tried to remove corrupted CodeQL CLI at " +
-            `${this.getDistributionStoragePath()} but encountered an error: ${e}.`,
+            `${this.getDistributionStoragePath()} but encountered an error: ${getErrorMessage(e)}.`,
         );
       }
     }
@@ -351,9 +431,21 @@ class ExtensionSpecificDistributionManager {
     release: Release,
     progressCallback?: ProgressCallback,
   ): Promise<void> {
-    await this.downloadDistribution(release, progressCallback);
-    // Store the installed release within the global extension state.
-    await this.storeInstalledRelease(release);
+    if (!this.distributionState) {
+      await this.ensureDistributionStateExists();
+    }
+
+    const distributionStatePath = this.getDistributionStatePath();
+
+    await withDistributionUpdateLock(
+      // .lock will be appended to this filename
+      distributionStatePath,
+      async () => {
+        await this.downloadDistribution(release, progressCallback);
+        // Store the installed release within the global extension state.
+        await this.storeInstalledRelease(release);
+      },
+    );
   }
 
   private async downloadDistribution(
@@ -365,7 +457,7 @@ class ExtensionSpecificDistributionManager {
     } catch (e) {
       void extLogger.log(
         `Tried to clean up old version of CLI at ${this.getDistributionStoragePath()} ` +
-          `but encountered an error: ${e}.`,
+          `but encountered an error: ${getErrorMessage(e)}.`,
       );
     }
 
@@ -404,6 +496,11 @@ class ExtensionSpecificDistributionManager {
           signal,
         );
 
+      const body = assetStream.body;
+      if (!body) {
+        throw new Error("No body in asset stream");
+      }
+
       const archivePath = join(tmpDirectory, "distributionDownload.zip");
       archiveFile = createWriteStream(archivePath);
 
@@ -411,27 +508,40 @@ class ExtensionSpecificDistributionManager {
       const totalNumBytes = contentLength
         ? parseInt(contentLength, 10)
         : undefined;
-      reportStreamProgress(
-        assetStream.body,
+
+      const reportProgress = reportStreamProgress(
         `Downloading CodeQL CLI ${release.name}…`,
         totalNumBytes,
         progressCallback,
       );
 
-      assetStream.body.on("data", onData);
-
-      await new Promise((resolve, reject) => {
-        if (!archiveFile) {
-          throw new Error("Invariant violation: archiveFile not set");
+      const reader = body.getReader();
+      for (;;) {
+        const { done, value } = await reader.read();
+        if (done) {
+          break;
         }
 
-        assetStream.body
-          .pipe(archiveFile)
-          .on("finish", resolve)
-          .on("error", reject);
+        onData();
+        reportProgress(value?.length ?? 0);
+
+        await new Promise((resolve, reject) => {
+          archiveFile?.write(value, (err) => {
+            if (err) {
+              reject(err);
+            }
+            resolve(undefined);
+          });
+        });
+      }
 
-        // If an error occurs on the body, we also want to reject the promise (e.g. during a timeout error).
-        assetStream.body.on("error", reject);
+      await new Promise((resolve, reject) => {
+        archiveFile?.close((err) => {
+          if (err) {
+            reject(err);
+          }
+          resolve(undefined);
+        });
       });
 
       disposeTimeout();
@@ -452,8 +562,8 @@ class ExtensionSpecificDistributionManager {
           : undefined,
       );
     } catch (e) {
-      if (e instanceof AbortError) {
-        const thrownError = new AbortError("The download timed out.");
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The download timed out.");
         thrownError.stack = e.stack;
         throw thrownError;
       }
@@ -547,23 +657,19 @@ class ExtensionSpecificDistributionManager {
   }
 
   private async bumpDistributionFolderIndex(): Promise<void> {
-    const index = this.extensionContext.globalState.get(
-      ExtensionSpecificDistributionManager._currentDistributionFolderIndexStateKey,
-      0,
-    );
-    await this.extensionContext.globalState.update(
-      ExtensionSpecificDistributionManager._currentDistributionFolderIndexStateKey,
-      index + 1,
-    );
+    await this.updateState((oldState) => {
+      return {
+        ...oldState,
+        folderIndex: (oldState.folderIndex ?? 0) + 1,
+      };
+    });
   }
 
   private getDistributionStoragePath(): string {
+    const distributionState = this.getDistributionState();
+
     // Use an empty string for the initial distribution for backwards compatibility.
-    const distributionFolderIndex =
-      this.extensionContext.globalState.get(
-        ExtensionSpecificDistributionManager._currentDistributionFolderIndexStateKey,
-        0,
-      ) || "";
+    const distributionFolderIndex = distributionState.folderIndex || "";
     return join(
       this.extensionContext.globalStorageUri.fsPath,
       ExtensionSpecificDistributionManager._currentDistributionFolderBaseName +
@@ -578,26 +684,65 @@ class ExtensionSpecificDistributionManager {
     );
   }
 
-  private getInstalledRelease(): Release | undefined {
-    return this.extensionContext.globalState.get(
-      ExtensionSpecificDistributionManager._installedReleaseStateKey,
+  private getDistributionStatePath(): string {
+    return join(
+      this.extensionContext.globalStorageUri.fsPath,
+      ExtensionSpecificDistributionManager._distributionStateFilename,
     );
   }
 
+  private getInstalledRelease(): Release | undefined {
+    return this.getDistributionState().release ?? undefined;
+  }
+
   private async storeInstalledRelease(
     release: Release | undefined,
   ): Promise<void> {
-    await this.extensionContext.globalState.update(
-      ExtensionSpecificDistributionManager._installedReleaseStateKey,
-      release,
-    );
+    await this.updateState((oldState) => ({
+      ...oldState,
+      release: release ?? null,
+    }));
+  }
+
+  private getDistributionState(): DistributionState {
+    const distributionState = this.distributionState;
+    if (distributionState === undefined) {
+      throw new Error(
+        "Invariant violation: distribution state not initialized",
+      );
+    }
+    return distributionState;
+  }
+
+  private async updateState(
+    f: (oldState: DistributionState) => DistributionState,
+  ) {
+    const oldState = this.distributionState;
+    if (oldState === undefined) {
+      throw new Error(
+        "Invariant violation: distribution state not initialized",
+      );
+    }
+    const newState = f(oldState);
+    this.distributionState = newState;
+
+    const distributionStatePath = this.getDistributionStatePath();
+    await outputJson(distributionStatePath, newState);
+  }
+
+  public get folderIndex() {
+    const distributionState = this.getDistributionState();
+
+    return distributionState.folderIndex;
+  }
+
+  public get distributionFolderPrefix() {
+    return ExtensionSpecificDistributionManager._currentDistributionFolderBaseName;
   }
 
   private static readonly _currentDistributionFolderBaseName = "distribution";
-  private static readonly _currentDistributionFolderIndexStateKey =
-    "distributionFolderIndex";
-  private static readonly _installedReleaseStateKey = "distributionRelease";
   private static readonly _codeQlExtractedFolderName = "codeql";
+  private static readonly _distributionStateFilename = "distribution.json";
 }
 
 /*
diff --git a/extensions/ql-vscode/src/codeql-cli/distribution/cleaner.ts b/extensions/ql-vscode/src/codeql-cli/distribution/cleaner.ts
new file mode 100644
index 00000000000..0b236cf66bd
--- /dev/null
+++ b/extensions/ql-vscode/src/codeql-cli/distribution/cleaner.ts
@@ -0,0 +1,127 @@
+import type { ExtensionContext } from "vscode";
+import { getDirectoryNamesInsidePath, isIOError } from "../../common/files";
+import { sleep } from "../../common/time";
+import type { BaseLogger } from "../../common/logging";
+import { join } from "path";
+import { getErrorMessage } from "../../common/helpers-pure";
+import { pathExists, remove } from "fs-extra";
+
+interface ExtensionManagedDistributionManager {
+  folderIndex: number;
+  distributionFolderPrefix: string;
+}
+
+interface DistributionDirectory {
+  directoryName: string;
+  folderIndex: number;
+}
+
+/**
+ * This class is responsible for cleaning up old distributions that are no longer needed. In normal operation, this
+ * should not be necessary as the old distribution is deleted when the distribution is updated. However, in some cases
+ * the extension may leave behind old distribution which can result in a significant amount of space (> 100 GB) being
+ * taking up by unused distributions.
+ */
+export class ExtensionManagedDistributionCleaner {
+  constructor(
+    private readonly extensionContext: ExtensionContext,
+    private readonly logger: BaseLogger,
+    private readonly manager: ExtensionManagedDistributionManager,
+  ) {}
+
+  public start() {
+    // Intentionally starting this without waiting for it
+    void this.cleanup().catch((e: unknown) => {
+      void this.logger.log(
+        `Failed to clean up old versions of the CLI: ${getErrorMessage(e)}`,
+      );
+    });
+  }
+
+  public async cleanup() {
+    if (!(await pathExists(this.extensionContext.globalStorageUri.fsPath))) {
+      return;
+    }
+
+    const currentFolderIndex = this.manager.folderIndex;
+
+    const distributionDirectoryRegex = new RegExp(
+      `^${this.manager.distributionFolderPrefix}(\\d+)$`,
+    );
+
+    const existingDirectories = await getDirectoryNamesInsidePath(
+      this.extensionContext.globalStorageUri.fsPath,
+    );
+    const distributionDirectories = existingDirectories
+      .map((dir): DistributionDirectory | null => {
+        const match = dir.match(distributionDirectoryRegex);
+        if (!match) {
+          // When the folderIndex is 0, the distributionFolderPrefix is used as the directory name
+          if (dir === this.manager.distributionFolderPrefix) {
+            return {
+              directoryName: dir,
+              folderIndex: 0,
+            };
+          }
+
+          return null;
+        }
+
+        return {
+          directoryName: dir,
+          folderIndex: parseInt(match[1]),
+        };
+      })
+      .filter((dir) => dir !== null);
+
+    // Clean up all directories that are older than the current one
+    const cleanableDirectories = distributionDirectories.filter(
+      (dir) => dir.folderIndex < currentFolderIndex,
+    );
+
+    if (cleanableDirectories.length === 0) {
+      return;
+    }
+
+    // Shuffle the array so that multiple VS Code processes don't all try to clean up the same directory at the same time
+    for (let i = cleanableDirectories.length - 1; i > 0; i--) {
+      const j = Math.floor(Math.random() * (i + 1));
+      [cleanableDirectories[i], cleanableDirectories[j]] = [
+        cleanableDirectories[j],
+        cleanableDirectories[i],
+      ];
+    }
+
+    void this.logger.log(
+      `Cleaning up ${cleanableDirectories.length} old versions of the CLI.`,
+    );
+
+    for (const cleanableDirectory of cleanableDirectories) {
+      // Wait 10 seconds between each cleanup to avoid overloading the system (even though the remove call should be async)
+      await sleep(10_000);
+
+      const path = join(
+        this.extensionContext.globalStorageUri.fsPath,
+        cleanableDirectory.directoryName,
+      );
+
+      // Delete this directory
+      try {
+        await remove(path);
+      } catch (e) {
+        if (isIOError(e) && e.code === "ENOENT") {
+          // If the directory doesn't exist, that's fine
+          continue;
+        }
+
+        void this.logger.log(
+          `Tried to clean up an old version of the CLI at ${path} but encountered an error: ${getErrorMessage(e)}.`,
+        );
+      }
+    }
+
+    void this.logger.log(
+      `Cleaned up ${cleanableDirectories.length} old versions of the CLI.`,
+    );
+  }
+}
diff --git a/extensions/ql-vscode/src/codeql-cli/distribution/releases-api-consumer.ts b/extensions/ql-vscode/src/codeql-cli/distribution/releases-api-consumer.ts
index ff482a7b2c3..4b28af44423 100644
--- a/extensions/ql-vscode/src/codeql-cli/distribution/releases-api-consumer.ts
+++ b/extensions/ql-vscode/src/codeql-cli/distribution/releases-api-consumer.ts
@@ -1,5 +1,3 @@
-import type { Response } from "node-fetch";
-import { default as fetch } from "node-fetch";
 import type { Range } from "semver";
 import { compare, parse, satisfies } from "semver";
 import { URL } from "url";
@@ -34,9 +32,9 @@ export class ReleasesApiConsumer {
     additionalCompatibilityCheck?: (release: GithubRelease) => boolean,
   ): Promise<Release> {
     const apiPath = `/repos/${this.repositoryNwo}/releases`;
-    const allReleases: GithubRelease[] = await (
+    const allReleases = (await (
       await this.makeApiCall(apiPath)
-    ).json();
+    ).json()) as GithubRelease[];
     const compatibleReleases = allReleases.filter((release) => {
       if (release.prerelease && !includePrerelease) {
         return false;
diff --git a/extensions/ql-vscode/src/codeql-cli/lock.ts b/extensions/ql-vscode/src/codeql-cli/lock.ts
new file mode 100644
index 00000000000..8dfc84d98d9
--- /dev/null
+++ b/extensions/ql-vscode/src/codeql-cli/lock.ts
@@ -0,0 +1,22 @@
+import { lock } from "proper-lockfile";
+
+export async function withDistributionUpdateLock(
+  lockFile: string,
+  f: () => Promise<void>,
+) {
+  const release = await lock(lockFile, {
+    stale: 60_000, // 1 minute. We can take the lock longer than this because that's based on the update interval.
+    update: 10_000, // 10 seconds
+    retries: {
+      minTimeout: 10_000,
+      maxTimeout: 60_000,
+      retries: 100,
+    },
+  });
+
+  try {
+    await f();
+  } finally {
+    await release();
+  }
+}
diff --git a/extensions/ql-vscode/src/codeql-cli/query-language.ts b/extensions/ql-vscode/src/codeql-cli/query-language.ts
index ba327560dde..d5cef76e697 100644
--- a/extensions/ql-vscode/src/codeql-cli/query-language.ts
+++ b/extensions/ql-vscode/src/codeql-cli/query-language.ts
@@ -36,7 +36,7 @@ export async function findLanguage(
       void extLogger.log(
         "Query language is unsupported. Select language manually.",
       );
-    } catch (e) {
+    } catch {
       void extLogger.log(
         "Could not autodetect query language. Select language manually.",
       );
@@ -89,7 +89,7 @@ export async function askForLanguage(
   if (!isQueryLanguage(language)) {
     void showAndLogErrorMessage(
       extLogger,
-      `Language '${language}' is not supported. Only languages ${Object.values(
+      `Language '${language as string}' is not supported. Only languages ${Object.values(
         QueryLanguage,
       ).join(", ")} are supported.`,
     );
diff --git a/extensions/ql-vscode/src/codeql-cli/query-metadata.ts b/extensions/ql-vscode/src/codeql-cli/query-metadata.ts
index 0991bf952d3..88fe52d49ba 100644
--- a/extensions/ql-vscode/src/codeql-cli/query-metadata.ts
+++ b/extensions/ql-vscode/src/codeql-cli/query-metadata.ts
@@ -1,6 +1,7 @@
 import type { CodeQLCliServer } from "./cli";
 import type { QueryMetadata } from "../common/interface-types";
 import { extLogger } from "../common/logging/vscode";
+import { getErrorMessage } from "../common/helpers-pure";
 
 /**
  * Gets metadata for a query, if it exists.
@@ -16,7 +17,9 @@ export async function tryGetQueryMetadata(
     return await cliServer.resolveMetadata(queryPath);
   } catch (e) {
     // Ignore errors and provide no metadata.
-    void extLogger.log(`Couldn't resolve metadata for ${queryPath}: ${e}`);
+    void extLogger.log(
+      `Couldn't resolve metadata for ${queryPath}: ${getErrorMessage(e)}`,
+    );
     return;
   }
 }
diff --git a/extensions/ql-vscode/src/common/bqrs-cli-types.ts b/extensions/ql-vscode/src/common/bqrs-cli-types.ts
index 2eb565a7215..e9e726957e3 100644
--- a/extensions/ql-vscode/src/common/bqrs-cli-types.ts
+++ b/extensions/ql-vscode/src/common/bqrs-cli-types.ts
@@ -11,6 +11,7 @@ export namespace BqrsColumnKindCode {
   export const BOOLEAN = "b";
   export const DATE = "d";
   export const ENTITY = "e";
+  export const BIGINT = "z";
 }
 
 export type BqrsColumnKind =
@@ -19,7 +20,8 @@ export type BqrsColumnKind =
   | typeof BqrsColumnKindCode.STRING
   | typeof BqrsColumnKindCode.BOOLEAN
   | typeof BqrsColumnKindCode.DATE
-  | typeof BqrsColumnKindCode.ENTITY;
+  | typeof BqrsColumnKindCode.ENTITY
+  | typeof BqrsColumnKindCode.BIGINT;
 
 export interface BqrsSchemaColumn {
   name?: string;
@@ -79,7 +81,8 @@ export type BqrsKind =
   | "Integer"
   | "Boolean"
   | "Date"
-  | "Entity";
+  | "Entity"
+  | "BigInt";
 
 interface BqrsColumn {
   name?: string;
diff --git a/extensions/ql-vscode/src/common/bqrs-raw-results-mapper.ts b/extensions/ql-vscode/src/common/bqrs-raw-results-mapper.ts
index 1074f9b8979..10bd5fe9e33 100644
--- a/extensions/ql-vscode/src/common/bqrs-raw-results-mapper.ts
+++ b/extensions/ql-vscode/src/common/bqrs-raw-results-mapper.ts
@@ -76,6 +76,8 @@ function mapColumnKind(kind: BqrsColumnKind): ColumnKind {
       return ColumnKind.Date;
     case BqrsColumnKindCode.ENTITY:
       return ColumnKind.Entity;
+    case BqrsColumnKindCode.BIGINT:
+      return ColumnKind.BigInt;
     default:
       assertNever(kind);
   }
diff --git a/extensions/ql-vscode/src/common/commands.ts b/extensions/ql-vscode/src/common/commands.ts
index 7b1cadcda7b..64585a8c9e8 100644
--- a/extensions/ql-vscode/src/common/commands.ts
+++ b/extensions/ql-vscode/src/common/commands.ts
@@ -138,6 +138,7 @@ export type LocalQueryCommands = {
   "codeQLQueries.createQuery": () => Promise<void>;
   "codeQL.runLocalQueryFromFileTab": (uri: Uri) => Promise<void>;
   "codeQL.runQueries": ExplorerSelectionCommandFunction<Uri>;
+  "codeQL.runQuerySuite": ExplorerSelectionCommandFunction<Uri>;
   "codeQL.quickEval": (uri: Uri) => Promise<void>;
   "codeQL.quickEvalCount": (uri: Uri) => Promise<void>;
   "codeQL.quickEvalContextEditor": (uri: Uri) => Promise<void>;
@@ -180,6 +181,7 @@ export type QueryHistoryCommands = {
   "codeQLQueryHistory.removeHistoryItemContextInline": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.renameItem": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.compareWith": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.comparePerformanceWith": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.showEvalLog": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.showEvalLogSummary": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.showEvalLogViewer": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
@@ -195,6 +197,7 @@ export type QueryHistoryCommands = {
   "codeQLQueryHistory.itemClicked": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.openOnGithub": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
   "codeQLQueryHistory.copyRepoList": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
+  "codeQLQueryHistory.viewAutofixes": TreeViewContextMultiSelectionCommandFunction<QueryHistoryInfo>;
 
   // Commands in the command palette
   "codeQL.exportSelectedVariantAnalysisResults": () => Promise<void>;
@@ -211,12 +214,14 @@ export type LanguageSelectionCommands = {
 export type LocalDatabasesCommands = {
   // Command palette commands
   "codeQL.chooseDatabaseFolder": () => Promise<void>;
+  "codeQL.chooseDatabaseFoldersParent": () => Promise<void>;
   "codeQL.chooseDatabaseArchive": () => Promise<void>;
   "codeQL.chooseDatabaseInternet": () => Promise<void>;
   "codeQL.chooseDatabaseGithub": () => Promise<void>;
   "codeQL.upgradeCurrentDatabase": () => Promise<void>;
   "codeQL.clearCache": () => Promise<void>;
   "codeQL.trimCache": () => Promise<void>;
+  "codeQL.trimOverlayBaseCache": () => Promise<void>;
 
   // Explorer context menu
   "codeQL.setCurrentDatabase": (uri: Uri) => Promise<void>;
@@ -348,7 +353,9 @@ export type MockGitHubApiServerCommands = {
   "codeQL.mockGitHubApiServer.startRecording": () => Promise<void>;
   "codeQL.mockGitHubApiServer.saveScenario": () => Promise<void>;
   "codeQL.mockGitHubApiServer.cancelRecording": () => Promise<void>;
-  "codeQL.mockGitHubApiServer.loadScenario": () => Promise<void>;
+  "codeQL.mockGitHubApiServer.loadScenario": (
+    scenario?: string,
+  ) => Promise<void>;
   "codeQL.mockGitHubApiServer.unloadScenario": () => Promise<void>;
 };
 
diff --git a/extensions/ql-vscode/src/common/github-url-identifier-helper.ts b/extensions/ql-vscode/src/common/github-url-identifier-helper.ts
index 3f5a8e2dbe7..1ea4e327b9d 100644
--- a/extensions/ql-vscode/src/common/github-url-identifier-helper.ts
+++ b/extensions/ql-vscode/src/common/github-url-identifier-helper.ts
@@ -78,7 +78,7 @@ function getNwoOrOwnerFromGitHubUrl(
     }
     const nwo = `${paths[0]}/${paths[1]}`;
     return paths[1] ? nwo : undefined;
-  } catch (e) {
+  } catch {
     // Ignore the error here, since we catch failures at a higher level.
     return;
   }
diff --git a/extensions/ql-vscode/src/common/helpers-pure.ts b/extensions/ql-vscode/src/common/helpers-pure.ts
index 20c1a780cb3..861e250b93f 100644
--- a/extensions/ql-vscode/src/common/helpers-pure.ts
+++ b/extensions/ql-vscode/src/common/helpers-pure.ts
@@ -69,7 +69,7 @@ export function getErrorMessage(e: unknown): string {
 }
 
 export function getErrorStack(e: unknown): string {
-  return e instanceof Error ? e.stack ?? "" : "";
+  return e instanceof Error ? (e.stack ?? "") : "";
 }
 
 export function asError(e: unknown): Error {
diff --git a/extensions/ql-vscode/src/common/interface-types.ts b/extensions/ql-vscode/src/common/interface-types.ts
index 2188fce86fc..eca0779966a 100644
--- a/extensions/ql-vscode/src/common/interface-types.ts
+++ b/extensions/ql-vscode/src/common/interface-types.ts
@@ -27,6 +27,7 @@ import type {
 } from "./raw-result-types";
 import type { AccessPathSuggestionOptions } from "../model-editor/suggestions";
 import type { ModelEvaluationRunState } from "../model-editor/shared/model-evaluation-run-state";
+import type { PerformanceComparisonDataFromLog } from "../log-insights/performance-comparison";
 
 /**
  * This module contains types and code that are shared between
@@ -162,6 +163,25 @@ interface SetUserSettingsMsg {
   userSettings: UserSettings;
 }
 
+export interface VariantAnalysisUserSettings {
+  /** Whether to display the "View Autofixes" button. */
+  shouldShowViewAutofixesButton: boolean;
+}
+
+export const DEFAULT_VARIANT_ANALYSIS_USER_SETTINGS: VariantAnalysisUserSettings =
+  {
+    shouldShowViewAutofixesButton: false,
+  };
+
+/**
+ * Message indicating that the user's variant analysis configuration
+ * settings have changed.
+ */
+interface SetVariantAnalysisUserSettingsMsg {
+  t: "setVariantAnalysisUserSettings";
+  variantAnalysisUserSettings: VariantAnalysisUserSettings;
+}
+
 /**
  * Message indicating that the results view should display interpreted
  * results.
@@ -360,6 +380,9 @@ interface ChangeCompareMessage {
 export type ToCompareViewMessage =
   | SetComparisonQueryInfoMessage
   | SetComparisonsMessage
+  | StreamingComparisonSetupMessage
+  | StreamingComparisonAddResultsMessage
+  | StreamingComparisonCompleteMessage
   | SetUserSettingsMsg;
 
 /**
@@ -393,6 +416,17 @@ export interface SetComparisonsMessage {
   readonly message: string | undefined;
 }
 
+export type ToComparePerformanceViewMessage = SetPerformanceComparisonQueries;
+
+export interface SetPerformanceComparisonQueries {
+  readonly t: "setPerformanceComparison";
+  readonly from: PerformanceComparisonDataFromLog;
+  readonly to: PerformanceComparisonDataFromLog;
+  readonly comparison: boolean;
+}
+
+export type FromComparePerformanceViewMessage = CommonFromViewMessages;
+
 export type QueryCompareResult =
   | RawQueryCompareResult
   | InterpretedQueryCompareResult;
@@ -419,6 +453,28 @@ export type InterpretedQueryCompareResult = {
   to: Result[];
 };
 
+export interface StreamingComparisonSetupMessage {
+  readonly t: "streamingComparisonSetup";
+  // The id of this streaming comparison
+  readonly id: string;
+  readonly currentResultSetName: string;
+  readonly message: string | undefined;
+  // The from and to fields will only contain a chunk of the results
+  readonly result: QueryCompareResult;
+}
+
+interface StreamingComparisonAddResultsMessage {
+  readonly t: "streamingComparisonAddResults";
+  readonly id: string;
+  // The from and to fields will only contain a chunk of the results
+  readonly result: QueryCompareResult;
+}
+
+interface StreamingComparisonCompleteMessage {
+  readonly t: "streamingComparisonComplete";
+  readonly id: string;
+}
+
 /**
  * Extract the name of the default result. Prefer returning
  * 'alerts', or '#select'. Otherwise return the first in the list.
@@ -490,6 +546,11 @@ interface OpenQueryTextMessage {
   t: "openQueryText";
 }
 
+interface ViewAutofixesMessage {
+  t: "viewAutofixes";
+  filterSort?: RepositoriesFilterSortStateWithIds;
+}
+
 interface CopyRepositoryListMessage {
   t: "copyRepositoryList";
   filterSort?: RepositoriesFilterSortStateWithIds;
@@ -517,13 +578,15 @@ export type ToVariantAnalysisMessage =
   | SetVariantAnalysisMessage
   | SetFilterSortStateMessage
   | SetRepoResultsMessage
-  | SetRepoStatesMessage;
+  | SetRepoStatesMessage
+  | SetVariantAnalysisUserSettingsMsg;
 
 export type FromVariantAnalysisMessage =
   | CommonFromViewMessages
   | RequestRepositoryResultsMessage
   | OpenQueryFileMessage
   | OpenQueryTextMessage
+  | ViewAutofixesMessage
   | CopyRepositoryListMessage
   | ExportResultsMessage
   | OpenLogsMessage
@@ -560,16 +623,6 @@ interface SetModifiedMethodsMessage {
   methodSignatures: string[];
 }
 
-interface SetInProgressMethodsMessage {
-  t: "setInProgressMethods";
-  methods: string[];
-}
-
-interface SetProcessedByAutoModelMethodsMessage {
-  t: "setProcessedByAutoModelMethods";
-  methods: string[];
-}
-
 interface SwitchModeMessage {
   t: "switchMode";
   mode: Mode;
@@ -601,17 +654,6 @@ interface GenerateMethodMessage {
   t: "generateMethod";
 }
 
-interface GenerateMethodsFromLlmMessage {
-  t: "generateMethodsFromLlm";
-  packageName: string;
-  methodSignatures: string[];
-}
-
-interface StopGeneratingMethodsFromLlmMessage {
-  t: "stopGeneratingMethodsFromLlm";
-  packageName: string;
-}
-
 interface StartModelEvaluationMessage {
   t: "startModelEvaluation";
 }
@@ -649,16 +691,6 @@ interface SetInModelingModeMessage {
   inModelingMode: boolean;
 }
 
-interface SetInProgressMessage {
-  t: "setInProgress";
-  inProgress: boolean;
-}
-
-interface SetProcessedByAutoModelMessage {
-  t: "setProcessedByAutoModel";
-  processedByAutoModel: boolean;
-}
-
 interface RevealMethodMessage {
   t: "revealMethod";
   methodSignature: string;
@@ -679,8 +711,6 @@ export type ToModelEditorMessage =
   | SetMethodsMessage
   | SetModeledAndModifiedMethodsMessage
   | SetModifiedMethodsMessage
-  | SetInProgressMethodsMessage
-  | SetProcessedByAutoModelMethodsMessage
   | RevealMethodMessage
   | SetAccessPathSuggestionsMessage
   | SetModelEvaluationRunMessage;
@@ -694,8 +724,6 @@ export type FromModelEditorMessage =
   | JumpToMethodMessage
   | SaveModeledMethods
   | GenerateMethodMessage
-  | GenerateMethodsFromLlmMessage
-  | StopGeneratingMethodsFromLlmMessage
   | ModelDependencyMessage
   | HideModeledMethodsMessage
   | SetMultipleModeledMethodsMessage
@@ -738,8 +766,6 @@ interface SetSelectedMethodMessage {
   method: Method;
   modeledMethods: ModeledMethod[];
   isModified: boolean;
-  isInProgress: boolean;
-  processedByAutoModel: boolean;
 }
 
 export type ToMethodModelingMessage =
@@ -748,9 +774,7 @@ export type ToMethodModelingMessage =
   | SetMethodModifiedMessage
   | SetNoMethodSelectedMessage
   | SetSelectedMethodMessage
-  | SetInModelingModeMessage
-  | SetInProgressMessage
-  | SetProcessedByAutoModelMessage;
+  | SetInModelingModeMessage;
 
 interface SetModelAlertsViewStateMessage {
   t: "setModelAlertsViewState";
diff --git a/extensions/ql-vscode/src/common/jsonl-reader.ts b/extensions/ql-vscode/src/common/jsonl-reader.ts
index a20488c48d2..cff0dcf0ec2 100644
--- a/extensions/ql-vscode/src/common/jsonl-reader.ts
+++ b/extensions/ql-vscode/src/common/jsonl-reader.ts
@@ -1,26 +1,62 @@
-import { readFile } from "fs-extra";
+import { stat } from "fs/promises";
+import { createReadStream } from "fs-extra";
+import type { BaseLogger } from "./logging";
+import { asError } from "./helpers-pure";
+
+const doubleLineBreakRegexp = /\n\r?\n/;
 
 /**
  * Read a file consisting of multiple JSON objects. Each object is separated from the previous one
  * by a double newline sequence. This is basically a more human-readable form of JSONL.
  *
- * The current implementation reads the entire text of the document into memory, but in the future
- * it will stream the document to improve the performance with large documents.
- *
  * @param path The path to the file.
  * @param handler Callback to be invoked for each top-level JSON object in order.
  */
 export async function readJsonlFile<T>(
   path: string,
   handler: (value: T) => Promise<void>,
+  logger?: BaseLogger,
 ): Promise<void> {
-  const logSummary = await readFile(path, "utf-8");
-
-  // Remove newline delimiters because summary is in .jsonl format.
-  const jsonSummaryObjects: string[] = logSummary.split(/\r?\n\r?\n/g);
+  // Stream the data as large evaluator logs won't fit in memory.
+  // Also avoid using 'readline' as it is slower than our manual line splitting.
+  void logger?.log(
+    `Parsing ${path} (${(await stat(path)).size / 1024 / 1024} MB)...`,
+  );
+  return new Promise((resolve, reject) => {
+    const stream = createReadStream(path, { encoding: "utf8" });
+    let buffer = "";
+    stream.on("data", async (chunk: string | Buffer) => {
+      if (typeof chunk !== "string") {
+        // This should never happen because we specify the encoding as "utf8".
+        throw new Error("Invalid chunk");
+      }
 
-  for (const obj of jsonSummaryObjects) {
-    const jsonObj = JSON.parse(obj) as T;
-    await handler(jsonObj);
-  }
+      const parts = (buffer + chunk).split(doubleLineBreakRegexp);
+      buffer = parts.pop()!;
+      if (parts.length > 0) {
+        try {
+          stream.pause();
+          for (const part of parts) {
+            await handler(JSON.parse(part));
+          }
+          stream.resume();
+        } catch (e) {
+          stream.destroy();
+          reject(asError(e));
+        }
+      }
+    });
+    stream.on("end", async () => {
+      try {
+        if (buffer.trim().length > 0) {
+          await handler(JSON.parse(buffer));
+        }
+        void logger?.log(`Finished parsing ${path}`);
+        resolve();
+      } catch (e) {
+        reject(asError(e));
+      }
+    });
+    stream.on("error", reject);
+  });
 }
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/gh-api-request.ts b/extensions/ql-vscode/src/common/mock-gh-api/gh-api-request.ts
index b9c08955cd5..b27533bccd1 100644
--- a/extensions/ql-vscode/src/common/mock-gh-api/gh-api-request.ts
+++ b/extensions/ql-vscode/src/common/mock-gh-api/gh-api-request.ts
@@ -14,7 +14,6 @@ export enum RequestKind {
   GetVariantAnalysisRepo = "getVariantAnalysisRepo",
   GetVariantAnalysisRepoResult = "getVariantAnalysisRepoResult",
   CodeSearch = "codeSearch",
-  AutoModel = "autoModel",
 }
 
 export interface BasicErrorResponse {
@@ -69,7 +68,7 @@ export interface GetVariantAnalysisRepoResultRequest {
   };
   response: {
     status: number;
-    body?: Buffer | string;
+    body?: ArrayBuffer | string;
     contentType: string;
   };
 }
@@ -92,31 +91,13 @@ interface CodeSearchRequest {
   };
 }
 
-export interface AutoModelResponse {
-  models: string;
-}
-
-interface AutoModelRequest {
-  request: {
-    kind: RequestKind.AutoModel;
-    body?: {
-      candidates: string;
-    };
-  };
-  response: {
-    status: number;
-    body?: AutoModelResponse | BasicErrorResponse;
-  };
-}
-
 export type GitHubApiRequest =
   | GetRepoRequest
   | SubmitVariantAnalysisRequest
   | GetVariantAnalysisRequest
   | GetVariantAnalysisRepoRequest
   | GetVariantAnalysisRepoResultRequest
-  | CodeSearchRequest
-  | AutoModelRequest;
+  | CodeSearchRequest;
 
 export const isGetRepoRequest = (
   request: GitHubApiRequest,
@@ -146,8 +127,3 @@ export const isCodeSearchRequest = (
   request: GitHubApiRequest,
 ): request is CodeSearchRequest =>
   request.request.kind === RequestKind.CodeSearch;
-
-export const isAutoModelRequest = (
-  request: GitHubApiRequest,
-): request is AutoModelRequest =>
-  request.request.kind === RequestKind.AutoModel;
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/mock-gh-api-server.ts b/extensions/ql-vscode/src/common/mock-gh-api/mock-gh-api-server.ts
index 41f19ccb9eb..34f1a954861 100644
--- a/extensions/ql-vscode/src/common/mock-gh-api/mock-gh-api-server.ts
+++ b/extensions/ql-vscode/src/common/mock-gh-api/mock-gh-api-server.ts
@@ -2,6 +2,7 @@ import { join, resolve } from "path";
 import { pathExists } from "fs-extra";
 import type { SetupServer } from "msw/node";
 import { setupServer } from "msw/node";
+import type { UnhandledRequestStrategy } from "msw/lib/core/utils/request/onUnhandledRequest";
 
 import { DisposableObject } from "../disposable-object";
 
@@ -26,12 +27,14 @@ export class MockGitHubApiServer extends DisposableObject {
     this.recorder = this.push(new Recorder(this.server));
   }
 
-  public startServer(): void {
+  public startServer(
+    onUnhandledRequest: UnhandledRequestStrategy = "bypass",
+  ): void {
     if (this._isListening) {
       return;
     }
 
-    this.server.listen({ onUnhandledRequest: "bypass" });
+    this.server.listen({ onUnhandledRequest });
     this._isListening = true;
   }
 
@@ -54,8 +57,7 @@ export class MockGitHubApiServer extends DisposableObject {
     const scenarioPath = join(scenariosPath, scenarioName);
 
     const handlers = await createRequestHandlers(scenarioPath);
-    this.server.resetHandlers();
-    this.server.use(...handlers);
+    this.server.resetHandlers(...handlers);
   }
 
   public async saveScenario(
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/recorder.ts b/extensions/ql-vscode/src/common/mock-gh-api/recorder.ts
index 234e42a7936..4f82b0f5493 100644
--- a/extensions/ql-vscode/src/common/mock-gh-api/recorder.ts
+++ b/extensions/ql-vscode/src/common/mock-gh-api/recorder.ts
@@ -1,14 +1,12 @@
 import { ensureDir, writeFile } from "fs-extra";
 import { join } from "path";
 
-import fetch from "node-fetch";
 import type { SetupServer } from "msw/node";
 
 import { DisposableObject } from "../disposable-object";
 import { gzipDecode } from "../zlib";
 
 import type {
-  AutoModelResponse,
   BasicErrorResponse,
   CodeSearchResponse,
   GetVariantAnalysisRepoResultRequest,
@@ -91,7 +89,14 @@ export class Recorder extends DisposableObject {
 
         let bodyFileLink = undefined;
         if (writtenRequest.response.body) {
-          await writeFile(bodyFilePath, writtenRequest.response.body);
+          if (typeof writtenRequest.response.body === "string") {
+            await writeFile(bodyFilePath, writtenRequest.response.body);
+          } else {
+            await writeFile(
+              bodyFilePath,
+              Buffer.from(writtenRequest.response.body),
+            );
+          }
           bodyFileLink = `file:${bodyFileName}`;
         }
 
@@ -226,7 +231,7 @@ async function createGitHubApiRequest(
         "x-vscode-codeql-msw-bypass": "true",
       },
     });
-    const responseBuffer = await response.buffer();
+    const responseBuffer = await response.arrayBuffer();
 
     return {
       request: {
@@ -258,23 +263,6 @@ async function createGitHubApiRequest(
     };
   }
 
-  const autoModelMatch = url.match(
-    /\/repos\/github\/codeql\/code-scanning\/codeql\/auto-model/,
-  );
-  if (autoModelMatch) {
-    return {
-      request: {
-        kind: RequestKind.AutoModel,
-      },
-      response: {
-        status,
-        body: await jsonResponseBody<
-          BasicErrorResponse | AutoModelResponse | undefined
-        >(response),
-      },
-    };
-  }
-
   return undefined;
 }
 
@@ -295,7 +283,7 @@ async function jsonResponseBody<T>(response: Response): Promise<T> {
   const body = await responseBody(response);
   const text = new TextDecoder("utf-8").decode(body);
 
-  return JSON.parse(text);
+  return JSON.parse(text) as T;
 }
 
 function shouldWriteBodyToFile(
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/request-handlers.ts b/extensions/ql-vscode/src/common/mock-gh-api/request-handlers.ts
index d445434a509..b6d3dc8b403 100644
--- a/extensions/ql-vscode/src/common/mock-gh-api/request-handlers.ts
+++ b/extensions/ql-vscode/src/common/mock-gh-api/request-handlers.ts
@@ -4,7 +4,6 @@ import type { RequestHandler } from "msw";
 import { http } from "msw";
 import type { GitHubApiRequest } from "./gh-api-request";
 import {
-  isAutoModelRequest,
   isCodeSearchRequest,
   isGetRepoRequest,
   isGetVariantAnalysisRepoRequest,
@@ -41,7 +40,6 @@ export async function createRequestHandlers(
     createGetVariantAnalysisRepoRequestHandler(requests),
     createGetVariantAnalysisRepoResultRequestHandler(requests),
     createCodeSearchRequestHandler(requests),
-    createAutoModelRequestHandler(requests),
   ];
 
   return handlers;
@@ -73,9 +71,10 @@ async function readRequestFiles(
       typeof request.response.body === "string" &&
       request.response.body.startsWith("file:")
     ) {
-      request.response.body = await readFile(
+      const buffer = await readFile(
         join(scenarioDirPath, request.response.body.substring(5)),
       );
+      request.response.body = buffer.buffer;
     }
 
     requests.push(request);
@@ -230,29 +229,3 @@ function createCodeSearchRequestHandler(
     });
   });
 }
-
-function createAutoModelRequestHandler(
-  requests: GitHubApiRequest[],
-): RequestHandler {
-  const autoModelRequests = requests.filter(isAutoModelRequest);
-  let requestIndex = 0;
-
-  // During automodeling there can be multiple API requests for each batch
-  // of candidates we want to model. We need to return different responses for each request,
-  // so keep an index of the request and return the appropriate response.
-  return http.post(
-    `${baseUrl}/repos/github/codeql/code-scanning/codeql/auto-model`,
-    () => {
-      const request = autoModelRequests[requestIndex];
-
-      if (requestIndex < autoModelRequests.length - 1) {
-        // If there are more requests to come, increment the index.
-        requestIndex++;
-      }
-
-      return jsonResponse(request.response.body, {
-        status: request.response.status,
-      });
-    },
-  );
-}
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/0-autoModel.json b/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/0-autoModel.json
deleted file mode 100644
index 1aef8ebaceb..00000000000
--- a/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/0-autoModel.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
-  "request": {
-    "kind": "autoModel"
-  },
-  "response": {
-    "status": 200,
-    "body": {
-      "models": "extensions:\n- addsTo: {extensible: sinkModel, pack: codeql/java-all}\n  data:\n  - [javax.servlet.http, HttpServletResponse, true, sendRedirect, (String), '', 'Argument[this]',\n    request-forgery, ai-generated]\n  - [javax.servlet.http, HttpServletResponse, true, sendRedirect, (String), '', 'Argument[0]',\n    request-forgery, ai-generated]\n"
-    }
-  }
-}
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/1-autoModel.json b/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/1-autoModel.json
deleted file mode 100644
index 44aa6a14f5d..00000000000
--- a/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/1-autoModel.json
+++ /dev/null
@@ -1,11 +0,0 @@
-{
-  "request": {
-    "kind": "autoModel"
-  },
-  "response": {
-    "status": 200,
-    "body": {
-      "models": "extensions:\n- addsTo: {extensible: sinkModel, pack: codeql/java-all}\n  data:\n  - [javax.servlet, MultipartConfigElement, true, MultipartConfigElement, (String),\n    '', 'Argument[0]', request-forgery, ai-generated]\n"
-    }
-  }
-}
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/README.md b/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/README.md
deleted file mode 100644
index 02382bce1f9..00000000000
--- a/extensions/ql-vscode/src/common/mock-gh-api/scenarios/auto-model-success/README.md
+++ /dev/null
@@ -1 +0,0 @@
-This scenario is best when modeling the `javax.servlet-api` package.
diff --git a/extensions/ql-vscode/src/common/mock-gh-api/vscode/vscode-mock-gh-api-server.ts b/extensions/ql-vscode/src/common/mock-gh-api/vscode/vscode-mock-gh-api-server.ts
index b194bc360ad..8e1e04e9daa 100644
--- a/extensions/ql-vscode/src/common/mock-gh-api/vscode/vscode-mock-gh-api-server.ts
+++ b/extensions/ql-vscode/src/common/mock-gh-api/vscode/vscode-mock-gh-api-server.ts
@@ -63,26 +63,33 @@ export class VSCodeMockGitHubApiServer extends DisposableObject {
     );
   }
 
-  public async loadScenario(): Promise<void> {
+  public async loadScenario(scenario?: string): Promise<void> {
     const scenariosPath = await this.getScenariosPath();
     if (!scenariosPath) {
       return;
     }
 
-    const scenarioNames = await this.server.getScenarioNames(scenariosPath);
-    const scenarioQuickPickItems = scenarioNames.map((s) => ({ label: s }));
-    const quickPickOptions = {
-      placeHolder: "Select a scenario to load",
-    };
-    const selectedScenario = await window.showQuickPick<QuickPickItem>(
-      scenarioQuickPickItems,
-      quickPickOptions,
-    );
-    if (!selectedScenario) {
-      return;
+    let scenarioName = scenario;
+    if (!scenarioName) {
+      const scenarioNames = await this.server.getScenarioNames(scenariosPath);
+      const scenarioQuickPickItems = scenarioNames.map((s) => ({ label: s }));
+      const quickPickOptions = {
+        placeHolder: "Select a scenario to load",
+      };
+      const selectedScenario = await window.showQuickPick<QuickPickItem>(
+        scenarioQuickPickItems,
+        quickPickOptions,
+      );
+      if (!selectedScenario) {
+        return;
+      }
+
+      scenarioName = selectedScenario.label;
     }
 
-    const scenarioName = selectedScenario.label;
+    if (!this.server.isListening && this.app.mode === AppMode.Test) {
+      await this.startServer();
+    }
 
     await this.server.loadScenario(scenarioName, scenariosPath);
 
@@ -94,12 +101,12 @@ export class VSCodeMockGitHubApiServer extends DisposableObject {
       true,
     );
 
-    await window.showInformationMessage(`Loaded scenario '${scenarioName}'`);
+    void window.showInformationMessage(`Loaded scenario '${scenarioName}'`);
   }
 
   public async unloadScenario(): Promise<void> {
     if (!this.server.isScenarioLoaded) {
-      await window.showInformationMessage("No scenario currently loaded");
+      void window.showInformationMessage("No scenario currently loaded");
     } else {
       await this.server.unloadScenario();
       await this.app.commands.execute(
@@ -107,7 +114,11 @@ export class VSCodeMockGitHubApiServer extends DisposableObject {
         "codeQL.mockGitHubApiServer.scenarioLoaded",
         false,
       );
-      await window.showInformationMessage("Unloaded scenario");
+      void window.showInformationMessage("Unloaded scenario");
+    }
+
+    if (this.server.isListening && this.app.mode === AppMode.Test) {
+      await this.stopServer();
     }
   }
 
@@ -139,7 +150,7 @@ export class VSCodeMockGitHubApiServer extends DisposableObject {
       true,
     );
 
-    await window.showInformationMessage(
+    void window.showInformationMessage(
       'Recording scenario. To save the scenario, use the "CodeQL Mock GitHub API Server: Save Scenario" command.',
     );
   }
@@ -221,7 +232,10 @@ export class VSCodeMockGitHubApiServer extends DisposableObject {
       return scenariosPath;
     }
 
-    if (this.app.mode === AppMode.Development) {
+    if (
+      this.app.mode === AppMode.Development ||
+      this.app.mode === AppMode.Test
+    ) {
       const developmentScenariosPath = path.join(
         this.app.extensionPath,
         "src/common/mock-gh-api/scenarios",
diff --git a/extensions/ql-vscode/src/common/octokit.ts b/extensions/ql-vscode/src/common/octokit.ts
index f0d97f182d4..f3717c5b2e9 100644
--- a/extensions/ql-vscode/src/common/octokit.ts
+++ b/extensions/ql-vscode/src/common/octokit.ts
@@ -1,10 +1,13 @@
 import { Octokit } from "@octokit/rest";
 import { retry } from "@octokit/plugin-retry";
-import fetch from "node-fetch";
 
 export const AppOctokit = Octokit.defaults({
   request: {
-    fetch,
+    // MSW replaces the global fetch object, so we can't just pass a reference to the
+    // fetch object at initialization time. Instead, we pass a function that will
+    // always call the global fetch object.
+    fetch: (input: string | URL | Request, init?: RequestInit) =>
+      fetch(input, init),
   },
   retry,
 });
diff --git a/extensions/ql-vscode/src/common/query-language.ts b/extensions/ql-vscode/src/common/query-language.ts
index 2cf0155b578..03feb4b1353 100644
--- a/extensions/ql-vscode/src/common/query-language.ts
+++ b/extensions/ql-vscode/src/common/query-language.ts
@@ -1,4 +1,5 @@
 export enum QueryLanguage {
+  Actions = "actions",
   CSharp = "csharp",
   Cpp = "cpp",
   Go = "go",
@@ -6,11 +7,14 @@ export enum QueryLanguage {
   Javascript = "javascript",
   Python = "python",
   Ruby = "ruby",
+  Rust = "rust",
   Swift = "swift",
 }
 
 export function getLanguageDisplayName(language: string): string {
-  switch (language) {
+  switch (language as QueryLanguage) {
+    case QueryLanguage.Actions:
+      return "Actions";
     case QueryLanguage.CSharp:
       return "C#";
     case QueryLanguage.Cpp:
@@ -25,6 +29,8 @@ export function getLanguageDisplayName(language: string): string {
       return "Python";
     case QueryLanguage.Ruby:
       return "Ruby";
+    case QueryLanguage.Rust:
+      return "Rust";
     case QueryLanguage.Swift:
       return "Swift";
     default:
@@ -33,6 +39,7 @@ export function getLanguageDisplayName(language: string): string {
 }
 
 export const PACKS_BY_QUERY_LANGUAGE = {
+  [QueryLanguage.Actions]: ["codeql/actions-queries"],
   [QueryLanguage.Cpp]: ["codeql/cpp-queries"],
   [QueryLanguage.CSharp]: [
     "codeql/csharp-queries",
@@ -43,19 +50,33 @@ export const PACKS_BY_QUERY_LANGUAGE = {
   [QueryLanguage.Javascript]: ["codeql/javascript-queries"],
   [QueryLanguage.Python]: ["codeql/python-queries"],
   [QueryLanguage.Ruby]: ["codeql/ruby-queries"],
+  [QueryLanguage.Rust]: ["codeql/rust-queries"],
 };
 
 export const dbSchemeToLanguage: Record<string, QueryLanguage> = {
-  "semmlecode.javascript.dbscheme": QueryLanguage.Javascript,
+  "semmlecode.javascript.dbscheme": QueryLanguage.Javascript, // This can also be QueryLanguage.Actions
   "semmlecode.cpp.dbscheme": QueryLanguage.Cpp,
   "semmlecode.dbscheme": QueryLanguage.Java,
   "semmlecode.python.dbscheme": QueryLanguage.Python,
   "semmlecode.csharp.dbscheme": QueryLanguage.CSharp,
   "go.dbscheme": QueryLanguage.Go,
   "ruby.dbscheme": QueryLanguage.Ruby,
+  "rust.dbscheme": QueryLanguage.Rust,
   "swift.dbscheme": QueryLanguage.Swift,
 };
 
+export const languageToDbScheme = Object.entries(dbSchemeToLanguage).reduce(
+  (acc, [k, v]) => {
+    acc[v] = k;
+    return acc;
+  },
+  {} as { [k: string]: string },
+);
+
+// Actions dbscheme is the same as Javascript dbscheme
+languageToDbScheme[QueryLanguage.Actions] =
+  languageToDbScheme[QueryLanguage.Javascript];
+
 export function isQueryLanguage(language: string): language is QueryLanguage {
   return Object.values(QueryLanguage).includes(language as QueryLanguage);
 }
diff --git a/extensions/ql-vscode/src/common/raw-result-types.ts b/extensions/ql-vscode/src/common/raw-result-types.ts
index 9dbca7fc46f..4b5a03e243d 100644
--- a/extensions/ql-vscode/src/common/raw-result-types.ts
+++ b/extensions/ql-vscode/src/common/raw-result-types.ts
@@ -5,6 +5,7 @@ export enum ColumnKind {
   Boolean = "boolean",
   Date = "date",
   Entity = "entity",
+  BigInt = "bigint",
 }
 
 export type Column = {
@@ -61,6 +62,11 @@ type CellValueNumber = {
   value: number;
 };
 
+type CellValueBigInt = {
+  type: "number";
+  value: number;
+};
+
 type CellValueString = {
   type: "string";
   value: string;
@@ -75,7 +81,8 @@ export type CellValue =
   | CellValueEntity
   | CellValueNumber
   | CellValueString
-  | CellValueBoolean;
+  | CellValueBoolean
+  | CellValueBigInt;
 
 export type Row = CellValue[];
 
diff --git a/extensions/ql-vscode/src/common/readonly.ts b/extensions/ql-vscode/src/common/readonly.ts
index 19a4ad963ef..e202bea52bd 100644
--- a/extensions/ql-vscode/src/common/readonly.ts
+++ b/extensions/ql-vscode/src/common/readonly.ts
@@ -1,14 +1,14 @@
 export type DeepReadonly<T> =
   T extends Array<infer R>
     ? DeepReadonlyArray<R>
-    : // eslint-disable-next-line @typescript-eslint/ban-types
+    : // eslint-disable-next-line @typescript-eslint/no-unsafe-function-type
       T extends Function
       ? T
       : T extends object
         ? DeepReadonlyObject<T>
         : T;
 
-interface DeepReadonlyArray<T> extends ReadonlyArray<DeepReadonly<T>> {}
+type DeepReadonlyArray<T> = ReadonlyArray<DeepReadonly<T>>;
 
 type DeepReadonlyObject<T> = {
   readonly [P in keyof T]: DeepReadonly<T[P]>;
diff --git a/extensions/ql-vscode/src/common/short-paths.ts b/extensions/ql-vscode/src/common/short-paths.ts
index 838dac031e1..860544c38d4 100644
--- a/extensions/ql-vscode/src/common/short-paths.ts
+++ b/extensions/ql-vscode/src/common/short-paths.ts
@@ -1,7 +1,9 @@
-import { platform } from "os";
+import { arch, platform } from "os";
 import { basename, dirname, join, normalize, resolve } from "path";
 import { lstat, readdir } from "fs/promises";
 import type { BaseLogger } from "./logging";
+import type { KoffiFunction } from "koffi";
+import { getErrorMessage } from "./helpers-pure";
 
 /**
  * Expands a path that potentially contains 8.3 short names (e.g. "C:\PROGRA~1" instead of "C:\Program Files").
@@ -32,7 +34,23 @@ export async function expandShortPaths(
     return absoluteShortPath;
   }
 
-  return await expandShortPathRecursive(absoluteShortPath, logger);
+  const longPath = await expandShortPathRecursive(absoluteShortPath, logger);
+  if (longPath.indexOf("~") < 0) {
+    return longPath;
+  }
+
+  void logger.log(
+    "Short path was not resolved to long path, using native method",
+  );
+
+  try {
+    return await expandShortPathNative(absoluteShortPath, logger);
+  } catch (e) {
+    void logger.log(
+      `Failed to expand short path using native method: ${getErrorMessage(e)}`,
+    );
+    return longPath;
+  }
 }
 
 /**
@@ -74,12 +92,12 @@ async function expandShortPathComponent(
         }
       } catch (e) {
         // Can't read stats for the child, so skip it.
-        void logger.log(`Error reading stats for child: ${e}`);
+        void logger.log(`Error reading stats for child: ${getErrorMessage(e)}`);
       }
     }
   } catch (e) {
     // Can't read the directory, so we won't be able to find this in the directory listing.
-    void logger.log(`Error reading directory: ${e}`);
+    void logger.log(`Error reading directory: ${getErrorMessage(e)}`);
     return shortBase;
   }
 
@@ -115,3 +133,46 @@ async function expandShortPathRecursive(
   const longBase = await expandShortPathComponent(dir, shortBase, logger);
   return join(dir, longBase);
 }
+
+let GetLongPathNameW: KoffiFunction | undefined;
+
+async function expandShortPathNative(shortPath: string, logger: BaseLogger) {
+  if (platform() !== "win32") {
+    throw new Error("expandShortPathNative is only supported on Windows");
+  }
+
+  if (arch() !== "x64") {
+    throw new Error(
+      "expandShortPathNative is only supported on x64 architecture",
+    );
+  }
+
+  if (GetLongPathNameW === undefined) {
+    // We are using koffi/indirect here to avoid including the native addon for all
+    // platforms in the bundle since this is only used on Windows. Instead, the
+    // native addon is included in the Gulpfile.
+    const koffi = await import("koffi/indirect");
+
+    const lib = koffi.load("kernel32.dll");
+    GetLongPathNameW = lib.func("__stdcall", "GetLongPathNameW", "uint32", [
+      "str16",
+      "str16",
+      "uint32",
+    ]);
+  }
+
+  const MAX_PATH = 32767;
+  const buffer = Buffer.alloc(MAX_PATH * 2, 0);
+
+  const result = GetLongPathNameW(shortPath, buffer, MAX_PATH);
+
+  if (result === 0) {
+    throw new Error("Failed to get long path name");
+  }
+
+  const longPath = buffer.toString("utf16le", 0, (result - 1) * 2);
+
+  void logger.log(`Expanded short path ${shortPath} to ${longPath}`);
+
+  return longPath;
+}
diff --git a/extensions/ql-vscode/src/common/unzip.ts b/extensions/ql-vscode/src/common/unzip.ts
index 2c8c361f562..9a35eedad38 100644
--- a/extensions/ql-vscode/src/common/unzip.ts
+++ b/extensions/ql-vscode/src/common/unzip.ts
@@ -5,6 +5,7 @@ import { Transform } from "stream";
 import { dirname, join } from "path";
 import type { WriteStream } from "fs";
 import { createWriteStream, ensureDir } from "fs-extra";
+import { asError } from "./helpers-pure";
 
 // We can't use promisify because it picks up the wrong overload.
 export function openZip(
@@ -47,7 +48,7 @@ export function readZipEntries(zipFile: ZipFile): Promise<ZipEntry[]> {
     });
 
     zipFile.on("error", (err) => {
-      reject(err);
+      reject(asError(err));
     });
   });
 }
diff --git a/extensions/ql-vscode/src/common/vscode/abstract-webview.ts b/extensions/ql-vscode/src/common/vscode/abstract-webview.ts
index c38590e4feb..87c0583af1d 100644
--- a/extensions/ql-vscode/src/common/vscode/abstract-webview.ts
+++ b/extensions/ql-vscode/src/common/vscode/abstract-webview.ts
@@ -41,6 +41,13 @@ export abstract class AbstractWebview<
 
   constructor(protected readonly app: App) {}
 
+  public hidePanel() {
+    if (this.panel !== undefined) {
+      this.panel.dispose();
+      this.panel = undefined;
+    }
+  }
+
   public async restoreView(panel: WebviewPanel): Promise<void> {
     this.panel = panel;
     const config = await this.getPanelConfig();
diff --git a/extensions/ql-vscode/src/common/vscode/archive-filesystem-provider.ts b/extensions/ql-vscode/src/common/vscode/archive-filesystem-provider.ts
index c82225f42f1..1ee61468c36 100644
--- a/extensions/ql-vscode/src/common/vscode/archive-filesystem-provider.ts
+++ b/extensions/ql-vscode/src/common/vscode/archive-filesystem-provider.ts
@@ -135,7 +135,7 @@ const sourceArchiveUriAuthorityPattern = /^(\d+)-(\d+)$/;
 class InvalidSourceArchiveUriError extends Error {
   constructor(uri: Uri) {
     super(
-      `Can't decode uri ${uri}: authority should be of the form startIndex-endIndex (where both indices are integers).`,
+      `Can't decode uri ${uri.toString()}: authority should be of the form startIndex-endIndex (where both indices are integers).`,
     );
   }
 }
diff --git a/extensions/ql-vscode/src/common/vscode/dialog.ts b/extensions/ql-vscode/src/common/vscode/dialog.ts
index b6ad555fe0d..f580ea5f340 100644
--- a/extensions/ql-vscode/src/common/vscode/dialog.ts
+++ b/extensions/ql-vscode/src/common/vscode/dialog.ts
@@ -1,4 +1,4 @@
-import { env, Uri, window } from "vscode";
+import { window } from "vscode";
 
 /**
  * Opens a modal dialog for the user to make a yes/no choice.
@@ -34,50 +34,6 @@ export async function showBinaryChoiceDialog(
   return chosenItem?.title === yesItem.title;
 }
 
-/**
- * Opens a modal dialog for the user to make a yes/no choice.
- *
- * @param message The message to show.
- * @param modal If true (the default), show a modal dialog box, otherwise dialog is non-modal and can
- *        be closed even if the user does not make a choice.
- *
- * @return
- *  `true` if the user clicks 'Yes',
- *  `false` if the user clicks 'No' or cancels the dialog,
- *  `undefined` if the dialog is closed without the user making a choice.
- */
-export async function showBinaryChoiceWithUrlDialog(
-  message: string,
-  url: string,
-): Promise<boolean | undefined> {
-  const urlItem = { title: "More Information", isCloseAffordance: false };
-  const yesItem = { title: "Yes", isCloseAffordance: false };
-  const noItem = { title: "No", isCloseAffordance: true };
-  let chosenItem;
-
-  // Keep the dialog open as long as the user is clicking the 'more information' option.
-  // To prevent an infinite loop, if the user clicks 'more information' 5 times, close the dialog and return cancelled
-  let count = 0;
-  do {
-    chosenItem = await window.showInformationMessage(
-      message,
-      { modal: true },
-      urlItem,
-      yesItem,
-      noItem,
-    );
-    if (chosenItem === urlItem) {
-      await env.openExternal(Uri.parse(url, true));
-    }
-    count++;
-  } while (chosenItem === urlItem && count < 5);
-
-  if (!chosenItem || chosenItem.title === urlItem.title) {
-    return undefined;
-  }
-  return chosenItem.title === yesItem.title;
-}
-
 /**
  * Show an information message with a customisable action.
  * @param message The message to show.
diff --git a/extensions/ql-vscode/src/common/vscode/progress.ts b/extensions/ql-vscode/src/common/vscode/progress.ts
index 7d944cc4b89..baf3b2c4f28 100644
--- a/extensions/ql-vscode/src/common/vscode/progress.ts
+++ b/extensions/ql-vscode/src/common/vscode/progress.ts
@@ -97,17 +97,15 @@ export function withProgress<R>(
  * Displays a progress monitor that indicates how much progess has been made
  * reading from a stream.
  *
- * @param readable The stream to read progress from
  * @param messagePrefix A prefix for displaying the message
  * @param totalNumBytes Total number of bytes in this stream
  * @param progress The progress callback used to set messages
  */
 export function reportStreamProgress(
-  readable: NodeJS.ReadableStream,
   messagePrefix: string,
   totalNumBytes?: number,
   progress?: ProgressCallback,
-) {
+): (bytesRead: number) => void {
   if (progress && totalNumBytes) {
     let numBytesDownloaded = 0;
     const updateProgress = () => {
@@ -123,10 +121,10 @@ export function reportStreamProgress(
     // Display the progress straight away rather than waiting for the first chunk.
     updateProgress();
 
-    readable.on("data", (data) => {
-      numBytesDownloaded += data.length;
+    return (bytesRead: number) => {
+      numBytesDownloaded += bytesRead;
       updateProgress();
-    });
+    };
   } else if (progress) {
     progress({
       step: 1,
@@ -134,4 +132,6 @@ export function reportStreamProgress(
       message: `${messagePrefix} (Size unknown)`,
     });
   }
+
+  return () => {};
 }
diff --git a/extensions/ql-vscode/src/common/vscode/selection-commands.ts b/extensions/ql-vscode/src/common/vscode/selection-commands.ts
index 93db99584a1..bfe107ff0a3 100644
--- a/extensions/ql-vscode/src/common/vscode/selection-commands.ts
+++ b/extensions/ql-vscode/src/common/vscode/selection-commands.ts
@@ -18,7 +18,7 @@ type SelectionCommand<T extends NotArray> = CreateSupertypeOf<
   TreeViewContextMultiSelectionCommandFunction<T> &
     TreeViewContextSingleSelectionCommandFunction<T> &
     ExplorerSelectionCommandFunction<T>,
-  (singleItem: T, multiSelect?: T[] | undefined) => Promise<void>
+  (singleItem: T, multiSelect?: T[]) => Promise<void>
 >;
 
 export function createSingleSelectionCommand<T extends NotArray>(
diff --git a/extensions/ql-vscode/src/common/vscode/telemetry.ts b/extensions/ql-vscode/src/common/vscode/telemetry.ts
index 451eff486a2..d8c6f54c6c8 100644
--- a/extensions/ql-vscode/src/common/vscode/telemetry.ts
+++ b/extensions/ql-vscode/src/common/vscode/telemetry.ts
@@ -1,26 +1,15 @@
-import type {
-  Extension,
-  ExtensionContext,
-  ConfigurationChangeEvent,
-} from "vscode";
-import { ConfigurationTarget, env } from "vscode";
+import type { Extension, ExtensionContext } from "vscode";
+import { ConfigurationTarget, env, Uri, window } from "vscode";
 import TelemetryReporter from "vscode-extension-telemetry";
-import {
-  ConfigListener,
-  CANARY_FEATURES,
-  ENABLE_TELEMETRY,
-  LOG_TELEMETRY,
-  isIntegrationTestMode,
-  isCanary,
-} from "../../config";
+import { ENABLE_TELEMETRY, isCanary, LOG_TELEMETRY } from "../../config";
 import type { TelemetryClient } from "applicationinsights";
 import { extLogger } from "../logging/vscode";
 import { UserCancellationException } from "./progress";
-import { showBinaryChoiceWithUrlDialog } from "./dialog";
 import type { RedactableError } from "../errors";
 import type { SemVer } from "semver";
 import type { AppTelemetry } from "../telemetry";
 import type { EnvelopeTelemetry } from "applicationinsights/out/Declarations/Contracts";
+import type { Disposable } from "../disposable-object";
 
 // Key is injected at build time through the APP_INSIGHTS_KEY environment variable.
 const key = "REPLACE-APP-INSIGHTS-KEY";
@@ -55,80 +44,25 @@ const baseDataPropertiesToRemove = [
 
 const NOT_SET_CLI_VERSION = "not-set";
 
-export class ExtensionTelemetryListener
-  extends ConfigListener
-  implements AppTelemetry
-{
-  private reporter?: TelemetryReporter;
+export class ExtensionTelemetryListener implements AppTelemetry, Disposable {
+  private readonly reporter: TelemetryReporter;
 
   private cliVersionStr = NOT_SET_CLI_VERSION;
 
-  constructor(
-    private readonly id: string,
-    private readonly version: string,
-    private readonly key: string,
-    private readonly ctx: ExtensionContext,
-  ) {
-    super();
-
-    env.onDidChangeTelemetryEnabled(async () => {
-      await this.initialize();
-    });
-  }
-
-  /**
-   * This function handles changes to relevant configuration elements. There are 2 configuration
-   * ids that this function cares about:
-   *
-   *     * `codeQL.telemetry.enableTelemetry`: If this one has changed, then we need to re-initialize
-   *        the reporter and the reporter may wind up being removed.
-   *     * `codeQL.canary`: A change here could possibly re-trigger a dialog popup.
-   *
-   * Note that the global telemetry setting also gate-keeps whether or not to send telemetry events
-   * to Application Insights. However, this gatekeeping happens inside of the vscode-extension-telemetry
-   * package. So, this does not need to be handled here.
-   *
-   * @param e the configuration change event
-   */
-  async handleDidChangeConfiguration(
-    e: ConfigurationChangeEvent,
-  ): Promise<void> {
-    if (e.affectsConfiguration(ENABLE_TELEMETRY.qualifiedName)) {
-      await this.initialize();
-    }
-
-    // Re-request telemetry so that users can see the dialog again.
-    // Re-request if codeQL.canary is being set to `true` and telemetry
-    // is not currently enabled.
-    if (
-      e.affectsConfiguration(CANARY_FEATURES.qualifiedName) &&
-      CANARY_FEATURES.getValue() &&
-      !ENABLE_TELEMETRY.getValue()
-    ) {
-      await this.setTelemetryRequested(false);
-      await this.requestTelemetryPermission();
-    }
-  }
-
-  async initialize() {
-    await this.requestTelemetryPermission();
-
-    this.disposeReporter();
-
-    if (ENABLE_TELEMETRY.getValue<boolean>()) {
-      this.createReporter();
-    }
-  }
-
-  private createReporter() {
+  constructor(id: string, version: string, key: string) {
+    // We can always initialize this and send events using it because the vscode-extension-telemetry will check
+    // whether the `telemetry.telemetryLevel` setting is enabled.
     this.reporter = new TelemetryReporter(
-      this.id,
-      this.version,
-      this.key,
+      id,
+      version,
+      key,
       /* anonymize stack traces */ true,
     );
-    this.push(this.reporter);
 
+    this.addTelemetryProcessor();
+  }
+
+  private addTelemetryProcessor() {
     // The appInsightsClient field is private but we want to access it anyway
     const client = this.reporter["appInsightsClient"] as TelemetryClient;
     if (client) {
@@ -151,14 +85,10 @@ export class ExtensionTelemetryListener
   }
 
   dispose() {
-    super.dispose();
-    void this.reporter?.dispose();
+    void this.reporter.dispose();
   }
 
   sendCommandUsage(name: string, executionTime: number, error?: Error): void {
-    if (!this.reporter) {
-      return;
-    }
     const status = !error
       ? CommandCompletion.Success
       : error instanceof UserCancellationException
@@ -178,10 +108,6 @@ export class ExtensionTelemetryListener
   }
 
   sendUIInteraction(name: string): void {
-    if (!this.reporter) {
-      return;
-    }
-
     this.reporter.sendTelemetryEvent(
       "ui-interaction",
       {
@@ -197,10 +123,6 @@ export class ExtensionTelemetryListener
     error: RedactableError,
     extraProperties?: { [key: string]: string },
   ): void {
-    if (!this.reporter) {
-      return;
-    }
-
     const properties: { [key: string]: string } = {
       isCanary: isCanary().toString(),
       cliVersion: this.cliVersionStr,
@@ -215,10 +137,6 @@ export class ExtensionTelemetryListener
   }
 
   sendConfigInformation(config: Record<string, string>): void {
-    if (!this.reporter) {
-      return;
-    }
-
     this.reporter.sendTelemetryEvent(
       "config",
       {
@@ -230,37 +148,6 @@ export class ExtensionTelemetryListener
     );
   }
 
-  /**
-   * Displays a popup asking the user if they want to enable telemetry
-   * for this extension.
-   */
-  async requestTelemetryPermission() {
-    if (!this.wasTelemetryRequested()) {
-      // if global telemetry is disabled, avoid showing the dialog or making any changes
-      let result = undefined;
-      if (
-        env.isTelemetryEnabled &&
-        // Avoid showing the dialog if we are in integration test mode.
-        !isIntegrationTestMode()
-      ) {
-        // Extension won't start until this completes.
-        result = await showBinaryChoiceWithUrlDialog(
-          "Does the CodeQL Extension by GitHub have your permission to collect usage data and metrics to help us improve CodeQL for VSCode?",
-          "https://codeql.github.com/docs/codeql-for-visual-studio-code/about-telemetry-in-codeql-for-visual-studio-code",
-        );
-      }
-      if (result !== undefined) {
-        await Promise.all([
-          this.setTelemetryRequested(true),
-          ENABLE_TELEMETRY.updateValue<boolean>(
-            result,
-            ConfigurationTarget.Global,
-          ),
-        ]);
-      }
-    }
-  }
-
   /**
    * Exposed for testing
    */
@@ -271,21 +158,45 @@ export class ExtensionTelemetryListener
   set cliVersion(version: SemVer | undefined) {
     this.cliVersionStr = version ? version.toString() : NOT_SET_CLI_VERSION;
   }
+}
 
-  private disposeReporter() {
-    if (this.reporter) {
-      void this.reporter.dispose();
-      this.reporter = undefined;
+async function notifyTelemetryChange() {
+  const continueItem = { title: "Continue", isCloseAffordance: false };
+  const vsCodeTelemetryItem = {
+    title: "More Information about VS Code Telemetry",
+    isCloseAffordance: false,
+  };
+  const codeqlTelemetryItem = {
+    title: "More Information about CodeQL Telemetry",
+    isCloseAffordance: false,
+  };
+  let chosenItem;
+
+  do {
+    chosenItem = await window.showInformationMessage(
+      "The CodeQL extension now follows VS Code's telemetry settings. VS Code telemetry is currently enabled. Learn how to update your telemetry settings by clicking the links below.",
+      { modal: true },
+      continueItem,
+      vsCodeTelemetryItem,
+      codeqlTelemetryItem,
+    );
+    if (chosenItem === vsCodeTelemetryItem) {
+      await env.openExternal(
+        Uri.parse(
+          "https://code.visualstudio.com/docs/getstarted/telemetry",
+          true,
+        ),
+      );
     }
-  }
-
-  private wasTelemetryRequested(): boolean {
-    return !!this.ctx.globalState.get<boolean>("telemetry-request-viewed");
-  }
-
-  private async setTelemetryRequested(newValue: boolean): Promise<void> {
-    await this.ctx.globalState.update("telemetry-request-viewed", newValue);
-  }
+    if (chosenItem === codeqlTelemetryItem) {
+      await env.openExternal(
+        Uri.parse(
+          "https://docs.github.com/en/code-security/codeql-for-vs-code/using-the-advanced-functionality-of-the-codeql-for-vs-code-extension/telemetry-in-codeql-for-visual-studio-code",
+          true,
+        ),
+      );
+    }
+  } while (chosenItem !== continueItem);
 }
 
 /**
@@ -301,15 +212,28 @@ export async function initializeTelemetry(
   if (telemetryListener !== undefined) {
     throw new Error("Telemetry is already initialized");
   }
+
+  if (ENABLE_TELEMETRY.getValue<boolean | undefined>() === false) {
+    if (env.isTelemetryEnabled) {
+      // Await this so that the user is notified before any telemetry is sent
+      await notifyTelemetryChange();
+    }
+
+    // Remove the deprecated telemetry setting
+    ENABLE_TELEMETRY.updateValue(undefined, ConfigurationTarget.Global);
+    ENABLE_TELEMETRY.updateValue(undefined, ConfigurationTarget.Workspace);
+    ENABLE_TELEMETRY.updateValue(
+      undefined,
+      ConfigurationTarget.WorkspaceFolder,
+    );
+  }
+
   telemetryListener = new ExtensionTelemetryListener(
     extension.id,
     extension.packageJSON.version,
     key,
-    ctx,
   );
-  // do not await initialization, since doing so will sometimes cause a modal popup.
-  // this is a particular problem during integration tests, which will hang if a modal popup is displayed.
-  void telemetryListener.initialize();
   ctx.subscriptions.push(telemetryListener);
+
   return telemetryListener;
 }
diff --git a/extensions/ql-vscode/src/common/vscode/webview-html.ts b/extensions/ql-vscode/src/common/vscode/webview-html.ts
index 7ad1f5d08e4..e1eac40024c 100644
--- a/extensions/ql-vscode/src/common/vscode/webview-html.ts
+++ b/extensions/ql-vscode/src/common/vscode/webview-html.ts
@@ -7,6 +7,7 @@ import type { App } from "../app";
 export type WebviewKind =
   | "results"
   | "compare"
+  | "compare-performance"
   | "variant-analysis"
   | "data-flow-paths"
   | "model-editor"
@@ -88,7 +89,7 @@ export function getHtmlForWebview(
   <body>
     <div id=root data-view="${view}">
     </div>
-      <script nonce="${nonce}" src="https://github.com/$%7BscriptWebviewUri%7D">
+      <script nonce="${nonce}" src="https://github.com/$%7BscriptWebviewUri.toString()%7D">
     </script>
   </body>
 </html>`;
@@ -100,9 +101,9 @@ function getNonce(): string {
 }
 
 function createStylesLinkWithNonce(nonce: string, uri: Uri): string {
-  return `<link nonce="${nonce}" rel="stylesheet" href="https://github.com/$%7Buri%7D">`;
+  return `<link nonce="${nonce}" rel="stylesheet" href="https://github.com/$%7Buri.toString()%7D">`;
 }
 
 function createStylesLinkWithoutNonce(uri: Uri): string {
-  return `<link rel="stylesheet" href="https://github.com/$%7Buri%7D">`;
+  return `<link rel="stylesheet" href="https://github.com/$%7Buri.toString()%7D">`;
 }
diff --git a/extensions/ql-vscode/src/common/zlib.ts b/extensions/ql-vscode/src/common/zlib.ts
index 4f9f9b00bf0..deb0ecf6518 100644
--- a/extensions/ql-vscode/src/common/zlib.ts
+++ b/extensions/ql-vscode/src/common/zlib.ts
@@ -1,10 +1,5 @@
 import { promisify } from "util";
-import { gzip, gunzip } from "zlib";
-
-/**
- * Promisified version of zlib.gzip
- */
-export const gzipEncode = promisify(gzip);
+import { gunzip } from "zlib";
 
 /**
  * Promisified version of zlib.gunzip
diff --git a/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts b/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts
new file mode 100644
index 00000000000..a59367ea135
--- /dev/null
+++ b/extensions/ql-vscode/src/compare-performance/compare-performance-view.ts
@@ -0,0 +1,121 @@
+import { statSync } from "fs";
+import { ViewColumn } from "vscode";
+
+import type { App } from "../common/app";
+import { redactableError } from "../common/errors";
+import type {
+  FromComparePerformanceViewMessage,
+  ToComparePerformanceViewMessage,
+} from "../common/interface-types";
+import type { Logger } from "../common/logging";
+import { showAndLogExceptionWithTelemetry } from "../common/logging";
+import { extLogger } from "../common/logging/vscode";
+import type { WebviewPanelConfig } from "../common/vscode/abstract-webview";
+import { AbstractWebview } from "../common/vscode/abstract-webview";
+import { withProgress } from "../common/vscode/progress";
+import { telemetryListener } from "../common/vscode/telemetry";
+import type { HistoryItemLabelProvider } from "../query-history/history-item-label-provider";
+import { PerformanceOverviewScanner } from "../log-insights/performance-comparison";
+import type { ResultsView } from "../local-queries";
+import { readJsonlFile } from "../common/jsonl-reader";
+import type { SummaryEvent } from "../log-insights/log-summary";
+
+export class ComparePerformanceView extends AbstractWebview<
+  ToComparePerformanceViewMessage,
+  FromComparePerformanceViewMessage
+> {
+  constructor(
+    app: App,
+    public logger: Logger,
+    public labelProvider: HistoryItemLabelProvider,
+    private resultsView: ResultsView,
+  ) {
+    super(app);
+  }
+
+  async showResults(fromJsonLog: string, toJsonLog: string) {
+    const panel = await this.getPanel();
+    panel.reveal(undefined, false);
+
+    // Close the results viewer as it will have opened when the user clicked the query in the history view
+    // (which they must do as part of the UI interaction for opening the performance view).
+    // The performance view generally needs a lot of width so it's annoying to have the result viewer open.
+    this.resultsView.hidePanel();
+
+    await this.waitForPanelLoaded();
+
+    function scanLogWithProgress(log: string, logDescription: string) {
+      const bytes = statSync(log).size;
+      return withProgress(
+        async (progress) => {
+          progress?.({
+            // all scans have step 1 - the backing progress tracker allows increments instead of
+            // steps - but for now we are happy with a tiny UI that says what is happening
+            message: `Scanning ...`,
+            step: 1,
+            maxStep: 2,
+          });
+          const scanner = new PerformanceOverviewScanner();
+          await readJsonlFile<SummaryEvent>(log, async (obj) => {
+            scanner.onEvent(obj);
+          });
+          return scanner;
+        },
+
+        {
+          title: `Scanning evaluator log ${logDescription} (${(bytes / 1024 / 1024).toFixed(1)} MB)`,
+        },
+      );
+    }
+
+    const [fromPerf, toPerf] = await Promise.all([
+      fromJsonLog === ""
+        ? new PerformanceOverviewScanner()
+        : scanLogWithProgress(fromJsonLog, "1/2"),
+      scanLogWithProgress(toJsonLog, fromJsonLog === "" ? "1/1" : "2/2"),
+    ]);
+
+    await this.postMessage({
+      t: "setPerformanceComparison",
+      from: fromPerf.getData(),
+      to: toPerf.getData(),
+      comparison: fromJsonLog !== "",
+    });
+  }
+
+  protected getPanelConfig(): WebviewPanelConfig {
+    return {
+      viewId: "comparePerformanceView",
+      title: "Compare CodeQL Performance",
+      viewColumn: ViewColumn.Active,
+      preserveFocus: true,
+      view: "compare-performance",
+    };
+  }
+
+  protected onPanelDispose(): void {}
+
+  protected async onMessage(
+    msg: FromComparePerformanceViewMessage,
+  ): Promise<void> {
+    switch (msg.t) {
+      case "viewLoaded":
+        this.onWebViewLoaded();
+        break;
+
+      case "telemetry":
+        telemetryListener?.sendUIInteraction(msg.action);
+        break;
+
+      case "unhandledError":
+        void showAndLogExceptionWithTelemetry(
+          extLogger,
+          telemetryListener,
+          redactableError(
+            msg.error,
+          )`Unhandled error in performance comparison view: ${msg.error.message}`,
+        );
+        break;
+    }
+  }
+}
diff --git a/extensions/ql-vscode/src/compare/compare-view.ts b/extensions/ql-vscode/src/compare/compare-view.ts
index 8b762e29882..93538f52e6b 100644
--- a/extensions/ql-vscode/src/compare/compare-view.ts
+++ b/extensions/ql-vscode/src/compare/compare-view.ts
@@ -34,6 +34,7 @@ import {
 } from "./result-set-names";
 import { compareInterpretedResults } from "./interpreted-results";
 import { isCanary } from "../config";
+import { nanoid } from "nanoid";
 
 interface ComparePair {
   from: CompletedLocalQueryInfo;
@@ -69,22 +70,20 @@ export class CompareView extends AbstractWebview<
     selectedResultSetName?: string,
   ) {
     const [fromSchemas, toSchemas] = await Promise.all([
-      this.cliServer.bqrsInfo(
-        from.completedQuery.query.resultsPaths.resultsPath,
-      ),
-      this.cliServer.bqrsInfo(to.completedQuery.query.resultsPaths.resultsPath),
+      this.cliServer.bqrsInfo(from.completedQuery.query.resultsPath),
+      this.cliServer.bqrsInfo(to.completedQuery.query.resultsPath),
     ]);
 
     const [fromSchemaNames, toSchemaNames] = await Promise.all([
       getResultSetNames(
         fromSchemas,
         from.completedQuery.query.metadata,
-        from.completedQuery.query.resultsPaths.interpretedResultsPath,
+        from.completedQuery.query.interpretedResultsPath,
       ),
       getResultSetNames(
         toSchemas,
         to.completedQuery.query.metadata,
-        to.completedQuery.query.resultsPaths.interpretedResultsPath,
+        to.completedQuery.query.interpretedResultsPath,
       ),
     ]);
 
@@ -100,15 +99,14 @@ export class CompareView extends AbstractWebview<
         schemaNames: fromSchemaNames,
         metadata: from.completedQuery.query.metadata,
         interpretedResultsPath:
-          from.completedQuery.query.resultsPaths.interpretedResultsPath,
+          from.completedQuery.query.interpretedResultsPath,
       },
       to,
       toInfo: {
         schemas: toSchemas,
         schemaNames: toSchemaNames,
         metadata: to.completedQuery.query.metadata,
-        interpretedResultsPath:
-          to.completedQuery.query.resultsPaths.interpretedResultsPath,
+        interpretedResultsPath: to.completedQuery.query.interpretedResultsPath,
       },
       commonResultSetNames,
     };
@@ -183,13 +181,97 @@ export class CompareView extends AbstractWebview<
         message = getErrorMessage(e);
       }
 
+      await this.streamResults(result, currentResultSetDisplayName, message);
+    }
+  }
+
+  private async streamResults(
+    result: QueryCompareResult | undefined,
+    currentResultSetName: string,
+    message: string | undefined,
+  ) {
+    // Since there is a string limit of 1GB in Node.js, the comparison is send as a JSON.stringified string to the webview
+    // and some comparisons may be larger than that, we sometimes need to stream results. This uses a heuristic of 2,000 results
+    // to determine if we should stream results.
+
+    if (!this.shouldStreamResults(result)) {
       await this.postMessage({
         t: "setComparisons",
         result,
-        currentResultSetName: currentResultSetDisplayName,
+        currentResultSetName,
         message,
       });
+      return;
     }
+
+    const id = nanoid();
+
+    // Streaming itself is implemented like this:
+    // - 1 setup message which contains the first 1,000 results
+    // - n "add results" messages which contain 1,000 results each
+    // - 1 complete message which just tells the webview that we're done
+
+    await this.postMessage({
+      t: "streamingComparisonSetup",
+      id,
+      result: this.chunkResults(result, 0, 1000),
+      currentResultSetName,
+      message,
+    });
+
+    const { from, to } = result;
+
+    const maxResults = Math.max(from.length, to.length);
+    for (let i = 1000; i < maxResults; i += 1000) {
+      const chunk = this.chunkResults(result, i, i + 1000);
+
+      await this.postMessage({
+        t: "streamingComparisonAddResults",
+        id,
+        result: chunk,
+      });
+    }
+
+    await this.postMessage({
+      t: "streamingComparisonComplete",
+      id,
+    });
+  }
+
+  private shouldStreamResults(
+    result: QueryCompareResult | undefined,
+  ): result is QueryCompareResult {
+    if (result === undefined) {
+      return false;
+    }
+
+    // We probably won't run into limits if we have less than 2,000 total results
+    const totalResults = result.from.length + result.to.length;
+    return totalResults > 2000;
+  }
+
+  private chunkResults(
+    result: QueryCompareResult,
+    start: number,
+    end: number,
+  ): QueryCompareResult {
+    if (result.kind === "raw") {
+      return {
+        ...result,
+        from: result.from.slice(start, end),
+        to: result.to.slice(start, end),
+      };
+    }
+
+    if (result.kind === "interpreted") {
+      return {
+        ...result,
+        from: result.from.slice(start, end),
+        to: result.to.slice(start, end),
+      };
+    }
+
+    assertNever(result);
   }
 
   protected getPanelConfig(): WebviewPanelConfig {
@@ -307,12 +389,12 @@ export class CompareView extends AbstractWebview<
       this.getResultSet(
         fromInfo.schemas,
         fromResultSetName,
-        from.completedQuery.query.resultsPaths.resultsPath,
+        from.completedQuery.query.resultsPath,
       ),
       this.getResultSet(
         toInfo.schemas,
         toResultSetName,
-        to.completedQuery.query.resultsPaths.resultsPath,
+        to.completedQuery.query.resultsPath,
       ),
     ]);
 
diff --git a/extensions/ql-vscode/src/compare/interpreted-results.ts b/extensions/ql-vscode/src/compare/interpreted-results.ts
index d5ca255ca4d..f98913a15e8 100644
--- a/extensions/ql-vscode/src/compare/interpreted-results.ts
+++ b/extensions/ql-vscode/src/compare/interpreted-results.ts
@@ -36,11 +36,9 @@ export async function compareInterpretedResults(
 
   const [fromResultSet, toResultSet, sourceLocationPrefix] = await Promise.all([
     getInterpretedResults(
-      fromQuery.completedQuery.query.resultsPaths.interpretedResultsPath,
-    ),
-    getInterpretedResults(
-      toQuery.completedQuery.query.resultsPaths.interpretedResultsPath,
+      fromQuery.completedQuery.query.interpretedResultsPath,
     ),
+    getInterpretedResults(toQuery.completedQuery.query.interpretedResultsPath),
     database.getSourceLocationPrefix(cliServer),
   ]);
 
diff --git a/extensions/ql-vscode/src/compare/sarif-diff.ts b/extensions/ql-vscode/src/compare/sarif-diff.ts
index 67e8e2ed976..158c63ae487 100644
--- a/extensions/ql-vscode/src/compare/sarif-diff.ts
+++ b/extensions/ql-vscode/src/compare/sarif-diff.ts
@@ -1,4 +1,4 @@
-import type { Location, Result } from "sarif";
+import type { Location, Result, ThreadFlowLocation } from "sarif";
 
 function toCanonicalLocation(location: Location): Location {
   if (location.physicalLocation?.artifactLocation?.index !== undefined) {
@@ -25,6 +25,19 @@ function toCanonicalLocation(location: Location): Location {
   return location;
 }
 
+function toCanonicalThreadFlowLocation(
+  threadFlowLocation: ThreadFlowLocation,
+): ThreadFlowLocation {
+  if (threadFlowLocation.location) {
+    return {
+      ...threadFlowLocation,
+      location: toCanonicalLocation(threadFlowLocation.location),
+    };
+  }
+
+  return threadFlowLocation;
+}
+
 function toCanonicalResult(result: Result): Result {
   const canonicalResult = {
     ...result,
@@ -40,37 +53,30 @@ function toCanonicalResult(result: Result): Result {
       canonicalResult.relatedLocations.map(toCanonicalLocation);
   }
 
-  if (canonicalResult.codeFlows) {
-    canonicalResult.codeFlows = canonicalResult.codeFlows.map((codeFlow) => {
-      if (codeFlow.threadFlows) {
-        return {
-          ...codeFlow,
-          threadFlows: codeFlow.threadFlows.map((threadFlow) => {
-            if (threadFlow.locations) {
-              return {
-                ...threadFlow,
-                locations: threadFlow.locations.map((threadFlowLocation) => {
-                  if (threadFlowLocation.location) {
-                    return {
-                      ...threadFlowLocation,
-                      location: toCanonicalLocation(
-                        threadFlowLocation.location,
-                      ),
-                    };
-                  }
-
-                  return threadFlowLocation;
-                }),
-              };
-            }
-
-            return threadFlow;
-          }),
-        };
-      }
-
-      return codeFlow;
-    });
+  if (canonicalResult.codeFlows && canonicalResult.codeFlows.length > 0) {
+    // If there are codeFlows, we don't want to compare the full codeFlows. Instead, we just want to compare the
+    // source and the sink (i.e. the first and last item). CodeQL should guarantee that the first and last threadFlow
+    // of every codeFlow is the same (i.e. every codeFlow has the same source and sink). Therefore, we just compare the
+    // first codeFlow and ignore the other codeFlows completely.
+    // If the codeFlow has a length of 1, this doesn't change the result.
+
+    const source = {
+      ...canonicalResult.codeFlows[0].threadFlows[0],
+    };
+    const sink = {
+      ...canonicalResult.codeFlows[0].threadFlows[
+        canonicalResult.codeFlows[0].threadFlows.length - 1
+      ],
+    };
+    source.locations = source.locations.map(toCanonicalThreadFlowLocation);
+    sink.locations = sink.locations.map(toCanonicalThreadFlowLocation);
+
+    canonicalResult.codeFlows = [
+      {
+        ...canonicalResult.codeFlows[0],
+        threadFlows: [source, sink],
+      },
+    ];
   }
 
   return canonicalResult;
@@ -79,11 +85,9 @@ function toCanonicalResult(result: Result): Result {
 /**
  * Compare the alerts of two queries. Use deep equality to determine if
  * results have been added or removed across two invocations of a query.
- *
- * Assumptions:
- *
- * 1. Queries have the same sort order
- * 2. Results are not changed or re-ordered, they are only added or removed
+ * It first canonicalizes the results to ensure that when small changes
+ * to the query are made, the results are still considered the same. This
+ * includes the removal of all paths except for the source and sink.
  *
  * @param fromResults the source query
  * @param toResults the target query
@@ -104,19 +108,30 @@ export function sarifDiff(fromResults: Result[], toResults: Result[]) {
   const canonicalFromResults = fromResults.map(toCanonicalResult);
   const canonicalToResults = toResults.map(toCanonicalResult);
 
-  const results = {
+  const diffResults = {
     from: arrayDiff(canonicalFromResults, canonicalToResults),
     to: arrayDiff(canonicalToResults, canonicalFromResults),
   };
 
   if (
-    fromResults.length === results.from.length &&
-    toResults.length === results.to.length
+    fromResults.length === diffResults.from.length &&
+    toResults.length === diffResults.to.length
   ) {
     throw new Error("CodeQL Compare: No overlap between the selected queries.");
   }
 
-  return results;
+  // We don't want to return the canonical results, we want to return the original results.
+  // We can retrieve this by finding the index of the canonical result in the canonical results
+  // and then using that index to find the original result. This is possible because we know that
+  // we did a 1-to-1 map between the canonical results and the original results.
+  return {
+    from: diffResults.from.map(
+      (result) => fromResults[canonicalFromResults.indexOf(result)],
+    ),
+    to: diffResults.to.map(
+      (result) => toResults[canonicalToResults.indexOf(result)],
+    ),
+  };
 }
 
 function arrayDiff<T>(source: readonly T[], toRemove: readonly T[]): T[] {
diff --git a/extensions/ql-vscode/src/config.ts b/extensions/ql-vscode/src/config.ts
index 377199da766..7e24fe26c5c 100644
--- a/extensions/ql-vscode/src/config.ts
+++ b/extensions/ql-vscode/src/config.ts
@@ -165,6 +165,8 @@ const ROOT_SETTING = new Setting("codeQL");
 const TELEMETRY_SETTING = new Setting("telemetry", ROOT_SETTING);
 
 export const LOG_TELEMETRY = new Setting("logTelemetry", TELEMETRY_SETTING);
+
+// Legacy setting that is no longer used, but is used for showing a message when the user upgrades.
 export const ENABLE_TELEMETRY = new Setting(
   "enableTelemetry",
   TELEMETRY_SETTING,
@@ -404,7 +406,7 @@ export class QueryServerConfigListener
   ): Promise<QueryServerConfigListener> {
     const codeQlPath =
       await distributionManager.getCodeQlPathWithoutVersionCheck();
-    const config = new QueryServerConfigListener(codeQlPath!);
+    const config = new QueryServerConfigListener(codeQlPath);
     if (distributionManager.onDidChangeDistribution) {
       config.push(
         distributionManager.onDidChangeDistribution(async () => {
@@ -828,15 +830,6 @@ export async function setAutogenerateQlPacks(choice: AutogenerateQLPacks) {
 
 const MODEL_SETTING = new Setting("model", ROOT_SETTING);
 const FLOW_GENERATION = new Setting("flowGeneration", MODEL_SETTING);
-const LLM_GENERATION = new Setting("llmGeneration", MODEL_SETTING);
-const LLM_GENERATION_BATCH_SIZE = new Setting(
-  "llmGenerationBatchSize",
-  MODEL_SETTING,
-);
-const LLM_GENERATION_DEV_ENDPOINT = new Setting(
-  "llmGenerationDevEndpoint",
-  MODEL_SETTING,
-);
 const MODEL_EVALUATION = new Setting("evaluation", MODEL_SETTING);
 const MODEL_PACK_LOCATION = new Setting("packLocation", MODEL_SETTING);
 const MODEL_PACK_NAME = new Setting("packName", MODEL_SETTING);
@@ -850,7 +843,6 @@ export type ModelConfigPackVariables = {
 
 export interface ModelConfig {
   flowGeneration: boolean;
-  llmGeneration: boolean;
   getPackLocation(
     languageId: string,
     variables: ModelConfigPackVariables,
@@ -870,26 +862,6 @@ export class ModelConfigListener extends ConfigListener implements ModelConfig {
     return !!FLOW_GENERATION.getValue<boolean>();
   }
 
-  public get llmGeneration(): boolean {
-    return !!LLM_GENERATION.getValue<boolean>() && !hasEnterpriseUri();
-  }
-
-  /**
-   * Limits the number of candidates we send to the model in each request to avoid long requests.
-   * Note that the model may return fewer than this number of candidates.
-   */
-  public get llmGenerationBatchSize(): number {
-    return LLM_GENERATION_BATCH_SIZE.getValue<number | null>() || 5;
-  }
-
-  /**
-   * The URL of the endpoint to use for LLM generation. This should only be set
-   * if you want to test against a dev server.
-   */
-  public get llmGenerationDevEndpoint(): string | undefined {
-    return LLM_GENERATION_DEV_ENDPOINT.getValue<string | undefined>();
-  }
-
   public get modelEvaluation(): boolean {
     return !!MODEL_EVALUATION.getValue<boolean>();
   }
@@ -982,3 +954,17 @@ export class GitHubDatabaseConfigListener
     await GITHUB_DATABASE_UPDATE.updateValue(value, target);
   }
 }
+
+const AUTOFIX_SETTING = new Setting("autofix", ROOT_SETTING);
+
+export const AUTOFIX_PATH = new Setting("path", AUTOFIX_SETTING);
+
+export function getAutofixPath(): string | undefined {
+  return AUTOFIX_PATH.getValue<string>() || undefined;
+}
+
+export const AUTOFIX_MODEL = new Setting("model", AUTOFIX_SETTING);
+
+export function getAutofixModel(): string | undefined {
+  return AUTOFIX_MODEL.getValue<string>() || undefined;
+}
diff --git a/extensions/ql-vscode/src/databases/config/db-config-store.ts b/extensions/ql-vscode/src/databases/config/db-config-store.ts
index 9d69567da94..b08406c9764 100644
--- a/extensions/ql-vscode/src/databases/config/db-config-store.ts
+++ b/extensions/ql-vscode/src/databases/config/db-config-store.ts
@@ -298,7 +298,7 @@ export class DbConfigStore extends DisposableObject {
     let newConfig: DbConfig | undefined = undefined;
     try {
       newConfig = await readJSON(this.configPath);
-    } catch (e) {
+    } catch {
       this.configErrors = [
         {
           kind: DbConfigValidationErrorKind.InvalidJson,
@@ -332,7 +332,7 @@ export class DbConfigStore extends DisposableObject {
     let newConfig: DbConfig | undefined = undefined;
     try {
       newConfig = readJSONSync(this.configPath);
-    } catch (e) {
+    } catch {
       this.configErrors = [
         {
           kind: DbConfigValidationErrorKind.InvalidJson,
diff --git a/extensions/ql-vscode/src/databases/database-fetcher.ts b/extensions/ql-vscode/src/databases/database-fetcher.ts
index 9e3c7321304..6f7f1356648 100644
--- a/extensions/ql-vscode/src/databases/database-fetcher.ts
+++ b/extensions/ql-vscode/src/databases/database-fetcher.ts
@@ -1,5 +1,3 @@
-import type { Response } from "node-fetch";
-import fetch, { AbortError } from "node-fetch";
 import type { InputBoxOptions } from "vscode";
 import { Uri, window } from "vscode";
 import type { CodeQLCliServer } from "../codeql-cli/cli";
@@ -30,11 +28,8 @@ import {
   allowHttp,
   downloadTimeout,
   getGitHubInstanceUrl,
-  hasGhecDrUri,
-  isCanary,
 } from "../config";
 import { showAndLogInformationMessage } from "../common/logging";
-import { AppOctokit } from "../common/octokit";
 import type { DatabaseOrigin } from "./local-databases/database-origin";
 import { createTimeoutSignal } from "../common/fetch-stream";
 import type { App } from "../common/app";
@@ -189,12 +184,7 @@ export class DatabaseFetcher {
       throw new Error(`Invalid GitHub repository: ${githubRepo}`);
     }
 
-    const credentials =
-      isCanary() || hasGhecDrUri() ? this.app.credentials : undefined;
-
-    const octokit = credentials
-      ? await credentials.getOctokit()
-      : new AppOctokit();
+    const octokit = await this.app.credentials.getOctokit();
 
     const result = await convertGithubNwoToDatabaseUrl(
       nwo,
@@ -454,7 +444,7 @@ export class DatabaseFetcher {
     let uri;
     try {
       uri = Uri.parse(databaseUrl, true);
-    } catch (e) {
+    } catch {
       throw new Error(`Invalid url: ${databaseUrl}`);
     }
 
@@ -536,8 +526,8 @@ export class DatabaseFetcher {
     } catch (e) {
       disposeTimeout();
 
-      if (e instanceof AbortError) {
-        const thrownError = new AbortError("The request timed out.");
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The request timed out.");
         thrownError.stack = e.stack;
         throw thrownError;
       }
@@ -545,30 +535,52 @@ export class DatabaseFetcher {
       throw e;
     }
 
+    const body = response.body;
+    if (!body) {
+      throw new Error("No response body found");
+    }
+
     const archiveFileStream = createWriteStream(archivePath);
 
     const contentLength = response.headers.get("content-length");
     const totalNumBytes = contentLength
       ? parseInt(contentLength, 10)
       : undefined;
-    reportStreamProgress(
-      response.body,
+
+    const reportProgress = reportStreamProgress(
       "Downloading database",
       totalNumBytes,
       progress,
     );
 
-    response.body.on("data", onData);
-
     try {
-      await new Promise((resolve, reject) => {
-        response.body
-          .pipe(archiveFileStream)
-          .on("finish", resolve)
-          .on("error", reject);
+      const reader = body.getReader();
+      for (;;) {
+        const { done, value } = await reader.read();
+        if (done) {
+          break;
+        }
+
+        onData();
+        reportProgress(value?.length ?? 0);
+
+        await new Promise((resolve, reject) => {
+          archiveFileStream.write(value, (err) => {
+            if (err) {
+              reject(err);
+            }
+            resolve(undefined);
+          });
+        });
+      }
 
-        // If an error occurs on the body, we also want to reject the promise (e.g. during a timeout error).
-        response.body.on("error", reject);
+      await new Promise((resolve, reject) => {
+        archiveFileStream.close((err) => {
+          if (err) {
+            reject(err);
+          }
+          resolve(undefined);
+        });
       });
     } catch (e) {
       // Close and remove the file if an error occurs
@@ -576,8 +588,8 @@ export class DatabaseFetcher {
         void remove(archivePath);
       });
 
-      if (e instanceof AbortError) {
-        const thrownError = new AbortError("The download timed out.");
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The download timed out.");
         thrownError.stack = e.stack;
         throw thrownError;
       }
@@ -600,7 +612,7 @@ export class DatabaseFetcher {
   private async checkForFailingResponse(
     response: Response,
     errorMessage: string,
-  ): Promise<Response | never> {
+  ): Promise<Response> {
     if (response.ok) {
       return response;
     }
@@ -612,7 +624,7 @@ export class DatabaseFetcher {
       const obj = JSON.parse(text);
       msg =
         obj.error || obj.message || obj.reason || JSON.stringify(obj, null, 2);
-    } catch (e) {
+    } catch {
       msg = text;
     }
     throw new Error(`${errorMessage}.\n\nReason: ${msg}`);
diff --git a/extensions/ql-vscode/src/databases/local-databases-ui.ts b/extensions/ql-vscode/src/databases/local-databases-ui.ts
index 8a12983951c..823093bfe49 100644
--- a/extensions/ql-vscode/src/databases/local-databases-ui.ts
+++ b/extensions/ql-vscode/src/databases/local-databases-ui.ts
@@ -16,6 +16,7 @@ import {
   ThemeIcon,
   ThemeColor,
   workspace,
+  FileType,
 } from "vscode";
 import { pathExists, stat, readdir, remove } from "fs-extra";
 
@@ -36,6 +37,7 @@ import {
 import {
   showAndLogExceptionWithTelemetry,
   showAndLogErrorMessage,
+  showAndLogInformationMessage,
 } from "../common/logging";
 import type { DatabaseFetcher } from "./database-fetcher";
 import { asError, asyncFilter, getErrorMessage } from "../common/helpers-pure";
@@ -267,6 +269,8 @@ export class DatabaseUI extends DisposableObject {
       "codeQL.getCurrentDatabase": this.handleGetCurrentDatabase.bind(this),
       "codeQL.chooseDatabaseFolder":
         this.handleChooseDatabaseFolderFromPalette.bind(this),
+      "codeQL.chooseDatabaseFoldersParent":
+        this.handleChooseDatabaseFoldersParentFromPalette.bind(this),
       "codeQL.chooseDatabaseArchive":
         this.handleChooseDatabaseArchiveFromPalette.bind(this),
       "codeQL.chooseDatabaseInternet":
@@ -280,6 +284,7 @@ export class DatabaseUI extends DisposableObject {
         this.handleUpgradeCurrentDatabase.bind(this),
       "codeQL.clearCache": this.handleClearCache.bind(this),
       "codeQL.trimCache": this.handleTrimCache.bind(this),
+      "codeQL.trimOverlayBaseCache": this.handleTrimOverlayBaseCache.bind(this),
       "codeQLDatabases.chooseDatabaseFolder":
         this.handleChooseDatabaseFolder.bind(this),
       "codeQLDatabases.chooseDatabaseArchive":
@@ -359,6 +364,12 @@ export class DatabaseUI extends DisposableObject {
     );
   }
 
+  private async handleChooseDatabaseFoldersParentFromPalette(): Promise<void> {
+    return withProgress(async (progress) => {
+      await this.chooseDatabasesParentFolder(progress);
+    });
+  }
+
   private async handleSetDefaultTourDatabase(): Promise<void> {
     return withProgress(
       async () => {
@@ -369,7 +380,7 @@ export class DatabaseUI extends DisposableObject {
             // This specifically refers to the database folder in
             // https://github.com/github/codespaces-codeql
             const uri = Uri.parse(
-              `${workspace.workspaceFolders[0].uri}/.tours/codeql-tutorial-database`,
+              `${workspace.workspaceFolders[0].uri.toString()}/.tours/codeql-tutorial-database`,
             );
 
             const databaseItem = this.databaseManager.findDatabaseItem(uri);
@@ -495,7 +506,7 @@ export class DatabaseUI extends DisposableObject {
   ): Promise<void> {
     try {
       await this.chooseAndSetDatabase(false, progress);
-    } catch (e: unknown) {
+    } catch (e) {
       void showAndLogExceptionWithTelemetry(
         this.app.logger,
         this.app.telemetry,
@@ -678,6 +689,25 @@ export class DatabaseUI extends DisposableObject {
     );
   }
 
+  private async handleTrimOverlayBaseCache(): Promise<void> {
+    return withProgress(
+      async () => {
+        if (
+          this.queryServer !== undefined &&
+          this.databaseManager.currentDatabaseItem !== undefined
+        ) {
+          await this.queryServer.trimCacheWithModeInDatabase(
+            this.databaseManager.currentDatabaseItem,
+            "overlay",
+          );
+        }
+      },
+      {
+        title: "Removing all overlay-dependent data from cache",
+      },
+    );
+  }
+
   private async handleGetCurrentDatabase(): Promise<string | undefined> {
     const dbItem = await this.getDatabaseItemInternal(undefined);
     return dbItem?.databaseUri.fsPath;
@@ -957,26 +987,22 @@ export class DatabaseUI extends DisposableObject {
   }
 
   /**
-   * Ask the user for a database directory. Returns the chosen database, or `undefined` if the
-   * operation was canceled.
+   * Import database from uri. Returns the imported database, or `undefined` if the
+   * operation was unsuccessful or canceled.
    */
-  private async chooseAndSetDatabase(
+  private async importDatabase(
+    uri: Uri,
     byFolder: boolean,
     progress: ProgressCallback,
   ): Promise<DatabaseItem | undefined> {
-    const uri = await chooseDatabaseDir(byFolder);
-    if (!uri) {
-      return undefined;
-    }
-
-    if (byFolder && !uri.fsPath.endsWith("testproj")) {
+    if (byFolder && !uri.fsPath.endsWith(".testproj")) {
       const fixedUri = await this.fixDbUri(uri);
       // we are selecting a database folder
       return await this.databaseManager.openDatabase(fixedUri, {
         type: "folder",
       });
     } else {
-      // we are selecting a database archive or a testproj.
+      // we are selecting a database archive or a .testproj.
       // Unzip archives (if an archive) and copy into a workspace-controlled area
       // before importing.
       return await this.databaseFetcher.importLocalDatabase(
@@ -986,6 +1012,104 @@ export class DatabaseUI extends DisposableObject {
     }
   }
 
+  /**
+   * Ask the user for a database directory. Returns the chosen database, or `undefined` if the
+   * operation was canceled.
+   */
+  private async chooseAndSetDatabase(
+    byFolder: boolean,
+    progress: ProgressCallback,
+  ): Promise<DatabaseItem | undefined> {
+    const uri = await chooseDatabaseDir(byFolder);
+    if (!uri) {
+      return undefined;
+    }
+
+    return await this.importDatabase(uri, byFolder, progress);
+  }
+
+  /**
+   * Ask the user for a parent directory that contains all databases.
+   * Returns all valid databases, or `undefined` if the operation was canceled.
+   */
+  private async chooseDatabasesParentFolder(
+    progress: ProgressCallback,
+  ): Promise<DatabaseItem[] | undefined> {
+    const uri = await chooseDatabaseDir(true);
+    if (!uri) {
+      return undefined;
+    }
+
+    const databases: DatabaseItem[] = [];
+    const failures: string[] = [];
+    const entries = await workspace.fs.readDirectory(uri);
+    const validFileTypes = [FileType.File, FileType.Directory];
+
+    for (const [index, entry] of entries.entries()) {
+      progress({
+        step: index + 1,
+        maxStep: entries.length,
+        message: `Importing '${entry[0]}'`,
+      });
+
+      const subProgress: ProgressCallback = (p) => {
+        progress({
+          step: index + 1,
+          maxStep: entries.length,
+          message: `Importing '${entry[0]}': (${p.step}/${p.maxStep}) ${p.message}`,
+        });
+      };
+
+      if (!validFileTypes.includes(entry[1])) {
+        void this.app.logger.log(
+          `Skipping import for '${entry[0]}', invalid file type: ${entry[1]}`,
+        );
+        continue;
+      }
+
+      try {
+        const databaseUri = Uri.joinPath(uri, entry[0]);
+        void this.app.logger.log(`Importing from ${databaseUri.toString()}`);
+
+        const database = await this.importDatabase(
+          databaseUri,
+          entry[1] === FileType.Directory,
+          subProgress,
+        );
+        if (database) {
+          databases.push(database);
+        } else {
+          failures.push(entry[0]);
+        }
+      } catch (e) {
+        failures.push(`${entry[0]}: ${getErrorMessage(e)}`.trim());
+      }
+    }
+
+    if (failures.length) {
+      void showAndLogErrorMessage(
+        this.app.logger,
+        `Failed to import ${failures.length} database(s), successfully imported ${databases.length} database(s).`,
+        {
+          fullMessage: `Failed to import ${failures.length} database(s), successfully imported ${databases.length} database(s).\nFailed databases:\n  - ${failures.join("\n  - ")}`,
+        },
+      );
+    } else if (databases.length === 0) {
+      void showAndLogErrorMessage(
+        this.app.logger,
+        `No database folder to import.`,
+      );
+      return undefined;
+    } else {
+      void showAndLogInformationMessage(
+        this.app.logger,
+        `Successfully imported ${databases.length} database(s).`,
+      );
+    }
+
+    return databases;
+  }
+
   /**
    * Perform some heuristics to ensure a proper database location is chosen.
    *
diff --git a/extensions/ql-vscode/src/databases/local-databases/database-manager.ts b/extensions/ql-vscode/src/databases/local-databases/database-manager.ts
index 7b4eb482fbc..5685f5f997a 100644
--- a/extensions/ql-vscode/src/databases/local-databases/database-manager.ts
+++ b/extensions/ql-vscode/src/databases/local-databases/database-manager.ts
@@ -64,12 +64,13 @@ const DB_LIST = "databaseList";
  */
 function eventFired<T>(
   event: vscode.Event<T>,
+  eventName: string,
   timeoutMs = 1000,
 ): Promise<T | undefined> {
   return new Promise((res, _rej) => {
     const timeout = setTimeout(() => {
       void extLogger.log(
-        `Waiting for event ${event} timed out after ${timeoutMs}ms`,
+        `Waiting for event '${eventName}' timed out after ${timeoutMs}ms`,
       );
       res(undefined);
       dispose();
@@ -231,7 +232,7 @@ export class DatabaseManager extends DisposableObject {
     let originStat;
     try {
       originStat = await stat(originDbYml);
-    } catch (e) {
+    } catch {
       // if there is an error here, assume that the origin database
       // is no longer available. Safely ignore and do not try to re-import.
       return false;
@@ -240,7 +241,7 @@ export class DatabaseManager extends DisposableObject {
     try {
       const importedStat = await stat(importedDbYml);
       return originStat.mtimeMs > importedStat.mtimeMs;
-    } catch (e) {
+    } catch {
       // If either of the files does not exist, we assume the origin is newer.
       // This shouldn't happen unless the user manually deleted one of the files.
       return true;
@@ -256,7 +257,7 @@ export class DatabaseManager extends DisposableObject {
   private async reimportTestDatabase(databaseUri: vscode.Uri): Promise<void> {
     const dbItem = this.findDatabaseItem(databaseUri);
     if (dbItem === undefined || dbItem.origin?.type !== "testproj") {
-      throw new Error(`Database ${databaseUri} is not a testproj.`);
+      throw new Error(`Database ${databaseUri.toString()} is not a testproj.`);
     }
 
     await this.removeDatabaseItem(dbItem);
@@ -411,7 +412,7 @@ export class DatabaseManager extends DisposableObject {
         qlpackStoragePath,
       );
       await qlPackGenerator.generate();
-    } catch (e: unknown) {
+    } catch (e) {
       void this.logger.log(
         `Could not create skeleton QL pack: ${getErrorMessage(e)}`,
       );
@@ -474,7 +475,10 @@ export class DatabaseManager extends DisposableObject {
       });
       // vscode api documentation says we must to wait for this event
       // between multiple `updateWorkspaceFolders` calls.
-      await eventFired(vscode.workspace.onDidChangeWorkspaceFolders);
+      await eventFired(
+        vscode.workspace.onDidChangeWorkspaceFolders,
+        "vscode.workspace.onDidChangeWorkspaceFolders",
+      );
     }
   }
 
@@ -561,7 +565,7 @@ export class DatabaseManager extends DisposableObject {
             // When loading from persisted state, leave invalid databases in the list. They will be
             // marked as invalid, and cannot be set as the current database.
             void this.logger.log(
-              `Error loading database ${database.uri}: ${e}.`,
+              `Error loading database ${database.uri}: ${getErrorMessage(e)}.`,
             );
           }
         }
diff --git a/extensions/ql-vscode/src/databases/ui/db-panel.ts b/extensions/ql-vscode/src/databases/ui/db-panel.ts
index 0605721d3ea..dbc61469d5a 100644
--- a/extensions/ql-vscode/src/databases/ui/db-panel.ts
+++ b/extensions/ql-vscode/src/databases/ui/db-panel.ts
@@ -432,7 +432,7 @@ export class DbPanel extends DisposableObject {
     try {
       // This will also validate that the controller repository is valid
       await getControllerRepo(this.app.credentials);
-    } catch (e: unknown) {
+    } catch (e) {
       if (e instanceof UserCancellationException) {
         return;
       }
diff --git a/extensions/ql-vscode/src/debugger/debug-protocol.ts b/extensions/ql-vscode/src/debugger/debug-protocol.ts
index d50bcee2221..c24d72e412b 100644
--- a/extensions/ql-vscode/src/debugger/debug-protocol.ts
+++ b/extensions/ql-vscode/src/debugger/debug-protocol.ts
@@ -39,6 +39,7 @@ export interface EvaluationCompletedEvent extends Event {
     resultType: QueryResultType;
     message: string | undefined;
     evaluationTime: number;
+    outputBaseName: string;
   };
 }
 
@@ -96,7 +97,7 @@ export type Response = DebugProtocol.Response & { type: "response" };
 export type InitializeResponse = DebugProtocol.InitializeResponse &
   Response & { command: "initialize" };
 
-export interface QuickEvalResponse extends Response {}
+export type QuickEvalResponse = Response;
 
 export type AnyResponse = InitializeResponse | QuickEvalResponse;
 
diff --git a/extensions/ql-vscode/src/debugger/debug-session.ts b/extensions/ql-vscode/src/debugger/debug-session.ts
index 1a51df30a30..64100a7831f 100644
--- a/extensions/ql-vscode/src/debugger/debug-session.ts
+++ b/extensions/ql-vscode/src/debugger/debug-session.ts
@@ -16,7 +16,7 @@ import type { BaseLogger, LogOptions } from "../common/logging";
 import { queryServerLogger } from "../common/logging/vscode";
 import { QueryResultType } from "../query-server/messages";
 import type {
-  CoreQueryResults,
+  CoreQueryResult,
   CoreQueryRun,
   QueryRunner,
 } from "../query-server";
@@ -25,6 +25,7 @@ import type * as CodeQLProtocol from "./debug-protocol";
 import type { QuickEvalContext } from "../run-queries-shared";
 import { getErrorMessage } from "../common/helpers-pure";
 import { DisposableObject } from "../common/disposable-object";
+import { basename } from "path";
 
 // More complete implementations of `Event` for certain events, because the classes from
 // `@vscode/debugadapter` make it more difficult to provide some of the message values.
@@ -107,9 +108,9 @@ class EvaluationCompletedEvent
   public readonly event = "codeql-evaluation-completed";
   public readonly body: CodeQLProtocol.EvaluationCompletedEvent["body"];
 
-  constructor(results: CoreQueryResults) {
+  constructor(result: CoreQueryResult) {
     super("codeql-evaluation-completed");
-    this.body = results;
+    this.body = result;
   }
 }
 
@@ -143,6 +144,7 @@ const QUERY_THREAD_NAME = "Evaluation thread";
 class RunningQuery extends DisposableObject {
   private readonly tokenSource = this.push(new CancellationTokenSource());
   public readonly queryRun: CoreQueryRun;
+  private readonly queryPath: string;
 
   public constructor(
     queryRunner: QueryRunner,
@@ -154,21 +156,25 @@ class RunningQuery extends DisposableObject {
   ) {
     super();
 
+    this.queryPath = config.query;
     // Create the query run, which will give us some information about the query even before the
     // evaluation has completed.
     this.queryRun = queryRunner.createQueryRun(
       config.database,
-      {
-        queryPath: config.query,
-        quickEvalPosition: quickEvalContext?.quickEvalPosition,
-        quickEvalCountOnly: quickEvalContext?.quickEvalCount,
-      },
+      [
+        {
+          queryPath: this.queryPath,
+          outputBaseName: "results",
+          quickEvalPosition: quickEvalContext?.quickEvalPosition,
+          quickEvalCountOnly: quickEvalContext?.quickEvalCount,
+        },
+      ],
       true,
       config.additionalPacks,
       config.extensionPacks,
       config.additionalRunQueryArgs,
       queryStorageDir,
-      undefined,
+      basename(config.query),
       undefined,
     );
   }
@@ -208,7 +214,7 @@ class RunningQuery extends DisposableObject {
       progressStart.body.cancellable = true;
       this.sendEvent(progressStart);
       try {
-        return await this.queryRun.evaluate(
+        const completedQuery = await this.queryRun.evaluate(
           (p) => {
             const progressUpdate = new ProgressUpdateEvent(
               this.queryRun.id,
@@ -220,6 +226,14 @@ class RunningQuery extends DisposableObject {
           this.tokenSource.token,
           this.logger,
         );
+        return (
+          completedQuery.results.get(this.queryPath) ?? {
+            resultType: QueryResultType.OTHER_ERROR,
+            message: "Missing query results",
+            evaluationTime: 0,
+            outputBaseName: "unknown",
+          }
+        );
       } finally {
         this.sendEvent(new ProgressEndEvent(this.queryRun.id));
       }
@@ -229,6 +243,7 @@ class RunningQuery extends DisposableObject {
         resultType: QueryResultType.OTHER_ERROR,
         message,
         evaluationTime: 0,
+        outputBaseName: "unknown",
       };
     }
   }
diff --git a/extensions/ql-vscode/src/debugger/debugger-ui.ts b/extensions/ql-vscode/src/debugger/debugger-ui.ts
index 6eb9a2d9fc7..8d401897055 100644
--- a/extensions/ql-vscode/src/debugger/debugger-ui.ts
+++ b/extensions/ql-vscode/src/debugger/debugger-ui.ts
@@ -8,7 +8,7 @@ import { debug, Uri, CancellationTokenSource } from "vscode";
 import type { DebuggerCommands } from "../common/commands";
 import type { DatabaseManager } from "../databases/local-databases";
 import { DisposableObject } from "../common/disposable-object";
-import type { CoreQueryResults } from "../query-server";
+import type { CoreQueryResult } from "../query-server";
 import {
   getQuickEvalContext,
   saveBeforeStart,
@@ -134,8 +134,15 @@ class QLDebugAdapterTracker
     body: EvaluationCompletedEvent["body"],
   ): Promise<void> {
     if (this.localQueryRun !== undefined) {
-      const results: CoreQueryResults = body;
-      await this.localQueryRun.complete(results, (_) => {});
+      const results: CoreQueryResult = body;
+      await this.localQueryRun.complete(
+        {
+          results: new Map<string, CoreQueryResult>([
+            [this.configuration.query, results],
+          ]),
+        },
+        (_) => {},
+      );
       this.localQueryRun = undefined;
     }
   }
diff --git a/extensions/ql-vscode/src/extension.ts b/extensions/ql-vscode/src/extension.ts
index 6a2a922c398..bd73929ad63 100644
--- a/extensions/ql-vscode/src/extension.ts
+++ b/extensions/ql-vscode/src/extension.ts
@@ -28,7 +28,6 @@ import {
   CliConfigListener,
   DistributionConfigListener,
   GitHubDatabaseConfigListener,
-  joinOrderWarningThreshold,
   QueryHistoryConfigListener,
   QueryServerConfigListener,
   VariantAnalysisConfigListener,
@@ -102,7 +101,6 @@ import { getPackagingCommands } from "./packaging";
 import { HistoryItemLabelProvider } from "./query-history/history-item-label-provider";
 import { EvalLogViewer } from "./query-evaluation-logging";
 import { SummaryLanguageSupport } from "./log-insights/summary-language-support";
-import { JoinOrderScannerProvider } from "./log-insights/join-order";
 import { LogScannerService } from "./log-insights/log-scanner-service";
 import { VariantAnalysisView } from "./variant-analysis/variant-analysis-view";
 import { VariantAnalysisViewSerializer } from "./variant-analysis/variant-analysis-view-serializer";
@@ -135,6 +133,7 @@ import { LanguageContextStore } from "./language-context-store";
 import { LanguageSelectionPanel } from "./language-selection-panel/language-selection-panel";
 import { GitHubDatabasesModule } from "./databases/github-databases";
 import { DatabaseFetcher } from "./databases/database-fetcher";
+import { ComparePerformanceView } from "./compare-performance/compare-performance-view";
 
 /**
  * extension.ts
@@ -219,7 +218,7 @@ function getCommands(
     "codeQL.copyVersion": async () => {
       const text = `CodeQL extension version: ${
         extension?.packageJSON.version
-      } \nCodeQL CLI version: ${await getCliVersion()} \nPlatform: ${platform()} ${arch()}`;
+      } \nCodeQL CLI version: ${(await getCliVersion()).toString()} \nPlatform: ${platform()} ${arch()}`;
       await env.clipboard.writeText(text);
       void showAndLogInformationMessage(extLogger, text);
     },
@@ -252,7 +251,7 @@ function registerErrorStubs(
   stubGenerator: (command: string) => () => Promise<void>,
 ): void {
   // Remove existing stubs
-  errorStubs.forEach((stub) => stub.dispose());
+  errorStubs.forEach((stub) => void stub.dispose());
 
   if (extension === undefined) {
     throw new Error(`Can't find extension ${extensionId}`);
@@ -300,12 +299,12 @@ const shouldUpdateOnNextActivationKey = "shouldUpdateOnNextActivation";
 
 const codeQlVersionRange = DEFAULT_DISTRIBUTION_VERSION_RANGE;
 
-// This is the minimum version of vscode that we _want_ to support. We want to update to Node 18, but that
-// requires 1.82 or later. If we change the minimum version in the package.json, then anyone on an older version of vscode will
+// This is the minimum version of vscode that we _want_ to support. We want to update to Node 20, but that
+// requires 1.90 or later. If we change the minimum version in the package.json, then anyone on an older version of vscode will
 // silently be unable to upgrade. So, the solution is to first bump the minimum version here and release. Then
 // bump the version in the package.json and release again. This way, anyone on an older version of vscode will get a warning
 // before silently being refused to upgrade.
-const MIN_VERSION = "1.82.0";
+const MIN_VERSION = "1.90.0";
 
 function sendConfigTelemetryData() {
   const config: Record<string, string> = {};
@@ -362,7 +361,9 @@ export async function activate(
     distributionConfigListener,
     codeQlVersionRange,
     ctx,
+    app.logger,
   );
+  await distributionManager.initialize();
 
   registerErrorStubs([checkForUpdatesCommand], (command) => async () => {
     void showAndLogErrorMessage(
@@ -456,12 +457,31 @@ export async function activate(
 
       void showAndLogWarningMessage(
         extLogger,
-        `You are using an unsupported version of the CodeQL CLI (${ver.version}). ` +
-          `The minimum supported version is ${CliVersionConstraint.OLDEST_SUPPORTED_CLI_VERSION}. ` +
+        `You are using an unsupported version of the CodeQL CLI (${ver.version.toString()}). ` +
+          `The minimum supported version is ${CliVersionConstraint.OLDEST_SUPPORTED_CLI_VERSION.toString()}. ` +
           `Please upgrade to a newer version of the CodeQL CLI.`,
       );
       unsupportedWarningShown = true;
     });
+
+    // Expose the CodeQL CLI features to the extension context under `codeQL.cliFeatures.*`.
+    let cliFeatures: { [feature: string]: boolean | undefined } = {};
+    codeQlExtension.cliServer.addVersionChangedListener(async (ver) => {
+      for (const feat of Object.keys(cliFeatures)) {
+        cliFeatures[feat] = false;
+      }
+      cliFeatures = {
+        ...cliFeatures,
+        ...(ver?.features ?? {}),
+      };
+      for (const feat of Object.keys(cliFeatures)) {
+        await app.commands.execute(
+          "setContext",
+          `codeQL.cliFeatures.${feat}`,
+          cliFeatures[feat] ?? false,
+        );
+      }
+    });
   }
 
   return codeQlExtension;
@@ -595,10 +615,13 @@ async function installOrUpdateDistribution(
     } else if (e instanceof GithubApiError) {
       void alertFunction(
         extLogger,
-        `Encountered GitHub API error while trying to ${taskDescription}. ${e}`,
+        `Encountered GitHub API error while trying to ${taskDescription}. ${getErrorMessage(e)}`,
       );
     }
-    void alertFunction(extLogger, `Unable to ${taskDescription}. ${e}`);
+    void alertFunction(
+      extLogger,
+      `Unable to ${taskDescription}. ${getErrorMessage(e)}`,
+    );
   } finally {
     isInstallingOrUpdatingDistribution = false;
   }
@@ -620,11 +643,11 @@ async function getDistributionDisplayingDistributionWarnings(
           case DistributionKind.ExtensionManaged:
             return 'Please update the CodeQL CLI by running the "CodeQL: Check for CLI Updates" command.';
           case DistributionKind.CustomPathConfig:
-            return `Please update the "CodeQL CLI Executable Path" setting to point to a CLI in the version range ${codeQlVersionRange}.`;
+            return `Please update the "CodeQL CLI Executable Path" setting to point to a CLI in the version range ${codeQlVersionRange.toString()}.`;
           case DistributionKind.PathEnvironmentVariable:
             return (
-              `Please update the CodeQL CLI on your PATH to a version compatible with ${codeQlVersionRange}, or ` +
-              `set the "CodeQL CLI Executable Path" setting to the path of a CLI version compatible with ${codeQlVersionRange}.`
+              `Please update the CodeQL CLI on your PATH to a version compatible with ${codeQlVersionRange.toString()}, or ` +
+              `set the "CodeQL CLI Executable Path" setting to the path of a CLI version compatible with ${codeQlVersionRange.toString()}.`
             );
         }
       })();
@@ -666,7 +689,7 @@ async function installOrUpdateThenTryActivate(
 
   try {
     await prepareCodeTour(app.commands);
-  } catch (e: unknown) {
+  } catch (e) {
     void extLogger.log(
       `Could not open tutorial workspace automatically: ${getErrorMessage(e)}`,
     );
@@ -737,7 +760,7 @@ async function activateWithInstalledDistribution(
   beganMainExtensionActivation = true;
   // Remove any error stubs command handlers left over from first part
   // of activation.
-  errorStubs.forEach((stub) => stub.dispose());
+  errorStubs.forEach((stub) => void stub.dispose());
 
   void extLogger.log("Initializing configuration listener...");
   const qlConfigurationListener =
@@ -746,9 +769,13 @@ async function activateWithInstalledDistribution(
     );
   ctx.subscriptions.push(qlConfigurationListener);
 
+  void extLogger.log("Initializing CodeQL language server.");
+  const languageClient = createLanguageClient(qlConfigurationListener);
+
   void extLogger.log("Initializing CodeQL cli server...");
   const cliServer = new CodeQLCliServer(
     app,
+    languageClient,
     distributionManager,
     new CliConfigListener(),
     extLogger,
@@ -922,6 +949,11 @@ async function activateWithInstalledDistribution(
       from: CompletedLocalQueryInfo,
       to: CompletedLocalQueryInfo,
     ): Promise<void> => showResultsForComparison(compareView, from, to),
+    async (
+      from: CompletedLocalQueryInfo,
+      to: CompletedLocalQueryInfo | undefined,
+    ): Promise<void> =>
+      showPerformanceComparison(comparePerformanceView, from, to),
   );
 
   ctx.subscriptions.push(qhm);
@@ -929,11 +961,6 @@ async function activateWithInstalledDistribution(
   void extLogger.log("Initializing evaluation log scanners.");
   const logScannerService = new LogScannerService(qhm);
   ctx.subscriptions.push(logScannerService);
-  ctx.subscriptions.push(
-    logScannerService.scanners.registerLogScannerProvider(
-      new JoinOrderScannerProvider(() => joinOrderWarningThreshold()),
-    ),
-  );
 
   void extLogger.log("Initializing compare view.");
   const compareView = new CompareView(
@@ -947,6 +974,15 @@ async function activateWithInstalledDistribution(
   );
   ctx.subscriptions.push(compareView);
 
+  void extLogger.log("Initializing performance comparison view.");
+  const comparePerformanceView = new ComparePerformanceView(
+    app,
+    queryServerLogger,
+    labelProvider,
+    localQueryResultsView,
+  );
+  ctx.subscriptions.push(comparePerformanceView);
+
   void extLogger.log("Initializing source archive filesystem provider.");
   archiveFilesystemProvider_activate(ctx, dbm);
 
@@ -959,9 +995,6 @@ async function activateWithInstalledDistribution(
 
   ctx.subscriptions.push(tmpDirDisposal);
 
-  void extLogger.log("Initializing CodeQL language server.");
-  const languageClient = createLanguageClient(qlConfigurationListener);
-
   const localQueries = new LocalQueries(
     app,
     qs,
@@ -1123,6 +1156,8 @@ async function activateWithInstalledDistribution(
   void extLogger.log("Reading query history");
   await qhm.readQueryHistory();
 
+  distributionManager.startCleanup();
+
   void extLogger.log("Successfully finished extension initialization.");
 
   return {
@@ -1135,7 +1170,7 @@ async function activateWithInstalledDistribution(
     databaseUI,
     variantAnalysisManager,
     dispose: () => {
-      ctx.subscriptions.forEach((d) => d.dispose());
+      ctx.subscriptions.forEach((d) => void d.dispose());
     },
   };
 }
@@ -1186,6 +1221,30 @@ async function showResultsForComparison(
   }
 }
 
+async function showPerformanceComparison(
+  view: ComparePerformanceView,
+  from: CompletedLocalQueryInfo,
+  to: CompletedLocalQueryInfo | undefined,
+): Promise<void> {
+  let fromLog = from.evaluatorLogPaths?.jsonSummary;
+  let toLog = to?.evaluatorLogPaths?.jsonSummary;
+
+  if (to === undefined) {
+    toLog = fromLog;
+    fromLog = "";
+  }
+  if (fromLog === undefined || toLog === undefined) {
+    return extLogger.showWarningMessage(
+      `Cannot compare performance as the structured logs are missing. Did they queries complete normally?`,
+    );
+  }
+  await extLogger.log(
+    `Comparing performance of ${from.getQueryName()} and ${to?.getQueryName() ?? "baseline"}`,
+  );
+
+  await view.showResults(fromLog, toLog);
+}
+
 function addUnhandledRejectionListener() {
   const handler = (error: unknown) => {
     // This listener will be triggered for errors from other extensions as
diff --git a/extensions/ql-vscode/src/koffi.d.ts b/extensions/ql-vscode/src/koffi.d.ts
new file mode 100644
index 00000000000..48cabce7265
--- /dev/null
+++ b/extensions/ql-vscode/src/koffi.d.ts
@@ -0,0 +1,4 @@
+// koffi/indirect is untyped in the upstream package, but it exports the same functions as koffi.
+declare module "koffi/indirect" {
+  export * from "koffi";
+}
diff --git a/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts b/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts
index f2e06b50cb8..fe0fb4c072c 100644
--- a/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts
+++ b/extensions/ql-vscode/src/language-selection-panel/language-selection-data-provider.ts
@@ -9,6 +9,7 @@ import {
 
 const ALL_LANGUAGE_SELECTION_OPTIONS = [
   undefined, // All languages
+  QueryLanguage.Actions,
   QueryLanguage.Cpp,
   QueryLanguage.CSharp,
   QueryLanguage.Go,
@@ -16,6 +17,7 @@ const ALL_LANGUAGE_SELECTION_OPTIONS = [
   QueryLanguage.Javascript,
   QueryLanguage.Python,
   QueryLanguage.Ruby,
+  QueryLanguage.Rust,
   QueryLanguage.Swift,
 ];
 
diff --git a/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts b/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts
index fd2203c0615..a8fd32a3276 100644
--- a/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts
+++ b/extensions/ql-vscode/src/language-support/ast-viewer/ast-builder.ts
@@ -7,7 +7,6 @@ import type {
 import type { DatabaseItem } from "../../databases/local-databases";
 import type { ChildAstItem, AstItem } from "./ast-viewer";
 import type { Uri } from "vscode";
-import type { QueryOutputDir } from "../../local-queries/query-output-dir";
 import { fileRangeFromURI } from "../contextual/file-range-from-uri";
 import { mapUrlValue } from "../../common/bqrs-raw-results-mapper";
 
@@ -17,15 +16,12 @@ import { mapUrlValue } from "../../common/bqrs-raw-results-mapper";
  */
 export class AstBuilder {
   private roots: AstItem[] | undefined;
-  private bqrsPath: string;
   constructor(
-    outputDir: QueryOutputDir,
+    private readonly bqrsPath: string,
     private cli: CodeQLCliServer,
     public db: DatabaseItem,
     public fileName: Uri,
-  ) {
-    this.bqrsPath = outputDir.bqrsPath;
-  }
+  ) {}
 
   async getRoots(): Promise<AstItem[]> {
     if (!this.roots) {
diff --git a/extensions/ql-vscode/src/language-support/ast-viewer/ast-viewer.ts b/extensions/ql-vscode/src/language-support/ast-viewer/ast-viewer.ts
index 71c057aa62c..f186674c08e 100644
--- a/extensions/ql-vscode/src/language-support/ast-viewer/ast-viewer.ts
+++ b/extensions/ql-vscode/src/language-support/ast-viewer/ast-viewer.ts
@@ -80,11 +80,11 @@ class AstViewerDataProvider
     const treeItem = new TreeItem(item.label || "", state);
     treeItem.description = line ? `Line ${line}` : "";
     treeItem.id = String(item.id);
-    treeItem.tooltip = `${treeItem.description} ${treeItem.label}`;
+    treeItem.tooltip = `${treeItem.description} ${typeof treeItem.label === "string" ? treeItem.label : (treeItem.label?.label ?? "")}`;
     treeItem.command = {
       command: "codeQLAstViewer.gotoCode",
       title: "Go To Code",
-      tooltip: `Go To ${item.location}`,
+      tooltip: "Go To Code",
       arguments: [item],
     };
     return treeItem;
diff --git a/extensions/ql-vscode/src/language-support/contextual/cached-operation.ts b/extensions/ql-vscode/src/language-support/contextual/cached-operation.ts
index a50e7d03b01..3c6e845d740 100644
--- a/extensions/ql-vscode/src/language-support/contextual/cached-operation.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/cached-operation.ts
@@ -7,6 +7,7 @@ export class CachedOperation<S extends unknown[], U> {
   private readonly operation: (t: string, ...args: S) => Promise<U>;
   private readonly cached: Map<string, U>;
   private readonly lru: string[];
+  private generation: number;
   private readonly inProgressCallbacks: Map<
     string,
     Array<[(u: U) => void, (reason?: Error) => void]>
@@ -17,6 +18,7 @@ export class CachedOperation<S extends unknown[], U> {
     private cacheSize = 100,
   ) {
     this.operation = operation;
+    this.generation = 0;
     this.lru = [];
     this.inProgressCallbacks = new Map<
       string,
@@ -46,7 +48,7 @@ export class CachedOperation<S extends unknown[], U> {
         inProgressCallback.push([resolve, reject]);
       });
     }
-
+    const origGeneration = this.generation;
     // Otherwise compute the new value, but leave a callback to allow sharing work
     const callbacks: Array<[(u: U) => void, (reason?: Error) => void]> = [];
     this.inProgressCallbacks.set(t, callbacks);
@@ -54,6 +56,11 @@ export class CachedOperation<S extends unknown[], U> {
       const result = await this.operation(t, ...args);
       callbacks.forEach((f) => f[0](result));
       this.inProgressCallbacks.delete(t);
+      if (this.generation !== origGeneration) {
+        // Cache was reset in the meantime so don't trust this
+        // result enough to cache it.
+        return result;
+      }
       if (this.lru.length > this.cacheSize) {
         const toRemove = this.lru.shift()!;
         this.cached.delete(toRemove);
@@ -69,4 +76,11 @@ export class CachedOperation<S extends unknown[], U> {
       this.inProgressCallbacks.delete(t);
     }
   }
+
+  reset() {
+    this.cached.clear();
+    this.lru.length = 0;
+    this.generation++;
+    this.inProgressCallbacks.clear();
+  }
 }
diff --git a/extensions/ql-vscode/src/language-support/contextual/file-range-from-uri.ts b/extensions/ql-vscode/src/language-support/contextual/file-range-from-uri.ts
index 1aeb1fee51e..5274dc32f28 100644
--- a/extensions/ql-vscode/src/language-support/contextual/file-range-from-uri.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/file-range-from-uri.ts
@@ -31,7 +31,7 @@ export function fileRangeFromURI(
         return new Location(db.resolveSourceFile(uri.uri), range);
       }
       return undefined;
-    } catch (e) {
+    } catch {
       return undefined;
     }
   }
diff --git a/extensions/ql-vscode/src/language-support/contextual/location-finder.ts b/extensions/ql-vscode/src/language-support/contextual/location-finder.ts
index 01b8a5bbe76..0d3c25de93d 100644
--- a/extensions/ql-vscode/src/language-support/contextual/location-finder.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/location-finder.ts
@@ -21,7 +21,6 @@ import {
 } from "./query-resolver";
 import type { CancellationToken, LocationLink } from "vscode";
 import { Uri } from "vscode";
-import type { QueryOutputDir } from "../../local-queries/query-output-dir";
 import type { QueryRunner } from "../../query-server";
 import { QueryResultType } from "../../query-server/messages";
 import { fileRangeFromURI } from "./file-range-from-uri";
@@ -84,9 +83,15 @@ export async function getLocationsForUriString(
       token,
       templates,
     );
-    if (results.resultType === QueryResultType.SUCCESS) {
+    const queryResult = results.results.get(query);
+    if (queryResult?.resultType === QueryResultType.SUCCESS) {
       links.push(
-        ...(await getLinksFromResults(results.outputDir, cli, db, filter)),
+        ...(await getLinksFromResults(
+          results.outputDir.getBqrsPath(queryResult.outputBaseName),
+          cli,
+          db,
+          filter,
+        )),
       );
     }
   }
@@ -94,13 +99,12 @@ export async function getLocationsForUriString(
 }
 
 async function getLinksFromResults(
-  outputDir: QueryOutputDir,
+  bqrsPath: string,
   cli: CodeQLCliServer,
   db: DatabaseItem,
   filter: (srcFile: string, destFile: string) => boolean,
 ): Promise<FullLocationLink[]> {
   const localLinks: FullLocationLink[] = [];
-  const bqrsPath = outputDir.bqrsPath;
   const info = await cli.bqrsInfo(bqrsPath);
   const selectInfo = info["result-sets"].find(
     (schema) => schema.name === SELECT_QUERY_NAME,
diff --git a/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts b/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts
index 4302b18fa92..0fe2a08d1fc 100644
--- a/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/query-resolver.ts
@@ -14,6 +14,7 @@ import type { CancellationToken } from "vscode";
 import type { ProgressCallback } from "../../common/vscode/progress";
 import type { CoreCompletedQuery, QueryRunner } from "../../query-server";
 import { createLockFileForStandardQuery } from "../../local-queries/standard-queries";
+import { basename } from "path";
 
 /**
  * This wil try to determine the qlpacks for a given database. If it can't find a matching
@@ -28,7 +29,7 @@ export async function resolveContextualQlPacksForDatabase(
 ): Promise<QlPacksForLanguage> {
   try {
     return await qlpackOfDatabase(cli, databaseItem);
-  } catch (e) {
+  } catch {
     // If we can't find the qlpacks for the database, use the defaults instead
   }
 
@@ -80,13 +81,19 @@ export async function runContextualQuery(
   const { cleanup } = await createLockFileForStandardQuery(cli, query);
   const queryRun = qs.createQueryRun(
     db.databaseUri.fsPath,
-    { queryPath: query, quickEvalPosition: undefined },
+    [
+      {
+        queryPath: query,
+        outputBaseName: "results",
+        quickEvalPosition: undefined,
+      },
+    ],
     false,
     getOnDiskWorkspaceFolders(),
     undefined,
     {},
     queryStorageDir,
-    undefined,
+    basename(query),
     templates,
   );
   void extLogger.log(
diff --git a/extensions/ql-vscode/src/language-support/contextual/template-provider.ts b/extensions/ql-vscode/src/language-support/contextual/template-provider.ts
index 19927bd8903..8d9cf6327ec 100644
--- a/extensions/ql-vscode/src/language-support/contextual/template-provider.ts
+++ b/extensions/ql-vscode/src/language-support/contextual/template-provider.ts
@@ -133,7 +133,7 @@ export class TemplateQueryReferenceProvider implements ReferenceProvider {
 
     const locLinks: Location[] = [];
     for (const link of fileLinks) {
-      if (link.targetRange!.contains(position)) {
+      if (link.targetRange.contains(position)) {
         locLinks.push({
           range: link.originSelectionRange!,
           uri: link.originUri,
@@ -209,8 +209,14 @@ export class TemplatePrintAstProvider {
       ? await this.cache.get(fileUri.toString(), progress, token)
       : await this.getAst(fileUri.toString(), progress, token);
 
+    const queryResults = Array.from(completedQuery.results.values());
+    if (queryResults.length !== 1) {
+      throw new Error(
+        `Expected exactly one query result, but found ${queryResults.length}.`,
+      );
+    }
     return new AstBuilder(
-      completedQuery.outputDir,
+      completedQuery.outputDir.getBqrsPath(queryResults[0].outputBaseName),
       this.cli,
       this.dbm.findDatabaseItem(Uri.file(completedQuery.dbPath))!,
       fileUri,
diff --git a/extensions/ql-vscode/src/language-support/language-client.ts b/extensions/ql-vscode/src/language-support/language-client.ts
index 7b27a3fdaa5..07a3296b1af 100644
--- a/extensions/ql-vscode/src/language-support/language-client.ts
+++ b/extensions/ql-vscode/src/language-support/language-client.ts
@@ -79,7 +79,7 @@ async function spawnLanguageServer(
           languageServerLogger.log(data.toString(), { trailingNewline: false }),
         progressReporter,
       );
-      return { writer: child.stdin!, reader: child.stdout! };
+      return { writer: child.stdin, reader: child.stdout };
     },
   );
 }
diff --git a/extensions/ql-vscode/src/language-support/language-support.ts b/extensions/ql-vscode/src/language-support/language-support.ts
index e73bab07f6b..bded793fdf6 100644
--- a/extensions/ql-vscode/src/language-support/language-support.ts
+++ b/extensions/ql-vscode/src/language-support/language-support.ts
@@ -12,7 +12,7 @@ import { languages, IndentAction } from "vscode";
  * See https://github.com/microsoft/vscode/blob/master/src/vs/editor/test/common/modes/supports/javascriptOnEnterRules.ts
  */
 export function install() {
-  // eslint-disable-next-line @typescript-eslint/no-var-requires
+  // eslint-disable-next-line @typescript-eslint/no-require-imports
   const langConfig = require("../../language-configuration.json");
   // setLanguageConfiguration requires a regexp for the wordpattern, not a string
   langConfig.wordPattern = new RegExp(langConfig.wordPattern);
diff --git a/extensions/ql-vscode/src/language-support/query-editor.ts b/extensions/ql-vscode/src/language-support/query-editor.ts
index 71e66900037..a7567e1f1be 100644
--- a/extensions/ql-vscode/src/language-support/query-editor.ts
+++ b/extensions/ql-vscode/src/language-support/query-editor.ts
@@ -99,7 +99,7 @@ async function previewQueryHelp(
         telemetryListener,
         errorMessage,
         {
-          fullMessage: `${errorMessage}\n${getErrorMessage(e)}`,
+          fullMessage: `${errorMessage.fullMessage}\n${getErrorMessage(e)}`,
         },
       );
     }
diff --git a/extensions/ql-vscode/src/local-queries/local-queries.ts b/extensions/ql-vscode/src/local-queries/local-queries.ts
index 2961586650b..4444ade8293 100644
--- a/extensions/ql-vscode/src/local-queries/local-queries.ts
+++ b/extensions/ql-vscode/src/local-queries/local-queries.ts
@@ -19,7 +19,11 @@ import { basename } from "path";
 import { showBinaryChoiceDialog } from "../common/vscode/dialog";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import { displayQuickQuery } from "./quick-query";
-import type { CoreCompletedQuery, QueryRunner } from "../query-server";
+import type {
+  CoreCompletedQuery,
+  CoreQueryTarget,
+  QueryRunner,
+} from "../query-server";
 import type { QueryHistoryManager } from "../query-history/query-history-manager";
 import type {
   DatabaseQuickPickItem,
@@ -37,6 +41,7 @@ import {
   createTimestampFile,
   getQuickEvalContext,
   saveBeforeStart,
+  validateQuerySuiteUri,
   validateQueryUri,
 } from "../run-queries-shared";
 import type { CompletedLocalQueryInfo } from "../query-results";
@@ -51,6 +56,7 @@ import { LocalQueryRun } from "./local-query-run";
 import { createMultiSelectionCommand } from "../common/vscode/selection-commands";
 import { findLanguage } from "../codeql-cli/query-language";
 import type { QueryTreeViewItem } from "../queries-panel/query-tree-view-item";
+import type { QueryLanguage } from "../common/query-language";
 import { tryGetQueryLanguage } from "../common/query-language";
 import type { LanguageContextStore } from "../language-context-store";
 import type { ExtensionApp } from "../common/vscode/extension-app";
@@ -107,6 +113,7 @@ export class LocalQueries extends DisposableObject {
       "codeQL.runQueries": createMultiSelectionCommand(
         this.runQueries.bind(this),
       ),
+      "codeQL.runQuerySuite": this.runQuerySuite.bind(this),
       "codeQL.quickEval": this.quickEval.bind(this),
       "codeQL.quickEvalCount": this.quickEvalCount.bind(this),
       "codeQL.quickEvalContextEditor": this.quickEval.bind(this),
@@ -178,7 +185,7 @@ export class LocalQueries extends DisposableObject {
   private async runQueries(fileURIs: Uri[]): Promise<void> {
     await withProgress(
       async (progress, token) => {
-        const maxQueryCount = MAX_QUERIES.getValue() as number;
+        const maxQueryCount = MAX_QUERIES.getValue<number>();
         const [files, dirFound] = await gatherQlFiles(
           fileURIs.map((uri) => uri.fsPath),
         );
@@ -239,6 +246,94 @@ export class LocalQueries extends DisposableObject {
     );
   }
 
+  private async runQuerySuite(fileUri: Uri): Promise<void> {
+    await withProgress(
+      async (progress, token) => {
+        const suitePath = validateQuerySuiteUri(fileUri);
+        const databaseItem = await this.databaseUI.getDatabaseItem(progress);
+        if (databaseItem === undefined) {
+          throw new Error("Can't run query suite without a selected database");
+        }
+        const selectedQuery: SelectedQuery = {
+          queryPath: suitePath,
+        };
+        const additionalPacks = getOnDiskWorkspaceFolders();
+        const extensionPacks =
+          await this.getDefaultExtensionPacks(additionalPacks);
+        const queries = await this.cliServer.resolveQueriesInSuite(
+          suitePath,
+          additionalPacks,
+        );
+        if (
+          !(await showBinaryChoiceDialog(
+            `You are about to run ${basename(suitePath)}, which contains ${queries.length} queries. Do you want to continue?`,
+          ))
+        ) {
+          return;
+        }
+        const queryTargets: CoreQueryTarget[] = [];
+        queries.forEach((query, index) => {
+          queryTargets.push({
+            queryPath: query,
+            outputBaseName: `${index.toString().padStart(3, "0")}-${basename(query)}`,
+            quickEvalPosition: undefined,
+            quickEvalCountOnly: false,
+          });
+        });
+        const coreQueryRun = this.queryRunner.createQueryRun(
+          databaseItem.databaseUri.fsPath,
+          queryTargets,
+          true,
+          additionalPacks,
+          extensionPacks,
+          {},
+          this.queryStorageDir,
+          basename(suitePath),
+          undefined,
+        );
+        // handle cancellation from the history view.
+        const source = new CancellationTokenSource();
+        try {
+          token.onCancellationRequested(() => source.cancel());
+
+          const localQueryRun = await this.createLocalQueryRun(
+            selectedQuery,
+            databaseItem,
+            coreQueryRun.outputDir,
+            source,
+          );
+
+          try {
+            const results = await coreQueryRun.evaluate(
+              progress,
+              source.token,
+              localQueryRun.logger,
+            );
+
+            await localQueryRun.complete(results, progress);
+
+            return results;
+          } catch (e) {
+            const err = asError(e);
+            await localQueryRun.fail(err);
+
+            if (token.isCancellationRequested) {
+              throw new UserCancellationException(err.message, true);
+            } else {
+              throw e;
+            }
+          }
+        } finally {
+          source.dispose();
+        }
+      },
+      {
+        title: "Running query suite",
+        cancellable: true,
+      },
+    );
+  }
+
   private async quickEval(uri: Uri): Promise<void> {
     await withProgress(
       async (progress, token) => {
@@ -452,17 +547,20 @@ export class LocalQueries extends DisposableObject {
 
     const coreQueryRun = this.queryRunner.createQueryRun(
       databaseItem.databaseUri.fsPath,
-      {
-        queryPath: selectedQuery.queryPath,
-        quickEvalPosition: selectedQuery.quickEval?.quickEvalPosition,
-        quickEvalCountOnly: selectedQuery.quickEval?.quickEvalCount,
-      },
+      [
+        {
+          queryPath: selectedQuery.queryPath,
+          outputBaseName: "results",
+          quickEvalPosition: selectedQuery.quickEval?.quickEvalPosition,
+          quickEvalCountOnly: selectedQuery.quickEval?.quickEvalCount,
+        },
+      ],
       true,
       additionalPacks,
       extensionPacks,
       {},
       this.queryStorageDir,
-      undefined,
+      basename(selectedQuery.queryPath),
       templates,
     );
 
@@ -524,7 +622,7 @@ export class LocalQueries extends DisposableObject {
     const queryLanguage = await findLanguage(this.cliServer, uri);
     if (queryLanguage) {
       filteredDBs = this.databaseManager.databaseItems.filter(
-        (db) => db.language === queryLanguage,
+        (db) => (db.language as QueryLanguage) === queryLanguage,
       );
       if (filteredDBs.length === 0) {
         void showAndLogErrorMessage(
diff --git a/extensions/ql-vscode/src/local-queries/local-query-run.ts b/extensions/ql-vscode/src/local-queries/local-query-run.ts
index 5ea2463caef..c2d6dec5972 100644
--- a/extensions/ql-vscode/src/local-queries/local-query-run.ts
+++ b/extensions/ql-vscode/src/local-queries/local-query-run.ts
@@ -4,7 +4,7 @@ import {
   showAndLogExceptionWithTelemetry,
   showAndLogWarningMessage,
 } from "../common/logging";
-import type { CoreQueryResults } from "../query-server";
+import type { CoreQueryResult, CoreQueryResults } from "../query-server";
 import type { QueryHistoryManager } from "../query-history/query-history-manager";
 import type { DatabaseItem } from "../databases/local-databases";
 import type {
@@ -29,7 +29,7 @@ import type { Disposable } from "../common/disposable-object";
 import type { ProgressCallback } from "../common/vscode/progress";
 import { progressUpdate } from "../common/vscode/progress";
 
-function formatResultMessage(result: CoreQueryResults): string {
+function formatResultMessage(result: CoreQueryResult): string {
   switch (result.resultType) {
     case QueryResultType.CANCELLATION:
       return `cancelled after ${Math.round(
@@ -86,7 +86,9 @@ export class LocalQueryRun {
     progress: ProgressCallback,
   ): Promise<void> {
     const evalLogPaths = await this.summarizeEvalLog(
-      results.resultType,
+      Array.from(results.results.values()).every(
+        (result) => result.resultType === QueryResultType.SUCCESS,
+      ),
       this.outputDir,
       this.logger,
       progress,
@@ -95,9 +97,12 @@ export class LocalQueryRun {
       this.queryInfo.setEvaluatorLogPaths(evalLogPaths);
     }
     progress(progressUpdate(1, 4, "Getting completed query info"));
-    const queryWithResults = await this.getCompletedQueryInfo(results);
+    const queriesWithResults = await this.getCompletedQueryInfo(results);
     progress(progressUpdate(2, 4, "Updating query history"));
-    this.queryHistoryManager.completeQuery(this.queryInfo, queryWithResults);
+    this.queryHistoryManager.completeQueries(
+      this.queryInfo,
+      queriesWithResults,
+    );
     progress(progressUpdate(3, 4, "Showing results"));
     await this.localQueries.showResultsForCompletedQuery(
       this.queryInfo as CompletedLocalQueryInfo,
@@ -116,7 +121,7 @@ export class LocalQueryRun {
    */
   public async fail(err: Error): Promise<void> {
     const evalLogPaths = await this.summarizeEvalLog(
-      QueryResultType.OTHER_ERROR,
+      false,
       this.outputDir,
       this.logger,
       (_) => {},
@@ -136,7 +141,7 @@ export class LocalQueryRun {
    * Generate summaries of the structured evaluator log.
    */
   private async summarizeEvalLog(
-    resultType: QueryResultType,
+    runSuccessful: boolean,
     outputDir: QueryOutputDir,
     logger: BaseLogger,
     progress: ProgressCallback,
@@ -152,7 +157,7 @@ export class LocalQueryRun {
       }
     } else {
       // Raw evaluator log was not found. Notify the user, unless we know why it wasn't found.
-      if (resultType === QueryResultType.SUCCESS) {
+      if (runSuccessful) {
         void showAndLogWarningMessage(
           extLogger,
           `Failed to write structured evaluator log to ${outputDir.evalLogPath}.`,
@@ -168,41 +173,43 @@ export class LocalQueryRun {
   }
 
   /**
-   * Gets a `QueryWithResults` containing information about the evaluation of the query and its
+   * Gets a `QueryWithResults` containing information about the evaluation of the queries and their
    * result, in the form expected by the query history UI.
    */
   private async getCompletedQueryInfo(
     results: CoreQueryResults,
-  ): Promise<QueryWithResults> {
-    // Read the query metadata if possible, to use in the UI.
-    const metadata = await tryGetQueryMetadata(
-      this.cliServer,
-      this.queryInfo.initialInfo.queryPath,
-    );
-    const query = new QueryEvaluationInfo(
-      this.outputDir.querySaveDir,
-      this.dbItem.databaseUri.fsPath,
-      await this.dbItem.hasMetadataFile(),
-      this.queryInfo.initialInfo.quickEvalPosition,
-      metadata,
-    );
+  ): Promise<QueryWithResults[]> {
+    const infos: QueryWithResults[] = [];
+    for (const [queryPath, result] of results.results) {
+      // Read the query metadata if possible, to use in the UI.
+      const metadata = await tryGetQueryMetadata(this.cliServer, queryPath);
+      const query = new QueryEvaluationInfo(
+        this.outputDir.querySaveDir,
+        result.outputBaseName,
+        this.dbItem.databaseUri.fsPath,
+        await this.dbItem.hasMetadataFile(),
+        this.queryInfo.initialInfo.quickEvalPosition,
+        metadata,
+      );
 
-    if (results.resultType !== QueryResultType.SUCCESS) {
-      const message = results.message
-        ? redactableError`Failed to run query: ${results.message}`
-        : redactableError`Failed to run query`;
-      void showAndLogExceptionWithTelemetry(
-        extLogger,
-        telemetryListener,
+      if (result.resultType !== QueryResultType.SUCCESS) {
+        const message = result.message
+          ? redactableError`Failed to run query: ${result.message}`
+          : redactableError`Failed to run query`;
+        void showAndLogExceptionWithTelemetry(
+          extLogger,
+          telemetryListener,
+          message,
+        );
+      }
+      const message = formatResultMessage(result);
+      const successful = result.resultType === QueryResultType.SUCCESS;
+      infos.push({
+        query,
         message,
-      );
+        successful,
+      });
     }
-    const message = formatResultMessage(results);
-    const successful = results.resultType === QueryResultType.SUCCESS;
-    return {
-      query,
-      message,
-      successful,
-    };
+    return infos;
   }
 }
diff --git a/extensions/ql-vscode/src/local-queries/query-contents.ts b/extensions/ql-vscode/src/local-queries/query-contents.ts
index 762965f70eb..a7302026952 100644
--- a/extensions/ql-vscode/src/local-queries/query-contents.ts
+++ b/extensions/ql-vscode/src/local-queries/query-contents.ts
@@ -15,7 +15,7 @@ import { dbSchemeToLanguage } from "../common/query-language";
  */
 export function getInitialQueryContents(language: string, dbscheme: string) {
   if (!language) {
-    const dbschemeBase = basename(dbscheme) as keyof typeof dbSchemeToLanguage;
+    const dbschemeBase = basename(dbscheme);
     language = dbSchemeToLanguage[dbschemeBase];
   }
 
diff --git a/extensions/ql-vscode/src/local-queries/query-output-dir.ts b/extensions/ql-vscode/src/local-queries/query-output-dir.ts
index a049849d54c..00be58078b7 100644
--- a/extensions/ql-vscode/src/local-queries/query-output-dir.ts
+++ b/extensions/ql-vscode/src/local-queries/query-output-dir.ts
@@ -30,10 +30,6 @@ function findQueryEvalLogEndSummaryFile(resultPath: string): string {
 export class QueryOutputDir {
   constructor(public readonly querySaveDir: string) {}
 
-  get dilPath() {
-    return join(this.querySaveDir, "results.dil");
-  }
-
   /**
    * Get the path that the compiled query is if it exists. Note that it only exists when using the legacy query server.
    */
@@ -41,10 +37,6 @@ export class QueryOutputDir {
     return join(this.querySaveDir, "compiledQuery.qlo");
   }
 
-  get csvPath() {
-    return join(this.querySaveDir, "results.csv");
-  }
-
   get logPath() {
     return findQueryLogFile(this.querySaveDir);
   }
@@ -69,7 +61,25 @@ export class QueryOutputDir {
     return findQueryEvalLogEndSummaryFile(this.querySaveDir);
   }
 
-  get bqrsPath() {
-    return join(this.querySaveDir, "results.bqrs");
+  getBqrsPath(outputBaseName: string): string {
+    return join(this.querySaveDir, `${outputBaseName}.bqrs`);
+  }
+
+  getInterpretedResultsPath(
+    metadataKind: string | undefined,
+    outputBaseName: string,
+  ): string {
+    return join(
+      this.querySaveDir,
+      `${outputBaseName}-${metadataKind === "graph" ? "graph" : `interpreted.sarif`}`,
+    );
+  }
+
+  getCsvPath(outputBaseName: string): string {
+    return join(this.querySaveDir, `${outputBaseName}.csv`);
+  }
+
+  getDilPath(outputBaseName: string): string {
+    return join(this.querySaveDir, `${outputBaseName}.dil`);
   }
 }
diff --git a/extensions/ql-vscode/src/local-queries/results-view.ts b/extensions/ql-vscode/src/local-queries/results-view.ts
index 18ee93f8543..55480c344f8 100644
--- a/extensions/ql-vscode/src/local-queries/results-view.ts
+++ b/extensions/ql-vscode/src/local-queries/results-view.ts
@@ -75,6 +75,7 @@ import type { App } from "../common/app";
 import type { Disposable } from "../common/disposable-object";
 import type { RawResultSet } from "../common/raw-result-types";
 import type { BqrsResultSetSchema } from "../common/bqrs-cli-types";
+import { CachedOperation } from "../language-support/contextual/cached-operation";
 
 /**
  * results-view.ts
@@ -177,6 +178,8 @@ export class ResultsView extends AbstractWebview<
   // Event listeners that should be disposed of when the view is disposed.
   private disposableEventListeners: Disposable[] = [];
 
+  private schemaCache: CachedOperation<[], BqrsResultSetSchema[]>;
+
   constructor(
     app: App,
     private databaseManager: DatabaseManager,
@@ -206,6 +209,10 @@ export class ResultsView extends AbstractWebview<
         }
       }),
     );
+
+    this.schemaCache = new CachedOperation(
+      this.getResultSetSchemasImpl.bind(this),
+    );
   }
 
   public getCommands(): ResultsViewCommands {
@@ -420,6 +427,7 @@ export class ResultsView extends AbstractWebview<
       );
       return;
     }
+    this.schemaCache.reset();
     // Notify the webview that it should expect new results.
     await this.postMessage({ t: "resultsUpdating" });
     await this._displayedQuery.completedQuery.updateSortState(
@@ -548,10 +556,14 @@ export class ResultsView extends AbstractWebview<
     await this.postMessage({
       t: "setState",
       interpretation: interpretationPage,
-      origResultsPaths: fullQuery.completedQuery.query.resultsPaths,
+      origResultsPaths: {
+        resultsPath: fullQuery.completedQuery.query.resultsPath,
+        interpretedResultsPath:
+          fullQuery.completedQuery.query.interpretedResultsPath,
+      },
       resultsPath: this.convertPathToWebviewUri(
         panel,
-        fullQuery.completedQuery.query.resultsPaths.resultsPath,
+        fullQuery.completedQuery.query.resultsPath,
       ),
       parsedResultSets,
       sortedResultsMap,
@@ -610,6 +622,12 @@ export class ResultsView extends AbstractWebview<
     selectedTable = "",
   ): Promise<BqrsResultSetSchema[]> {
     const resultsPath = completedQuery.getResultsPath(selectedTable);
+    return this.schemaCache.get(resultsPath);
+  }
+
+  private async getResultSetSchemasImpl(
+    resultsPath: string,
+  ): Promise<BqrsResultSetSchema[]> {
     const schemas = await this.cliServer.bqrsInfo(
       resultsPath,
       PAGE_SIZE.getValue(),
@@ -690,10 +708,14 @@ export class ResultsView extends AbstractWebview<
     await this.postMessage({
       t: "setState",
       interpretation: this._interpretation,
-      origResultsPaths: results.completedQuery.query.resultsPaths,
+      origResultsPaths: {
+        resultsPath: results.completedQuery.query.resultsPath,
+        interpretedResultsPath:
+          results.completedQuery.query.interpretedResultsPath,
+      },
       resultsPath: this.convertPathToWebviewUri(
         panel,
-        results.completedQuery.query.resultsPaths.resultsPath,
+        results.completedQuery.query.resultsPath,
       ),
       parsedResultSets,
       sortedResultsMap,
@@ -828,7 +850,10 @@ export class ResultsView extends AbstractWebview<
               };
         await this._getInterpretedResults(
           query.metadata,
-          query.resultsPaths,
+          {
+            resultsPath: query.resultsPath,
+            interpretedResultsPath: query.interpretedResultsPath,
+          },
           sourceInfo,
           sourceLocationPrefix,
           sortState,
@@ -930,7 +955,9 @@ export class ResultsView extends AbstractWebview<
       }
       const resultLocation = tryResolveLocation(sarifLoc, databaseItem);
       if (!resultLocation) {
-        void this.logger.log(`Sarif location was not resolvable ${sarifLoc}`);
+        void this.logger.log(
+          `Sarif location was not resolvable: ${sarifLoc.uri.toString()}`,
+        );
         continue;
       }
       const parsedMessage = parseSarifPlainTextMessage(message);
diff --git a/extensions/ql-vscode/src/local-queries/run-query.ts b/extensions/ql-vscode/src/local-queries/run-query.ts
index 1f06c656b56..06ed7037280 100644
--- a/extensions/ql-vscode/src/local-queries/run-query.ts
+++ b/extensions/ql-vscode/src/local-queries/run-query.ts
@@ -33,17 +33,20 @@ export async function runQuery({
   // Create a query run to execute
   const queryRun = queryRunner.createQueryRun(
     databaseItem.databaseUri.fsPath,
-    {
-      queryPath,
-      quickEvalPosition: undefined,
-      quickEvalCountOnly: false,
-    },
+    [
+      {
+        queryPath,
+        outputBaseName: "results",
+        quickEvalPosition: undefined,
+        quickEvalCountOnly: false,
+      },
+    ],
     false,
     additionalPacks,
     extensionPacks,
     {},
     queryStorageDir,
-    undefined,
+    basename(queryPath),
     undefined,
   );
 
@@ -54,13 +57,14 @@ export async function runQuery({
 
   try {
     const completedQuery = await queryRun.evaluate(progress, token, teeLogger);
+    const result = completedQuery.results.get(queryPath);
 
-    if (completedQuery.resultType !== QueryResultType.SUCCESS) {
+    if (result?.resultType !== QueryResultType.SUCCESS) {
       void showAndLogExceptionWithTelemetry(
         extLogger,
         telemetryListener,
         redactableError`Failed to run ${basename(queryPath)} query: ${
-          completedQuery.message ?? "No message"
+          result?.message ?? "No message"
         }`,
       );
       return;
diff --git a/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts b/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts
index 8d9390eab96..f99eb8d2fda 100644
--- a/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts
+++ b/extensions/ql-vscode/src/local-queries/skeleton-query-wizard.ts
@@ -38,6 +38,7 @@ import { getQlPackLanguage } from "../common/qlpack-language";
 type QueryLanguagesToDatabaseMap = Record<string, string>;
 
 export const QUERY_LANGUAGE_TO_DATABASE_REPO: QueryLanguagesToDatabaseMap = {
+  actions: "github/codeql",
   cpp: "google/brotli",
   csharp: "restsharp/RestSharp",
   go: "spf13/cobra",
@@ -45,6 +46,7 @@ export const QUERY_LANGUAGE_TO_DATABASE_REPO: QueryLanguagesToDatabaseMap = {
   javascript: "d3/d3",
   python: "pallets/flask",
   ruby: "jekyll/jekyll",
+  rust: "sharkdp/bat",
   swift: "Alamofire/Alamofire",
 };
 
@@ -130,7 +132,7 @@ export class SkeletonQueryWizard {
     // open the query file
     try {
       await this.openExampleFile();
-    } catch (e: unknown) {
+    } catch (e) {
       void this.app.logger.log(
         `Could not open example query file: ${getErrorMessage(e)}`,
       );
@@ -277,7 +279,7 @@ export class SkeletonQueryWizard {
       const qlPackGenerator = this.createQlPackGenerator();
 
       await qlPackGenerator.generate();
-    } catch (e: unknown) {
+    } catch (e) {
       void this.app.logger.log(
         `Could not create skeleton QL pack: ${getErrorMessage(e)}`,
       );
@@ -297,7 +299,7 @@ export class SkeletonQueryWizard {
 
       this.fileName = await this.determineNextFileName();
       await qlPackGenerator.createExampleQlFile(this.fileName);
-    } catch (e: unknown) {
+    } catch (e) {
       void this.app.logger.log(
         `Could not create query example file: ${getErrorMessage(e)}`,
       );
@@ -340,7 +342,7 @@ export class SkeletonQueryWizard {
       void withProgress(async (progress) => {
         try {
           await this.downloadDatabase(progress);
-        } catch (e: unknown) {
+        } catch (e) {
           if (e instanceof UserCancellationException) {
             return;
           }
diff --git a/extensions/ql-vscode/src/log-insights/join-order.ts b/extensions/ql-vscode/src/log-insights/join-order.ts
index 788da0a98e6..4bf85c89402 100644
--- a/extensions/ql-vscode/src/log-insights/join-order.ts
+++ b/extensions/ql-vscode/src/log-insights/join-order.ts
@@ -1,8 +1,5 @@
-import type {
-  EvaluationLogProblemReporter,
-  EvaluationLogScanner,
-  EvaluationLogScannerProvider,
-} from "./log-scanner";
+import { readJsonlFile } from "../common/jsonl-reader";
+import type { EvaluationLogProblemReporter } from "./log-scanner";
 import type {
   InLayer,
   ComputeRecursive,
@@ -19,23 +16,6 @@ function safeMax(it?: Iterable<number>) {
   return Number.isFinite(m) ? m : 0;
 }
 
-/**
- * Compute a key for the maps that that is sent to report generation.
- * Should only be used on events that are known to define queryCausingWork.
- */
-function makeKey(
-  queryCausingWork: string | undefined,
-  predicate: string,
-  suffix = "",
-): string {
-  if (queryCausingWork === undefined) {
-    throw new Error(
-      "queryCausingWork was not defined on an event we expected it to be defined for!",
-    );
-  }
-  return `${queryCausingWork}:${predicate}${suffix ? ` ${suffix}` : ""}`;
-}
-
 function getDependentPredicates(operations: string[]): string[] {
   const id = String.raw`[0-9a-zA-Z:#_\./]+`;
   const idWithAngleBrackets = String.raw`[0-9a-zA-Z:#_<>\./]+`;
@@ -128,14 +108,6 @@ function pointwiseSum(
   return result;
 }
 
-function pushValue<K, V>(m: Map<K, V[]>, k: K, v: V) {
-  if (!m.has(k)) {
-    m.set(k, []);
-  }
-  m.get(k)!.push(v);
-  return m;
-}
-
 function computeJoinOrderBadness(
   maxTupleCount: number,
   maxDependentPredicateSize: number,
@@ -154,41 +126,18 @@ interface Bucket {
   dependentPredicateSizes: Map<string, number>;
 }
 
-class JoinOrderScanner implements EvaluationLogScanner {
+class PredicateSizeScanner {
   // Map a predicate hash to its result size
-  private readonly predicateSizes = new Map<string, number>();
-  private readonly layerEvents = new Map<
-    string,
-    Array<ComputeRecursive | InLayer>
-  >();
-  // Map a key of the form 'query-with-demand : predicate name' to its badness input.
-  private readonly maxTupleCountMap = new Map<string, number[]>();
-  private readonly resultSizeMap = new Map<string, number[]>();
-  private readonly maxDependentPredicateSizeMap = new Map<string, number[]>();
-  private readonly joinOrderMetricMap = new Map<string, number>();
-
-  constructor(
-    private readonly problemReporter: EvaluationLogProblemReporter,
-    private readonly warningThreshold: number,
-  ) {}
+  readonly predicateSizes = new Map<string, number>();
+  readonly layerEvents = new Map<string, Array<ComputeRecursive | InLayer>>();
 
-  public onEvent(event: SummaryEvent): void {
+  onEvent(event: SummaryEvent): void {
     if (
       event.completionType !== undefined &&
       event.completionType !== "SUCCESS"
     ) {
       return; // Skip any evaluation that wasn't successful
     }
-
-    this.recordPredicateSizes(event);
-    this.computeBadnessMetric(event);
-  }
-
-  public onDone(): void {
-    void this;
-  }
-
-  private recordPredicateSizes(event: SummaryEvent): void {
     switch (event.evaluationStrategy) {
       case "EXTENSIONAL":
       case "COMPUTED_EXTENSIONAL":
@@ -215,29 +164,20 @@ class JoinOrderScanner implements EvaluationLogScanner {
       }
     }
   }
+}
 
-  private reportProblemIfNecessary(
-    event: SummaryEvent,
-    iteration: number,
-    metric: number,
-  ): void {
-    if (metric >= this.warningThreshold) {
-      this.problemReporter.reportProblem(
-        event.predicateName,
-        event.raHash,
-        iteration,
-        `Relation '${
-          event.predicateName
-        }' has an inefficient join order. Its join order metric is ${metric.toFixed(
-          2,
-        )}, which is larger than the threshold of ${this.warningThreshold.toFixed(
-          2,
-        )}.`,
-      );
-    }
-  }
+class JoinOrderScanner {
+  constructor(
+    private readonly predicateSizes: Map<string, number>,
+    private readonly layerEvents: Map<
+      string,
+      Array<ComputeRecursive | InLayer>
+    >,
+    private readonly problemReporter: EvaluationLogProblemReporter,
+    private readonly warningThreshold: number,
+  ) {}
 
-  private computeBadnessMetric(event: SummaryEvent): void {
+  public onEvent(event: SummaryEvent): void {
     if (
       event.completionType !== undefined &&
       event.completionType !== "SUCCESS"
@@ -252,7 +192,6 @@ class JoinOrderScanner implements EvaluationLogScanner {
         }
         // Compute the badness metric for a non-recursive predicate. The metric in this case is defined as:
         // badness = (max tuple count in the pipeline) / (largest predicate this pipeline depends on)
-        const key = makeKey(event.queryCausingWork, event.predicateName);
         const resultSize = event.resultSize;
 
         // There is only one entry in `pipelineRuns` if it's a non-recursive predicate.
@@ -260,20 +199,26 @@ class JoinOrderScanner implements EvaluationLogScanner {
           this.badnessInputsForNonRecursiveDelta(event.pipelineRuns[0], event);
 
         if (maxDependentPredicateSize > 0) {
-          pushValue(this.maxTupleCountMap, key, maxTupleCount);
-          pushValue(this.resultSizeMap, key, resultSize);
-          pushValue(
-            this.maxDependentPredicateSizeMap,
-            key,
-            maxDependentPredicateSize,
-          );
           const metric = computeJoinOrderBadness(
             maxTupleCount,
             maxDependentPredicateSize,
-            resultSize!,
+            resultSize,
           );
-          this.joinOrderMetricMap.set(key, metric);
-          this.reportProblemIfNecessary(event, 0, metric);
+          if (metric >= this.warningThreshold) {
+            const message = `'${event.predicateName}@${event.raHash.substring(
+              0,
+              8,
+            )}' has an inefficient join order. Its join order metric is ${metric.toFixed(
+              2,
+            )}, which is larger than the threshold of ${this.warningThreshold.toFixed(
+              2,
+            )}.`;
+            this.problemReporter.reportProblemNonRecursive(
+              event.predicateName,
+              event.raHash,
+              message,
+            );
+          }
         }
         break;
       }
@@ -282,39 +227,40 @@ class JoinOrderScanner implements EvaluationLogScanner {
         // Compute the badness metric for a recursive predicate for each ordering.
         const sccMetricInput = this.badnessInputsForRecursiveDelta(event);
         // Loop through each predicate in the SCC
-        sccMetricInput.forEach((buckets, predicate) => {
-          // Loop through each ordering of the predicate
-          buckets.forEach((bucket, raReference) => {
-            // Format the key as demanding-query:name (ordering)
-            const key = makeKey(
-              event.queryCausingWork,
-              predicate,
-              `(${raReference})`,
-            );
-            const maxTupleCount = Math.max(...bucket.tupleCounts);
-            const resultSize = bucket.resultSize;
-            const maxDependentPredicateSize = Math.max(
-              ...bucket.dependentPredicateSizes.values(),
-            );
-
-            if (maxDependentPredicateSize > 0) {
-              pushValue(this.maxTupleCountMap, key, maxTupleCount);
-              pushValue(this.resultSizeMap, key, resultSize);
-              pushValue(
-                this.maxDependentPredicateSizeMap,
-                key,
-                maxDependentPredicateSize,
-              );
-              const metric = computeJoinOrderBadness(
-                maxTupleCount,
-                maxDependentPredicateSize,
-                resultSize,
+        sccMetricInput.forEach((hashToOrderToBucket, predicateName) => {
+          hashToOrderToBucket.forEach((orderToBucket, raHash) => {
+            // Loop through each ordering of the predicate.
+            orderToBucket.forEach((bucket, raReference) => {
+              const maxDependentPredicateSize = Math.max(
+                ...bucket.dependentPredicateSizes.values(),
               );
-              const oldMetric = this.joinOrderMetricMap.get(key);
-              if (oldMetric === undefined || metric > oldMetric) {
-                this.joinOrderMetricMap.set(key, metric);
+
+              if (maxDependentPredicateSize > 0) {
+                const maxTupleCount = Math.max(...bucket.tupleCounts);
+                const resultSize = bucket.resultSize;
+                const metric = computeJoinOrderBadness(
+                  maxTupleCount,
+                  maxDependentPredicateSize,
+                  resultSize,
+                );
+                if (metric >= this.warningThreshold) {
+                  const message = `The ${raReference} pipeline for '${predicateName}@${raHash.substring(
+                    0,
+                    8,
+                  )}' has an inefficient join order. Its join order metric is ${metric.toFixed(
+                    2,
+                  )}, which is larger than the threshold of ${this.warningThreshold.toFixed(
+                    2,
+                  )}.`;
+                  this.problemReporter.reportProblemForRecursionSummary(
+                    predicateName,
+                    raHash,
+                    raReference,
+                    message,
+                  );
+                }
               }
-            }
+            });
           });
         });
         break;
@@ -457,20 +403,28 @@ class JoinOrderScanner implements EvaluationLogScanner {
    */
   private badnessInputsForRecursiveDelta(
     event: ComputeRecursive,
-  ): Map<string, Map<string, Bucket>> {
-    // nameToOrderToBucket : predicate name -> ordering (i.e., standard, order_500000, etc.) -> bucket
-    const nameToOrderToBucket = new Map<string, Map<string, Bucket>>();
+  ): Map<string, Map<string, Map<string, Bucket>>> {
+    // nameToHashToOrderToBucket : predicate name -> RA hash -> ordering (i.e., standard, order_500000, etc.) -> bucket
+    const nameToHashToOrderToBucket = new Map<
+      string,
+      Map<string, Map<string, Bucket>>
+    >();
 
     // Iterate through the SCC and compute the metric inputs
     this.iterateSCC(event, (inLayerEvent, run, iteration) => {
       const raReference = run.raReference;
       const predicateName = inLayerEvent.predicateName;
-      if (!nameToOrderToBucket.has(predicateName)) {
-        nameToOrderToBucket.set(predicateName, new Map());
+      if (!nameToHashToOrderToBucket.has(predicateName)) {
+        nameToHashToOrderToBucket.set(predicateName, new Map());
       }
-      const orderTobucket = nameToOrderToBucket.get(predicateName)!;
-      if (!orderTobucket.has(raReference)) {
-        orderTobucket.set(raReference, {
+      const hashToOrderToBucket = nameToHashToOrderToBucket.get(predicateName)!;
+      const raHash = inLayerEvent.raHash;
+      if (!hashToOrderToBucket.has(raHash)) {
+        hashToOrderToBucket.set(raHash, new Map());
+      }
+      const orderToBucket = hashToOrderToBucket.get(raHash)!;
+      if (!orderToBucket.has(raReference)) {
+        orderToBucket.set(raReference, {
           tupleCounts: new Int32Array(0),
           resultSize: 0,
           dependentPredicateSizes: new Map(),
@@ -484,7 +438,7 @@ class JoinOrderScanner implements EvaluationLogScanner {
         iteration,
       );
 
-      const bucket = orderTobucket.get(raReference)!;
+      const bucket = orderToBucket.get(raReference)!;
       // Pointwise sum the tuple counts
       const newTupleCounts = pointwiseSum(
         bucket.tupleCounts,
@@ -504,23 +458,36 @@ class JoinOrderScanner implements EvaluationLogScanner {
         );
       }
 
-      orderTobucket.set(raReference, {
+      orderToBucket.set(raReference, {
         tupleCounts: newTupleCounts,
         resultSize,
         dependentPredicateSizes: newDependentPredicateSizes,
       });
     });
-    return nameToOrderToBucket;
+    return nameToHashToOrderToBucket;
   }
 }
 
-export class JoinOrderScannerProvider implements EvaluationLogScannerProvider {
-  constructor(private readonly getThreshdold: () => number) {}
+export async function scanAndReportJoinOrderProblems(
+  jsonSummaryLocation: string,
+  problemReporter: EvaluationLogProblemReporter,
+  warningThreshold: number,
+) {
+  // Do two passes over the summary JSON. The first pass collects the sizes of predicates, along
+  // with collecting layer events for each recursive SCC.
+  const predicateSizeScanner = new PredicateSizeScanner();
+  await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
+    predicateSizeScanner.onEvent(obj);
+  });
 
-  public createScanner(
-    problemReporter: EvaluationLogProblemReporter,
-  ): EvaluationLogScanner {
-    const threshold = this.getThreshdold();
-    return new JoinOrderScanner(problemReporter, threshold);
-  }
+  // The second pass takes the information from the first pass, computes join order scores, and reports those that exceed the threshold.
+  const joinOrderScanner = new JoinOrderScanner(
+    predicateSizeScanner.predicateSizes,
+    predicateSizeScanner.layerEvents,
+    problemReporter,
+    warningThreshold,
+  );
+  await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
+    joinOrderScanner.onEvent(obj);
+  });
 }
diff --git a/extensions/ql-vscode/src/log-insights/log-scanner-service.ts b/extensions/ql-vscode/src/log-insights/log-scanner-service.ts
index d2fe1311907..e8e79d60bc5 100644
--- a/extensions/ql-vscode/src/log-insights/log-scanner-service.ts
+++ b/extensions/ql-vscode/src/log-insights/log-scanner-service.ts
@@ -2,11 +2,12 @@ import { Diagnostic, DiagnosticSeverity, languages, Range, Uri } from "vscode";
 import { DisposableObject } from "../common/disposable-object";
 import type { QueryHistoryInfo } from "../query-history/query-history-info";
 import type { EvaluationLogProblemReporter } from "./log-scanner";
-import { EvaluationLogScannerSet } from "./log-scanner";
 import type { PipelineInfo, SummarySymbols } from "./summary-parser";
 import { readFile } from "fs-extra";
 import { extLogger } from "../common/logging/vscode";
 import type { QueryHistoryManager } from "../query-history/query-history-manager";
+import { scanAndReportJoinOrderProblems } from "./join-order";
+import { joinOrderWarningThreshold } from "../config";
 
 /**
  * Compute the key used to find a predicate in the summary symbols.
@@ -28,17 +29,41 @@ class ProblemReporter implements EvaluationLogProblemReporter {
 
   constructor(private readonly symbols: SummarySymbols | undefined) {}
 
-  public reportProblem(
+  public reportProblemNonRecursive(
     predicateName: string,
     raHash: string,
-    iteration: number,
     message: string,
   ): void {
     const nameWithHash = predicateSymbolKey(predicateName, raHash);
     const predicateSymbol = this.symbols?.predicates[nameWithHash];
     let predicateInfo: PipelineInfo | undefined = undefined;
     if (predicateSymbol !== undefined) {
-      predicateInfo = predicateSymbol.iterations[iteration];
+      predicateInfo = predicateSymbol.iterations[0];
+    }
+    if (predicateInfo !== undefined) {
+      const range = new Range(
+        predicateInfo.raStartLine,
+        0,
+        predicateInfo.raEndLine + 1,
+        0,
+      );
+      this.diagnostics.push(
+        new Diagnostic(range, message, DiagnosticSeverity.Error),
+      );
+    }
+  }
+
+  public reportProblemForRecursionSummary(
+    predicateName: string,
+    raHash: string,
+    order: string,
+    message: string,
+  ): void {
+    const nameWithHash = predicateSymbolKey(predicateName, raHash);
+    const predicateSymbol = this.symbols?.predicates[nameWithHash];
+    let predicateInfo: PipelineInfo | undefined = undefined;
+    if (predicateSymbol !== undefined) {
+      predicateInfo = predicateSymbol.recursionSummaries[order];
     }
     if (predicateInfo !== undefined) {
       const range = new Range(
@@ -59,7 +84,6 @@ class ProblemReporter implements EvaluationLogProblemReporter {
 }
 
 export class LogScannerService extends DisposableObject {
-  public readonly scanners = new EvaluationLogScannerSet();
   private readonly diagnosticCollection = this.push(
     languages.createDiagnosticCollection("ql-eval-log"),
   );
@@ -94,19 +118,19 @@ export class LogScannerService extends DisposableObject {
   public async scanEvalLog(query: QueryHistoryInfo | undefined): Promise<void> {
     this.diagnosticCollection.clear();
 
-    if (
-      query?.t !== "local" ||
-      query.evalLogSummaryLocation === undefined ||
-      query.jsonEvalLogSummaryLocation === undefined
-    ) {
+    if (query?.t !== "local" || query.evaluatorLogPaths === undefined) {
       return;
     }
 
-    const diagnostics = await this.scanLog(
-      query.jsonEvalLogSummaryLocation,
-      query.evalLogSummarySymbolsLocation,
-    );
-    const uri = Uri.file(query.evalLogSummaryLocation);
+    const { summarySymbols, jsonSummary, humanReadableSummary } =
+      query.evaluatorLogPaths;
+
+    if (jsonSummary === undefined || humanReadableSummary === undefined) {
+      return;
+    }
+
+    const diagnostics = await this.scanLog(jsonSummary, summarySymbols);
+    const uri = Uri.file(humanReadableSummary);
     this.diagnosticCollection.set(uri, diagnostics);
   }
 
@@ -127,9 +151,11 @@ export class LogScannerService extends DisposableObject {
       );
     }
     const problemReporter = new ProblemReporter(symbols);
-
-    await this.scanners.scanLog(jsonSummaryLocation, problemReporter);
-
+    await scanAndReportJoinOrderProblems(
+      jsonSummaryLocation,
+      problemReporter,
+      joinOrderWarningThreshold(),
+    );
     return problemReporter.diagnostics;
   }
 }
diff --git a/extensions/ql-vscode/src/log-insights/log-scanner.ts b/extensions/ql-vscode/src/log-insights/log-scanner.ts
index 7a8efcd5605..22a9a5cdf78 100644
--- a/extensions/ql-vscode/src/log-insights/log-scanner.ts
+++ b/extensions/ql-vscode/src/log-insights/log-scanner.ts
@@ -1,114 +1,38 @@
-import type { SummaryEvent } from "./log-summary";
-import { readJsonlFile } from "../common/jsonl-reader";
-import type { Disposable } from "../common/disposable-object";
-
 /**
  * Callback interface used to report diagnostics from a log scanner.
  */
 export interface EvaluationLogProblemReporter {
   /**
-   * Report a potential problem detected in the evaluation log.
+   * Report a potential problem detected in the evaluation log for a non-recursive predicate.
    *
    * @param predicateName The mangled name of the predicate with the problem.
    * @param raHash The RA hash of the predicate with the problem.
-   * @param iteration The iteration number with the problem. For a non-recursive predicate, this
-   * must be zero.
    * @param message The problem message.
    */
-  reportProblem(
+  reportProblemNonRecursive(
     predicateName: string,
     raHash: string,
-    iteration: number,
     message: string,
   ): void;
 
   /**
-   * Log a message about a problem in the implementation of the scanner. These will typically be
-   * displayed separate from any problems reported via `reportProblem()`.
-   */
-  log(message: string): void;
-}
-
-/**
- * Interface implemented by a log scanner. Instances are created via
- * `EvaluationLogScannerProvider.createScanner()`.
- */
-export interface EvaluationLogScanner {
-  /**
-   * Called for each event in the log summary, in order. The implementation can report problems via
-   * the `EvaluationLogProblemReporter` interface that was supplied to `createScanner()`.
-   * @param event The log summary event.
-   */
-  onEvent(event: SummaryEvent): void;
-  /**
-   * Called after all events in the log summary have been processed. The implementation can report
-   * problems via the `EvaluationLogProblemReporter` interface that was supplied to
-   * `createScanner()`.
-   */
-  onDone(): void;
-}
-
-/**
- * A factory for log scanners. When a log is to be scanned, all registered
- * `EvaluationLogScannerProviders` will be asked to create a new instance of `EvaluationLogScanner`
- * to do the scanning.
- */
-export interface EvaluationLogScannerProvider {
-  /**
-   * Create a new instance of `EvaluationLogScanner` to scan a single summary log.
-   * @param problemReporter Callback interface for reporting any problems discovered.
-   */
-  createScanner(
-    problemReporter: EvaluationLogProblemReporter,
-  ): EvaluationLogScanner;
-}
-
-export class EvaluationLogScannerSet {
-  private readonly scannerProviders = new Map<
-    number,
-    EvaluationLogScannerProvider
-  >();
-  private nextScannerProviderId = 0;
-
-  /**
-   * Register a provider that can create instances of `EvaluationLogScanner` to scan evaluation logs
-   * for problems.
-   * @param provider The provider.
-   * @returns A `Disposable` that, when disposed, will unregister the provider.
+   * Report a potential problem detected in the evaluation log for the summary of a recursive pipeline.
+   *
+   * @param predicateName The mangled name of the predicate with the problem.
+   * @param raHash The RA hash of the predicate with the problem.
+   * @param order The particular order (pipeline name) that had the problem.
+   * @param message The problem message.
    */
-  public registerLogScannerProvider(
-    provider: EvaluationLogScannerProvider,
-  ): Disposable {
-    const id = this.nextScannerProviderId;
-    this.nextScannerProviderId++;
-
-    this.scannerProviders.set(id, provider);
-    return {
-      dispose: () => {
-        this.scannerProviders.delete(id);
-      },
-    };
-  }
+  reportProblemForRecursionSummary(
+    predicateName: string,
+    raHash: string,
+    order: string,
+    message: string,
+  ): void;
 
   /**
-   * Scan the evaluator summary log for problems, using the scanners for all registered providers.
-   * @param jsonSummaryLocation The file path of the JSON summary log.
-   * @param problemReporter Callback interface for reporting any problems discovered.
+   * Log a message about a problem in the implementation of the scanner. These will typically be
+   * displayed separate from any problems reported via `reportProblem()`.
    */
-  public async scanLog(
-    jsonSummaryLocation: string,
-    problemReporter: EvaluationLogProblemReporter,
-  ): Promise<void> {
-    const scanners = [...this.scannerProviders.values()].map((p) =>
-      p.createScanner(problemReporter),
-    );
-
-    await readJsonlFile<SummaryEvent>(jsonSummaryLocation, async (obj) => {
-      scanners.forEach((scanner) => {
-        scanner.onEvent(obj);
-      });
-    });
-
-    scanners.forEach((scanner) => scanner.onDone());
-  }
+  log(message: string): void;
 }
diff --git a/extensions/ql-vscode/src/log-insights/log-summary.ts b/extensions/ql-vscode/src/log-insights/log-summary.ts
index 50435d51e1e..6919210f98c 100644
--- a/extensions/ql-vscode/src/log-insights/log-summary.ts
+++ b/extensions/ql-vscode/src/log-insights/log-summary.ts
@@ -16,7 +16,8 @@ type EvaluationStrategy =
   | "EXTENSIONAL"
   | "SENTINEL_EMPTY"
   | "CACHACA"
-  | "CACHE_HIT";
+  | "CACHE_HIT"
+  | "NAMED_LOCAL";
 
 interface SummaryEventBase {
   evaluationStrategy: EvaluationStrategy;
@@ -28,11 +29,14 @@ interface SummaryEventBase {
 
 interface ResultEventBase extends SummaryEventBase {
   resultSize: number;
+  dependencies?: { [key: string]: string };
+  mainHash?: string;
 }
 
 export interface ComputeSimple extends ResultEventBase {
   evaluationStrategy: "COMPUTE_SIMPLE";
   ra: Ra;
+  millis: number;
   pipelineRuns?: [PipelineRun];
   queryCausingWork?: string;
   dependencies: { [key: string]: string };
@@ -42,6 +46,7 @@ export interface ComputeRecursive extends ResultEventBase {
   evaluationStrategy: "COMPUTE_RECURSIVE";
   deltaSizes: number[];
   ra: Ra;
+  millis: number;
   pipelineRuns: PipelineRun[];
   queryCausingWork?: string;
   dependencies: { [key: string]: string };
@@ -58,6 +63,15 @@ export interface InLayer extends ResultEventBase {
   predicateIterationMillis: number[];
 }
 
+interface NamedLocal extends ResultEventBase {
+  evaluationStrategy: "NAMED_LOCAL";
+  deltaSizes: number[];
+  ra: Ra;
+  pipelineRuns: PipelineRun[];
+  queryCausingWork?: string;
+  predicateIterationMillis: number[];
+}
+
 interface ComputedExtensional extends ResultEventBase {
   evaluationStrategy: "COMPUTED_EXTENSIONAL";
   queryCausingWork?: string;
@@ -90,4 +104,5 @@ export type SummaryEvent =
   | Extensional
   | SentinelEmpty
   | Cachaca
-  | CacheHit;
+  | CacheHit
+  | NamedLocal;
diff --git a/extensions/ql-vscode/src/log-insights/performance-comparison.ts b/extensions/ql-vscode/src/log-insights/performance-comparison.ts
new file mode 100644
index 00000000000..7dfb516b9c3
--- /dev/null
+++ b/extensions/ql-vscode/src/log-insights/performance-comparison.ts
@@ -0,0 +1,242 @@
+import { createHash } from "crypto";
+import type { SummaryEvent } from "./log-summary";
+
+export interface PipelineSummary {
+  steps: string[];
+  /** Total counts for each step in the RA array, across all iterations */
+  counts: number[];
+  hash: string;
+}
+
+/**
+ * Data extracted from a log for the purpose of doing a performance comparison.
+ *
+ * Memory compactness is important since we keep this data in memory; once for
+ * each side of the comparison.
+ *
+ * This object must be able to survive a `postMessage` transfer from the extension host
+ * to a web view (which rules out `Map` values, for example).
+ */
+export interface PerformanceComparisonDataFromLog {
+  /**
+   * Names of predicates mentioned in the log.
+   *
+   * For compactness, details of these predicates are stored in a "struct of arrays" style.
+   *
+   * All fields (except those ending with `Indices`) should contain an array of the same length as `names`;
+   * details of a given predicate should be stored at the same index in each of those arrays.
+   */
+  names: string[];
+
+  /** RA hash of the `i`th predicate event */
+  raHashes: string[];
+
+  /** Number of milliseconds spent evaluating the `i`th predicate from the `names` array. */
+  timeCosts: number[];
+
+  /** Number of tuples seen in pipelines evaluating the `i`th predicate from the `names` array. */
+  tupleCosts: number[];
+
+  /** Number of iterations seen when evaluating the `i`th predicate from the `names` array. */
+  iterationCounts: number[];
+
+  /** Number of executions of pipelines evaluating the `i`th predicate from the `names` array. */
+  evaluationCounts: number[];
+
+  /**
+   * List of indices into the `names` array for which we have seen a cache hit.
+   */
+  cacheHitIndices: number[];
+
+  /**
+   * List of indices into the `names` array where the predicate was deemed empty due to a sentinel check.
+   */
+  sentinelEmptyIndices: number[];
+
+  /**
+   * All the pipeline runs seen for the `i`th predicate from the `names` array.
+   */
+  pipelineSummaryList: Array<Record<string, PipelineSummary>>;
+
+  /** All dependencies of the `i`th predicate from the `names` array, encoded as a list of indices in `names`. */
+  dependencyLists: number[][];
+}
+
+export class PerformanceOverviewScanner {
+  private readonly data: PerformanceComparisonDataFromLog = {
+    names: [],
+    raHashes: [],
+    timeCosts: [],
+    tupleCosts: [],
+    cacheHitIndices: [],
+    sentinelEmptyIndices: [],
+    pipelineSummaryList: [],
+    evaluationCounts: [],
+    iterationCounts: [],
+    dependencyLists: [],
+  };
+  private readonly raToIndex = new Map<string, number>();
+  private readonly mainHashToRepr = new Map<string, number>();
+  private readonly nameToIndex = new Map<string, number>();
+
+  private getPredicateIndex(name: string, ra: string): number {
+    let index = this.raToIndex.get(ra);
+    if (index === undefined) {
+      index = this.raToIndex.size;
+      this.raToIndex.set(ra, index);
+      const {
+        names,
+        raHashes,
+        timeCosts,
+        tupleCosts,
+        iterationCounts,
+        evaluationCounts,
+        pipelineSummaryList,
+        dependencyLists,
+      } = this.data;
+      names.push(name);
+      raHashes.push(ra);
+      timeCosts.push(0);
+      tupleCosts.push(0);
+      iterationCounts.push(0);
+      evaluationCounts.push(0);
+      pipelineSummaryList.push({});
+      dependencyLists.push([]);
+    }
+    return index;
+  }
+
+  getData(): PerformanceComparisonDataFromLog {
+    return this.data;
+  }
+
+  onEvent(event: SummaryEvent): void {
+    const { completionType, evaluationStrategy, predicateName, raHash } = event;
+    if (completionType !== undefined && completionType !== "SUCCESS") {
+      return; // Skip any evaluation that wasn't successful
+    }
+
+    switch (evaluationStrategy) {
+      case "EXTENSIONAL": {
+        break;
+      }
+      case "COMPUTED_EXTENSIONAL": {
+        if (predicateName.startsWith("cached_")) {
+          // Add a dependency from a cached COMPUTED_EXTENSIONAL to the predicate with the actual contents.
+          // The raHash of the this event may appear in a CACHE_HIT event in the other event log. The dependency
+          // we're adding here is needed in order to associate the original predicate with such a cache hit.
+          const originalName = predicateName.substring("cached_".length);
+          const originalIndex = this.nameToIndex.get(originalName);
+          if (originalIndex != null) {
+            const index = this.getPredicateIndex(predicateName, raHash);
+            this.data.dependencyLists[index].push(originalIndex);
+          }
+        }
+        break;
+      }
+      case "CACHE_HIT":
+      case "CACHACA": {
+        // Record a cache hit, but only if the predicate has not been seen before.
+        // We're mainly interested in the reuse of caches from an earlier query run as they can distort comparisons.
+        if (!this.raToIndex.has(raHash)) {
+          this.data.cacheHitIndices.push(
+            this.getPredicateIndex(predicateName, raHash),
+          );
+        }
+        break;
+      }
+      case "SENTINEL_EMPTY": {
+        const index = this.getPredicateIndex(predicateName, raHash);
+        this.data.sentinelEmptyIndices.push(index);
+        const sentinelIndex = this.raToIndex.get(event.sentinelRaHash);
+        if (sentinelIndex != null) {
+          this.data.dependencyLists[index].push(sentinelIndex); // needed for matching up cache hits
+        }
+        break;
+      }
+      case "COMPUTE_RECURSIVE":
+      case "COMPUTE_SIMPLE":
+      case "NAMED_LOCAL":
+      case "IN_LAYER": {
+        const index = this.getPredicateIndex(predicateName, raHash);
+        this.nameToIndex.set(predicateName, index);
+        let totalTime = 0;
+        let totalTuples = 0;
+        if (evaluationStrategy === "COMPUTE_SIMPLE") {
+          totalTime += event.millis;
+        } else {
+          // Make a best-effort estimate of the total time by adding up the positive iteration times (they can be negative).
+          // Note that for COMPUTE_RECURSIVE the "millis" field contain the total time of the SCC, not just that predicate,
+          // but we don't have a good way to show that in the UI, so we rely on the accumulated iteration times.
+          for (const millis of event.predicateIterationMillis ?? []) {
+            if (millis > 0) {
+              totalTime += millis;
+            }
+          }
+        }
+        const {
+          timeCosts,
+          tupleCosts,
+          iterationCounts,
+          evaluationCounts,
+          pipelineSummaryList,
+          dependencyLists,
+        } = this.data;
+        const pipelineSummaries = pipelineSummaryList[index];
+        const dependencyList = dependencyLists[index];
+        for (const { counts, raReference } of event.pipelineRuns ?? []) {
+          // Get or create the pipeline summary for this RA
+          const pipelineSummary = (pipelineSummaries[raReference] ??= {
+            steps: event.ra[raReference],
+            counts: counts.map(() => 0),
+            hash: getPipelineHash(event.ra[raReference]),
+          });
+          const { counts: totalTuplesPerStep } = pipelineSummary;
+          for (let i = 0, length = counts.length; i < length; ++i) {
+            const count = counts[i];
+            if (count < 0) {
+              // Empty RA lines have a tuple count of -1. Do not count them when aggregating.
+              // But retain the fact that this step had a negative count for rendering purposes.
+              totalTuplesPerStep[i] = count;
+              continue;
+            }
+            totalTuples += count;
+            totalTuplesPerStep[i] += count;
+          }
+        }
+        for (const dependencyHash of Object.values(event.dependencies ?? {})) {
+          const dependencyIndex = this.raToIndex.get(dependencyHash);
+          if (dependencyIndex != null) {
+            dependencyList.push(dependencyIndex);
+          }
+        }
+        // For predicates in the same SCC, add two-way dependencies with an arbitrary SCC member
+        const sccHash =
+          event.mainHash ??
+          (evaluationStrategy === "COMPUTE_RECURSIVE" ? raHash : null);
+        if (sccHash != null) {
+          const mainIndex = this.mainHashToRepr.get(sccHash);
+          if (mainIndex == null) {
+            this.mainHashToRepr.set(sccHash, index);
+          } else {
+            dependencyLists[index].push(mainIndex);
+            dependencyLists[mainIndex].push(index);
+          }
+        }
+        timeCosts[index] += totalTime;
+        tupleCosts[index] += totalTuples;
+        iterationCounts[index] += event.pipelineRuns?.length ?? 0;
+        evaluationCounts[index] += 1;
+        break;
+      }
+    }
+  }
+}
+
+function getPipelineHash(steps: string[]) {
+  const md5 = createHash("md5");
+  for (const step of steps) {
+    md5.write(step);
+  }
+  return md5.digest("base64");
+}
diff --git a/extensions/ql-vscode/src/log-insights/summary-language-support.ts b/extensions/ql-vscode/src/log-insights/summary-language-support.ts
index 9919db114da..6546fd04ce2 100644
--- a/extensions/ql-vscode/src/log-insights/summary-language-support.ts
+++ b/extensions/ql-vscode/src/log-insights/summary-language-support.ts
@@ -113,7 +113,7 @@ export class SummaryLanguageSupport extends DisposableObject {
         const sourceMapText = await readFile(mapPath, "utf-8");
         const rawMap: RawSourceMap = JSON.parse(sourceMapText);
         this.sourceMap = await new SourceMapConsumer(rawMap);
-      } catch (e: unknown) {
+      } catch (e) {
         // Error reading sourcemap. Pretend there was no sourcemap.
         void extLogger.log(
           `Error reading sourcemap file '${mapPath}': ${getErrorMessage(e)}`,
diff --git a/extensions/ql-vscode/src/log-insights/summary-parser.ts b/extensions/ql-vscode/src/log-insights/summary-parser.ts
index 6a42efca187..61a3a8af250 100644
--- a/extensions/ql-vscode/src/log-insights/summary-parser.ts
+++ b/extensions/ql-vscode/src/log-insights/summary-parser.ts
@@ -1,6 +1,3 @@
-import { createReadStream, writeFile } from "fs-extra";
-import { LINE_ENDINGS, splitStreamAtSeparators } from "../common/split-stream";
-
 /**
  * Location information for a single pipeline invocation in the RA.
  */
@@ -18,6 +15,11 @@ interface PredicateSymbol {
    * `PipelineInfo` for each iteration. A non-recursive predicate will have a single iteration `0`.
    */
   iterations: Record<number, PipelineInfo>;
+
+  /**
+   * `PipelineInfo` for each order, summarised for all iterations that used that order. Empty for non-recursive predicates.
+   */
+  recursionSummaries: Record<string, PipelineInfo>;
 }
 
 /**
@@ -27,102 +29,3 @@ interface PredicateSymbol {
 export interface SummarySymbols {
   predicates: Record<string, PredicateSymbol>;
 }
-
-// Tuple counts for Expr::Expr::getParent#dispred#f0820431#ff@76d6745o:
-const NON_RECURSIVE_TUPLE_COUNT_REGEXP =
-  /^Evaluated relational algebra for predicate (?<predicateName>\S+) with tuple counts:$/;
-// Tuple counts for Expr::Expr::getEnclosingStmt#f0820431#bf@923ddwj9 on iteration 0 running pipeline base:
-const RECURSIVE_TUPLE_COUNT_REGEXP =
-  /^Evaluated relational algebra for predicate (?<predicateName>\S+) on iteration (?<iteration>\d+) running pipeline (?<pipeline>\S+) with tuple counts:$/;
-const RETURN_REGEXP = /^\s*return /;
-
-/**
- * Parse a human-readable evaluation log summary to find the location of the RA for each pipeline
- * run.
- *
- * TODO: Once we're more certain about the symbol format, we should have the CLI generate this as it
- * generates the human-readabe summary to avoid having to rely on regular expression matching of the
- * human-readable text.
- *
- * @param summaryPath The path to the summary file.
- * @param symbolsPath The path to the symbols file to generate.
- */
-export async function generateSummarySymbolsFile(
-  summaryPath: string,
-  symbolsPath: string,
-): Promise<void> {
-  const symbols = await generateSummarySymbols(summaryPath);
-  await writeFile(symbolsPath, JSON.stringify(symbols));
-}
-
-/**
- * Parse a human-readable evaluation log summary to find the location of the RA for each pipeline
- * run.
- *
- * @param fileLocation The path to the summary file.
- * @returns Symbol information for the summary file.
- */
-async function generateSummarySymbols(
-  summaryPath: string,
-): Promise<SummarySymbols> {
-  const stream = createReadStream(summaryPath, {
-    encoding: "utf-8",
-  });
-  try {
-    const lines = splitStreamAtSeparators(stream, LINE_ENDINGS);
-
-    const symbols: SummarySymbols = {
-      predicates: {},
-    };
-
-    let lineNumber = 0;
-    let raStartLine = 0;
-    let iteration = 0;
-    let predicateName: string | undefined = undefined;
-    let startLine = 0;
-    for await (const line of lines) {
-      if (predicateName === undefined) {
-        // Looking for the start of the predicate.
-        const nonRecursiveMatch = line.match(NON_RECURSIVE_TUPLE_COUNT_REGEXP);
-        if (nonRecursiveMatch) {
-          iteration = 0;
-          predicateName = nonRecursiveMatch.groups!.predicateName;
-        } else {
-          const recursiveMatch = line.match(RECURSIVE_TUPLE_COUNT_REGEXP);
-          if (recursiveMatch?.groups) {
-            predicateName = recursiveMatch.groups.predicateName;
-            iteration = parseInt(recursiveMatch.groups.iteration);
-          }
-        }
-        if (predicateName !== undefined) {
-          startLine = lineNumber;
-          raStartLine = lineNumber + 1;
-        }
-      } else {
-        const returnMatch = line.match(RETURN_REGEXP);
-        if (returnMatch) {
-          let symbol = symbols.predicates[predicateName];
-          if (symbol === undefined) {
-            symbol = {
-              iterations: {},
-            };
-            symbols.predicates[predicateName] = symbol;
-          }
-          symbol.iterations[iteration] = {
-            startLine,
-            raStartLine,
-            raEndLine: lineNumber,
-          };
-
-          predicateName = undefined;
-        }
-      }
-
-      lineNumber++;
-    }
-
-    return symbols;
-  } finally {
-    stream.close();
-  }
-}
diff --git a/extensions/ql-vscode/src/model-editor/auto-model-api.ts b/extensions/ql-vscode/src/model-editor/auto-model-api.ts
deleted file mode 100644
index 5433ce65461..00000000000
--- a/extensions/ql-vscode/src/model-editor/auto-model-api.ts
+++ /dev/null
@@ -1,65 +0,0 @@
-import type { Credentials } from "../common/authentication";
-import type { OctokitResponse } from "@octokit/types";
-import fetch from "node-fetch";
-import type { ModelConfigListener } from "../config";
-
-export enum AutomodelMode {
-  Unspecified = "AUTOMODEL_MODE_UNSPECIFIED",
-  Framework = "AUTOMODEL_MODE_FRAMEWORK",
-  Application = "AUTOMODEL_MODE_APPLICATION",
-}
-
-export interface ModelRequest {
-  mode: AutomodelMode;
-  // Base64-encoded GZIP-compressed SARIF log
-  candidates: string;
-}
-
-export interface ModelResponse {
-  models: string;
-}
-
-export async function autoModel(
-  credentials: Credentials,
-  request: ModelRequest,
-  modelingConfig: ModelConfigListener,
-): Promise<ModelResponse> {
-  const devEndpoint = modelingConfig.llmGenerationDevEndpoint;
-  if (devEndpoint) {
-    return callAutoModelDevEndpoint(devEndpoint, request);
-  } else {
-    const octokit = await credentials.getOctokit();
-
-    const response: OctokitResponse<ModelResponse> = await octokit.request(
-      "POST /repos/github/codeql/code-scanning/codeql/auto-model",
-      {
-        data: request,
-      },
-    );
-
-    return response.data;
-  }
-}
-
-async function callAutoModelDevEndpoint(
-  endpoint: string,
-  request: ModelRequest,
-): Promise<ModelResponse> {
-  const json = JSON.stringify(request);
-  const response = await fetch(endpoint, {
-    method: "POST",
-    headers: {
-      "Content-Type": "application/json",
-    },
-    body: json,
-  });
-
-  if (!response.ok) {
-    throw new Error(
-      `Error calling auto-model API: ${response.status} ${response.statusText}`,
-    );
-  }
-
-  const data = await response.json();
-  return data as ModelResponse;
-}
diff --git a/extensions/ql-vscode/src/model-editor/auto-model-codeml-queries.ts b/extensions/ql-vscode/src/model-editor/auto-model-codeml-queries.ts
deleted file mode 100644
index 58b6a253510..00000000000
--- a/extensions/ql-vscode/src/model-editor/auto-model-codeml-queries.ts
+++ /dev/null
@@ -1,233 +0,0 @@
-import type { CodeQLCliServer, SourceInfo } from "../codeql-cli/cli";
-import type { CoreCompletedQuery, QueryRunner } from "../query-server";
-import type { DatabaseItem } from "../databases/local-databases";
-import type { ProgressCallback } from "../common/vscode/progress";
-import type { Log } from "sarif";
-import type { Mode } from "./shared/mode";
-import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
-import { interpretResultsSarif } from "../query-results";
-import { join } from "path";
-import { dir } from "tmp-promise";
-import { writeFile, outputFile } from "fs-extra";
-import { dump as dumpYaml } from "js-yaml";
-import type { MethodSignature } from "./method";
-import { runQuery } from "../local-queries/run-query";
-import type { QueryMetadata } from "../common/interface-types";
-import type { CancellationTokenSource } from "vscode";
-import { resolveQueries } from "../local-queries";
-import { modeTag } from "./mode-tag";
-
-type AutoModelQueriesOptions = {
-  mode: Mode;
-  candidateMethods: MethodSignature[];
-  cliServer: CodeQLCliServer;
-  queryRunner: QueryRunner;
-  databaseItem: DatabaseItem;
-  queryStorageDir: string;
-
-  progress: ProgressCallback;
-  cancellationTokenSource: CancellationTokenSource;
-};
-
-export type AutoModelQueriesResult = {
-  candidates: Log;
-};
-
-export async function runAutoModelQueries({
-  mode,
-  candidateMethods,
-  cliServer,
-  queryRunner,
-  databaseItem,
-  queryStorageDir,
-  progress,
-  cancellationTokenSource,
-}: AutoModelQueriesOptions): Promise<AutoModelQueriesResult | undefined> {
-  // First, resolve the query that we want to run.
-  const queryPath = await resolveAutomodelQuery(
-    cliServer,
-    databaseItem,
-    "candidates",
-    mode,
-  );
-
-  // Generate a pack containing the candidate filters
-  const { packDir: filterPackDir, cleanup: cleanupFilterPack } =
-    await generateCandidateFilterPack(databaseItem.language, candidateMethods);
-
-  const additionalPacks = [...getOnDiskWorkspaceFolders(), filterPackDir];
-  const extensionPacks = Object.keys(
-    await cliServer.resolveQlpacks(additionalPacks, true),
-  );
-
-  // Run the actual query
-  const completedQuery = await runQuery({
-    queryRunner,
-    databaseItem,
-    queryPath,
-    queryStorageDir,
-    additionalPacks,
-    extensionPacks,
-    progress,
-    token: cancellationTokenSource.token,
-  });
-
-  await cleanupFilterPack();
-
-  if (!completedQuery) {
-    return undefined;
-  }
-
-  // Get metadata for the query. This is required to interpret the results. We already know the kind is problem
-  // (because of the constraint in resolveQueries), so we don't need any more checks on the metadata.
-  const metadata = await cliServer.resolveMetadata(queryPath);
-
-  // CodeQL needs to have access to the database to be able to retrieve the
-  // snippets from it. The source location prefix is used to determine the
-  // base path of the database.
-  const sourceLocationPrefix =
-    await databaseItem.getSourceLocationPrefix(cliServer);
-  const sourceArchiveUri = databaseItem.sourceArchive;
-  const sourceInfo =
-    sourceArchiveUri === undefined
-      ? undefined
-      : {
-          sourceArchive: sourceArchiveUri.fsPath,
-          sourceLocationPrefix,
-        };
-
-  const candidates = await interpretAutomodelResults(
-    cliServer,
-    completedQuery,
-    metadata,
-    sourceInfo,
-  );
-
-  return {
-    candidates,
-  };
-}
-
-async function resolveAutomodelQuery(
-  cliServer: CodeQLCliServer,
-  databaseItem: DatabaseItem,
-  queryTag: string,
-  mode: Mode,
-): Promise<string> {
-  const packsToSearch = [`codeql/${databaseItem.language}-automodel-queries`];
-
-  // First, resolve the query that we want to run.
-  // All queries are tagged like this:
-  // internal extract automodel <mode> <queryTag>
-  // Example: internal extract automodel framework-mode candidates
-  const queries = await resolveQueries(
-    cliServer,
-    packsToSearch,
-    `Extract automodel ${queryTag}`,
-    {
-      kind: "problem",
-      "tags contain all": ["automodel", modeTag(mode), ...queryTag.split(" ")],
-    },
-  );
-  if (queries.length > 1) {
-    throw new Error(
-      `Found multiple auto model queries for ${mode} ${queryTag}. Can't continue`,
-    );
-  }
-  if (queries.length === 0) {
-    throw new Error(
-      `Did not found any auto model queries for ${mode} ${queryTag}. Can't continue`,
-    );
-  }
-
-  return queries[0];
-}
-
-type CandidateFilterPackResult = {
-  packDir: string;
-  cleanup: () => Promise<void>;
-};
-
-/**
- * generateCandidateFilterPack will create a temporary extension pack.
- * This pack will contain a filter that will restrict the automodel queries
- * to the specified candidate methods only.
- * This is done using the `extensible` predicate "automodelCandidateFilter".
- * @param language
- * @param candidateMethods
- * @returns
- */
-export async function generateCandidateFilterPack(
-  language: string,
-  candidateMethods: MethodSignature[],
-): Promise<CandidateFilterPackResult> {
-  // Pack resides in a temporary directory, to not pollute the workspace.
-  const { path: packDir, cleanup } = await dir({ unsafeCleanup: true });
-
-  const syntheticConfigPack = {
-    name: "codeql/automodel-filter",
-    version: "0.0.0",
-    library: true,
-    extensionTargets: {
-      [`codeql/${language}-automodel-queries`]: "*",
-    },
-    dataExtensions: ["filter.yml"],
-  };
-
-  const qlpackFile = join(packDir, "codeql-pack.yml");
-  await outputFile(qlpackFile, dumpYaml(syntheticConfigPack), "utf8");
-
-  // The predicate has the following defintion:
-  // extensible predicate automodelCandidateFilter(string package, string type, string name, string signature)
-  const dataRows = candidateMethods.map((method) => [
-    method.packageName,
-    method.typeName,
-    method.methodName,
-    method.methodParameters,
-  ]);
-
-  const filter = {
-    extensions: [
-      {
-        addsTo: {
-          pack: `codeql/${language}-automodel-queries`,
-          extensible: "automodelCandidateFilter",
-        },
-        data: dataRows,
-      },
-    ],
-  };
-
-  const filterFile = join(packDir, "filter.yml");
-  await writeFile(filterFile, dumpYaml(filter), "utf8");
-
-  return {
-    packDir,
-    cleanup,
-  };
-}
-
-async function interpretAutomodelResults(
-  cliServer: CodeQLCliServer,
-  completedQuery: CoreCompletedQuery,
-  metadata: QueryMetadata,
-  sourceInfo: SourceInfo | undefined,
-): Promise<Log> {
-  const interpretedResultsPath = join(
-    completedQuery.outputDir.querySaveDir,
-    "results.sarif",
-  );
-
-  const { ...sarif } = await interpretResultsSarif(
-    cliServer,
-    metadata,
-    {
-      resultsPath: completedQuery.outputDir.bqrsPath,
-      interpretedResultsPath,
-    },
-    sourceInfo,
-    ["--sarif-add-snippets"],
-  );
-
-  return sarif;
-}
diff --git a/extensions/ql-vscode/src/model-editor/auto-model.ts b/extensions/ql-vscode/src/model-editor/auto-model.ts
deleted file mode 100644
index e0099fae518..00000000000
--- a/extensions/ql-vscode/src/model-editor/auto-model.ts
+++ /dev/null
@@ -1,41 +0,0 @@
-import type { ModelRequest } from "./auto-model-api";
-import { AutomodelMode } from "./auto-model-api";
-import { Mode } from "./shared/mode";
-import type { AutoModelQueriesResult } from "./auto-model-codeml-queries";
-import { assertNever } from "../common/helpers-pure";
-import type { Log } from "sarif";
-import { gzipEncode } from "../common/zlib";
-
-/**
- * Encode a SARIF log to the format expected by the server: JSON, GZIP-compressed, base64-encoded
- * @param log SARIF log to encode
- * @returns base64-encoded GZIP-compressed SARIF log
- */
-export async function encodeSarif(log: Log): Promise<string> {
-  const json = JSON.stringify(log);
-  const buffer = Buffer.from(json, "utf-8");
-  const compressed = await gzipEncode(buffer);
-  return compressed.toString("base64");
-}
-
-export async function createAutoModelRequest(
-  mode: Mode,
-  result: AutoModelQueriesResult,
-): Promise<ModelRequest> {
-  let requestMode: AutomodelMode;
-  switch (mode) {
-    case Mode.Application:
-      requestMode = AutomodelMode.Application;
-      break;
-    case Mode.Framework:
-      requestMode = AutomodelMode.Framework;
-      break;
-    default:
-      assertNever(mode);
-  }
-
-  return {
-    mode: requestMode,
-    candidates: await encodeSarif(result.candidates),
-  };
-}
diff --git a/extensions/ql-vscode/src/model-editor/auto-modeler.ts b/extensions/ql-vscode/src/model-editor/auto-modeler.ts
deleted file mode 100644
index e3f62ba3be8..00000000000
--- a/extensions/ql-vscode/src/model-editor/auto-modeler.ts
+++ /dev/null
@@ -1,249 +0,0 @@
-import type { Method, MethodSignature } from "./method";
-import type { ModeledMethod } from "./modeled-method";
-import { load as loadYaml } from "js-yaml";
-import type { ProgressCallback } from "../common/vscode/progress";
-import { withProgress } from "../common/vscode/progress";
-import { createAutoModelRequest } from "./auto-model";
-import { getCandidates } from "./shared/auto-model-candidates";
-import { runAutoModelQueries } from "./auto-model-codeml-queries";
-import { loadDataExtensionYaml } from "./yaml";
-import type { ModelRequest, ModelResponse } from "./auto-model-api";
-import { autoModel } from "./auto-model-api";
-import { RequestError } from "@octokit/request-error";
-import { showAndLogExceptionWithTelemetry } from "../common/logging";
-import { redactableError } from "../common/errors";
-import type { App } from "../common/app";
-import type { CodeQLCliServer } from "../codeql-cli/cli";
-import type { QueryRunner } from "../query-server";
-import type { DatabaseItem } from "../databases/local-databases";
-import type { Mode } from "./shared/mode";
-import { CancellationTokenSource } from "vscode";
-import type { ModelingStore } from "./modeling-store";
-import type { ModelConfigListener } from "../config";
-import type { QueryLanguage } from "../common/query-language";
-
-/**
- * The auto-modeler holds state around auto-modeling jobs and allows
- * starting and stopping them.
- */
-export class AutoModeler {
-  // Keep track of auto-modeling jobs that are in progress
-  // so that we can stop them.
-  private readonly jobs: Map<string, CancellationTokenSource>;
-
-  constructor(
-    private readonly app: App,
-    private readonly cliServer: CodeQLCliServer,
-    private readonly queryRunner: QueryRunner,
-    private readonly modelConfig: ModelConfigListener,
-    private readonly modelingStore: ModelingStore,
-    private readonly queryStorageDir: string,
-    private readonly databaseItem: DatabaseItem,
-    private readonly language: QueryLanguage,
-    private readonly addModeledMethods: (
-      modeledMethods: Record<string, ModeledMethod[]>,
-    ) => Promise<void>,
-  ) {
-    this.jobs = new Map<string, CancellationTokenSource>();
-  }
-
-  /**
-   * Models the given package's external API usages, except
-   * the ones that are already modeled.
-   * @param packageName The name of the package to model.
-   * @param methods The methods.
-   * @param modeledMethods The currently modeled methods.
-   * @param mode The mode we are modeling in.
-   */
-  public async startModeling(
-    packageName: string,
-    methods: readonly Method[],
-    modeledMethods: Record<string, readonly ModeledMethod[]>,
-    processedByAutoModelMethods: Set<string>,
-    mode: Mode,
-  ): Promise<void> {
-    if (this.jobs.has(packageName)) {
-      return;
-    }
-
-    const cancellationTokenSource = new CancellationTokenSource();
-    this.jobs.set(packageName, cancellationTokenSource);
-
-    try {
-      await this.modelPackage(
-        packageName,
-        methods,
-        modeledMethods,
-        processedByAutoModelMethods,
-        mode,
-        cancellationTokenSource,
-      );
-    } finally {
-      this.jobs.delete(packageName);
-    }
-  }
-
-  /**
-   * Stops modeling the given package.
-   * @param packageName The name of the package to stop modeling.
-   */
-  public async stopModeling(packageName: string): Promise<void> {
-    void this.app.logger.log(`Stopping modeling for package ${packageName}`);
-    const cancellationTokenSource = this.jobs.get(packageName);
-    if (cancellationTokenSource) {
-      cancellationTokenSource.cancel();
-    }
-  }
-
-  /**
-   * Stops all in-progress modeling jobs.
-   */
-  public async stopAllModeling(): Promise<void> {
-    for (const cancellationTokenSource of this.jobs.values()) {
-      cancellationTokenSource.cancel();
-    }
-  }
-
-  private async modelPackage(
-    packageName: string,
-    methods: readonly Method[],
-    modeledMethods: Record<string, readonly ModeledMethod[]>,
-    processedByAutoModelMethods: Set<string>,
-    mode: Mode,
-    cancellationTokenSource: CancellationTokenSource,
-  ): Promise<void> {
-    void this.app.logger.log(`Modeling package ${packageName}`);
-
-    const candidateBatchSize = this.modelConfig.llmGenerationBatchSize;
-
-    await withProgress(async (progress) => {
-      // Fetch the candidates to send to the model
-      const allCandidateMethods = getCandidates(
-        mode,
-        methods,
-        modeledMethods,
-        processedByAutoModelMethods,
-      );
-
-      // If there are no candidates, there is nothing to model and we just return
-      if (allCandidateMethods.length === 0) {
-        void this.app.logger.log("No candidates to model. Stopping.");
-        return;
-      }
-
-      // Find number of slices to make
-      const batchNumber = Math.ceil(
-        allCandidateMethods.length / candidateBatchSize,
-      );
-      try {
-        for (let i = 0; i < batchNumber; i++) {
-          // Check if we should stop
-          if (cancellationTokenSource.token.isCancellationRequested) {
-            break;
-          }
-
-          const start = i * candidateBatchSize;
-          const end = start + candidateBatchSize;
-          const candidatesToProcess = allCandidateMethods.slice(start, end);
-          const candidateSignatures = candidatesToProcess.map(
-            (c) => c.signature,
-          );
-
-          // Let the UI know which candidates we are modeling
-          this.modelingStore.addInProgressMethods(
-            this.databaseItem,
-            candidateSignatures,
-          );
-
-          // Kick off the process to model the slice of candidates
-          await this.modelCandidates(
-            candidatesToProcess,
-            mode,
-            progress,
-            cancellationTokenSource,
-          );
-
-          // Let the UI know which candidates we are done modeling
-          this.modelingStore.removeInProgressMethods(
-            this.databaseItem,
-            candidateSignatures,
-          );
-
-          // Let the UI know which methods have been sent to the LLM
-          this.modelingStore.addProcessedByAutoModelMethods(
-            this.databaseItem,
-            candidateSignatures,
-          );
-        }
-      } finally {
-        // Clear out in progress methods in case anything went wrong
-        this.modelingStore.removeInProgressMethods(
-          this.databaseItem,
-          allCandidateMethods.map((c) => c.signature),
-        );
-      }
-    });
-  }
-
-  private async modelCandidates(
-    candidateMethods: MethodSignature[],
-    mode: Mode,
-    progress: ProgressCallback,
-    cancellationTokenSource: CancellationTokenSource,
-  ): Promise<void> {
-    void this.app.logger.log("Executing auto-model queries");
-
-    const usages = await runAutoModelQueries({
-      mode,
-      candidateMethods,
-      cliServer: this.cliServer,
-      queryRunner: this.queryRunner,
-      queryStorageDir: this.queryStorageDir,
-      databaseItem: this.databaseItem,
-      progress: (update) => progress({ ...update }),
-      cancellationTokenSource,
-    });
-    if (!usages) {
-      return;
-    }
-
-    const request = await createAutoModelRequest(mode, usages);
-
-    void this.app.logger.log("Calling auto-model API");
-
-    const response = await this.callAutoModelApi(request);
-    if (!response) {
-      return;
-    }
-
-    const models = loadYaml(response.models, {
-      filename: "auto-model.yml",
-    });
-
-    const loadedMethods = loadDataExtensionYaml(models, this.language);
-    if (!loadedMethods) {
-      return;
-    }
-
-    await this.addModeledMethods(loadedMethods);
-  }
-
-  private async callAutoModelApi(
-    request: ModelRequest,
-  ): Promise<ModelResponse | null> {
-    try {
-      return await autoModel(this.app.credentials, request, this.modelConfig);
-    } catch (e) {
-      if (e instanceof RequestError && e.status === 429) {
-        void showAndLogExceptionWithTelemetry(
-          this.app.logger,
-          this.app.telemetry,
-          redactableError`Rate limit hit, please try again soon.`,
-        );
-        return null;
-      } else {
-        throw e;
-      }
-    }
-  }
-}
diff --git a/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts b/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts
index 959a727e7e0..d5e8f0d78a5 100644
--- a/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts
+++ b/extensions/ql-vscode/src/model-editor/extension-pack-picker.ts
@@ -115,7 +115,7 @@ export async function pickExtensionPack(
         existingExtensionPackPaths[0],
         databaseItem.language,
       );
-    } catch (e: unknown) {
+    } catch (e) {
       void showAndLogErrorMessage(
         logger,
         `Could not read extension pack ${formatPackName(packName)}`,
diff --git a/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts b/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts
index d5606574ab0..f3736748805 100644
--- a/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts
+++ b/extensions/ql-vscode/src/model-editor/extensions-workspace-folder.ts
@@ -133,7 +133,7 @@ async function findGitFolder(
             const stat = await workspace.fs.stat(gitFolder);
             // Check whether it's a directory
             return (stat.type & FileType.Directory) !== 0;
-          } catch (e) {
+          } catch {
             return false;
           }
         }),
diff --git a/extensions/ql-vscode/src/model-editor/generate.ts b/extensions/ql-vscode/src/model-editor/generate.ts
index 9f4b20c13da..157ed78b78d 100644
--- a/extensions/ql-vscode/src/model-editor/generate.ts
+++ b/extensions/ql-vscode/src/model-editor/generate.ts
@@ -91,6 +91,14 @@ async function runSingleGenerateQuery(
   if (!completedQuery) {
     return undefined;
   }
+  const queryResults = Array.from(completedQuery.results.values());
+  if (queryResults.length !== 1) {
+    throw new Error(
+      `Expected exactly one query result, but got ${queryResults.length}`,
+    );
+  }
 
-  return cliServer.bqrsDecodeAll(completedQuery.outputDir.bqrsPath);
+  return cliServer.bqrsDecodeAll(
+    completedQuery.outputDir.getBqrsPath(queryResults[0].outputBaseName),
+  );
 }
diff --git a/extensions/ql-vscode/src/model-editor/library.ts b/extensions/ql-vscode/src/model-editor/library.ts
index bedf40f0786..7cc12514de9 100644
--- a/extensions/ql-vscode/src/model-editor/library.ts
+++ b/extensions/ql-vscode/src/model-editor/library.ts
@@ -32,7 +32,7 @@ export function parseLibraryFilename(filename: string): Library {
   semverRegex.lastIndex = 0;
 
   // Find the last occurence of the regex within the library name
-  // eslint-disable-next-line no-constant-condition
+
   while (true) {
     const currentMatch = semverRegex.exec(libraryName);
     if (currentMatch === null) {
diff --git a/extensions/ql-vscode/src/model-editor/method-modeling/method-modeling-view-provider.ts b/extensions/ql-vscode/src/model-editor/method-modeling/method-modeling-view-provider.ts
index d325bb72fd7..53fc6f1275e 100644
--- a/extensions/ql-vscode/src/model-editor/method-modeling/method-modeling-view-provider.ts
+++ b/extensions/ql-vscode/src/model-editor/method-modeling/method-modeling-view-provider.ts
@@ -70,8 +70,6 @@ export class MethodModelingViewProvider extends AbstractWebviewViewProvider<
     method: Method,
     modeledMethods: readonly ModeledMethod[],
     isModified: boolean,
-    isInProgress: boolean,
-    processedByAutoModel: boolean,
   ): Promise<void> {
     this.method = method;
     this.databaseItem = databaseItem;
@@ -82,8 +80,6 @@ export class MethodModelingViewProvider extends AbstractWebviewViewProvider<
       method,
       modeledMethods,
       isModified,
-      isInProgress,
-      processedByAutoModel,
     });
   }
 
@@ -104,8 +100,6 @@ export class MethodModelingViewProvider extends AbstractWebviewViewProvider<
         selectedMethod.method,
         selectedMethod.modeledMethods,
         selectedMethod.isModified,
-        selectedMethod.isInProgress,
-        selectedMethod.processedByAutoModel,
       );
     }
   }
@@ -203,8 +197,6 @@ export class MethodModelingViewProvider extends AbstractWebviewViewProvider<
             e.method,
             e.modeledMethods,
             e.isModified,
-            e.isInProgress,
-            e.processedByAutoModel,
           );
         }
       }),
@@ -232,36 +224,6 @@ export class MethodModelingViewProvider extends AbstractWebviewViewProvider<
         }
       }),
     );
-
-    this.push(
-      this.modelingEvents.onInProgressMethodsChanged(async (e) => {
-        if (this.method && this.databaseItem) {
-          const dbUri = this.databaseItem.databaseUri.toString();
-          if (e.dbUri === dbUri) {
-            const inProgress = e.methods.has(this.method.signature);
-            await this.postMessage({
-              t: "setInProgress",
-              inProgress,
-            });
-          }
-        }
-      }),
-    );
-
-    this.push(
-      this.modelingEvents.onProcessedByAutoModelMethodsChanged(async (e) => {
-        if (this.method && this.databaseItem) {
-          const dbUri = this.databaseItem.databaseUri.toString();
-          if (e.dbUri === dbUri) {
-            const processedByAutoModel = e.methods.has(this.method.signature);
-            await this.postMessage({
-              t: "setProcessedByAutoModel",
-              processedByAutoModel,
-            });
-          }
-        }
-      }),
-    );
   }
 
   private registerToModelConfigEvents(): void {
diff --git a/extensions/ql-vscode/src/model-editor/model-editor-module.ts b/extensions/ql-vscode/src/model-editor/model-editor-module.ts
index 2aa914e377f..ebd234b7825 100644
--- a/extensions/ql-vscode/src/model-editor/model-editor-module.ts
+++ b/extensions/ql-vscode/src/model-editor/model-editor-module.ts
@@ -204,7 +204,6 @@ export class ModelEditorModule extends DisposableObject {
             this.app.logger,
             queryDir,
             language,
-            this.modelConfig,
             initialMode,
           );
           if (!success) {
diff --git a/extensions/ql-vscode/src/model-editor/model-editor-queries-setup.ts b/extensions/ql-vscode/src/model-editor/model-editor-queries-setup.ts
index a39103e3974..14b42572f71 100644
--- a/extensions/ql-vscode/src/model-editor/model-editor-queries-setup.ts
+++ b/extensions/ql-vscode/src/model-editor/model-editor-queries-setup.ts
@@ -8,7 +8,6 @@ import {
   syntheticQueryPackName,
 } from "./model-editor-queries";
 import type { CodeQLCliServer } from "../codeql-cli/cli";
-import type { ModelConfig } from "../config";
 import type { Mode } from "./shared/mode";
 import type { NotificationLogger } from "../common/logging";
 
@@ -30,7 +29,6 @@ import type { NotificationLogger } from "../common/logging";
  * @param logger The logger to use.
  * @param queryDir The directory to set up.
  * @param language The language to use for the queries.
- * @param modelConfig The model config to use.
  * @param initialMode The initial mode to use to check the existence of the queries.
  * @returns true if the setup was successful, false otherwise.
  */
@@ -39,7 +37,6 @@ export async function setUpPack(
   logger: NotificationLogger,
   queryDir: string,
   language: QueryLanguage,
-  modelConfig: ModelConfig,
   initialMode: Mode,
 ): Promise<boolean> {
   // Download the required query packs
@@ -91,10 +88,5 @@ export async function setUpPack(
     await cliServer.packInstall(queryDir);
   }
 
-  // Download any other required packs
-  if (language === "java" && modelConfig.llmGeneration) {
-    await cliServer.packDownload([`codeql/${language}-automodel-queries`]);
-  }
-
   return true;
 }
diff --git a/extensions/ql-vscode/src/model-editor/model-editor-queries.ts b/extensions/ql-vscode/src/model-editor/model-editor-queries.ts
index 0e7ddd48c4e..f1e7429afbd 100644
--- a/extensions/ql-vscode/src/model-editor/model-editor-queries.ts
+++ b/extensions/ql-vscode/src/model-editor/model-editor-queries.ts
@@ -172,10 +172,19 @@ export async function runModelEditorQueries(
     maxStep: externalApiQueriesProgressMaxStep,
   });
 
+  const queryResults = Array.from(completedQuery.results.values());
+  if (queryResults.length !== 1) {
+    throw new Error(
+      `Expected exactly one query result, but got ${queryResults.length}`,
+    );
+  }
+
   const bqrsChunk = await readQueryResults({
     cliServer,
     logger,
-    bqrsPath: completedQuery.outputDir.bqrsPath,
+    bqrsPath: completedQuery.outputDir.getBqrsPath(
+      queryResults[0].outputBaseName,
+    ),
   });
   if (!bqrsChunk) {
     return;
diff --git a/extensions/ql-vscode/src/model-editor/model-editor-view.ts b/extensions/ql-vscode/src/model-editor/model-editor-view.ts
index 3e2d233bc09..8f0ac3c75a0 100644
--- a/extensions/ql-vscode/src/model-editor/model-editor-view.ts
+++ b/extensions/ql-vscode/src/model-editor/model-editor-view.ts
@@ -49,7 +49,6 @@ import {
 import { pickExtensionPack } from "./extension-pack-picker";
 import type { QueryLanguage } from "../common/query-language";
 import { getLanguageDisplayName } from "../common/query-language";
-import { AutoModeler } from "./auto-modeler";
 import { telemetryListener } from "../common/vscode/telemetry";
 import type { ModelingStore } from "./modeling-store";
 import type { ModelingEvents } from "./modeling-events";
@@ -77,7 +76,6 @@ export class ModelEditorView extends AbstractWebview<
   ToModelEditorMessage,
   FromModelEditorMessage
 > {
-  private readonly autoModeler: AutoModeler;
   private readonly modelEvaluator: ModelEvaluator;
   private readonly languageDefinition: ModelsAsDataLanguage;
   // Cancellation token source that can be used for passing into long-running operations. Should only
@@ -114,19 +112,6 @@ export class ModelEditorView extends AbstractWebview<
     this.registerToModelingEvents();
     this.registerToModelConfigEvents();
 
-    this.autoModeler = new AutoModeler(
-      app,
-      cliServer,
-      queryRunner,
-      this.modelConfig,
-      modelingStore,
-      queryStorageDir,
-      databaseItem,
-      language,
-      async (modeledMethods) => {
-        this.addModeledMethods(modeledMethods);
-      },
-    );
     this.languageDefinition = getModelsAsDataLanguage(language);
 
     this.modelEvaluator = new ModelEvaluator(
@@ -317,21 +302,6 @@ export class ModelEditorView extends AbstractWebview<
           "model-editor-generate-modeled-methods",
         );
 
-        break;
-      case "generateMethodsFromLlm":
-        await this.generateModeledMethodsFromLlm(
-          msg.packageName,
-          msg.methodSignatures,
-        );
-        void telemetryListener?.sendUIInteraction(
-          "model-editor-generate-methods-from-llm",
-        );
-        break;
-      case "stopGeneratingMethodsFromLlm":
-        await this.autoModeler.stopModeling(msg.packageName);
-        void telemetryListener?.sendUIInteraction(
-          "model-editor-stop-generating-methods-from-llm",
-        );
         break;
       case "modelDependency":
         await this.modelDependency();
@@ -438,9 +408,6 @@ export class ModelEditorView extends AbstractWebview<
         this.modelConfig.flowGeneration) &&
       !!modelsAsDataLanguage.modelGeneration;
 
-    const showLlmButton =
-      this.databaseItem.language === "java" && this.modelConfig.llmGeneration;
-
     const showEvaluationUi = this.modelConfig.modelEvaluation;
 
     const sourceArchiveAvailable =
@@ -456,7 +423,6 @@ export class ModelEditorView extends AbstractWebview<
         extensionPack: this.extensionPack,
         language: this.language,
         showGenerateButton,
-        showLlmButton,
         showEvaluationUi,
         mode: this.modelingStore.getMode(this.databaseItem),
         showModeSwitchButton,
@@ -489,7 +455,7 @@ export class ModelEditorView extends AbstractWebview<
         this.app.logger,
       );
       this.modelingStore.setModeledMethods(this.databaseItem, modeledMethods);
-    } catch (e: unknown) {
+    } catch (e) {
       void showAndLogErrorMessage(
         this.app.logger,
         `Unable to read data extension YAML: ${getErrorMessage(e)}`,
@@ -595,7 +561,7 @@ export class ModelEditorView extends AbstractWebview<
             t: "setAccessPathSuggestions",
             accessPathSuggestions: options,
           });
-        } catch (e: unknown) {
+        } catch (e) {
           void showAndLogExceptionWithTelemetry(
             this.app.logger,
             this.app.telemetry,
@@ -639,7 +605,7 @@ export class ModelEditorView extends AbstractWebview<
             return;
           }
 
-          if (addedDatabase.language !== this.language) {
+          if ((addedDatabase.language as QueryLanguage) !== this.language) {
             void showAndLogErrorMessage(
               this.app.logger,
               `The selected database is for ${addedDatabase.language}, but the current database is for ${this.language}.`,
@@ -679,7 +645,7 @@ export class ModelEditorView extends AbstractWebview<
             progress,
             token: this.cancellationTokenSource.token,
           });
-        } catch (e: unknown) {
+        } catch (e) {
           void showAndLogExceptionWithTelemetry(
             this.app.logger,
             this.app.telemetry,
@@ -767,7 +733,7 @@ export class ModelEditorView extends AbstractWebview<
             progress,
             token: this.cancellationTokenSource.token,
           });
-        } catch (e: unknown) {
+        } catch (e) {
           void showAndLogExceptionWithTelemetry(
             this.app.logger,
             this.app.telemetry,
@@ -805,33 +771,6 @@ export class ModelEditorView extends AbstractWebview<
     );
   }
 
-  private async generateModeledMethodsFromLlm(
-    packageName: string,
-    methodSignatures: string[],
-  ): Promise<void> {
-    const methods = this.modelingStore.getMethods(
-      this.databaseItem,
-      methodSignatures,
-    );
-    const modeledMethods = this.modelingStore.getModeledMethods(
-      this.databaseItem,
-      methodSignatures,
-    );
-    const processedByAutoModelMethods =
-      this.modelingStore.getProcessedByAutoModelMethods(
-        this.databaseItem,
-        methodSignatures,
-      );
-    const mode = this.modelingStore.getMode(this.databaseItem);
-    await this.autoModeler.startModeling(
-      packageName,
-      methods,
-      modeledMethods,
-      processedByAutoModelMethods,
-      mode,
-    );
-  }
-
   private async modelDependency(): Promise<void> {
     return withProgress(
       async (progress, token) => {
@@ -983,30 +922,6 @@ export class ModelEditorView extends AbstractWebview<
       }),
     );
 
-    this.push(
-      this.modelingEvents.onInProgressMethodsChanged(async (event) => {
-        if (event.dbUri === this.databaseItem.databaseUri.toString()) {
-          await this.postMessage({
-            t: "setInProgressMethods",
-            methods: Array.from(event.methods),
-          });
-        }
-      }),
-    );
-
-    this.push(
-      this.modelingEvents.onProcessedByAutoModelMethodsChanged(
-        async (event) => {
-          if (event.dbUri === this.databaseItem.databaseUri.toString()) {
-            await this.postMessage({
-              t: "setProcessedByAutoModelMethods",
-              methods: Array.from(event.methods),
-            });
-          }
-        },
-      ),
-    );
-
     this.push(
       this.modelingEvents.onRevealInModelEditor(async (event) => {
         if (event.dbUri === this.databaseItem.databaseUri.toString()) {
diff --git a/extensions/ql-vscode/src/model-editor/modeled-method.ts b/extensions/ql-vscode/src/model-editor/modeled-method.ts
index 2f7c40d27aa..7156ee93e54 100644
--- a/extensions/ql-vscode/src/model-editor/modeled-method.ts
+++ b/extensions/ql-vscode/src/model-editor/modeled-method.ts
@@ -1,6 +1,5 @@
 import { assertNever } from "../common/helpers-pure";
 import type { MethodSignature } from "./method";
-import type { ModelingStatus } from "./shared/modeling-status";
 
 export type ModeledMethodType =
   | "none"
@@ -15,10 +14,6 @@ export type Provenance =
   | "df-generated"
   // Generated by the dataflow model and manually edited
   | "df-manual"
-  // Generated by the auto-model
-  | "ai-generated"
-  // Generated by the auto-model and manually edited
-  | "ai-manual"
   // Entered by the user in the editor manually
   | "manual";
 
@@ -112,30 +107,6 @@ export function modeledMethodSupportsProvenance(
   );
 }
 
-export function isModelPending(
-  modeledMethod: ModeledMethod | undefined,
-  modelingStatus: ModelingStatus,
-  processedByAutoModel: boolean,
-): boolean {
-  if (
-    (!modeledMethod || modeledMethod.type === "none") &&
-    processedByAutoModel
-  ) {
-    return true;
-  }
-
-  if (!modeledMethod) {
-    return false;
-  }
-
-  return (
-    modelingStatus === "unsaved" &&
-    modeledMethod.type !== "none" &&
-    modeledMethodSupportsProvenance(modeledMethod) &&
-    modeledMethod.provenance === "ai-generated"
-  );
-}
-
 /**
  * Calculates the new provenance for a modeled method based on the current provenance.
  * @param modeledMethod The modeled method if there is one.
@@ -158,13 +129,6 @@ export function calculateNewProvenance(
     case "df-manual":
       // If the method has had manual edits, we want the provenance to stay the same.
       return "df-manual";
-    case "ai-generated":
-      // If the method has been generated and there has been a change, we assume
-      // that the user has manually edited it.
-      return "ai-manual";
-    case "ai-manual":
-      // If the method has had manual edits, we want the provenance to stay the same.
-      return "ai-manual";
     default:
       // The method has been modeled manually.
       return "manual";
diff --git a/extensions/ql-vscode/src/model-editor/modeling-events.ts b/extensions/ql-vscode/src/model-editor/modeling-events.ts
index 06de166add7..2b7322f0ed7 100644
--- a/extensions/ql-vscode/src/model-editor/modeling-events.ts
+++ b/extensions/ql-vscode/src/model-editor/modeling-events.ts
@@ -37,18 +37,6 @@ interface SelectedMethodChangedEvent {
   readonly usage: Usage;
   readonly modeledMethods: readonly ModeledMethod[];
   readonly isModified: boolean;
-  readonly isInProgress: boolean;
-  readonly processedByAutoModel: boolean;
-}
-
-interface InProgressMethodsChangedEvent {
-  readonly dbUri: string;
-  readonly methods: ReadonlySet<string>;
-}
-
-interface ProcessedByAutoModelMethodsChangedEvent {
-  readonly dbUri: string;
-  readonly methods: ReadonlySet<string>;
 }
 
 interface ModelEvaluationRunChangedEvent {
@@ -83,8 +71,6 @@ export class ModelingEvents extends DisposableObject {
   public readonly onModeChanged: AppEvent<ModeChangedEvent>;
   public readonly onModeledAndModifiedMethodsChanged: AppEvent<ModeledAndModifiedMethodsChangedEvent>;
   public readonly onSelectedMethodChanged: AppEvent<SelectedMethodChangedEvent>;
-  public readonly onInProgressMethodsChanged: AppEvent<InProgressMethodsChangedEvent>;
-  public readonly onProcessedByAutoModelMethodsChanged: AppEvent<ProcessedByAutoModelMethodsChangedEvent>;
   public readonly onModelEvaluationRunChanged: AppEvent<ModelEvaluationRunChangedEvent>;
   public readonly onRevealInModelEditor: AppEvent<RevealInModelEditorEvent>;
   public readonly onFocusModelEditor: AppEvent<FocusModelEditorEvent>;
@@ -99,8 +85,6 @@ export class ModelingEvents extends DisposableObject {
   private readonly onModeChangedEventEmitter: AppEventEmitter<ModeChangedEvent>;
   private readonly onModeledAndModifiedMethodsChangedEventEmitter: AppEventEmitter<ModeledAndModifiedMethodsChangedEvent>;
   private readonly onSelectedMethodChangedEventEmitter: AppEventEmitter<SelectedMethodChangedEvent>;
-  private readonly onInProgressMethodsChangedEventEmitter: AppEventEmitter<InProgressMethodsChangedEvent>;
-  private readonly onProcessedByAutoModelMethodsChangedEventEmitter: AppEventEmitter<ProcessedByAutoModelMethodsChangedEvent>;
   private readonly onModelEvaluationRunChangedEventEmitter: AppEventEmitter<ModelEvaluationRunChangedEvent>;
   private readonly onRevealInModelEditorEventEmitter: AppEventEmitter<RevealInModelEditorEvent>;
   private readonly onFocusModelEditorEventEmitter: AppEventEmitter<FocusModelEditorEvent>;
@@ -151,18 +135,6 @@ export class ModelingEvents extends DisposableObject {
     this.onSelectedMethodChanged =
       this.onSelectedMethodChangedEventEmitter.event;
 
-    this.onInProgressMethodsChangedEventEmitter = this.push(
-      app.createEventEmitter<InProgressMethodsChangedEvent>(),
-    );
-    this.onInProgressMethodsChanged =
-      this.onInProgressMethodsChangedEventEmitter.event;
-
-    this.onProcessedByAutoModelMethodsChangedEventEmitter = this.push(
-      app.createEventEmitter<ProcessedByAutoModelMethodsChangedEvent>(),
-    );
-    this.onProcessedByAutoModelMethodsChanged =
-      this.onProcessedByAutoModelMethodsChangedEventEmitter.event;
-
     this.onModelEvaluationRunChangedEventEmitter = this.push(
       app.createEventEmitter<ModelEvaluationRunChangedEvent>(),
     );
@@ -254,8 +226,6 @@ export class ModelingEvents extends DisposableObject {
     usage: Usage,
     modeledMethods: ModeledMethod[],
     isModified: boolean,
-    isInProgress: boolean,
-    processedByAutoModel: boolean,
   ) {
     this.onSelectedMethodChangedEventEmitter.fire({
       databaseItem,
@@ -263,28 +233,6 @@ export class ModelingEvents extends DisposableObject {
       usage,
       modeledMethods,
       isModified,
-      isInProgress,
-      processedByAutoModel,
-    });
-  }
-
-  public fireInProgressMethodsChangedEvent(
-    dbUri: string,
-    methods: ReadonlySet<string>,
-  ) {
-    this.onInProgressMethodsChangedEventEmitter.fire({
-      dbUri,
-      methods,
-    });
-  }
-
-  public fireProcessedByAutoModelMethodsChangedEvent(
-    dbUri: string,
-    methods: ReadonlySet<string>,
-  ) {
-    this.onProcessedByAutoModelMethodsChangedEventEmitter.fire({
-      dbUri,
-      methods,
     });
   }
 
diff --git a/extensions/ql-vscode/src/model-editor/modeling-store.ts b/extensions/ql-vscode/src/model-editor/modeling-store.ts
index d4ac7e46df7..d964ad9897a 100644
--- a/extensions/ql-vscode/src/model-editor/modeling-store.ts
+++ b/extensions/ql-vscode/src/model-editor/modeling-store.ts
@@ -15,8 +15,6 @@ interface InternalDbModelingState {
   mode: Mode;
   modeledMethods: Record<string, ModeledMethod[]>;
   modifiedMethodSignatures: Set<string>;
-  inProgressMethods: Set<string>;
-  processedByAutoModelMethods: Set<string>;
   selectedMethod: Method | undefined;
   selectedUsage: Usage | undefined;
   modelEvaluationRun: ModelEvaluationRun | undefined;
@@ -30,8 +28,6 @@ export interface DbModelingState {
   readonly mode: Mode;
   readonly modeledMethods: Readonly<Record<string, readonly ModeledMethod[]>>;
   readonly modifiedMethodSignatures: ReadonlySet<string>;
-  readonly inProgressMethods: ReadonlySet<string>;
-  readonly processedByAutoModelMethods: ReadonlySet<string>;
   readonly selectedMethod: Method | undefined;
   readonly selectedUsage: Usage | undefined;
   readonly modelEvaluationRun: ModelEvaluationRun | undefined;
@@ -44,8 +40,6 @@ export interface SelectedMethodDetails {
   readonly usage: Usage | undefined;
   readonly modeledMethods: readonly ModeledMethod[];
   readonly isModified: boolean;
-  readonly isInProgress: boolean;
-  readonly processedByAutoModel: boolean;
 }
 
 export class ModelingStore extends DisposableObject {
@@ -68,10 +62,8 @@ export class ModelingStore extends DisposableObject {
       mode,
       modeledMethods: {},
       modifiedMethodSignatures: new Set(),
-      processedByAutoModelMethods: new Set(),
       selectedMethod: undefined,
       selectedUsage: undefined,
-      inProgressMethods: new Set(),
       modelEvaluationRun: undefined,
       isModelAlertsViewOpen: false,
     });
@@ -160,7 +152,6 @@ export class ModelingStore extends DisposableObject {
         methods,
         state.modeledMethods,
         state.modifiedMethodSignatures,
-        state.processedByAutoModelMethods,
       );
     });
   }
@@ -171,7 +162,6 @@ export class ModelingStore extends DisposableObject {
         state.methods,
         state.modeledMethods,
         state.modifiedMethodSignatures,
-        state.processedByAutoModelMethods,
       );
     });
   }
@@ -308,75 +298,15 @@ export class ModelingStore extends DisposableObject {
 
     const modeledMethods = dbState.modeledMethods[method.signature] ?? [];
     const isModified = dbState.modifiedMethodSignatures.has(method.signature);
-    const isInProgress = dbState.inProgressMethods.has(method.signature);
-    const processedByAutoModel = dbState.processedByAutoModelMethods.has(
-      method.signature,
-    );
     this.modelingEvents.fireSelectedMethodChangedEvent(
       dbItem,
       method,
       usage,
       modeledMethods,
       isModified,
-      isInProgress,
-      processedByAutoModel,
-    );
-  }
-
-  public addInProgressMethods(
-    dbItem: DatabaseItem,
-    inProgressMethods: string[],
-  ) {
-    this.changeInProgressMethods(dbItem, (state) => {
-      state.inProgressMethods = new Set([
-        ...state.inProgressMethods,
-        ...inProgressMethods,
-      ]);
-    });
-  }
-
-  public removeInProgressMethods(
-    dbItem: DatabaseItem,
-    methodSignatures: string[],
-  ) {
-    this.changeInProgressMethods(dbItem, (state) => {
-      state.inProgressMethods = new Set(
-        Array.from(state.inProgressMethods).filter(
-          (s) => !methodSignatures.includes(s),
-        ),
-      );
-    });
-  }
-
-  public getProcessedByAutoModelMethods(
-    dbItem: DatabaseItem,
-    methodSignatures?: string[],
-  ): Set<string> {
-    const processedByAutoModelMethods =
-      this.getState(dbItem).processedByAutoModelMethods;
-    if (!methodSignatures) {
-      return processedByAutoModelMethods;
-    }
-    return new Set(
-      Array.from(processedByAutoModelMethods).filter((x) =>
-        methodSignatures.includes(x),
-      ),
     );
   }
 
-  public addProcessedByAutoModelMethods(
-    dbItem: DatabaseItem,
-    processedByAutoModelMethods: string[],
-  ) {
-    this.changeProcessedByAutoModelMethods(dbItem, (state) => {
-      state.processedByAutoModelMethods = new Set([
-        ...state.processedByAutoModelMethods,
-        ...processedByAutoModelMethods,
-      ]);
-    });
-    this.updateMethodSorting(dbItem);
-  }
-
   public updateModelEvaluationRun(
     dbItem: DatabaseItem,
     evaluationRun: ModelEvaluationRun | undefined,
@@ -405,10 +335,6 @@ export class ModelingStore extends DisposableObject {
       isModified: dbState.modifiedMethodSignatures.has(
         selectedMethod.signature,
       ),
-      isInProgress: dbState.inProgressMethods.has(selectedMethod.signature),
-      processedByAutoModel: dbState.processedByAutoModelMethods.has(
-        selectedMethod.signature,
-      ),
     };
   }
 
@@ -460,34 +386,6 @@ export class ModelingStore extends DisposableObject {
     );
   }
 
-  private changeInProgressMethods(
-    dbItem: DatabaseItem,
-    updateState: (state: InternalDbModelingState) => void,
-  ) {
-    const state = this.getState(dbItem);
-
-    updateState(state);
-
-    this.modelingEvents.fireInProgressMethodsChangedEvent(
-      dbItem.databaseUri.toString(),
-      state.inProgressMethods,
-    );
-  }
-
-  private changeProcessedByAutoModelMethods(
-    dbItem: DatabaseItem,
-    updateState: (state: InternalDbModelingState) => void,
-  ) {
-    const state = this.getState(dbItem);
-
-    updateState(state);
-
-    this.modelingEvents.fireProcessedByAutoModelMethodsChangedEvent(
-      dbItem.databaseUri.toString(),
-      state.processedByAutoModelMethods,
-    );
-  }
-
   private changeModelEvaluationRun(
     dbItem: DatabaseItem,
     updateState: (state: InternalDbModelingState) => void,
diff --git a/extensions/ql-vscode/src/model-editor/shared/auto-model-candidates.ts b/extensions/ql-vscode/src/model-editor/shared/auto-model-candidates.ts
deleted file mode 100644
index 879be09505d..00000000000
--- a/extensions/ql-vscode/src/model-editor/shared/auto-model-candidates.ts
+++ /dev/null
@@ -1,48 +0,0 @@
-import type { Method, MethodSignature } from "../method";
-import type { ModeledMethod } from "../modeled-method";
-import type { Mode } from "./mode";
-import { groupMethods, sortGroupNames } from "./sorting";
-
-/**
- * Return the candidates that the model should be run on. This includes limiting the number of
- * candidates to the candidate limit and filtering out anything that is already modeled and respecting
- * the order in the UI.
- * @param mode Whether it is application or framework mode.
- * @param methods all methods.
- * @param modeledMethodsBySignature the currently modeled methods.
- * @returns list of modeled methods that are candidates for modeling.
- */
-
-export function getCandidates(
-  mode: Mode,
-  methods: readonly Method[],
-  modeledMethodsBySignature: Record<string, readonly ModeledMethod[]>,
-  processedByAutoModelMethods: Set<string>,
-): MethodSignature[] {
-  const candidateMethods = methods.filter((method) => {
-    // Filter out any methods already processed by auto-model
-    if (processedByAutoModelMethods.has(method.signature)) {
-      return false;
-    }
-
-    const modeledMethods: ModeledMethod[] = [
-      ...(modeledMethodsBySignature[method.signature] ?? []),
-    ];
-
-    // Anything that is modeled is not a candidate
-    if (modeledMethods.some((m) => m.type !== "none")) {
-      return false;
-    }
-
-    // A method that is supported is modeled outside of the model file, so it is not a candidate.
-    if (method.supported) {
-      return false;
-    }
-
-    return true;
-  });
-
-  // Sort the same way as the UI so we send the first ones listed in the UI first
-  const grouped = groupMethods(candidateMethods, mode);
-  return sortGroupNames(grouped).flatMap((name) => grouped[name]);
-}
diff --git a/extensions/ql-vscode/src/model-editor/shared/sorting.ts b/extensions/ql-vscode/src/model-editor/shared/sorting.ts
index f09304b1c6a..fb6614ba199 100644
--- a/extensions/ql-vscode/src/model-editor/shared/sorting.ts
+++ b/extensions/ql-vscode/src/model-editor/shared/sorting.ts
@@ -47,7 +47,6 @@ export function sortMethods(
   methods: readonly Method[],
   modeledMethodsMap: Record<string, readonly ModeledMethod[]>,
   modifiedSignatures: ReadonlySet<string>,
-  processedByAutoModelMethods: ReadonlySet<string>,
 ): Method[] {
   const sortedMethods = [...methods];
   sortedMethods.sort((a, b) => {
@@ -56,13 +55,11 @@ export function sortMethods(
       a,
       modeledMethodsMap[a.signature] ?? [],
       modifiedSignatures.has(a.signature),
-      processedByAutoModelMethods.has(a.signature),
     );
     const methodBPrimarySortOrdinal = getMethodPrimarySortOrdinal(
       b,
       modeledMethodsMap[b.signature] ?? [],
       modifiedSignatures.has(b.signature),
-      processedByAutoModelMethods.has(b.signature),
     );
     if (methodAPrimarySortOrdinal !== methodBPrimarySortOrdinal) {
       return methodAPrimarySortOrdinal - methodBPrimarySortOrdinal;
@@ -82,32 +79,25 @@ export function sortMethods(
 
 /**
  * Assigns numbers to the following classes of methods:
- * - Unsaved positive AutoModel predictions => 0
- * - Negative AutoModel predictions => 1
- * - Unsaved manual models + unmodeled methods => 2
- * - Saved models from this model pack (AutoModel and manual) => 3
- * - Methods not modelable in this model pack => 4
+ * - Unsaved manual models + unmodeled methods => 0
+ * - Saved models from this model pack (AutoModel and manual) => 1
+ * - Methods not modelable in this model pack => 2
  */
 function getMethodPrimarySortOrdinal(
   method: Method,
   modeledMethods: readonly ModeledMethod[],
   isUnsaved: boolean,
-  isProcessedByAutoModel: boolean,
 ): number {
   const canBeModeled = canMethodBeModeled(method, modeledMethods, isUnsaved);
   const isModeled = modeledMethods.length > 0;
   if (canBeModeled) {
-    if (isModeled && isUnsaved && isProcessedByAutoModel) {
+    if ((isModeled && isUnsaved) || !isModeled) {
       return 0;
-    } else if (!isModeled && isProcessedByAutoModel) {
-      return 1;
-    } else if ((isModeled && isUnsaved) || !isModeled) {
-      return 2;
     } else {
-      return 3;
+      return 1;
     }
   } else {
-    return 4;
+    return 2;
   }
 }
 
diff --git a/extensions/ql-vscode/src/model-editor/shared/view-state.ts b/extensions/ql-vscode/src/model-editor/shared/view-state.ts
index 1389103bc10..658909dbc04 100644
--- a/extensions/ql-vscode/src/model-editor/shared/view-state.ts
+++ b/extensions/ql-vscode/src/model-editor/shared/view-state.ts
@@ -7,7 +7,6 @@ export interface ModelEditorViewState {
   extensionPack: ExtensionPack;
   language: QueryLanguage;
   showGenerateButton: boolean;
-  showLlmButton: boolean;
   showEvaluationUi: boolean;
   mode: Mode;
   showModeSwitchButton: boolean;
diff --git a/extensions/ql-vscode/src/model-editor/suggestion-queries.ts b/extensions/ql-vscode/src/model-editor/suggestion-queries.ts
index 37ce78fd3a5..f325fc2a4d5 100644
--- a/extensions/ql-vscode/src/model-editor/suggestion-queries.ts
+++ b/extensions/ql-vscode/src/model-editor/suggestion-queries.ts
@@ -109,7 +109,15 @@ export async function runSuggestionsQuery(
     maxStep,
   });
 
-  const bqrs = await cliServer.bqrsDecodeAll(completedQuery.outputDir.bqrsPath);
+  const queryResults = Array.from(completedQuery.results.values());
+  if (queryResults.length !== 1) {
+    throw new Error(
+      `Expected exactly one query result, but got ${queryResults.length}`,
+    );
+  }
+  const bqrs = await cliServer.bqrsDecodeAll(
+    completedQuery.outputDir.getBqrsPath(queryResults[0].outputBaseName),
+  );
 
   progress({
     message: "Finalizing results",
diff --git a/extensions/ql-vscode/src/query-evaluation-logging/eval-log-viewer.ts b/extensions/ql-vscode/src/query-evaluation-logging/eval-log-viewer.ts
index a35b1cd72c4..0bd7a572b44 100644
--- a/extensions/ql-vscode/src/query-evaluation-logging/eval-log-viewer.ts
+++ b/extensions/ql-vscode/src/query-evaluation-logging/eval-log-viewer.ts
@@ -45,7 +45,10 @@ class EvalLogDataProvider
       ? TreeItemCollapsibleState.Collapsed
       : TreeItemCollapsibleState.None;
     const treeItem = new TreeItem(element.label || "", state);
-    treeItem.tooltip = `${treeItem.label} || ''}`;
+    treeItem.tooltip =
+      typeof treeItem.label === "string"
+        ? treeItem.label
+        : (treeItem.label?.label ?? "");
     return treeItem;
   }
 
diff --git a/extensions/ql-vscode/src/query-history/history-item-label-provider.ts b/extensions/ql-vscode/src/query-history/history-item-label-provider.ts
index b2bb24b049a..8787e025daf 100644
--- a/extensions/ql-vscode/src/query-history/history-item-label-provider.ts
+++ b/extensions/ql-vscode/src/query-history/history-item-label-provider.ts
@@ -12,17 +12,36 @@ import type { VariantAnalysisHistoryItem } from "./variant-analysis-history-item
 import { assertNever } from "../common/helpers-pure";
 import { pluralize } from "../common/word";
 import { humanizeQueryStatus } from "./query-status";
+import { substituteConfigVariables } from "../common/config-template";
 
-interface InterpolateReplacements {
-  t: string; // Start time
-  q: string; // Query name
-  d: string; // Database/repositories count
-  r: string; // Result count/Empty
-  s: string; // Status
-  f: string; // Query file name
-  l: string; // Query language
-  "%": "%"; // Percent sign
-}
+type LabelVariables = {
+  startTime: string;
+  queryName: string;
+  databaseName: string;
+  resultCount: string;
+  status: string;
+  queryFileBasename: string;
+  queryLanguage: string;
+};
+
+const legacyVariableInterpolateReplacements: Record<
+  keyof LabelVariables,
+  string
+> = {
+  startTime: "t",
+  queryName: "q",
+  databaseName: "d",
+  resultCount: "r",
+  status: "s",
+  queryFileBasename: "f",
+  queryLanguage: "l",
+};
+
+// If any of the "legacy" variables are used, we need to use legacy interpolation.
+const legacyLabelRegex = new RegExp(
+  `%([${Object.values(legacyVariableInterpolateReplacements).join("")}%])`,
+  "g",
+);
 
 export class HistoryItemLabelProvider {
   constructor(private config: QueryHistoryConfig) {
@@ -30,21 +49,27 @@ export class HistoryItemLabelProvider {
   }
 
   getLabel(item: QueryHistoryInfo) {
-    let replacements: InterpolateReplacements;
+    let variables: LabelVariables;
     switch (item.t) {
       case "local":
-        replacements = this.getLocalInterpolateReplacements(item);
+        variables = this.getLocalVariables(item);
         break;
       case "variant-analysis":
-        replacements = this.getVariantAnalysisInterpolateReplacements(item);
+        variables = this.getVariantAnalysisVariables(item);
         break;
       default:
         assertNever(item);
     }
 
-    const rawLabel = item.userSpecifiedLabel ?? (this.config.format || "%q");
+    const rawLabel =
+      item.userSpecifiedLabel ?? (this.config.format || "${queryName}");
 
-    return this.interpolate(rawLabel, replacements);
+    legacyLabelRegex.lastIndex = 0; // Reset the regex index to start searching from the start of the string if the strings are the same
+    if (legacyLabelRegex.test(rawLabel)) {
+      return this.legacyInterpolate(rawLabel, variables);
+    }
+
+    return substituteConfigVariables(rawLabel, variables).replace(/\s+/g, " ");
   }
 
   /**
@@ -59,55 +84,60 @@ export class HistoryItemLabelProvider {
       : getRawQueryName(item);
   }
 
-  private interpolate(
+  private legacyInterpolate(
     rawLabel: string,
-    replacements: InterpolateReplacements,
+    variables: LabelVariables,
   ): string {
-    const label = rawLabel.replace(
-      /%(.)/g,
-      (match, key: keyof InterpolateReplacements) => {
-        const replacement = replacements[key];
-        return replacement !== undefined ? replacement : match;
+    const replacements = Object.entries(variables).reduce(
+      (acc, [key, value]) => {
+        acc[
+          legacyVariableInterpolateReplacements[key as keyof LabelVariables]
+        ] = value;
+        return acc;
       },
+      {
+        "%": "%",
+      } as Record<string, string>,
     );
 
+    const label = rawLabel.replace(/%(.)/g, (match, key: string) => {
+      const replacement = replacements[key];
+      return replacement !== undefined ? replacement : match;
+    });
+
     return label.replace(/\s+/g, " ");
   }
 
-  private getLocalInterpolateReplacements(
-    item: LocalQueryInfo,
-  ): InterpolateReplacements {
+  private getLocalVariables(item: LocalQueryInfo): LabelVariables {
     const { resultCount = 0, message = "in progress" } =
       item.completedQuery || {};
     return {
-      t: item.startTime,
-      q: item.getQueryName(),
-      d: item.databaseName,
-      r: `(${resultCount} results)`,
-      s: message,
-      f: item.getQueryFileName(),
-      l: this.getLanguageLabel(item),
-      "%": "%",
+      startTime: item.startTime,
+      queryName: item.getQueryName(),
+      databaseName: item.databaseName,
+      resultCount: resultCount === -1 ? "" : `(${resultCount} results)`,
+      status: message,
+      queryFileBasename: item.getQueryFileName(),
+      queryLanguage: this.getLanguageLabel(item),
     };
   }
 
-  private getVariantAnalysisInterpolateReplacements(
+  private getVariantAnalysisVariables(
     item: VariantAnalysisHistoryItem,
-  ): InterpolateReplacements {
+  ): LabelVariables {
     const resultCount = item.resultCount
       ? `(${pluralize(item.resultCount, "result", "results")})`
       : "";
     return {
-      t: new Date(item.variantAnalysis.executionStartTime).toLocaleString(
-        env.language,
-      ),
-      q: `${item.variantAnalysis.query.name} (${item.variantAnalysis.language})`,
-      d: buildRepoLabel(item),
-      r: resultCount,
-      s: humanizeQueryStatus(item.status),
-      f: basename(item.variantAnalysis.query.filePath),
-      l: this.getLanguageLabel(item),
-      "%": "%",
+      startTime: new Date(
+        item.variantAnalysis.executionStartTime,
+      ).toLocaleString(env.language),
+      queryName: `${item.variantAnalysis.query.name} (${item.variantAnalysis.language})`,
+      databaseName: buildRepoLabel(item),
+      resultCount,
+      status: humanizeQueryStatus(item.status),
+      queryFileBasename: basename(item.variantAnalysis.query.filePath),
+      queryLanguage: this.getLanguageLabel(item),
     };
   }
 
diff --git a/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts b/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts
index 8f63d109eb5..7b355539a9a 100644
--- a/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts
+++ b/extensions/ql-vscode/src/query-history/history-tree-data-provider.ts
@@ -138,12 +138,12 @@ export class HistoryTreeDataProvider
 
             const resultCount1 =
               h1.t === "local"
-                ? h1.completedQuery?.resultCount ?? -1
-                : h1.resultCount ?? -1;
+                ? (h1.completedQuery?.resultCount ?? -1)
+                : (h1.resultCount ?? -1);
             const resultCount2 =
               h2.t === "local"
-                ? h2.completedQuery?.resultCount ?? -1
-                : h2.resultCount ?? -1;
+                ? (h2.completedQuery?.resultCount ?? -1)
+                : (h2.resultCount ?? -1);
 
             switch (this.sortOrder) {
               case SortOrder.NameAsc:
diff --git a/extensions/ql-vscode/src/query-history/query-history-manager.ts b/extensions/ql-vscode/src/query-history/query-history-manager.ts
index 22562d76a48..edf22f9b846 100644
--- a/extensions/ql-vscode/src/query-history/query-history-manager.ts
+++ b/extensions/ql-vscode/src/query-history/query-history-manager.ts
@@ -23,7 +23,8 @@ import { URLSearchParams } from "url";
 import { DisposableObject } from "../common/disposable-object";
 import { ONE_HOUR_IN_MS, TWO_HOURS_IN_MS } from "../common/time";
 import { assertNever, getErrorMessage } from "../common/helpers-pure";
-import type { CompletedLocalQueryInfo, LocalQueryInfo } from "../query-results";
+import type { CompletedLocalQueryInfo } from "../query-results";
+import { LocalQueryInfo } from "../query-results";
 import type { QueryHistoryInfo } from "./query-history-info";
 import {
   getActionsWorkflowRunUrl,
@@ -50,7 +51,10 @@ import type { QueryRunner } from "../query-server";
 import type { VariantAnalysisManager } from "../variant-analysis/variant-analysis-manager";
 import type { VariantAnalysisHistoryItem } from "./variant-analysis-history-item";
 import { getTotalResultCount } from "../variant-analysis/shared/variant-analysis";
-import { HistoryTreeDataProvider } from "./history-tree-data-provider";
+import {
+  HistoryTreeDataProvider,
+  SortOrder,
+} from "./history-tree-data-provider";
 import type { QueryHistoryDirs } from "./query-history-dirs";
 import type { QueryHistoryCommands } from "../common/commands";
 import type { App } from "../common/app";
@@ -97,15 +101,6 @@ const SHOW_QUERY_TEXT_QUICK_EVAL_MSG = `\
 
 `;
 
-enum SortOrder {
-  NameAsc = "NameAsc",
-  NameDesc = "NameDesc",
-  DateAsc = "DateAsc",
-  DateDesc = "DateDesc",
-  CountAsc = "CountAsc",
-  CountDesc = "CountDesc",
-}
-
 /**
  * Number of milliseconds two clicks have to arrive apart to be
  * considered a double-click.
@@ -149,6 +144,10 @@ export class QueryHistoryManager extends DisposableObject {
       from: CompletedLocalQueryInfo,
       to: CompletedLocalQueryInfo,
     ) => Promise<void>,
+    private readonly doComparePerformanceCallback: (
+      from: CompletedLocalQueryInfo,
+      to: CompletedLocalQueryInfo | undefined,
+    ) => Promise<void>,
   ) {
     super();
 
@@ -263,6 +262,8 @@ export class QueryHistoryManager extends DisposableObject {
         "query",
       ),
       "codeQLQueryHistory.compareWith": this.handleCompareWith.bind(this),
+      "codeQLQueryHistory.comparePerformanceWith":
+        this.handleComparePerformanceWith.bind(this),
       "codeQLQueryHistory.showEvalLog": createSingleSelectionCommand(
         this.app.logger,
         this.handleShowEvalLog.bind(this),
@@ -331,6 +332,11 @@ export class QueryHistoryManager extends DisposableObject {
         this.handleOpenOnGithub.bind(this),
         "query",
       ),
+      "codeQLQueryHistory.viewAutofixes": createSingleSelectionCommand(
+        this.app.logger,
+        this.handleViewAutofixes.bind(this),
+        "query",
+      ),
       "codeQLQueryHistory.copyRepoList": createSingleSelectionCommand(
         this.app.logger,
         this.handleCopyRepoList.bind(this),
@@ -342,8 +348,37 @@ export class QueryHistoryManager extends DisposableObject {
     };
   }
 
-  public completeQuery(info: LocalQueryInfo, results: QueryWithResults): void {
-    info.completeThisQuery(results);
+  public completeQueries(
+    info: LocalQueryInfo,
+    results: QueryWithResults[],
+  ): void {
+    let first = true;
+    // Sorting results by the output/results basename should produce a deterministic order.
+    results.sort((a, b) => {
+      const aPath = a.query.outputBaseName;
+      const bPath = b.query.outputBaseName;
+      return aPath.localeCompare(bPath);
+    });
+    for (const result of results) {
+      if (first) {
+        // This is the first query, so we can just update the existing info.
+        info.completeThisQuery(result);
+        first = false;
+      } else {
+        // For other queries in the same run, we'll add new entries to the history pane. In the long
+        // term, it would be better if we could have a single entry containing sub-entries for each
+        // query.
+        const clonedInfo = new LocalQueryInfo(
+          info.initialInfo,
+          undefined,
+          info.failureReason,
+          undefined,
+          info.evaluatorLogPaths,
+        );
+        clonedInfo.completeThisQuery(result);
+        this.addQuery(clonedInfo);
+      }
+    }
     this._onDidCompleteQuery.fire(info);
   }
 
@@ -549,6 +584,23 @@ export class QueryHistoryManager extends DisposableObject {
       }),
     );
 
+    await Promise.all(
+      this.treeDataProvider.allHistory.map(async (item) => {
+        // Remove any local queries whose directories no longer exist. This can happen when running
+        // a query suite, which produces multiple queries in the history pane that all share the
+        // same underlying directory, which we may have just deleted above. (Ideally, there would be
+        // a first-class concept of a local multi-query run in this pane that would group them all
+        // together, but doing it this way at least avoids cluttering the history pane with entries
+        // that can no longer be viewed).
+        if (item.t === "local") {
+          const dir = item.completedQuery?.query.querySaveDir;
+          if (dir && !(await pathExists(dir))) {
+            this.treeDataProvider.remove(item);
+          }
+        }
+      }),
+    );
+
     await this.writeQueryHistory();
     const current = this.treeDataProvider.getCurrent();
     if (current !== undefined) {
@@ -679,6 +731,39 @@ export class QueryHistoryManager extends DisposableObject {
     }
   }
 
+  async handleComparePerformanceWith(
+    singleItem: QueryHistoryInfo,
+    multiSelect: QueryHistoryInfo[] | undefined,
+  ) {
+    multiSelect ||= [singleItem];
+
+    if (
+      !this.isSuccessfulCompletedLocalQueryInfo(singleItem) ||
+      !multiSelect.every(this.isSuccessfulCompletedLocalQueryInfo)
+    ) {
+      throw new Error(
+        "Please only select local queries that have completed successfully.",
+      );
+    }
+
+    const fromItem = this.getFromQueryToCompare(singleItem, multiSelect);
+
+    let toItem: CompletedLocalQueryInfo | undefined = undefined;
+    try {
+      toItem = await this.findOtherQueryToComparePerformance(
+        fromItem,
+        multiSelect,
+      );
+    } catch (e) {
+      void showAndLogErrorMessage(
+        this.app.logger,
+        `Failed to compare queries: ${getErrorMessage(e)}`,
+      );
+    }
+
+    await this.doComparePerformanceCallback(fromItem, toItem);
+  }
+
   async handleItemClicked(item: QueryHistoryInfo) {
     this.treeDataProvider.setCurrentItem(item);
 
@@ -781,7 +866,7 @@ export class QueryHistoryManager extends DisposableObject {
 
   private async warnNoEvalLogSummary(item: LocalQueryInfo) {
     const evalLogLocation =
-      item.evalLogLocation ?? item.initialInfo.outputDir?.evalLogPath;
+      item.evaluatorLogPaths?.log ?? item.initialInfo.outputDir?.evalLogPath;
 
     // Summary log file doesn't exist.
     if (evalLogLocation && (await pathExists(evalLogLocation))) {
@@ -801,7 +886,7 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     const evalLogLocation =
-      item.evalLogLocation ?? item.initialInfo.outputDir?.evalLogPath;
+      item.evaluatorLogPaths?.log ?? item.initialInfo.outputDir?.evalLogPath;
 
     if (evalLogLocation && (await pathExists(evalLogLocation))) {
       await tryOpenExternalFile(this.app.commands, evalLogLocation);
@@ -816,12 +901,15 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     // If the summary file location wasn't saved, display error
-    if (!item.evalLogSummaryLocation) {
+    if (!item.evaluatorLogPaths?.humanReadableSummary) {
       await this.warnNoEvalLogSummary(item);
       return;
     }
 
-    await tryOpenExternalFile(this.app.commands, item.evalLogSummaryLocation);
+    await tryOpenExternalFile(
+      this.app.commands,
+      item.evaluatorLogPaths.humanReadableSummary,
+    );
   }
 
   async handleShowEvalLogViewer(item: QueryHistoryInfo) {
@@ -830,7 +918,7 @@ export class QueryHistoryManager extends DisposableObject {
     }
 
     // If the JSON summary file location wasn't saved, display error
-    if (item.jsonEvalLogSummaryLocation === undefined) {
+    if (item.evaluatorLogPaths?.jsonSummary === undefined) {
       await this.warnNoEvalLogSummary(item);
       return;
     }
@@ -838,16 +926,16 @@ export class QueryHistoryManager extends DisposableObject {
     // TODO(angelapwen): Stream the file in.
     try {
       const evalLogData: EvalLogData[] = await parseViewerData(
-        item.jsonEvalLogSummaryLocation,
+        item.evaluatorLogPaths.jsonSummary,
       );
       const evalLogTreeBuilder = new EvalLogTreeBuilder(
         item.getQueryName(),
         evalLogData,
       );
       this.evalLogViewer.updateRoots(await evalLogTreeBuilder.getRoots());
-    } catch (e) {
+    } catch {
       throw new Error(
-        `Could not read evaluator log summary JSON file to generate viewer data at ${item.jsonEvalLogSummaryLocation}.`,
+        `Could not read evaluator log summary JSON file to generate viewer data at ${item.evaluatorLogPaths.jsonSummary}.`,
       );
     }
   }
@@ -900,7 +988,7 @@ export class QueryHistoryManager extends DisposableObject {
     if (hasInterpretedResults) {
       await tryOpenExternalFile(
         this.app.commands,
-        query.resultsPaths.interpretedResultsPath,
+        query.interpretedResultsPath,
       );
     } else {
       const label = this.labelProvider.getLabel(item);
@@ -963,6 +1051,14 @@ export class QueryHistoryManager extends DisposableObject {
     );
   }
 
+  async handleViewAutofixes(item: QueryHistoryInfo) {
+    if (item.t !== "variant-analysis") {
+      return;
+    }
+
+    await this.variantAnalysisManager.viewAutofixes(item.variantAnalysis.id);
+  }
+
   async handleCopyRepoList(item: QueryHistoryInfo) {
     if (item.t !== "variant-analysis") {
       return;
@@ -1073,6 +1169,7 @@ export class QueryHistoryManager extends DisposableObject {
         detail: item.completedQuery.message,
         query: item,
       }));
+
     if (comparableQueryLabels.length < 1) {
       throw new Error("No other queries available to compare with.");
     }
@@ -1081,6 +1178,52 @@ export class QueryHistoryManager extends DisposableObject {
     return choice?.query;
   }
 
+  private async findOtherQueryToComparePerformance(
+    fromItem: CompletedLocalQueryInfo,
+    allSelectedItems: CompletedLocalQueryInfo[],
+  ): Promise<CompletedLocalQueryInfo | undefined> {
+    // If exactly 2 items are selected, return the one that
+    // isn't being used as the "from" item.
+    if (allSelectedItems.length === 2) {
+      const otherItem =
+        fromItem === allSelectedItems[0]
+          ? allSelectedItems[1]
+          : allSelectedItems[0];
+      return otherItem;
+    }
+
+    if (allSelectedItems.length > 2) {
+      throw new Error("Please select no more than 2 queries.");
+    }
+
+    // Otherwise, present a dialog so the user can choose the item they want to use.
+    const comparableQueryLabels = this.treeDataProvider.allHistory
+      .filter(this.isSuccessfulCompletedLocalQueryInfo)
+      .filter((otherItem) => otherItem !== fromItem)
+      .map((item) => ({
+        label: this.labelProvider.getLabel(item),
+        description: item.databaseName,
+        detail: item.completedQuery.message,
+        query: item,
+      }));
+    const comparableQueryLabelsWithDefault = [
+      {
+        label: "Single run",
+        description:
+          "Look at the performance of this run, compared to a trivial baseline",
+        detail: undefined,
+        query: undefined,
+      },
+      ...comparableQueryLabels,
+    ];
+    if (comparableQueryLabelsWithDefault.length < 1) {
+      throw new Error("No other queries available to compare with.");
+    }
+    const choice = await window.showQuickPick(comparableQueryLabelsWithDefault);
+
+    return choice?.query;
+  }
+
   /**
    * Updates the compare with source query. This ensures that all compare command invocations
    * when exactly 2 queries are selected always have the proper _from_ query. Always use
diff --git a/extensions/ql-vscode/src/query-history/query-history-scrubber.ts b/extensions/ql-vscode/src/query-history/query-history-scrubber.ts
index 961124116b6..1e31ccdf300 100644
--- a/extensions/ql-vscode/src/query-history/query-history-scrubber.ts
+++ b/extensions/ql-vscode/src/query-history/query-history-scrubber.ts
@@ -113,7 +113,9 @@ async function scrubQueries(
         throw new Error(EOL + errors.join(EOL));
       }
     } catch (e) {
-      void extLogger.log(`Error while scrubbing queries: ${e}`);
+      void extLogger.log(
+        `Error while scrubbing queries: ${getErrorMessage(e)}`,
+      );
     } finally {
       void extLogger.log(`Scrubbed ${scrubCount} old queries.`);
     }
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-dto.ts b/extensions/ql-vscode/src/query-history/store/query-history-dto.ts
index bec7a2ad5da..78cb5b6064e 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-dto.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-dto.ts
@@ -14,6 +14,7 @@ export type QueryHistoryItemDto =
   | QueryHistoryVariantAnalysisDto;
 
 export enum QueryLanguageDto {
+  Actions = "actions",
   CSharp = "csharp",
   Cpp = "cpp",
   Go = "go",
@@ -21,5 +22,6 @@ export enum QueryLanguageDto {
   Javascript = "javascript",
   Python = "python",
   Ruby = "ruby",
+  Rust = "rust",
   Swift = "swift",
 }
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts
index fe8c64b5e47..1df15d41dd2 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-language-domain-mapper.ts
@@ -6,6 +6,8 @@ export function mapQueryLanguageToDto(
   language: QueryLanguage,
 ): QueryLanguageDto {
   switch (language) {
+    case QueryLanguage.Actions:
+      return QueryLanguageDto.Actions;
     case QueryLanguage.CSharp:
       return QueryLanguageDto.CSharp;
     case QueryLanguage.Cpp:
@@ -20,6 +22,8 @@ export function mapQueryLanguageToDto(
       return QueryLanguageDto.Python;
     case QueryLanguage.Ruby:
       return QueryLanguageDto.Ruby;
+    case QueryLanguage.Rust:
+      return QueryLanguageDto.Rust;
     case QueryLanguage.Swift:
       return QueryLanguageDto.Swift;
     default:
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts
index deea1bfd80b..1e3ea1c18a8 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-language-dto-mapper.ts
@@ -6,6 +6,8 @@ export function mapQueryLanguageToDomainModel(
   language: QueryLanguageDto,
 ): QueryLanguage {
   switch (language) {
+    case QueryLanguageDto.Actions:
+      return QueryLanguage.Actions;
     case QueryLanguageDto.CSharp:
       return QueryLanguage.CSharp;
     case QueryLanguageDto.Cpp:
@@ -20,6 +22,8 @@ export function mapQueryLanguageToDomainModel(
       return QueryLanguage.Python;
     case QueryLanguageDto.Ruby:
       return QueryLanguage.Ruby;
+    case QueryLanguageDto.Rust:
+      return QueryLanguage.Rust;
     case QueryLanguageDto.Swift:
       return QueryLanguage.Swift;
     default:
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts
index 45c7b184c11..61fe2e0bc4b 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-local-query-domain-mapper.ts
@@ -25,10 +25,10 @@ export function mapLocalQueryInfoToDto(
   return {
     initialInfo: mapInitialQueryInfoToDto(query.initialInfo),
     t: "local",
-    evalLogLocation: query.evalLogLocation,
-    evalLogSummaryLocation: query.evalLogSummaryLocation,
-    jsonEvalLogSummaryLocation: query.jsonEvalLogSummaryLocation,
-    evalLogSummarySymbolsLocation: query.evalLogSummarySymbolsLocation,
+    evalLogLocation: query.evaluatorLogPaths?.log,
+    evalLogSummaryLocation: query.evaluatorLogPaths?.humanReadableSummary,
+    jsonEvalLogSummaryLocation: query.evaluatorLogPaths?.jsonSummary,
+    evalLogSummarySymbolsLocation: query.evaluatorLogPaths?.summarySymbols,
     failureReason: query.failureReason,
     completedQuery:
       query.completedQuery && mapCompletedQueryToDto(query.completedQuery),
@@ -118,6 +118,6 @@ function mapQueryEvaluationInfoToDto(
     databaseHasMetadataFile: queryEvaluationInfo.databaseHasMetadataFile,
     quickEvalPosition: queryEvaluationInfo.quickEvalPosition,
     metadata: queryEvaluationInfo.metadata,
-    resultsPaths: queryEvaluationInfo.resultsPaths,
+    outputBaseName: queryEvaluationInfo.outputBaseName,
   };
 }
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts
index ee6765c80d7..aa42dd8c1a0 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto-mapper.ts
@@ -32,10 +32,15 @@ export function mapLocalQueryItemToDomainModel(
     localQuery.failureReason,
     localQuery.completedQuery &&
       mapCompletedQueryInfoToDomainModel(localQuery.completedQuery),
-    localQuery.evalLogLocation,
-    localQuery.evalLogSummaryLocation,
-    localQuery.jsonEvalLogSummaryLocation,
-    localQuery.evalLogSummarySymbolsLocation,
+    localQuery.evalLogLocation
+      ? {
+          log: localQuery.evalLogLocation,
+          humanReadableSummary: localQuery.evalLogSummaryLocation,
+          jsonSummary: localQuery.jsonEvalLogSummaryLocation,
+          summarySymbols: localQuery.evalLogSummarySymbolsLocation,
+          endSummary: undefined,
+        }
+      : undefined,
   );
 }
 
@@ -99,6 +104,7 @@ function mapQueryEvaluationInfoToDomainModel(
 ): QueryEvaluationInfo {
   return new QueryEvaluationInfo(
     evaluationInfo.querySaveDir,
+    evaluationInfo.outputBaseName ?? "results",
     evaluationInfo.dbItemPath,
     evaluationInfo.databaseHasMetadataFile,
     evaluationInfo.quickEvalPosition,
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts
index b9a2f3448fa..2a6b3c78ea0 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-local-query-dto.ts
@@ -86,7 +86,10 @@ export interface QueryEvaluationInfoDto {
   databaseHasMetadataFile: boolean;
   quickEvalPosition?: PositionDto;
   metadata?: QueryMetadataDto;
-  resultsPaths: {
+  outputBaseName?: string;
+
+  // Superceded by outputBaseName
+  resultsPaths?: {
     resultsPath: string;
     interpretedResultsPath: string;
   };
diff --git a/extensions/ql-vscode/src/query-history/store/query-history-store.ts b/extensions/ql-vscode/src/query-history/store/query-history-store.ts
index 279c17c4dc0..0b54908ceba 100644
--- a/extensions/ql-vscode/src/query-history/store/query-history-store.ts
+++ b/extensions/ql-vscode/src/query-history/store/query-history-store.ts
@@ -61,7 +61,7 @@ export async function readQueryHistoryFromFile(
           // to see if they exist on disk.
           return true;
         }
-        const resultsPath = q.completedQuery?.query.resultsPaths.resultsPath;
+        const resultsPath = q.completedQuery?.query.resultsPath;
         return !!resultsPath && (await pathExists(resultsPath));
       },
     );
diff --git a/extensions/ql-vscode/src/query-results.ts b/extensions/ql-vscode/src/query-results.ts
index 95f5fcb2641..3e81762bc08 100644
--- a/extensions/ql-vscode/src/query-results.ts
+++ b/extensions/ql-vscode/src/query-results.ts
@@ -64,7 +64,7 @@ export class CompletedQueryInfo implements QueryWithResults {
      * sarif file.
      */
     public interpretedResultsSortState: InterpretedResultsSortState | undefined,
-    public resultCount: number = 0,
+    public resultCount: number = -1,
 
     /**
      * Map from result set name to SortedResultSetInfo.
@@ -78,11 +78,11 @@ export class CompletedQueryInfo implements QueryWithResults {
 
   getResultsPath(selectedTable: string, useSorted = true): string {
     if (!useSorted) {
-      return this.query.resultsPaths.resultsPath;
+      return this.query.resultsPath;
     }
     return (
       this.sortedResultsInfo[selectedTable]?.resultsPath ||
-      this.query.resultsPaths.resultsPath
+      this.query.resultsPath
     );
   }
 
@@ -102,7 +102,7 @@ export class CompletedQueryInfo implements QueryWithResults {
     };
 
     await server.sortBqrs(
-      this.query.resultsPaths.resultsPath,
+      this.query.resultsPath,
       sortedResultSetInfo.resultsPath,
       resultSetName,
       [sortState.columnIndex],
@@ -200,10 +200,7 @@ export class LocalQueryInfo {
     private cancellationSource?: CancellationTokenSource, // used to cancel in progress queries
     public failureReason?: string,
     public completedQuery?: CompletedQueryInfo,
-    public evalLogLocation?: string,
-    public evalLogSummaryLocation?: string,
-    public jsonEvalLogSummaryLocation?: string,
-    public evalLogSummarySymbolsLocation?: string,
+    public evaluatorLogPaths?: EvaluatorLogPaths,
   ) {
     /**/
   }
@@ -229,10 +226,7 @@ export class LocalQueryInfo {
 
   /** Sets the paths to the various structured evaluator logs. */
   public setEvaluatorLogPaths(logPaths: EvaluatorLogPaths): void {
-    this.evalLogLocation = logPaths.log;
-    this.evalLogSummaryLocation = logPaths.humanReadableSummary;
-    this.jsonEvalLogSummaryLocation = logPaths.jsonSummary;
-    this.evalLogSummarySymbolsLocation = logPaths.summarySymbols;
+    this.evaluatorLogPaths = logPaths;
   }
 
   /**
diff --git a/extensions/ql-vscode/src/query-server/messages.ts b/extensions/ql-vscode/src/query-server/messages.ts
index 44e0d515458..548e93ad32b 100644
--- a/extensions/ql-vscode/src/query-server/messages.ts
+++ b/extensions/ql-vscode/src/query-server/messages.ts
@@ -42,6 +42,22 @@ export interface TrimCacheParams {
   db: string;
 }
 
+/**
+ * Parameters for trimming the cache of a dataset with a specific mode.
+ */
+export interface TrimCacheWithModeParams {
+  /**
+   * The dataset that we want to trim the cache of.
+   */
+  db: string;
+  /**
+   * The cache cleanup mode to use.
+   */
+  mode: ClearCacheMode;
+}
+
+export type ClearCacheMode = "clear" | "trim" | "fit" | "overlay";
+
 /**
  * The result of trimming or clearing the cache.
  */
@@ -130,13 +146,29 @@ export interface RunQueryParams {
   extensionPacks?: string[];
 }
 
-interface RunQueryResult {
+export interface RunQueryResult {
   resultType: QueryResultType;
   message?: string;
   expectedDbschemeName?: string;
   evaluationTime: number;
 }
 
+export interface RunQueryInputOutput {
+  queryPath: string;
+  outputPath: string;
+  dilPath: string;
+}
+
+export interface RunQueriesParams {
+  inputOutputPaths: RunQueryInputOutput[];
+  db: string;
+  additionalPacks: string[];
+  externalInputs: Record<string, string>;
+  singletonExternalInputs: Record<string, string>;
+  logPath?: string;
+  extensionPacks?: string[];
+}
+
 interface UpgradeParams {
   db: string;
   additionalPacks: string[];
@@ -177,6 +209,14 @@ export const trimCache = new RequestType<
   ClearCacheResult,
   void
 >("evaluation/trimCache");
+/**
+ * Trim the cache of a dataset with a specific mode.
+ */
+export const trimCacheWithMode = new RequestType<
+  WithProgressId<TrimCacheWithModeParams>,
+  ClearCacheResult,
+  void
+>("evaluation/trimCacheWithMode");
 
 /**
  * Clear the pack cache
@@ -196,6 +236,12 @@ export const runQuery = new RequestType<
   void
 >("evaluation/runQuery");
 
+export const runQueries = new RequestType<
+  WithProgressId<RunQueriesParams>,
+  Record<string, RunQueryResult>,
+  void
+>("evaluation/runQueries");
+
 export const registerDatabases = new RequestType<
   WithProgressId<RegisterDatabasesParams>,
   RegisterDatabasesResult,
diff --git a/extensions/ql-vscode/src/query-server/query-runner.ts b/extensions/ql-vscode/src/query-server/query-runner.ts
index 7fbb3446575..5d42e6056d7 100644
--- a/extensions/ql-vscode/src/query-server/query-runner.ts
+++ b/extensions/ql-vscode/src/query-server/query-runner.ts
@@ -6,10 +6,12 @@ import { UserCancellationException } from "../common/vscode/progress";
 import type { DatabaseItem } from "../databases/local-databases/database-item";
 import { QueryOutputDir } from "../local-queries/query-output-dir";
 import type {
+  ClearCacheMode,
   ClearCacheParams,
   Position,
   QueryResultType,
   TrimCacheParams,
+  TrimCacheWithModeParams,
 } from "./messages";
 import {
   clearCache,
@@ -17,21 +19,29 @@ import {
   deregisterDatabases,
   registerDatabases,
   trimCache,
+  trimCacheWithMode,
   upgradeDatabase,
 } from "./messages";
 import type { BaseLogger, Logger } from "../common/logging";
-import { basename, join } from "path";
+import { join } from "path";
 import { nanoid } from "nanoid";
 import type { QueryServerClient } from "./query-server-client";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import { compileAndRunQueryAgainstDatabaseCore } from "./run-queries";
 
 export interface CoreQueryTarget {
-  /** The full path to the query. */
+  /** Path to the query source file. */
   queryPath: string;
+
+  /**
+   * Base name to use for output files, without extension. For example, "foo" will result in the
+   * BQRS file being written to "<outputdir>/foo.bqrs".
+   */
+  outputBaseName: string;
+
   /**
    * Optional position of text to be used as QuickEval target. This need not be in the same file as
-   * `query`.
+   * `queryPath`.
    */
   quickEvalPosition?: Position;
   /**
@@ -40,14 +50,25 @@ export interface CoreQueryTarget {
   quickEvalCountOnly?: boolean;
 }
 
-export interface CoreQueryResults {
+export interface CoreQueryResult {
   readonly resultType: QueryResultType;
   readonly message: string | undefined;
   readonly evaluationTime: number;
+
+  /**
+   * The base name of the output file. Append '.bqrs' and join with the output directory to get the
+   * path to the BQRS.
+   */
+  readonly outputBaseName: string;
+}
+
+export interface CoreQueryResults {
+  /** A map from query path to its results. */
+  readonly results: Map<string, CoreQueryResult>;
 }
 
 export interface CoreQueryRun {
-  readonly queryTarget: CoreQueryTarget;
+  readonly queryTargets: CoreQueryTarget[];
   readonly dbPath: string;
   readonly id: string;
   readonly outputDir: QueryOutputDir;
@@ -124,9 +145,25 @@ export class QueryRunner {
     await this.qs.sendRequest(trimCache, params);
   }
 
+  async trimCacheWithModeInDatabase(
+    dbItem: DatabaseItem,
+    mode: ClearCacheMode,
+  ): Promise<void> {
+    if (dbItem.contents === undefined) {
+      throw new Error("Can't clean the cache in an invalid database.");
+    }
+
+    const db = dbItem.databaseUri.fsPath;
+    const params: TrimCacheWithModeParams = {
+      db,
+      mode,
+    };
+    await this.qs.sendRequest(trimCacheWithMode, params);
+  }
+
   public async compileAndRunQueryAgainstDatabaseCore(
     dbPath: string,
-    query: CoreQueryTarget,
+    queries: CoreQueryTarget[],
     additionalPacks: string[],
     extensionPacks: string[] | undefined,
     additionalRunQueryArgs: Record<string, unknown>,
@@ -142,7 +179,7 @@ export class QueryRunner {
     return await compileAndRunQueryAgainstDatabaseCore(
       this.qs,
       dbPath,
-      query,
+      queries,
       generateEvalLog,
       additionalPacks,
       extensionPacks,
@@ -213,19 +250,20 @@ export class QueryRunner {
    */
   public createQueryRun(
     dbPath: string,
-    query: CoreQueryTarget,
+    queries: CoreQueryTarget[],
     generateEvalLog: boolean,
     additionalPacks: string[],
     extensionPacks: string[] | undefined,
     additionalRunQueryArgs: Record<string, unknown>,
     queryStorageDir: string,
-    id = `${basename(query.queryPath)}-${nanoid()}`,
+    queryBasename: string,
     templates: Record<string, string> | undefined,
   ): CoreQueryRun {
+    const id = `${queryBasename}-${nanoid()}`;
     const outputDir = new QueryOutputDir(join(queryStorageDir, id));
 
     return {
-      queryTarget: query,
+      queryTargets: queries,
       dbPath,
       id,
       outputDir,
@@ -238,10 +276,10 @@ export class QueryRunner {
           id,
           outputDir,
           dbPath,
-          queryTarget: query,
+          queryTargets: queries,
           ...(await this.compileAndRunQueryAgainstDatabaseCore(
             dbPath,
-            query,
+            queries,
             additionalPacks,
             extensionPacks,
             additionalRunQueryArgs,
diff --git a/extensions/ql-vscode/src/query-server/query-server-client.ts b/extensions/ql-vscode/src/query-server/query-server-client.ts
index c342e3b4996..e62637ff3ad 100644
--- a/extensions/ql-vscode/src/query-server/query-server-client.ts
+++ b/extensions/ql-vscode/src/query-server/query-server-client.ts
@@ -95,6 +95,14 @@ export class QueryServerClient extends DisposableObject {
     return this.opts.logger;
   }
 
+  /**
+   * Whether this query server supports the 'evaluation/runQueries' method for running multiple
+   * queries at once.
+   */
+  async supportsRunQueriesMethod(): Promise<boolean> {
+    return await this.cliServer.cliConstraints.supportsQueryServerRunQueries();
+  }
+
   /** Stops the query server by disposing of the current server process. */
   private stopQueryServer(): void {
     if (this.serverProcess !== undefined) {
@@ -296,7 +304,7 @@ export class QueryServerClient extends DisposableObject {
     }
   }
 
-  public dispose(disposeHandler?: DisposeHandler | undefined): void {
+  public dispose(disposeHandler?: DisposeHandler): void {
     this.progressCallbacks = {};
     this.stopQueryServer();
     super.dispose(disposeHandler);
diff --git a/extensions/ql-vscode/src/query-server/run-queries.ts b/extensions/ql-vscode/src/query-server/run-queries.ts
index 593979118e7..5a35144728f 100644
--- a/extensions/ql-vscode/src/query-server/run-queries.ts
+++ b/extensions/ql-vscode/src/query-server/run-queries.ts
@@ -1,10 +1,19 @@
 import type { CancellationToken } from "vscode";
 import type { ProgressCallback } from "../common/vscode/progress";
-import type { RunQueryParams } from "./messages";
-import { runQuery } from "./messages";
+import type {
+  RunQueryParams,
+  RunQueryResult,
+  RunQueriesParams,
+  RunQueryInputOutput,
+} from "./messages";
+import { runQueries, runQuery } from "./messages";
 import type { QueryOutputDir } from "../local-queries/query-output-dir";
 import type { QueryServerClient } from "./query-server-client";
-import type { CoreQueryResults, CoreQueryTarget } from "./query-runner";
+import type {
+  CoreQueryResult,
+  CoreQueryResults,
+  CoreQueryTarget,
+} from "./query-runner";
 import type { BaseLogger } from "../common/logging";
 
 /**
@@ -24,7 +33,7 @@ import type { BaseLogger } from "../common/logging";
 export async function compileAndRunQueryAgainstDatabaseCore(
   qs: QueryServerClient,
   dbPath: string,
-  query: CoreQueryTarget,
+  targets: CoreQueryTarget[],
   generateEvalLog: boolean,
   additionalPacks: string[],
   extensionPacks: string[] | undefined,
@@ -35,12 +44,36 @@ export async function compileAndRunQueryAgainstDatabaseCore(
   templates: Record<string, string> | undefined,
   logger: BaseLogger,
 ): Promise<CoreQueryResults> {
-  const target =
-    query.quickEvalPosition !== undefined
+  if (targets.length > 1) {
+    // We are running a batch of multiple queries; use the new query server API for that.
+    if (targets.some((target) => target.quickEvalPosition !== undefined)) {
+      throw new Error(
+        "Quick evaluation is not supported when running multiple queries.",
+      );
+    }
+    return compileAndRunQueriesAgainstDatabaseCore(
+      qs,
+      dbPath,
+      targets,
+      generateEvalLog,
+      additionalPacks,
+      extensionPacks,
+      additionalRunQueryArgs,
+      outputDir,
+      progress,
+      token,
+      templates,
+      logger,
+    );
+  }
+
+  const target = targets[0];
+  const compilationTarget =
+    target.quickEvalPosition !== undefined
       ? {
           quickEval: {
-            quickEvalPos: query.quickEvalPosition,
-            countOnly: query.quickEvalCountOnly,
+            quickEvalPos: target.quickEvalPosition,
+            countOnly: target.quickEvalCountOnly,
           },
         }
       : { query: {} };
@@ -51,11 +84,11 @@ export async function compileAndRunQueryAgainstDatabaseCore(
     additionalPacks,
     externalInputs: {},
     singletonExternalInputs: templates || {},
-    outputPath: outputDir.bqrsPath,
-    queryPath: query.queryPath,
-    dilPath: outputDir.dilPath,
+    queryPath: target.queryPath,
+    outputPath: outputDir.getBqrsPath(target.outputBaseName),
+    dilPath: outputDir.getDilPath(target.outputBaseName),
     logPath: evalLogPath,
-    target,
+    target: compilationTarget,
     extensionPacks,
     // Add any additional arguments without interpretation.
     ...additionalRunQueryArgs,
@@ -67,10 +100,83 @@ export async function compileAndRunQueryAgainstDatabaseCore(
   // properly will require a change in the query server.
   qs.activeQueryLogger = logger;
   const result = await qs.sendRequest(runQuery, queryToRun, token, progress);
+  return {
+    results: new Map<string, CoreQueryResult>([
+      [
+        target.queryPath,
+        {
+          resultType: result.resultType,
+          message: result.message,
+          evaluationTime: result.evaluationTime,
+          outputBaseName: target.outputBaseName,
+        },
+      ],
+    ]),
+  };
+}
+
+async function compileAndRunQueriesAgainstDatabaseCore(
+  qs: QueryServerClient,
+  dbPath: string,
+  targets: CoreQueryTarget[],
+  generateEvalLog: boolean,
+  additionalPacks: string[],
+  extensionPacks: string[] | undefined,
+  additionalRunQueryArgs: Record<string, unknown>,
+  outputDir: QueryOutputDir,
+  progress: ProgressCallback,
+  token: CancellationToken,
+  templates: Record<string, string> | undefined,
+  logger: BaseLogger,
+): Promise<CoreQueryResults> {
+  if (!(await qs.supportsRunQueriesMethod())) {
+    throw new Error(
+      "The CodeQL CLI does not support the 'evaluation/runQueries' query-server command. Please update to the latest version.",
+    );
+  }
+  const inputOutputPaths: RunQueryInputOutput[] = targets.map((target) => {
+    return {
+      queryPath: target.queryPath,
+      outputPath: outputDir.getBqrsPath(target.outputBaseName),
+      dilPath: outputDir.getDilPath(target.outputBaseName),
+    };
+  });
 
+  const evalLogPath = generateEvalLog ? outputDir.evalLogPath : undefined;
+  const queriesToRun: RunQueriesParams = {
+    db: dbPath,
+    additionalPacks,
+    externalInputs: {},
+    singletonExternalInputs: templates || {},
+    inputOutputPaths,
+    logPath: evalLogPath,
+    extensionPacks,
+    // Add any additional arguments without interpretation.
+    ...additionalRunQueryArgs,
+  };
+
+  // Update the active query logger every time there is a new request to compile.
+  // This isn't ideal because in situations where there are queries running
+  // in parallel, each query's log messages are interleaved. Fixing this
+  // properly will require a change in the query server.
+  qs.activeQueryLogger = logger;
+  const queryResults: Record<string, RunQueryResult> = await qs.sendRequest(
+    runQueries,
+    queriesToRun,
+    token,
+    progress,
+  );
+  const coreQueryResults = new Map<string, CoreQueryResult>();
+  targets.forEach((target) => {
+    const queryResult = queryResults[target.queryPath];
+    coreQueryResults.set(target.queryPath, {
+      resultType: queryResult.resultType,
+      message: queryResult.message,
+      evaluationTime: queryResult.evaluationTime,
+      outputBaseName: target.outputBaseName,
+    });
+  });
   return {
-    resultType: result.resultType,
-    message: result.message,
-    evaluationTime: result.evaluationTime,
+    results: coreQueryResults,
   };
 }
diff --git a/extensions/ql-vscode/src/query-testing/test-runner.ts b/extensions/ql-vscode/src/query-testing/test-runner.ts
index 23da9d0c1eb..8c38fca4ab6 100644
--- a/extensions/ql-vscode/src/query-testing/test-runner.ts
+++ b/extensions/ql-vscode/src/query-testing/test-runner.ts
@@ -61,7 +61,7 @@ export class TestRunner extends DisposableObject {
       })) {
         await eventHandler(event);
       }
-    } catch (e) {
+    } catch {
       // CodeQL testing can throw exception even in normal scenarios. For example, if the test run
       // produces no output (which is normal), the testing command would throw an exception on
       // unexpected EOF during json parsing. So nothing needs to be done here - all the relevant
@@ -125,7 +125,7 @@ export class TestRunner extends DisposableObject {
           // So we need to display the error message ourselves and then rethrow.
           void showAndLogWarningMessage(
             extLogger,
-            `Cannot reopen database ${uri}: ${e}`,
+            `Cannot reopen database ${uri.toString()}: ${getErrorMessage(e)}`,
           );
           throw e;
         }
diff --git a/extensions/ql-vscode/src/run-queries-shared.ts b/extensions/ql-vscode/src/run-queries-shared.ts
index 4a91cad5e58..03e25df46dc 100644
--- a/extensions/ql-vscode/src/run-queries-shared.ts
+++ b/extensions/ql-vscode/src/run-queries-shared.ts
@@ -27,7 +27,6 @@ import type {
 import type { BaseLogger } from "./common/logging";
 import { showAndLogWarningMessage } from "./common/logging";
 import { extLogger } from "./common/logging/vscode";
-import { generateSummarySymbolsFile } from "./log-insights/summary-parser";
 import { getErrorMessage } from "./common/helpers-pure";
 import { createHash } from "crypto";
 import { QueryOutputDir } from "./local-queries/query-output-dir";
@@ -65,6 +64,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
    */
   constructor(
     querySaveDir: string,
+    public readonly outputBaseName: string,
     public readonly dbItemPath: string,
     public readonly databaseHasMetadataFile: boolean,
     public readonly quickEvalPosition?: Position,
@@ -73,23 +73,30 @@ export class QueryEvaluationInfo extends QueryOutputDir {
     super(querySaveDir);
   }
 
-  get resultsPaths() {
-    return {
-      resultsPath: this.bqrsPath,
-      interpretedResultsPath: join(
-        this.querySaveDir,
-        this.metadata?.kind === "graph"
-          ? "graphResults"
-          : "interpretedResults.sarif",
-      ),
-    };
+  get resultsPath() {
+    return this.getBqrsPath(this.outputBaseName);
   }
+
+  get interpretedResultsPath() {
+    return this.getInterpretedResultsPath(
+      this.metadata?.kind,
+      this.outputBaseName,
+    );
+  }
+
+  get csvPath() {
+    return this.getCsvPath(this.outputBaseName);
+  }
+
+  get dilPath() {
+    return this.getDilPath(this.outputBaseName);
+  }
+
   getSortedResultSetPath(resultSetName: string) {
     const hasher = createHash("sha256");
     hasher.update(resultSetName);
-    return join(
-      this.querySaveDir,
-      `sortedResults-${hasher.digest("hex")}.bqrs`,
+    return this.getBqrsPath(
+      `${this.outputBaseName}-sorted-${hasher.digest("hex")}`,
     );
   }
 
@@ -127,7 +134,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
    * Holds if this query actually has produced interpreted results.
    */
   async hasInterpretedResults(): Promise<boolean> {
-    return pathExists(this.resultsPaths.interpretedResultsPath);
+    return pathExists(this.interpretedResultsPath);
   }
 
   /**
@@ -205,7 +212,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
     let nextOffset: number | undefined = 0;
     do {
       const chunk: DecodedBqrsChunk = await cliServer.bqrsDecode(
-        this.resultsPaths.resultsPath,
+        this.resultsPath,
         resultSet,
         {
           pageSize: 100,
@@ -218,7 +225,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
             .map((v, i) => {
               if (chunk.columns[i].kind === "String") {
                 return `"${
-                  typeof v === "string" ? v.replaceAll('"', '""') : v
+                  typeof v === "string" ? v.replaceAll('"', '""') : v.toString()
                 }"`;
               } else if (chunk.columns[i].kind === "Entity") {
                 return (v as BqrsEntityValue).label;
@@ -243,9 +250,9 @@ export class QueryEvaluationInfo extends QueryOutputDir {
    * If the query has no result sets, then return undefined.
    */
   async chooseResultSet(cliServer: CodeQLCliServer) {
-    const resultSets = (
-      await cliServer.bqrsInfo(this.resultsPaths.resultsPath, 0)
-    )["result-sets"];
+    const resultSets = (await cliServer.bqrsInfo(this.resultsPath))[
+      "result-sets"
+    ];
     if (!resultSets.length) {
       return undefined;
     }
@@ -284,7 +291,7 @@ export class QueryEvaluationInfo extends QueryOutputDir {
     }
     await cliServer.generateResultsCsv(
       ensureMetadataIsComplete(this.metadata),
-      this.resultsPaths.resultsPath,
+      this.resultsPath,
       this.csvPath,
       sourceInfo,
     );
@@ -348,6 +355,23 @@ export function validateQueryPath(
   }
 }
 
+/**
+ * Validates that the specified URI represents a QL query suite (QLS), and returns the file system
+ * path to that suite.
+ */
+export function validateQuerySuiteUri(suiteUri: Uri): string {
+  if (suiteUri.scheme !== "file") {
+    throw new Error("Can only run queries that are on disk.");
+  }
+  const suitePath = suiteUri.fsPath;
+  if (!suitePath.endsWith(".qls")) {
+    throw new Error(
+      'The selected resource is not a CodeQL query suite; It should have the extension ".qls".',
+    );
+  }
+  return suitePath;
+}
+
 export interface QuickEvalContext {
   quickEvalPosition: Position;
   quickEvalText: string;
@@ -545,15 +569,6 @@ export async function generateEvalLogSummaries(
 
     if (humanReadableSummary !== undefined) {
       summarySymbols = outputDir.evalLogSummarySymbolsPath;
-      if (
-        !(await cliServer.cliConstraints.supportsGenerateSummarySymbolMap())
-      ) {
-        // We're using an old CLI that cannot generate the summary symbols file while generating the
-        // human-readable log summary. As a fallback, create it by parsing the human-readable
-        // summary.
-        progress(progressUpdate(3, 3, "Generating summary symbols file"));
-        await generateSummarySymbolsFile(humanReadableSummary, summarySymbols);
-      }
     }
   }
 
@@ -607,7 +622,7 @@ export async function logEndSummary(
     const endSummaryContent = await readFile(endSummary, "utf-8");
     void logger.log(" --- Evaluator Log Summary --- ");
     void logger.log(endSummaryContent);
-  } catch (e) {
+  } catch {
     void showAndLogWarningMessage(
       extLogger,
       `Could not read structured evaluator log end of summary file at ${endSummary}.`,
diff --git a/extensions/ql-vscode/src/status-bar.ts b/extensions/ql-vscode/src/status-bar.ts
index 4dd9f2523c2..66b7d2270c3 100644
--- a/extensions/ql-vscode/src/status-bar.ts
+++ b/extensions/ql-vscode/src/status-bar.ts
@@ -55,7 +55,7 @@ export class CodeQlStatusBarHandler extends DisposableObject {
     this.item.text = `CodeQL${canary}`;
 
     const version = await this.cli.getVersion();
-    this.item.text = `CodeQL CLI v${version}${canary}`;
+    this.item.text = `CodeQL CLI v${version.toString()}${canary}`;
     this.item.show();
   }
 }
diff --git a/extensions/ql-vscode/src/stories/Overview.mdx b/extensions/ql-vscode/src/stories/Overview.mdx
index cc06ee5cfca..7d9939cb4d9 100644
--- a/extensions/ql-vscode/src/stories/Overview.mdx
+++ b/extensions/ql-vscode/src/stories/Overview.mdx
@@ -1,7 +1,5 @@
 import { Canvas, Meta, Story } from '@storybook/blocks';
 
-import { VSCodeButton } from '@vscode/webview-ui-toolkit/react';
-
 import iframeImage from './images/update-css-variables-iframe.png';
 import stylesImage from './images/update-css-variables-styles.png';
 import bodyImage from './images/update-css-variables-body.png';
diff --git a/extensions/ql-vscode/src/stories/common/Alert.stories.tsx b/extensions/ql-vscode/src/stories/common/Alert.stories.tsx
index f82eaa17100..2267ccb2696 100644
--- a/extensions/ql-vscode/src/stories/common/Alert.stories.tsx
+++ b/extensions/ql-vscode/src/stories/common/Alert.stories.tsx
@@ -1,8 +1,9 @@
 import type { Meta, StoryFn } from "@storybook/react";
-import { VSCodeButton, VSCodeLink } from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 import { VariantAnalysisContainer } from "../../view/variant-analysis/VariantAnalysisContainer";
 import { Alert } from "../../view/common";
+import { Link } from "../../view/common/Link";
 
 export default {
   title: "Alert",
@@ -24,7 +25,7 @@ Warning.args = {
   title: "This query found a warning",
   message: (
     <>
-      Warning content with <VSCodeLink>links</VSCodeLink>
+      Warning content with <Link>links</Link>
     </>
   ),
 };
@@ -50,7 +51,7 @@ Error.args = {
   title: "This query found an error",
   message: (
     <>
-      Error content with <VSCodeLink>links</VSCodeLink>
+      Error content with <Link>links</Link>
     </>
   ),
 };
@@ -70,8 +71,7 @@ ErrorExample.args = {
     <>
       Request to
       https://api.github.com/repos/octodemo/Hello-World/code-scanning/codeql/queries
-      failed. <VSCodeLink>View actions logs</VSCodeLink> and try running this
-      query again.
+      failed. <Link>View actions logs</Link> and try running this query again.
     </>
   ),
 };
@@ -84,8 +84,8 @@ ErrorWithButtons.args = {
     "Request to https://api.github.com/repos/octodemo/Hello-World/code-scanning/codeql/queries failed. Try running this query again.",
   actions: (
     <>
-      <VSCodeButton appearance="secondary">View actions logs</VSCodeButton>
-      <VSCodeButton>Retry</VSCodeButton>
+      <VscodeButton secondary>View actions logs</VscodeButton>
+      <VscodeButton>Retry</VscodeButton>
     </>
   ),
 };
diff --git a/extensions/ql-vscode/src/stories/common/ResponsiveContainer.stories.tsx b/extensions/ql-vscode/src/stories/common/ResponsiveContainer.stories.tsx
index 117a9570870..91bf0d9e156 100644
--- a/extensions/ql-vscode/src/stories/common/ResponsiveContainer.stories.tsx
+++ b/extensions/ql-vscode/src/stories/common/ResponsiveContainer.stories.tsx
@@ -7,7 +7,7 @@ export default {
   component: ResponsiveContainerComponent,
 } as Meta<typeof ResponsiveContainerComponent>;
 
-const Template: StoryFn<typeof ResponsiveContainerComponent> = (args) => (
+const Template: StoryFn<typeof ResponsiveContainerComponent> = () => (
   <ResponsiveContainerComponent>
     <span>Hello</span>
   </ResponsiveContainerComponent>
diff --git a/extensions/ql-vscode/src/stories/method-modeling/MethodModelingInputs.stories.tsx b/extensions/ql-vscode/src/stories/method-modeling/MethodModelingInputs.stories.tsx
index 8cea272943c..2220e81c132 100644
--- a/extensions/ql-vscode/src/stories/method-modeling/MethodModelingInputs.stories.tsx
+++ b/extensions/ql-vscode/src/stories/method-modeling/MethodModelingInputs.stories.tsx
@@ -53,20 +53,3 @@ FullyModeledMethod.args = {
   method,
   modeledMethod,
 };
-
-export const ModelingInProgress = Template.bind({});
-ModelingInProgress.args = {
-  method,
-  modeledMethod,
-  isModelingInProgress: true,
-};
-
-const generatedModeledMethod = createSinkModeledMethod({
-  provenance: "ai-generated",
-});
-export const ModelingNotAccepted = Template.bind({});
-ModelingNotAccepted.args = {
-  method,
-  modeledMethod: generatedModeledMethod,
-  modelPending: true,
-};
diff --git a/extensions/ql-vscode/src/stories/model-editor/InProgressDropdown.stories.tsx b/extensions/ql-vscode/src/stories/model-editor/InProgressDropdown.stories.tsx
deleted file mode 100644
index c9db432c043..00000000000
--- a/extensions/ql-vscode/src/stories/model-editor/InProgressDropdown.stories.tsx
+++ /dev/null
@@ -1,14 +0,0 @@
-import type { Meta, StoryFn } from "@storybook/react";
-
-import { InProgressDropdown as InProgressDropdownComponent } from "../../view/model-editor/InProgressDropdown";
-
-export default {
-  title: "CodeQL Model Editor/In Progress Dropdown",
-  component: InProgressDropdownComponent,
-} as Meta<typeof InProgressDropdownComponent>;
-
-const Template: StoryFn<typeof InProgressDropdownComponent> = (args) => (
-  <InProgressDropdownComponent />
-);
-
-export const InProgressDropdown = Template.bind({});
diff --git a/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx b/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx
index bcb51057606..16cb303b786 100644
--- a/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx
+++ b/extensions/ql-vscode/src/stories/model-editor/LibraryRow.stories.tsx
@@ -220,10 +220,9 @@ LibraryRow.args = {
     ],
   },
   modifiedSignatures: new Set(["org.sql2o.Sql2o#Sql2o(String)"]),
-  inProgressMethods: new Set(),
+  selectedSignatures: new Set(["org.sql2o.Sql2o#Sql2o(String)"]),
   viewState: createMockModelEditorViewState({
     showGenerateButton: true,
-    showLlmButton: true,
   }),
   hideModeledMethods: false,
 };
diff --git a/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx b/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx
index 6fdc64a1a41..f7bf0748b20 100644
--- a/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx
+++ b/extensions/ql-vscode/src/stories/model-editor/MethodRow.stories.tsx
@@ -96,7 +96,6 @@ const modeledMethod: ModeledMethod = {
 
 const viewState = createMockModelEditorViewState({
   showGenerateButton: true,
-  showLlmButton: true,
 });
 
 export const Unmodeled = Template.bind({});
@@ -113,6 +112,7 @@ Source.args = {
   modeledMethods: [{ ...modeledMethod, type: "source" }],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const Sink = Template.bind({});
@@ -121,6 +121,7 @@ Sink.args = {
   modeledMethods: [{ ...modeledMethod, type: "sink" }],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const Summary = Template.bind({});
@@ -137,6 +138,7 @@ Neutral.args = {
   modeledMethods: [{ ...modeledMethod, type: "neutral" }],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const AlreadyModeled = Template.bind({});
@@ -146,15 +148,6 @@ AlreadyModeled.args = {
   viewState,
 };
 
-export const ModelingInProgress = Template.bind({});
-ModelingInProgress.args = {
-  method,
-  modeledMethods: [modeledMethod],
-  modelingInProgress: true,
-  methodCanBeModeled: true,
-  viewState,
-};
-
 export const MultipleModelings = Template.bind({});
 MultipleModelings.args = {
   method,
@@ -165,6 +158,7 @@ MultipleModelings.args = {
   ],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const ValidationError = Template.bind({});
@@ -176,6 +170,7 @@ ValidationError.args = {
   ],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
 
 export const MultipleValidationErrors = Template.bind({});
@@ -190,4 +185,5 @@ MultipleValidationErrors.args = {
   ],
   methodCanBeModeled: true,
   viewState,
+  onChange: () => {},
 };
diff --git a/extensions/ql-vscode/src/stories/model-editor/ModelEditor.stories.tsx b/extensions/ql-vscode/src/stories/model-editor/ModelEditor.stories.tsx
index 71c199845f4..33569b77db5 100644
--- a/extensions/ql-vscode/src/stories/model-editor/ModelEditor.stories.tsx
+++ b/extensions/ql-vscode/src/stories/model-editor/ModelEditor.stories.tsx
@@ -27,7 +27,6 @@ ModelEditor.args = {
       dataExtensions: [],
     },
     showGenerateButton: true,
-    showLlmButton: true,
   }),
   initialMethods: [
     {
diff --git a/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx b/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx
index bfb179a1fed..d2cc19f3916 100644
--- a/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx
+++ b/extensions/ql-vscode/src/stories/results/AlertTable.stories.tsx
@@ -431,4 +431,7 @@ WithCodeFlows.args = {
       showRawResults={() => action("show-raw-results")}
     />
   ),
+  userSettings: {
+    shouldShowProvenance: true,
+  },
 };
diff --git a/extensions/ql-vscode/src/stories/tsconfig.json b/extensions/ql-vscode/src/stories/tsconfig.json
index 7c10f9902ac..498d867b626 100644
--- a/extensions/ql-vscode/src/stories/tsconfig.json
+++ b/extensions/ql-vscode/src/stories/tsconfig.json
@@ -2,7 +2,7 @@
   "compilerOptions": {
     "module": "esnext",
     "moduleResolution": "node",
-    "target": "es6",
+    "target": "es2021",
     "outDir": "out",
     "lib": ["ES2021", "dom"],
     "jsx": "react-jsx",
diff --git a/extensions/ql-vscode/src/tmp-dir.ts b/extensions/ql-vscode/src/tmp-dir.ts
index b556150a0df..51b1cc814ec 100644
--- a/extensions/ql-vscode/src/tmp-dir.ts
+++ b/extensions/ql-vscode/src/tmp-dir.ts
@@ -1,5 +1,6 @@
 import { dirSync } from "tmp-promise";
 import { extLogger } from "./common/logging/vscode";
+import { getErrorMessage } from "./common/helpers-pure";
 
 // Shared temporary folder for the extension.
 export const tmpDir = dirSync({
@@ -14,7 +15,7 @@ export const tmpDirDisposal = {
       tmpDir.removeCallback();
     } catch (e) {
       void extLogger.log(
-        `Failed to remove temporary directory ${tmpDir.name}: ${e}`,
+        `Failed to remove temporary directory ${tmpDir.name}: ${getErrorMessage(e)}`,
       );
     }
   },
diff --git a/extensions/ql-vscode/src/variant-analysis/gh-api/gh-api-client.ts b/extensions/ql-vscode/src/variant-analysis/gh-api/gh-api-client.ts
index 3855951865e..be8d323c7c4 100644
--- a/extensions/ql-vscode/src/variant-analysis/gh-api/gh-api-client.ts
+++ b/extensions/ql-vscode/src/variant-analysis/gh-api/gh-api-client.ts
@@ -1,4 +1,3 @@
-import type { OctokitResponse } from "@octokit/types/dist-types";
 import type { Credentials } from "../../common/authentication";
 import type { VariantAnalysisSubmission } from "../shared/variant-analysis";
 import type {
@@ -26,13 +25,12 @@ export async function submitVariantAnalysis(
     repository_owners: databases.repositoryOwners,
   };
 
-  const response: OctokitResponse<VariantAnalysis> = await octokit.request(
-    "POST /repositories/:controllerRepoId/code-scanning/codeql/variant-analyses",
-    {
-      controllerRepoId,
-      data,
-    },
-  );
+  const response = await octokit.request<VariantAnalysis>({
+    method: "POST",
+    url: "/repositories/:controllerRepoId/code-scanning/codeql/variant-analyses",
+    controllerRepoId,
+    data,
+  });
 
   return response.data;
 }
@@ -44,13 +42,12 @@ export async function getVariantAnalysis(
 ): Promise<VariantAnalysis> {
   const octokit = await credentials.getOctokit();
 
-  const response: OctokitResponse<VariantAnalysis> = await octokit.request(
-    "GET /repositories/:controllerRepoId/code-scanning/codeql/variant-analyses/:variantAnalysisId",
-    {
-      controllerRepoId,
-      variantAnalysisId,
-    },
-  );
+  const response = await octokit.request<VariantAnalysis>({
+    method: "GET",
+    url: "/repositories/:controllerRepoId/code-scanning/codeql/variant-analyses/:variantAnalysisId",
+    controllerRepoId,
+    variantAnalysisId,
+  });
 
   return response.data;
 }
@@ -63,15 +60,13 @@ export async function getVariantAnalysisRepo(
 ): Promise<VariantAnalysisRepoTask> {
   const octokit = await credentials.getOctokit();
 
-  const response: OctokitResponse<VariantAnalysisRepoTask> =
-    await octokit.request(
-      "GET /repositories/:controllerRepoId/code-scanning/codeql/variant-analyses/:variantAnalysisId/repositories/:repoId",
-      {
-        controllerRepoId,
-        variantAnalysisId,
-        repoId,
-      },
-    );
+  const response = await octokit.request<VariantAnalysisRepoTask>({
+    method: "GET",
+    url: "/repositories/:controllerRepoId/code-scanning/codeql/variant-analyses/:variantAnalysisId/repositories/:repoId",
+    controllerRepoId,
+    variantAnalysisId,
+    repoId,
+  });
 
   return response.data;
 }
@@ -104,9 +99,9 @@ export async function createGist(
   });
   if (response.status >= 300) {
     throw new Error(
-      `Error exporting variant analysis results: ${response.status} ${
-        response?.data || ""
-      }`,
+      `Error exporting variant analysis results: ${response.status} ${JSON.stringify(
+        response?.data,
+      )}`,
     );
   }
   return response.data.html_url;
diff --git a/extensions/ql-vscode/src/variant-analysis/repo-states-store/repo-states-store.ts b/extensions/ql-vscode/src/variant-analysis/repo-states-store/repo-states-store.ts
index f2acb35caf6..647e125821a 100644
--- a/extensions/ql-vscode/src/variant-analysis/repo-states-store/repo-states-store.ts
+++ b/extensions/ql-vscode/src/variant-analysis/repo-states-store/repo-states-store.ts
@@ -26,7 +26,7 @@ export async function readRepoStates(
     const repoStates = mapRepoStatesToDomainModel(repoStatesData);
 
     return repoStates;
-  } catch (e) {
+  } catch {
     // Ignore this error, we simply might not have downloaded anything yet
     return undefined;
   }
diff --git a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
index 2251afe4921..5b29eed8fd0 100644
--- a/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
+++ b/extensions/ql-vscode/src/variant-analysis/run-remote-query.ts
@@ -1,10 +1,9 @@
 import type { CancellationToken } from "vscode";
-import { Uri, window } from "vscode";
-import { join, sep, basename, relative } from "path";
-import { dump, load } from "js-yaml";
-import { copy, writeFile, readFile, mkdirp } from "fs-extra";
-import type { DirectoryResult } from "tmp-promise";
-import { dir, tmpName } from "tmp-promise";
+import { window } from "vscode";
+import { join, basename, relative } from "path";
+import { dump } from "js-yaml";
+import { copy, writeFile, readFile, mkdirp, remove } from "fs-extra";
+import { nanoid } from "nanoid";
 import { tmpDir } from "../tmp-dir";
 import { getOnDiskWorkspaceFolders } from "../common/vscode/workspace-folders";
 import type { Credentials } from "../common/authentication";
@@ -28,13 +27,7 @@ import {
 } from "./repository-selection";
 import type { Repository } from "./shared/repository";
 import type { DbManager } from "../databases/db-manager";
-import {
-  getQlPackFilePath,
-  FALLBACK_QLPACK_FILENAME,
-  QLPACK_FILENAMES,
-  QLPACK_LOCK_FILENAMES,
-} from "../common/ql";
-import type { QlPackFile } from "../packaging/qlpack-file";
+import { FALLBACK_QLPACK_FILENAME } from "../common/ql";
 import { expandShortPaths } from "../common/short-paths";
 import type { QlPackDetails } from "./ql-pack-details";
 import type { ModelPackDetails } from "../common/model-pack-details";
@@ -69,8 +62,6 @@ async function generateQueryPack(
   );
 
   const mustSynthesizePack = qlPackDetails.qlPackFilePath === undefined;
-  const cliSupportsMrvaPackCreate =
-    await cliServer.cliConstraints.supportsMrvaPackCreate();
 
   let targetPackPath: string;
   let needsInstall: boolean;
@@ -88,15 +79,6 @@ async function generateQueryPack(
 
     // Install packs, since we just synthesized a dependency on the language's standard library.
     needsInstall = true;
-  } else if (!cliSupportsMrvaPackCreate) {
-    // We need to copy the query pack to a temporary directory and then fix it up to work with MRVA.
-    targetPackPath = tmpDir.queryPackDir;
-    await copyExistingQueryPack(cliServer, qlPackDetails, targetPackPath);
-
-    // We should already have all the dependencies available, but these older versions of the CLI
-    // have a bug where they will not search `--additional-packs` during validation in `codeql pack bundle`.
-    // Installing the packs will ensure that any extension packs get put in the right place.
-    needsInstall = true;
   } else {
     // The CLI supports creating a MRVA query pack directly from the source pack.
     targetPackPath = qlPackDetails.qlPackRootPath;
@@ -114,36 +96,18 @@ async function generateQueryPack(
     await cliServer.clearCache();
   }
 
-  let precompilationOpts: string[];
-  if (cliSupportsMrvaPackCreate) {
-    if (
-      qlPackDetails.queryFiles.length > 1 &&
-      !(await cliServer.cliConstraints.supportsPackCreateWithMultipleQueries())
-    ) {
-      throw new Error(
-        `Installed CLI version does not allow creating a MRVA pack with multiple queries`,
-      );
-    }
-
-    const queryOpts = qlPackDetails.queryFiles.flatMap((q) => [
-      "--query",
-      join(targetPackPath, relative(qlPackDetails.qlPackRootPath, q)),
-    ]);
-
-    precompilationOpts = [
-      "--mrva",
-      ...queryOpts,
-      // We need to specify the extension packs as dependencies so that they are included in the MRVA pack.
-      // The version range doesn't matter, since they'll always be found by source lookup.
-      ...extensionPacks.map((p) => `--extension-pack=${p.name}@*`),
-    ];
-  } else {
-    precompilationOpts = ["--qlx"];
-
-    if (extensionPacks.length > 0) {
-      await addExtensionPacksAsDependencies(targetPackPath, extensionPacks);
-    }
-  }
+  const queryOpts = qlPackDetails.queryFiles.flatMap((q) => [
+    "--query",
+    join(targetPackPath, relative(qlPackDetails.qlPackRootPath, q)),
+  ]);
+
+  const precompilationOpts = [
+    "--mrva",
+    ...queryOpts,
+    // We need to specify the extension packs as dependencies so that they are included in the MRVA pack.
+    // The version range doesn't matter, since they'll always be found by source lookup.
+    ...extensionPacks.map((p) => `--extension-pack=${p.name}@*`),
+  ];
 
   const bundlePath = tmpDir.bundleFile;
   void extLogger.log(
@@ -191,93 +155,29 @@ async function createNewQueryPack(
   );
 }
 
-async function copyExistingQueryPack(
-  cliServer: CodeQLCliServer,
-  qlPackDetails: QlPackDetails,
-  targetPackPath: string,
-) {
-  const toCopy = await cliServer.packPacklist(
-    qlPackDetails.qlPackRootPath,
-    false,
-  );
-
-  // Also include query files that contain extensible predicates. These query files are not
-  // needed for the query to run, but they are needed for the query pack to pass deep validation
-  // of data extensions.
-  const metadata = await cliServer.generateExtensiblePredicateMetadata(
-    qlPackDetails.qlPackRootPath,
-  );
-  metadata.extensible_predicates.forEach((predicate) => {
-    if (predicate.path.endsWith(".ql")) {
-      toCopy.push(join(qlPackDetails.qlPackRootPath, predicate.path));
-    }
-  });
-
-  [
-    // also copy the lock file (either new name or old name) and the query file itself. These are not included in the packlist.
-    ...QLPACK_LOCK_FILENAMES.map((f) => join(qlPackDetails.qlPackRootPath, f)),
-    ...qlPackDetails.queryFiles,
-  ].forEach((absolutePath) => {
-    if (absolutePath) {
-      toCopy.push(absolutePath);
-    }
-  });
-
-  let copiedCount = 0;
-  await copy(qlPackDetails.qlPackRootPath, targetPackPath, {
-    filter: (file: string) =>
-      // copy file if it is in the packlist, or it is a parent directory of a file in the packlist
-      !!toCopy.find((f) => {
-        // Normalized paths ensure that Windows drive letters are capitalized consistently.
-        const normalizedPath = Uri.file(f).fsPath;
-        const matches =
-          normalizedPath === file || normalizedPath.startsWith(file + sep);
-        if (matches) {
-          copiedCount++;
-        }
-        return matches;
-      }),
-  });
-
-  void extLogger.log(`Copied ${copiedCount} files to ${targetPackPath}`);
-
-  await fixPackFile(targetPackPath, qlPackDetails);
-}
-
 interface RemoteQueryTempDir {
-  remoteQueryDir: DirectoryResult;
+  remoteQueryDir: string;
   queryPackDir: string;
   compiledPackDir: string;
   bundleFile: string;
 }
 
 async function createRemoteQueriesTempDirectory(): Promise<RemoteQueryTempDir> {
-  const shortRemoteQueryDir = await dir({
-    dir: tmpDir.name,
-    unsafeCleanup: true,
-  });
   // Expand 8.3 filenames here to work around a CLI bug where `codeql pack bundle` produces an empty
   // archive if the pack path contains any 8.3 components.
-  const remoteQueryDir = {
-    ...shortRemoteQueryDir,
-    path: await expandShortPaths(shortRemoteQueryDir.path, extLogger),
-  };
-  const queryPackDir = join(remoteQueryDir.path, "query-pack");
+  const tmpDirPath = await expandShortPaths(tmpDir.name, extLogger);
+
+  const remoteQueryDir = join(tmpDirPath, `remote-query-${nanoid()}`);
+  await mkdirp(remoteQueryDir);
+
+  const queryPackDir = join(remoteQueryDir, "query-pack");
   await mkdirp(queryPackDir);
-  const compiledPackDir = join(remoteQueryDir.path, "compiled-pack");
-  const bundleFile = await expandShortPaths(
-    await getPackedBundlePath(tmpDir.name),
-    extLogger,
-  );
-  return { remoteQueryDir, queryPackDir, compiledPackDir, bundleFile };
-}
 
-async function getPackedBundlePath(remoteQueryDir: string): Promise<string> {
-  return tmpName({
-    dir: remoteQueryDir,
-    postfix: "generated.tgz",
-    prefix: "qlpack",
-  });
+  const compiledPackDir = join(remoteQueryDir, "compiled-pack");
+
+  const bundleFile = join(remoteQueryDir, `qlpack-${nanoid()}-generated.tgz`);
+
+  return { remoteQueryDir, queryPackDir, compiledPackDir, bundleFile };
 }
 
 interface PreparedRemoteQuery {
@@ -346,7 +246,7 @@ export async function prepareRemoteQueryRun(
       token,
     );
   } finally {
-    await tempDir.remoteQueryDir.cleanup();
+    await remove(tempDir.remoteQueryDir);
   }
 
   if (token.isCancellationRequested) {
@@ -372,42 +272,6 @@ export async function prepareRemoteQueryRun(
   };
 }
 
-/**
- * Fixes the qlpack.yml or codeql-pack.yml file to be correct in the context of the MRVA request.
- *
- * Performs the following fixes:
- *
- * - Updates the default suite of the query pack. This is used to ensure
- *   only the specified query is run.
- * - Ensures the query pack name is set to the name expected by the server.
- * - Removes any `${workspace}` version references from the qlpack.yml or codeql-pack.yml file. Converts them
- *   to `*` versions.
- *
- * @param targetPackPath The path to the directory containing the target pack
- * @param qlPackDetails The details of the original QL pack
- */
-async function fixPackFile(
-  targetPackPath: string,
-  qlPackDetails: QlPackDetails,
-): Promise<void> {
-  const packPath = await getQlPackFilePath(targetPackPath);
-
-  // This should not happen since we create the pack ourselves.
-  if (!packPath) {
-    throw new Error(
-      `Could not find ${QLPACK_FILENAMES.join(
-        " or ",
-      )} file in '${targetPackPath}'`,
-    );
-  }
-  const qlpack = load(await readFile(packPath, "utf8")) as QlPackFile;
-
-  updateDefaultSuite(qlpack, qlPackDetails);
-  removeWorkspaceRefs(qlpack);
-
-  await writeFile(packPath, dump(qlpack));
-}
-
 async function getExtensionPacksToInject(
   cliServer: CodeQLCliServer,
   workspaceFolders: string[],
@@ -436,41 +300,6 @@ async function getExtensionPacksToInject(
   return result;
 }
 
-async function addExtensionPacksAsDependencies(
-  queryPackDir: string,
-  extensionPacks: ModelPackDetails[],
-): Promise<void> {
-  const qlpackFile = await getQlPackFilePath(queryPackDir);
-  if (!qlpackFile) {
-    throw new Error(
-      `Could not find ${QLPACK_FILENAMES.join(
-        " or ",
-      )} file in '${queryPackDir}'`,
-    );
-  }
-
-  const syntheticQueryPack = load(
-    await readFile(qlpackFile, "utf8"),
-  ) as QlPackFile;
-
-  const dependencies = syntheticQueryPack.dependencies ?? {};
-  extensionPacks.forEach(({ name }) => {
-    // Add this extension pack as a dependency. It doesn't matter which
-    // version we specify, since we are guaranteed that the extension pack
-    // is resolved from source at the given path.
-    dependencies[name] = "*";
-  });
-
-  syntheticQueryPack.dependencies = dependencies;
-
-  await writeFile(qlpackFile, dump(syntheticQueryPack));
-}
-
-function updateDefaultSuite(qlpack: QlPackFile, qlPackDetails: QlPackDetails) {
-  delete qlpack.defaultSuiteFile;
-  qlpack.defaultSuite = generateDefaultSuite(qlPackDetails);
-}
-
 function generateDefaultSuite(qlPackDetails: QlPackDetails) {
   const queries = qlPackDetails.queryFiles.map((query) => {
     const relativePath = relative(qlPackDetails.qlPackRootPath, query);
@@ -571,15 +400,3 @@ async function getControllerRepoFromApi(
     }
   }
 }
-
-function removeWorkspaceRefs(qlpack: QlPackFile) {
-  if (!qlpack.dependencies) {
-    return;
-  }
-
-  for (const [key, value] of Object.entries(qlpack.dependencies)) {
-    if (value === "${workspace}") {
-      qlpack.dependencies[key] = "*";
-    }
-  }
-}
diff --git a/extensions/ql-vscode/src/variant-analysis/sarif-processing.ts b/extensions/ql-vscode/src/variant-analysis/sarif-processing.ts
index aa643d9f576..f998f228e19 100644
--- a/extensions/ql-vscode/src/variant-analysis/sarif-processing.ts
+++ b/extensions/ql-vscode/src/variant-analysis/sarif-processing.ts
@@ -24,6 +24,7 @@ import type {
   ResultSeverity,
   ThreadFlow,
 } from "./shared/analysis-result";
+import { getErrorMessage } from "../common/helpers-pure";
 
 // A line of more than 8k characters is probably generated.
 const CODE_SNIPPET_LARGE_LINE_SIZE_LIMIT = 8192;
@@ -47,7 +48,9 @@ export function extractAnalysisAlerts(
       try {
         alerts.push(...extractResultAlerts(run, result, fileLinkPrefix));
       } catch (e) {
-        errors.push(`Error when processing SARIF result: ${e}`);
+        errors.push(
+          `Error when processing SARIF result: ${getErrorMessage(e)}`,
+        );
         continue;
       }
     }
@@ -67,7 +70,7 @@ function extractResultAlerts(
   const rule = tryGetRule(run, result);
   const severity = tryGetSeverity(run, result, rule) || defaultSeverity;
   const codeFlows = getCodeFlows(result, fileLinkPrefix);
-  const shortDescription = getShortDescription(rule, message!);
+  const shortDescription = getShortDescription(rule, message);
 
   for (const location of result.locations ?? []) {
     const physicalLocation = location.physicalLocation!;
@@ -266,7 +269,7 @@ function getCodeFlows(result: Result, fileLinkPrefix: string): CodeFlow[] {
       for (const threadFlow of codeFlow.threadFlows) {
         for (const threadFlowLocation of threadFlow.locations) {
           const physicalLocation =
-            threadFlowLocation!.location!.physicalLocation!;
+            threadFlowLocation.location!.physicalLocation!;
           const filePath = tryGetFilePath(physicalLocation);
           const codeSnippet = getCodeSnippet(
             physicalLocation.contextRegion,
@@ -299,7 +302,7 @@ function getCodeFlows(result: Result, fileLinkPrefix: string): CodeFlow[] {
 function getMessage(result: Result, fileLinkPrefix: string): AnalysisMessage {
   const tokens: AnalysisMessageToken[] = [];
 
-  const messageText = result.message!.text!;
+  const messageText = result.message.text!;
   const messageParts = parseSarifPlainTextMessage(messageText);
 
   for (const messagePart of messageParts) {
diff --git a/extensions/ql-vscode/src/variant-analysis/shared/variant-analysis.ts b/extensions/ql-vscode/src/variant-analysis/shared/variant-analysis.ts
index 2bb3a60e924..a83a5f2bbf6 100644
--- a/extensions/ql-vscode/src/variant-analysis/shared/variant-analysis.ts
+++ b/extensions/ql-vscode/src/variant-analysis/shared/variant-analysis.ts
@@ -34,7 +34,7 @@ export interface VariantAnalysis {
 export function parseVariantAnalysisQueryLanguage(
   language: string,
 ): QueryLanguage | undefined {
-  return Object.values(QueryLanguage).find((x) => x === language);
+  return Object.values(QueryLanguage).find((x) => x.toString() === language);
 }
 
 export enum VariantAnalysisStatus {
@@ -287,8 +287,9 @@ export function getSkippedRepoCount(
     return 0;
   }
 
-  return Object.values(skippedRepos).reduce(
-    (acc, group) => acc + group.repositoryCount,
+  return Object.values(skippedRepos).reduce<number>(
+    (acc, group: VariantAnalysisSkippedRepositoryGroup) =>
+      acc + group.repositoryCount,
     0,
   );
 }
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
index 9e05309f41c..4256d037cfc 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-manager.ts
@@ -73,12 +73,12 @@ import type {
   VariantAnalysisCommands,
 } from "../common/commands";
 import { exportVariantAnalysisResults } from "./export-results";
+import { viewAutofixesForVariantAnalysisResults } from "./view-autofixes";
 import {
   readRepoStates,
   REPO_STATES_FILENAME,
   writeRepoStates,
 } from "./repo-states-store";
-import { FetchError } from "node-fetch";
 import {
   showAndLogExceptionWithTelemetry,
   showAndLogInformationMessage,
@@ -332,7 +332,7 @@ export class VariantAnalysisManager
   ): Promise<number | undefined> {
     if (!isVariantAnalysisEnabledForGitHubHost()) {
       throw new Error(
-        `Multi-repository variant analysis is not enabled for ${getEnterpriseUri()}`,
+        `Multi-repository variant analysis is not enabled for ${getEnterpriseUri()?.toString()}`,
       );
     }
 
@@ -425,7 +425,7 @@ export class VariantAnalysisManager
         this.app.credentials,
         variantAnalysisSubmission,
       );
-    } catch (e: unknown) {
+    } catch (e) {
       // If the error is handled by the handleRequestError function, we don't need to throw
       if (
         e instanceof RequestError &&
@@ -562,7 +562,7 @@ export class VariantAnalysisManager
       });
       const doc = await workspace.openTextDocument(uri);
       await Window.showTextDocument(doc, { preview: false });
-    } catch (error) {
+    } catch {
       void showAndLogWarningMessage(
         this.app.logger,
         "Could not open variant analysis query text. Failed to open text document.",
@@ -586,7 +586,7 @@ export class VariantAnalysisManager
         variantAnalysis.query.filePath,
       );
       await Window.showTextDocument(textDocument, ViewColumn.One);
-    } catch (error) {
+    } catch {
       void showAndLogWarningMessage(
         this.app.logger,
         `Could not open file: ${variantAnalysis.query.filePath}`,
@@ -859,7 +859,9 @@ export class VariantAnalysisManager
           } catch (e) {
             if (
               retry++ < maxRetryCount &&
-              e instanceof FetchError &&
+              e &&
+              typeof e === "object" &&
+              "code" in e &&
               (e.code === "ETIMEDOUT" || e.code === "ECONNRESET")
             ) {
               void this.app.logger.log(
@@ -966,6 +968,21 @@ export class VariantAnalysisManager
     );
   }
 
+  public async viewAutofixes(
+    variantAnalysisId: number,
+    filterSort: RepositoriesFilterSortStateWithIds = defaultFilterSortState,
+  ) {
+    await viewAutofixesForVariantAnalysisResults(
+      this,
+      this.variantAnalysisResultsManager,
+      variantAnalysisId,
+      filterSort,
+      this.app.credentials,
+      this.app,
+      this.cliServer,
+    );
+  }
+
   public async copyRepoListToClipboard(
     variantAnalysisId: number,
     filterSort: RepositoriesFilterSortStateWithIds = defaultFilterSortState,
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-mapper.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-mapper.ts
index c3a72a26705..2b8858035a2 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-mapper.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-mapper.ts
@@ -76,15 +76,11 @@ function mapVariantAnalysis(
   let skippedRepos: VariantAnalysisSkippedRepositories = {};
 
   if (response.scanned_repositories) {
-    scannedRepos = mapScannedRepositories(
-      response.scanned_repositories as ApiVariantAnalysisScannedRepository[],
-    );
+    scannedRepos = mapScannedRepositories(response.scanned_repositories);
   }
 
   if (response.skipped_repositories) {
-    skippedRepos = mapSkippedRepositories(
-      response.skipped_repositories as ApiVariantAnalysisSkippedRepositories,
-    );
+    skippedRepos = mapSkippedRepositories(response.skipped_repositories);
   }
 
   // Maintain the canceling status if we are still canceling.
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts
index e7856ba59de..01e27410ff0 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-results-manager.ts
@@ -1,5 +1,4 @@
 import { appendFile, pathExists, rm } from "fs-extra";
-import fetch from "node-fetch";
 import { EOL } from "os";
 import { join } from "path";
 
@@ -45,6 +44,7 @@ export type LoadResultsOptions = {
 
 export class VariantAnalysisResultsManager extends DisposableObject {
   private static readonly RESULTS_DIRECTORY = "results";
+  private static readonly RESULTS_SARIF_FILENAME = "results.sarif";
 
   private readonly cachedResults: Map<
     CacheKey,
@@ -94,13 +94,23 @@ export class VariantAnalysisResultsManager extends DisposableObject {
 
     const response = await fetch(repoTask.artifactUrl);
 
-    let responseSize = parseInt(response.headers.get("content-length") || "0");
-    if (responseSize === 0 && response.size > 0) {
-      responseSize = response.size;
+    const responseSize = parseInt(
+      response.headers.get("content-length") || "1",
+    );
+
+    if (!response.body) {
+      throw new Error("No response body found");
     }
 
+    const reader = response.body.getReader();
+
     let amountDownloaded = 0;
-    for await (const chunk of response.body) {
+    for (;;) {
+      const { value: chunk, done } = await reader.read();
+      if (done) {
+        break;
+      }
+
       await appendFile(zipFilePath, Buffer.from(chunk));
       amountDownloaded += chunk.length;
       await onDownloadPercentageChanged(
@@ -203,7 +213,10 @@ export class VariantAnalysisResultsManager extends DisposableObject {
       storageDirectory,
       VariantAnalysisResultsManager.RESULTS_DIRECTORY,
     );
-    const sarifPath = join(resultsDirectory, "results.sarif");
+    const sarifPath = join(
+      resultsDirectory,
+      VariantAnalysisResultsManager.RESULTS_SARIF_FILENAME,
+    );
     const bqrsPath = join(resultsDirectory, "results.bqrs");
 
     let interpretedResults: AnalysisAlert[] | undefined;
@@ -285,6 +298,17 @@ export class VariantAnalysisResultsManager extends DisposableObject {
     return join(variantAnalysisStoragePath, fullName);
   }
 
+  public getRepoResultsSarifStoragePath(
+    variantAnalysisStoragePath: string,
+    fullName: string,
+  ): string {
+    return join(
+      this.getRepoStorageDirectory(variantAnalysisStoragePath, fullName),
+      VariantAnalysisResultsManager.RESULTS_DIRECTORY,
+      VariantAnalysisResultsManager.RESULTS_SARIF_FILENAME,
+    );
+  }
+
   private createGitHubFileLinkPrefix(fullName: string, sha: string): string {
     return new URL(
       `/${fullName}/blob/${sha}`,
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts
index cc531c558e7..db591ac3d95 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view-manager.ts
@@ -34,4 +34,8 @@ export interface VariantAnalysisViewManager<
     variantAnalysisId: number,
     filterSort?: RepositoriesFilterSortStateWithIds,
   ): Promise<void>;
+  viewAutofixes(
+    variantAnalysisId: number,
+    filterSort?: RepositoriesFilterSortStateWithIds,
+  ): Promise<void>;
 }
diff --git a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
index f8a87e47b87..555a3686e68 100644
--- a/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
+++ b/extensions/ql-vscode/src/variant-analysis/variant-analysis-view.ts
@@ -27,6 +27,7 @@ import type { App } from "../common/app";
 import {
   getVariantAnalysisDefaultResultsFilter,
   getVariantAnalysisDefaultResultsSort,
+  isCanary,
 } from "../config";
 
 export class VariantAnalysisView
@@ -53,6 +54,13 @@ export class VariantAnalysisView
     panel.reveal(undefined, true);
 
     await this.waitForPanelLoaded();
+
+    await this.postMessage({
+      t: "setVariantAnalysisUserSettings",
+      variantAnalysisUserSettings: {
+        shouldShowViewAutofixesButton: isCanary(),
+      },
+    });
   }
 
   public async updateView(variantAnalysis: VariantAnalysis): Promise<void> {
@@ -135,6 +143,12 @@ export class VariantAnalysisView
       case "openQueryText":
         await this.manager.openQueryText(this.variantAnalysisId);
         break;
+      case "viewAutofixes":
+        await this.manager.viewAutofixes(
+          this.variantAnalysisId,
+          msg.filterSort,
+        );
+        break;
       case "copyRepositoryList":
         await this.manager.copyRepoListToClipboard(
           this.variantAnalysisId,
diff --git a/extensions/ql-vscode/src/variant-analysis/view-autofixes.ts b/extensions/ql-vscode/src/variant-analysis/view-autofixes.ts
new file mode 100644
index 00000000000..0d0214b07cf
--- /dev/null
+++ b/extensions/ql-vscode/src/variant-analysis/view-autofixes.ts
@@ -0,0 +1,914 @@
+import type { RepositoriesFilterSortStateWithIds } from "./shared/variant-analysis-filter-sort";
+import {
+  defaultFilterSortState,
+  filterAndSortRepositoriesWithResults,
+} from "./shared/variant-analysis-filter-sort";
+import type {
+  VariantAnalysis,
+  VariantAnalysisRepositoryTask,
+} from "./shared/variant-analysis";
+import type { Credentials } from "../common/authentication";
+import { extLogger } from "../common/logging/vscode";
+import type { App } from "../common/app";
+import type { CodeQLCliServer } from "../codeql-cli/cli";
+import {
+  pathExists,
+  ensureDir,
+  remove,
+  unlink,
+  readFile,
+  writeFile,
+  createWriteStream,
+} from "fs-extra";
+import {
+  withProgress,
+  progressUpdate,
+  reportStreamProgress,
+} from "../common/vscode/progress";
+import type { ProgressCallback } from "../common/vscode/progress";
+import { join, parse } from "path";
+import { pluralize } from "../common/word";
+import { readRepoTask } from "./repo-tasks-store";
+import { tmpDir } from "../tmp-dir";
+import { spawn } from "child_process";
+import type { execFileSync } from "child_process";
+import { tryOpenExternalFile } from "../common/vscode/external-files";
+import type { VariantAnalysisManager } from "./variant-analysis-manager";
+import type { VariantAnalysisResultsManager } from "./variant-analysis-results-manager";
+import {
+  getAutofixPath,
+  getAutofixModel,
+  downloadTimeout,
+  AUTOFIX_PATH,
+  AUTOFIX_MODEL,
+} from "../config";
+import { asError, getErrorMessage } from "../common/helpers-pure";
+import { createTimeoutSignal } from "../common/fetch-stream";
+import { unzipToDirectoryConcurrently } from "../common/unzip-concurrently";
+import { reportUnzipProgress } from "../common/vscode/unzip-progress";
+import { getDirectoryNamesInsidePath } from "../common/files";
+import { Readable } from "stream";
+
+// Limit to three repos when generating autofixes so not sending
+// too many requests to autofix. Since we only need to validate
+// a handle of autofixes for each query, this should be sufficient.
+// Consider increasing this in the future if needed.
+const MAX_NUM_REPOS: number = 3;
+// Similarly, limit to three fixes per repo.
+const MAX_NUM_FIXES: number = 3;
+
+/**
+ * Generates autofixes for the results of a variant analysis.
+ */
+export async function viewAutofixesForVariantAnalysisResults(
+  variantAnalysisManager: VariantAnalysisManager,
+  variantAnalysisResultsManager: VariantAnalysisResultsManager,
+  variantAnalysisId: number,
+  filterSort: RepositoriesFilterSortStateWithIds = defaultFilterSortState,
+  credentials: Credentials,
+  app: App,
+  cliServer: CodeQLCliServer,
+): Promise<void> {
+  await withProgress(
+    async (progress: ProgressCallback) => {
+      // Get the path to the local autofix installation.
+      const localAutofixPath = await findLocalAutofix();
+
+      // Get the variant analysis with the given id.
+      const variantAnalysis =
+        variantAnalysisManager.tryGetVariantAnalysis(variantAnalysisId);
+      if (!variantAnalysis) {
+        throw new Error(`No variant analysis with id: ${variantAnalysisId}`);
+      }
+
+      // Generate the query help and output it to the override directory.
+      await overrideQueryHelp(variantAnalysis, cliServer, localAutofixPath);
+
+      // Get the full names (nwos) of the selected repositories.
+      const selectedRepoNames = getSelectedRepositoryNames(
+        variantAnalysis,
+        filterSort,
+      );
+
+      // Get storage paths for the autofix results.
+      const {
+        variantAnalysisIdStoragePath,
+        sourceRootsStoragePath,
+        autofixOutputStoragePath,
+      } = await getStoragePaths(variantAnalysisManager, variantAnalysisId);
+
+      // Process the selected repositories:
+      //  Get sarif
+      //  Download source root
+      //  Run autofix and output results
+      progress(
+        progressUpdate(
+          1,
+          2,
+          `Processing ${pluralize(selectedRepoNames.length, "repository", "repositories")}`,
+        ),
+      );
+      const outputTextFiles = await processSelectedRepositories(
+        variantAnalysisResultsManager,
+        selectedRepoNames,
+        variantAnalysisIdStoragePath,
+        sourceRootsStoragePath,
+        autofixOutputStoragePath,
+        localAutofixPath,
+        credentials,
+      );
+
+      // Output results from all repos to a combined markdown file.
+      progress(progressUpdate(2, 2, `Finalizing autofix results`));
+      const combinedOutputMarkdownFile = join(
+        autofixOutputStoragePath,
+        "autofix-output.md",
+      );
+      await mergeFiles(outputTextFiles, combinedOutputMarkdownFile, false);
+
+      // Open the combined markdown file.
+      await tryOpenExternalFile(app.commands, combinedOutputMarkdownFile);
+    },
+    {
+      title: "Generating Autofixes",
+      cancellable: false, // not cancellable for now
+    },
+  );
+}
+
+/**
+ * Finds the local autofix installation path from the `codeQL.autofix.path` setting.
+ * Throws an error if the path is not set or does not exist.
+ * @returns An object containing the local autofix path.
+ * @throws Error if the `codeQL.autofix.path` setting is not set or the path does not exist.
+ */
+async function findLocalAutofix(): Promise<string> {
+  const localAutofixPath = getAutofixPath();
+  if (!localAutofixPath) {
+    throw new Error(
+      `Path to local autofix installation not found. Make sure ${AUTOFIX_PATH.qualifiedName} is set correctly. Internal GitHub access required.`,
+    );
+  }
+  if (!(await pathExists(localAutofixPath))) {
+    throw new Error(`Local autofix path ${localAutofixPath} does not exist.`);
+  }
+  return localAutofixPath;
+}
+
+/**
+ * Overrides the query help from a given variant analysis
+ * at a location within the `localAutofixPath` directory .
+ */
+async function overrideQueryHelp(
+  variantAnalysis: VariantAnalysis,
+  cliServer: CodeQLCliServer,
+  localAutofixPath: string,
+): Promise<void> {
+  // Get path to the query used by the variant analysis.
+  const queryFilePath = variantAnalysis.query.filePath;
+  if (!(await pathExists(queryFilePath))) {
+    throw new Error(`Query file used by variant analysis not found.`);
+  }
+  const parsedQueryFilePath = parse(queryFilePath);
+  const queryFilePathNoExt = join(
+    parsedQueryFilePath.dir,
+    parsedQueryFilePath.name,
+  );
+
+  // Get the path to the query help, which may be either a `.qhelp` or a `.md` file.
+  // Note: we assume that the name of the query file is the same as the name of the query help file.
+  const queryHelpFilePathQhelp = `${queryFilePathNoExt}.qhelp`;
+  const queryHelpFilePathMarkdown = `${queryFilePathNoExt}.md`;
+
+  // Set `queryHelpFilePath` to the existing extension type.
+  let queryHelpFilePath: string;
+  if (await pathExists(queryHelpFilePathQhelp)) {
+    queryHelpFilePath = queryHelpFilePathQhelp;
+  } else if (await pathExists(queryHelpFilePathMarkdown)) {
+    queryHelpFilePath = queryHelpFilePathMarkdown;
+  } else {
+    throw new Error(
+      `Could not find query help file at either ${queryHelpFilePathQhelp} or ${queryHelpFilePathMarkdown}. Check that the query help file exists and is named correctly.`,
+    );
+  }
+
+  // Get the query metadata.
+  let metadata;
+  try {
+    metadata = await cliServer.resolveMetadata(queryFilePath);
+  } catch (e) {
+    throw new Error(
+      `Could not resolve query metadata for ${queryFilePath}. Reason: ${getErrorMessage(e)}`,
+    );
+  }
+  // Get the query ID (used for the overridden query help's filename).
+  const queryId = metadata.id;
+  if (!queryId) {
+    throw new Error(`Query metadata for ${queryFilePath} is missing an ID.`);
+  }
+  // Replace `/` with `-` for use with the overridden query help's filename.
+  // Use `replaceAll` since some query IDs have multiple slashes.
+  const queryIdWithDash = queryId.replaceAll("/", "-");
+
+  // Get the path to the output directory for overriding the query help.
+  // Note: the path to this directory may change in the future.
+  const queryHelpOverrideDirectory = join(
+    localAutofixPath,
+    "prompt-templates",
+    "qhelps",
+    `${queryIdWithDash}.md`,
+  );
+
+  await cliServer.generateQueryHelp(
+    queryHelpFilePath,
+    queryHelpOverrideDirectory,
+  );
+}
+
+/**
+ * Gets the full names (owner/repo) of the selected
+ * repositories from the given variant analysis while
+ * limiting the number of repositories to `MAX_NUM_REPOS`.
+ */
+function getSelectedRepositoryNames(
+  variantAnalysis: VariantAnalysis,
+  filterSort: RepositoriesFilterSortStateWithIds,
+): string[] {
+  // Get the repositories that were selected by the user.
+  const filteredRepositories = filterAndSortRepositoriesWithResults(
+    variantAnalysis.scannedRepos,
+    filterSort,
+  );
+
+  // Get the full names (owner/repo = nwo) of the selected repos.
+  let fullNames = filteredRepositories
+    ?.filter((a) => a.resultCount && a.resultCount > 0)
+    .map((a) => a.repository.fullName);
+  if (!fullNames || fullNames.length === 0) {
+    throw new Error("No repositories with results found.");
+  }
+
+  // Limit to MAX_NUM_REPOS by slicing the array.
+  if (fullNames.length > MAX_NUM_REPOS) {
+    fullNames = fullNames.slice(0, MAX_NUM_REPOS);
+    void extLogger.showWarningMessage(
+      `Only the first ${MAX_NUM_REPOS} repos (${fullNames.join(", ")}) will be included in the Autofix results.`,
+    );
+  }
+
+  return fullNames;
+}
+
+/**
+ * Gets the storage paths needed for the autofix results.
+ */
+async function getStoragePaths(
+  variantAnalysisManager: VariantAnalysisManager,
+  variantAnalysisId: number,
+): Promise<{
+  variantAnalysisIdStoragePath: string;
+  sourceRootsStoragePath: string;
+  autofixOutputStoragePath: string;
+}> {
+  // Confirm storage path for the variant analysis ID exists.
+  const variantAnalysisIdStoragePath =
+    variantAnalysisManager.getVariantAnalysisStorageLocation(variantAnalysisId);
+  if (!(await pathExists(variantAnalysisIdStoragePath))) {
+    throw new Error(
+      `Variant analysis storage location does not exist: ${variantAnalysisIdStoragePath}`,
+    );
+  }
+
+  // Storage path for all autofix info.
+  const autofixStoragePath = join(variantAnalysisIdStoragePath, "autofix");
+
+  // Storage path for the source roots used with autofix.
+  const sourceRootsStoragePath = join(autofixStoragePath, "source-roots");
+  await ensureDir(sourceRootsStoragePath);
+
+  // Storage path for the autofix output.
+  let autofixOutputStoragePath = join(autofixStoragePath, "output");
+  // If the path already exists, assume that it's a previous run
+  // and append "-n" to the end of the path where n is the next available number.
+  if (await pathExists(autofixOutputStoragePath)) {
+    let i = 1;
+    while (await pathExists(autofixOutputStoragePath + i.toString())) {
+      i++;
+    }
+    autofixOutputStoragePath = autofixOutputStoragePath += i.toString();
+  }
+  await ensureDir(autofixOutputStoragePath);
+
+  return {
+    variantAnalysisIdStoragePath,
+    sourceRootsStoragePath,
+    autofixOutputStoragePath,
+  };
+}
+
+/**
+ * Processes the selected repositories for autofix generation.
+ */
+async function processSelectedRepositories(
+  variantAnalysisResultsManager: VariantAnalysisResultsManager,
+  selectedRepoNames: string[],
+  variantAnalysisIdStoragePath: string,
+  sourceRootsStoragePath: string,
+  autofixOutputStoragePath: string,
+  localAutofixPath: string,
+  credentials: Credentials,
+): Promise<string[]> {
+  const outputTextFiles: string[] = [];
+  await Promise.all(
+    selectedRepoNames.map(async (nwo) =>
+      withProgress(
+        async (progressForRepo: ProgressCallback) => {
+          // Get the sarif file.
+          progressForRepo(progressUpdate(1, 3, `Getting sarif...`));
+          const sarifFile = await getRepoSarifFile(
+            variantAnalysisResultsManager,
+            variantAnalysisIdStoragePath,
+            nwo,
+          );
+
+          // Read the contents of the variant analysis' `repo_task.json` file,
+          // and confirm that the `databaseCommitSha` and `resultCount` exist.
+          const repoTask: VariantAnalysisRepositoryTask = await readRepoTask(
+            variantAnalysisResultsManager.getRepoStorageDirectory(
+              variantAnalysisIdStoragePath,
+              nwo,
+            ),
+          );
+          if (!repoTask.databaseCommitSha) {
+            throw new Error(`Missing database commit SHA for ${nwo}`);
+          }
+          if (!repoTask.resultCount) {
+            throw new Error(`Missing variant analysis result count for ${nwo}`);
+          }
+
+          // Download the source root.
+          // Using `0` as the progress step to force a dynamic vs static progress bar.
+          progressForRepo(progressUpdate(0, 3, `Fetching source root...`));
+          const srcRootPath = await downloadPublicCommitSource(
+            nwo,
+            repoTask.databaseCommitSha,
+            sourceRootsStoragePath,
+            credentials,
+            progressForRepo,
+          );
+
+          // Run autofix.
+          progressForRepo(progressUpdate(2, 3, `Running autofix...`));
+          await runAutofixForRepository(
+            nwo,
+            sarifFile,
+            srcRootPath,
+            localAutofixPath,
+            autofixOutputStoragePath,
+            repoTask.resultCount,
+            outputTextFiles,
+          );
+        },
+        {
+          title: `${nwo}`,
+          cancellable: false,
+        },
+      ),
+    ),
+  );
+
+  return outputTextFiles;
+}
+
+/**
+ * Gets the path to a SARIF file for a given `nwo`.
+ */
+async function getRepoSarifFile(
+  variantAnalysisResultsManager: VariantAnalysisResultsManager,
+  variantAnalysisIdStoragePath: string,
+  nwo: string,
+): Promise<string> {
+  if (
+    !(await variantAnalysisResultsManager.isVariantAnalysisRepoDownloaded(
+      variantAnalysisIdStoragePath,
+      nwo,
+    ))
+  ) {
+    throw new Error(`Variant analysis results not downloaded for ${nwo}`);
+  }
+  const sarifFile =
+    variantAnalysisResultsManager.getRepoResultsSarifStoragePath(
+      variantAnalysisIdStoragePath,
+      nwo,
+    );
+  if (!(await pathExists(sarifFile))) {
+    throw new Error(`SARIF file not found for ${nwo}`);
+  }
+  return sarifFile;
+}
+
+/**
+ * Downloads the source code of a public commit from a GitHub repository.
+ */
+async function downloadPublicCommitSource(
+  nwo: string,
+  sha: string,
+  outputPath: string,
+  credentials: Credentials,
+  progressCallback: ProgressCallback,
+): Promise<string> {
+  const [owner, repo] = nwo.split("/");
+  if (!owner || !repo) {
+    throw new Error(`Invalid repository name: ${nwo}`);
+  }
+
+  // Create output directory if it doesn't exist
+  await ensureDir(outputPath);
+
+  // Define the final checkout directory
+  const checkoutDir = join(
+    outputPath,
+    `${owner}-${repo}-${sha.substring(0, 7)}`,
+  );
+
+  // Check if directory already exists to avoid re-downloading
+  if (await pathExists(checkoutDir)) {
+    const dirNames = await getDirectoryNamesInsidePath(checkoutDir);
+    if (dirNames.length === 1) {
+      // The path to the source code should be a single directory inside `checkoutDir`.
+      const sourceRootDir = join(checkoutDir, dirNames[0]);
+      void extLogger.log(
+        `Source for ${nwo} at ${sha} already exists at ${sourceRootDir}.`,
+      );
+      return sourceRootDir;
+    } else {
+      // Remove `checkoutDir` to allow a re-download if the directory structure is unexpected.
+      void extLogger.log(
+        `Unexpected directory structure. Removing ${checkoutDir}`,
+      );
+      await remove(checkoutDir);
+    }
+  }
+
+  void extLogger.log(`Fetching source of repository ${nwo} at ${sha}...`);
+
+  try {
+    const octokit = await credentials.getOctokit();
+
+    // Get the zipball URL
+    const { url } = await octokit.rest.repos.downloadZipballArchive({
+      owner,
+      repo,
+      ref: sha,
+    });
+
+    // Create a temporary directory for downloading
+    const archivePath = join(
+      tmpDir.name,
+      `source-${owner}-${repo}-${Date.now()}.zip`,
+    );
+
+    // Set timeout
+    const {
+      signal,
+      onData,
+      dispose: disposeTimeout,
+    } = createTimeoutSignal(downloadTimeout());
+
+    // Fetch the url
+    let response: Response;
+    try {
+      response = await fetch(url, {
+        headers: {
+          Accept: "application/zip",
+        },
+        signal,
+      });
+    } catch (e) {
+      disposeTimeout();
+
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The request timed out.");
+        thrownError.stack = e.stack;
+        throw thrownError;
+      }
+      throw new Error(
+        `Error fetching source root. Reason: ${getErrorMessage(e)}`,
+      );
+    }
+
+    // Download the source root from the response body
+    const body = response.body;
+    if (!body) {
+      throw new Error("No response body found");
+    }
+
+    const archiveFileStream = createWriteStream(archivePath);
+
+    const contentLength = response.headers.get("content-length");
+    const totalNumBytes = contentLength
+      ? parseInt(contentLength, 10)
+      : undefined;
+
+    const reportProgress = reportStreamProgress(
+      "Downloading source root...",
+      totalNumBytes,
+      progressCallback,
+    );
+
+    try {
+      const readable = Readable.fromWeb(body);
+      readable.on("data", (chunk) => {
+        onData();
+        reportProgress(chunk?.length ?? 0);
+      });
+      await new Promise((resolve, reject) => {
+        readable
+          .pipe(archiveFileStream)
+          .on("error", (err) => {
+            reject(err);
+          })
+          .on("finish", () => resolve(undefined));
+      });
+
+      await new Promise((resolve, reject) => {
+        archiveFileStream.close((err) => {
+          if (err) {
+            reject(err);
+          }
+          resolve(undefined);
+        });
+      });
+    } catch (e) {
+      // Close and remove the file if an error occurs
+      archiveFileStream.close(() => {
+        void remove(archivePath);
+      });
+
+      if (e instanceof DOMException && e.name === "AbortError") {
+        const thrownError = new Error("The download timed out.");
+        thrownError.stack = e.stack;
+        throw thrownError;
+      }
+
+      throw new Error(
+        `Error downloading source root. Reason: ${getErrorMessage(e)}`,
+      );
+    } finally {
+      disposeTimeout();
+    }
+
+    void extLogger.log(`Download complete, extracting source...`);
+
+    // Extract the downloaded zip file
+    await unzipToDirectoryConcurrently(
+      archivePath,
+      checkoutDir,
+      reportUnzipProgress(`Unzipping source root...`, progressCallback),
+    );
+    await remove(archivePath);
+
+    // Since `unzipToDirectoryConcurrently` extracts to a directory within
+    // `checkoutDir`, we need to return the path to that extracted directory.
+    const dirNames = await getDirectoryNamesInsidePath(checkoutDir);
+    if (dirNames.length === 1) {
+      return join(checkoutDir, dirNames[0]);
+    } else {
+      throw new Error(
+        `Expected exactly one unzipped source directory for ${nwo}, but found ${dirNames.length}.`,
+      );
+    }
+  } catch (error) {
+    await remove(checkoutDir);
+    throw new Error(
+      `Failed to download ${nwo} at ${sha}:. Reason: ${getErrorMessage(error)}`,
+    );
+  }
+}
+
+/**
+ * Runs autofix for a given repository (nwo).
+ */
+async function runAutofixForRepository(
+  nwo: string,
+  sarifFile: string,
+  srcRootPath: string,
+  localAutofixPath: string,
+  autofixOutputStoragePath: string,
+  resultCount: number,
+  outputTextFiles: string[],
+): Promise<void> {
+  // Get storage paths for the autofix results for this repository.
+  const {
+    repoAutofixOutputStoragePath,
+    outputTextFilePath,
+    transcriptFilePath,
+    fixDescriptionFilePath,
+  } = await getRepoStoragePaths(autofixOutputStoragePath, nwo);
+
+  // Get autofix binary.
+  // Switch to Go binary in the future and have user pass full path
+  // in an environment variable instead of hardcoding part here.
+  const cocofixBin = join(process.cwd(), localAutofixPath, "bin", "cocofix.js");
+
+  // Limit number of fixes generated.
+  const limitFixesBoolean: boolean = resultCount > MAX_NUM_FIXES;
+  if (limitFixesBoolean) {
+    void extLogger.log(
+      `Only generating autofixes for the first ${MAX_NUM_FIXES} alerts for ${nwo}.`,
+    );
+
+    // Run autofix in a loop for the first MAX_NUM_FIXES alerts.
+    // Not an ideal solution, but avoids modifying the input SARIF file.
+    const tempOutputTextFiles: string[] = [];
+    const fixDescriptionFiles: string[] = [];
+    const transcriptFiles: string[] = [];
+    for (let i = 0; i < MAX_NUM_FIXES; i++) {
+      const tempOutputTextFilePath = appendSuffixToFilePath(
+        outputTextFilePath,
+        i.toString(),
+      );
+      const tempFixDescriptionFilePath = appendSuffixToFilePath(
+        fixDescriptionFilePath,
+        i.toString(),
+      );
+      const tempTranscriptFilePath = appendSuffixToFilePath(
+        transcriptFilePath,
+        i.toString(),
+      );
+
+      tempOutputTextFiles.push(tempOutputTextFilePath);
+      fixDescriptionFiles.push(tempFixDescriptionFilePath);
+      transcriptFiles.push(tempTranscriptFilePath);
+
+      await runAutofixOnResults(
+        cocofixBin,
+        sarifFile,
+        srcRootPath,
+        tempOutputTextFilePath,
+        tempFixDescriptionFilePath,
+        tempTranscriptFilePath,
+        repoAutofixOutputStoragePath,
+        i,
+      );
+    }
+
+    // Merge the output files together.
+    // Caveat that autofix will call each alert "alert 0", which will look a bit odd in the merged output file.
+    await mergeFiles(tempOutputTextFiles, outputTextFilePath);
+    await mergeFiles(fixDescriptionFiles, fixDescriptionFilePath);
+    await mergeFiles(transcriptFiles, transcriptFilePath);
+  } else {
+    // Run autofix once for all alerts.
+    await runAutofixOnResults(
+      cocofixBin,
+      sarifFile,
+      srcRootPath,
+      outputTextFilePath,
+      fixDescriptionFilePath,
+      transcriptFilePath,
+      repoAutofixOutputStoragePath,
+    );
+  }
+
+  // Format the output text file with markdown.
+  await formatWithMarkdown(outputTextFilePath, `${nwo}`);
+
+  // Save output text files from each repo to later merge
+  // into a single markdown file containing all results.
+  outputTextFiles.push(outputTextFilePath);
+}
+
+/**
+ * Gets the storage paths for the autofix results for a given repository.
+ */
+async function getRepoStoragePaths(
+  autofixOutputStoragePath: string,
+  nwo: string,
+) {
+  // Create output directories for repo's autofix results.
+  const repoAutofixOutputStoragePath = join(
+    autofixOutputStoragePath,
+    nwo.replaceAll("/", "-"),
+  );
+  await ensureDir(repoAutofixOutputStoragePath);
+  return {
+    repoAutofixOutputStoragePath,
+    outputTextFilePath: join(repoAutofixOutputStoragePath, "output.txt"),
+    transcriptFilePath: join(repoAutofixOutputStoragePath, "transcript.md"),
+    fixDescriptionFilePath: join(
+      repoAutofixOutputStoragePath,
+      "fix-description.md",
+    ),
+  };
+}
+
+/**
+ * Runs autofix on the results in the given SARIF file.
+ */
+async function runAutofixOnResults(
+  cocofixBin: string,
+  sarifFile: string,
+  srcRootPath: string,
+  outputTextFilePath: string,
+  fixDescriptionFilePath: string,
+  transcriptFilePath: string,
+  workDir: string,
+  alertNumber?: number, // Optional parameter for specific alert
+): Promise<void> {
+  // Get autofix model from user settings.
+  const autofixModel = getAutofixModel();
+  if (!autofixModel) {
+    throw new Error(
+      `Autofix model not found. Make sure ${AUTOFIX_MODEL.qualifiedName} is set correctly.`,
+    );
+  }
+  // Set up args for autofix command.
+  const autofixArgs = [
+    "--sarif",
+    sarifFile,
+    "--source-root",
+    srcRootPath,
+    "--model",
+    autofixModel,
+    "--dev",
+    "--no-cache",
+    "--format",
+    "text",
+    "--diff-style",
+    "diff", // could do "text" instead if want line of "=" between fixes
+    "--output",
+    outputTextFilePath,
+    "--fix-description",
+    fixDescriptionFilePath,
+    "--transcript",
+    transcriptFilePath,
+  ];
+
+  // Add alert number argument if provided
+  if (alertNumber !== undefined) {
+    autofixArgs.push("--only-alert-number", alertNumber.toString());
+  }
+
+  await execAutofix(
+    cocofixBin,
+    autofixArgs,
+    {
+      cwd: workDir,
+      env: {
+        CAPI_DEV_KEY: process.env.CAPI_DEV_KEY,
+        PATH: process.env.PATH,
+      },
+    },
+    true,
+  );
+}
+
+/**
+ * Executes the autofix command.
+ */
+function execAutofix(
+  bin: string,
+  args: string[],
+  options: Parameters<typeof execFileSync>[2],
+  showCommand?: boolean,
+): Promise<void> {
+  return new Promise((resolve, reject) => {
+    try {
+      const cwd = options?.cwd || process.cwd();
+      if (showCommand) {
+        void extLogger.log(
+          `Spawning '${bin} ${args.join(" ")}' in ${cwd.toString()}`,
+        );
+      }
+
+      let stdoutBuffer = "";
+      let stderrBuffer = "";
+
+      const p = spawn(bin, args, {
+        stdio: ["ignore", "pipe", "pipe"],
+        ...options,
+      });
+
+      // Listen for stdout
+      p.stdout?.on("data", (data) => {
+        stdoutBuffer += data.toString();
+      });
+
+      // Listen for stderr
+      p.stderr?.on("data", (data) => {
+        stderrBuffer += data.toString();
+      });
+
+      // Listen for errors
+      p.on("error", reject);
+
+      // Listen for process exit
+      p.on("exit", (code) => {
+        // Log collected output
+        if (stdoutBuffer.trim()) {
+          void extLogger.log(`Autofix stdout:\n${stdoutBuffer.trim()}`);
+        }
+
+        if (stderrBuffer.trim()) {
+          void extLogger.log(`Autofix stderr:\n${stderrBuffer.trim()}`);
+        }
+
+        if (code === 0) {
+          resolve();
+        } else {
+          reject(new Error(`Autofix process exited with code ${code}.`));
+        }
+      });
+    } catch (e) {
+      reject(asError(e));
+    }
+  });
+}
+
+/**
+ * Creates a new file path by appending the given suffix.
+ * @param filePath The original file path.
+ * @param suffix The suffix to append to the file name (before the extension).
+ * @returns The new file path with the suffix appended.
+ */
+function appendSuffixToFilePath(filePath: string, suffix: string): string {
+  const { dir, name, ext } = parse(filePath);
+  return join(dir, `${name}-${suffix}${ext}`);
+}
+
+/**
+ * Merges the given `inputFiles` into a single `outputFile`.
+ * @param inputFiles - The list of input files to merge.
+ * @param outputFile - The output file path.
+ * @param deleteOriginalFiles - Whether to delete the original input files after merging.
+ */
+async function mergeFiles(
+  inputFiles: string[],
+  outputFile: string,
+  deleteOriginalFiles: boolean = true,
+): Promise<void> {
+  try {
+    // Check if any input files do not exist and return if so.
+    const pathChecks = await Promise.all(
+      inputFiles.map(async (path) => ({
+        exists: await pathExists(path),
+      })),
+    );
+    const anyPathMissing = pathChecks.some((check) => !check.exists);
+    if (inputFiles.length === 0 || anyPathMissing) {
+      return;
+    }
+
+    // Merge the files
+    const contents = await Promise.all(
+      inputFiles.map((file) => readFile(file, "utf8")),
+    );
+
+    // Write merged content
+    await writeFile(outputFile, contents.join("\n"));
+
+    // Delete original files
+    if (deleteOriginalFiles) {
+      await Promise.all(inputFiles.map((file) => unlink(file)));
+    }
+  } catch (error) {
+    throw new Error(`Error merging files. Reason: ${getErrorMessage(error)}`);
+  }
+}
+
+/**
+ * Formats the given input file with the specified header.
+ * @param inputFile The path to the input file to format.
+ * @param header The header to include in the formatted output.
+ */
+async function formatWithMarkdown(
+  inputFile: string,
+  header: string,
+): Promise<void> {
+  try {
+    // Check if the input file exists
+    const exists = await pathExists(inputFile);
+    if (!exists) {
+      return;
+    }
+
+    // Read the input file content
+    const content = await readFile(inputFile, "utf8");
+
+    const frontFormatting: string =
+      "<details><summary>Fix suggestion details</summary>\n\n```diff\n";
+
+    const backFormatting: string =
+      "```\n\n</details>\n\n ### Notes\n - notes placeholder\n\n";
+
+    // Format the content with Markdown
+    // Replace ``` in the content with \``` to avoid breaking the Markdown code block
+    const formattedContent = `## ${header}\n\n${frontFormatting}${content.replaceAll("```", "\\```")}${backFormatting}`;
+
+    // Write the formatted content back to the file
+    await writeFile(inputFile, formattedContent);
+  } catch (error) {
+    throw new Error(`Error formatting file. Reason: ${getErrorMessage(error)}`);
+  }
+}
diff --git a/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css
new file mode 100644
index 00000000000..70a8e8a1577
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css
@@ -0,0 +1,56 @@
+/* Styles have been copied from https://vscode-elements.github.io/elements-lite/components/action-button/configurator/ */
+.actionButton {
+  align-items: center;
+  background-color: transparent;
+  border-color: transparent;
+  border-style: solid;
+  border-width: 1px;
+  border-radius: 5px;
+  color: var(--vscode-foreground);
+  display: inline-flex;
+  cursor: pointer;
+  padding: 0;
+  user-select: none;
+}
+
+.actionButton:disabled {
+  color: var(--vscode-disabledForeground);
+  cursor: default;
+  pointer-events: none;
+}
+
+.actionButton :global(.codicon),
+.actionButton svg {
+  color: var(--vscode-icon-foreground);
+  display: block;
+  padding: 2px;
+}
+
+.actionButton svg {
+  box-sizing: content-box;
+  height: 16px;
+  width: 16px;
+}
+
+.actionButton:disabled :global(.codicon),
+.actionButton:disabled svg {
+  color: var(--vscode-disabledForeground);
+}
+
+.actionButton:hover {
+  background-color: var(--vscode-toolbar-hoverBackground);
+  outline: 1px dotted var(--vscode-contrastActiveBorder, transparent);
+  outline-offset: -1px;
+}
+
+.actionButton:active {
+  background-color: var(--vscode-toolbar-activeBackground);
+}
+
+.actionButton:focus {
+  outline: none;
+}
+
+.actionButton:focus-visible {
+  border-color: var(--vscode-focusBorder);
+}
diff --git a/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css.d.ts b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css.d.ts
new file mode 100644
index 00000000000..e29a2ad9062
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.module.css.d.ts
@@ -0,0 +1,2 @@
+declare const styles: { [className: string]: string };
+export default styles;
diff --git a/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.tsx b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.tsx
new file mode 100644
index 00000000000..f673fd56f96
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/ActionButton/ActionButton.tsx
@@ -0,0 +1,9 @@
+import styles from "./ActionButton.module.css";
+
+// This is needed because vscode-elements/elements does not implement
+// the same styles for icon buttons as vscode/webview-ui-toolkit
+export const ActionButton = (props: React.ComponentProps<"button">) => (
+  <button type="button" {...props} className={styles.actionButton}>
+    {props.children}
+  </button>
+);
diff --git a/extensions/ql-vscode/src/view/common/Badge.tsx b/extensions/ql-vscode/src/view/common/Badge.tsx
new file mode 100644
index 00000000000..cb9826bcab8
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/Badge.tsx
@@ -0,0 +1,8 @@
+import { VscodeBadge } from "@vscode-elements/react-elements";
+
+// This applies the counter variant by default so the border-radius attribute is set
+export const Badge = (props: React.ComponentProps<typeof VscodeBadge>) => (
+  <VscodeBadge variant="counter" {...props}>
+    {props.children}
+  </VscodeBadge>
+);
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx b/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx
index 277013084f1..cc232060f0a 100644
--- a/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx
+++ b/extensions/ql-vscode/src/view/common/CodePaths/CodeFlowsDropdown.tsx
@@ -1,6 +1,9 @@
 import type { ChangeEvent, SetStateAction } from "react";
 import { useCallback } from "react";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 
 import type { CodeFlow } from "../../../variant-analysis/shared/analysis-result";
 
@@ -35,12 +38,12 @@ export const CodeFlowsDropdown = ({
     .toString();
 
   return (
-    <VSCodeDropdown value={value} onChange={handleChange}>
+    <VscodeSingleSelect value={value} onChange={handleChange}>
       {codeFlows.map((codeFlow, index) => (
-        <VSCodeOption key={index} value={index.toString()}>
+        <VscodeOption key={index} value={index.toString()}>
           {getCodeFlowName(codeFlow)}
-        </VSCodeOption>
+        </VscodeOption>
       ))}
-    </VSCodeDropdown>
+    </VscodeSingleSelect>
   );
 };
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx b/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx
index 301107afcc5..520d26a3d83 100644
--- a/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx
+++ b/extensions/ql-vscode/src/view/common/CodePaths/CodePaths.tsx
@@ -1,5 +1,5 @@
 import { styled } from "styled-components";
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
+import { Link } from "../Link";
 
 import type {
   AnalysisMessage,
@@ -8,7 +8,7 @@ import type {
 } from "../../../variant-analysis/shared/analysis-result";
 import { vscode } from "../../vscode-api";
 
-const ShowPathsLink = styled(VSCodeLink)`
+const ShowPathsLink = styled(Link)`
   cursor: pointer;
 `;
 
diff --git a/extensions/ql-vscode/src/view/common/CodePaths/ThreadPath.tsx b/extensions/ql-vscode/src/view/common/CodePaths/ThreadPath.tsx
index 99659a36c18..fd2204daab6 100644
--- a/extensions/ql-vscode/src/view/common/CodePaths/ThreadPath.tsx
+++ b/extensions/ql-vscode/src/view/common/CodePaths/ThreadPath.tsx
@@ -1,5 +1,5 @@
 import { styled } from "styled-components";
-import { VSCodeTag } from "@vscode/webview-ui-toolkit/react";
+import { Tag } from "../Tag";
 
 import type {
   AnalysisMessage,
@@ -56,12 +56,12 @@ export const ThreadPath = ({
       </TitleContainer>
       {isSource && (
         <TagContainer>
-          <VSCodeTag>Source</VSCodeTag>
+          <Tag>Source</Tag>
         </TagContainer>
       )}
       {isSink && (
         <TagContainer>
-          <VSCodeTag>Sink</VSCodeTag>
+          <Tag>Sink</Tag>
         </TagContainer>
       )}
     </HeaderContainer>
diff --git a/extensions/ql-vscode/src/view/common/FileCodeSnippet/CodeSnippetMessage.tsx b/extensions/ql-vscode/src/view/common/FileCodeSnippet/CodeSnippetMessage.tsx
index 6e209a340d4..09ec16d4288 100644
--- a/extensions/ql-vscode/src/view/common/FileCodeSnippet/CodeSnippetMessage.tsx
+++ b/extensions/ql-vscode/src/view/common/FileCodeSnippet/CodeSnippetMessage.tsx
@@ -1,5 +1,5 @@
 import { styled } from "styled-components";
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
+import { Link } from "../Link";
 
 import type {
   AnalysisMessage,
@@ -39,7 +39,7 @@ const CodeSnippetMessageContainer = styled.div<CodeSnippetMessageContainerProps>
   padding-bottom: 1em;
 `;
 
-const LocationLink = styled(VSCodeLink)`
+const LocationLink = styled(Link)`
   font-family: var(--vscode-editor-font-family);
 `;
 
diff --git a/extensions/ql-vscode/src/view/common/FileCodeSnippet/FileCodeSnippet.tsx b/extensions/ql-vscode/src/view/common/FileCodeSnippet/FileCodeSnippet.tsx
index c6fdb624156..b97c7d79c0c 100644
--- a/extensions/ql-vscode/src/view/common/FileCodeSnippet/FileCodeSnippet.tsx
+++ b/extensions/ql-vscode/src/view/common/FileCodeSnippet/FileCodeSnippet.tsx
@@ -1,5 +1,4 @@
 import { styled } from "styled-components";
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 
 import type {
   AnalysisMessage,
@@ -12,6 +11,7 @@ import { createRemoteFileRef } from "../../../common/location-link-utils";
 import { CodeSnippetMessage } from "./CodeSnippetMessage";
 import { CodeSnippetLine } from "./CodeSnippetLine";
 import { sendTelemetry } from "../telemetry";
+import { Link } from "../Link";
 
 const borderColor = "var(--vscode-editor-snippetFinalTabstopHighlightBorder)";
 
@@ -72,12 +72,9 @@ export const FileCodeSnippet = ({
     return (
       <Container>
         <TitleContainer>
-          <VSCodeLink
-            onClick={sendCodeSnippetTitleLinkTelemetry}
-            href={titleFileUri}
-          >
+          <Link onClick={sendCodeSnippetTitleLinkTelemetry} href={titleFileUri}>
             {fileLink.filePath}
-          </VSCodeLink>
+          </Link>
         </TitleContainer>
         {message && severity && (
           <CodeSnippetMessage message={message} severity={severity}>
@@ -93,12 +90,9 @@ export const FileCodeSnippet = ({
   return (
     <Container>
       <TitleContainer>
-        <VSCodeLink
-          onClick={sendCodeSnippetTitleLinkTelemetry}
-          href={titleFileUri}
-        >
+        <Link onClick={sendCodeSnippetTitleLinkTelemetry} href={titleFileUri}>
           {fileLink.filePath}
-        </VSCodeLink>
+        </Link>
       </TitleContainer>
       <CodeContainer>
         {code.map((line, index) => (
diff --git a/extensions/ql-vscode/src/view/common/Link.tsx b/extensions/ql-vscode/src/view/common/Link.tsx
new file mode 100644
index 00000000000..a0e37b92bcd
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/Link.tsx
@@ -0,0 +1,25 @@
+import { styled } from "styled-components";
+
+export const Link = styled.a`
+  background: transparent;
+  box-sizing: border-box;
+  color: var(--vscode-textLink-foreground);
+  cursor: pointer;
+  fill: currentcolor;
+  font-family: var(--vscode-font-family);
+  font-size: var(--vscode-font-size);
+  line-height: normal;
+  outline: none;
+
+  &:hover {
+    text-decoration: underline;
+  }
+
+  &:focus-visible {
+    border: 1px solid var(--vscode-focusBorder);
+  }
+
+  &:focus {
+    border: 1px solid var(--vscode-focusBorder);
+  }
+`;
diff --git a/extensions/ql-vscode/src/view/common/LinkIconButton.tsx b/extensions/ql-vscode/src/view/common/LinkIconButton.tsx
index 8a8e4bbeba5..f282fb646f3 100644
--- a/extensions/ql-vscode/src/view/common/LinkIconButton.tsx
+++ b/extensions/ql-vscode/src/view/common/LinkIconButton.tsx
@@ -1,7 +1,7 @@
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 import { styled } from "styled-components";
+import { Link } from "./Link";
 
-export const LinkIconButton = styled(VSCodeLink)`
+export const LinkIconButton = styled(Link)`
   .codicon {
     vertical-align: text-bottom;
   }
diff --git a/extensions/ql-vscode/src/view/common/SearchBox.tsx b/extensions/ql-vscode/src/view/common/SearchBox.tsx
index 464d303fa7e..7837c143e76 100644
--- a/extensions/ql-vscode/src/view/common/SearchBox.tsx
+++ b/extensions/ql-vscode/src/view/common/SearchBox.tsx
@@ -1,12 +1,16 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeTextField } from "@vscode/webview-ui-toolkit/react";
+import { VscodeTextfield } from "@vscode-elements/react-elements";
 import { Codicon } from "./icon";
 
-const TextField = styled(VSCodeTextField)`
+const TextField = styled(VscodeTextfield)`
   width: 100%;
 `;
 
+const SearchIcon = styled(Codicon)`
+  margin: 0 8px;
+`;
+
 type Props = {
   value: string;
   placeholder: string;
@@ -37,7 +41,7 @@ export const SearchBox = ({
       onInput={handleInput}
       className={className}
     >
-      <Codicon name="search" label="Search..." slot="start" />
+      <SearchIcon name="search" label="Search..." slot="content-before" />
     </TextField>
   );
 };
diff --git a/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx b/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx
index 32240fac67e..facfeedf0dd 100644
--- a/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx
+++ b/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBox.tsx
@@ -14,19 +14,23 @@ import {
   useRole,
 } from "@floating-ui/react";
 import { css, styled } from "styled-components";
-import { VSCodeTextField } from "@vscode/webview-ui-toolkit/react";
 import type { Option } from "./options";
 import { findMatchingOptions } from "./options";
 import { SuggestBoxItem } from "./SuggestBoxItem";
 import { LabelText } from "./LabelText";
 import type { Diagnostic } from "./diagnostics";
 import { useOpenKey } from "./useOpenKey";
+import { VscodeTextfield } from "@vscode-elements/react-elements";
 
-const Input = styled(VSCodeTextField)<{ $error: boolean }>`
+interface InputProps {
+  $error: boolean;
+}
+
+const Input = styled(VscodeTextfield)<InputProps>`
   width: 100%;
   font-family: var(--vscode-editor-font-family);
 
-  ${(props) =>
+  ${(props: InputProps) =>
     props.$error &&
     css`
       --dropdown-border: var(--vscode-inputValidation-errorBorder);
@@ -96,7 +100,7 @@ export type SuggestBoxProps<
 
   /**
    * Can be used to render a different component for the input. This is used
-   * in testing to use default HTML components rather than the VSCodeTextField
+   * in testing to use default HTML components rather than the VscodeTextfield
    * for easier testing.
    * @param props The props returned by `getReferenceProps` of {@link useInteractions}
    */
@@ -200,8 +204,6 @@ export const SuggestBox = <
   }, [disabled]);
 
   return (
-    // Disabled because the div is used to stop click propagation, it's not a button
-    // eslint-disable-next-line jsx-a11y/click-events-have-key-events, jsx-a11y/no-static-element-interactions
     <div onClick={stopClickPropagation}>
       {renderInputComponent(
         getReferenceProps({
diff --git a/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBoxItem.tsx b/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBoxItem.tsx
index 1693d46f1d2..97a9d1a7486 100644
--- a/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBoxItem.tsx
+++ b/extensions/ql-vscode/src/view/common/SuggestBox/SuggestBoxItem.tsx
@@ -64,23 +64,35 @@ type Props = {
 export const SuggestBoxItem = forwardRef<
   HTMLDivElement,
   Props & HTMLProps<HTMLDivElement>
->(({ children, active, icon, labelText, details, ...props }, ref) => {
-  const id = useId();
-  return (
-    <Container
-      ref={ref}
-      role="option"
-      id={id}
-      aria-selected={active}
-      $active={active}
-      {...props}
-    >
-      {icon}
-      <LabelContainer>
-        <Label>{labelText}</Label>
-        {details && <DetailsLabel>{details}</DetailsLabel>}
-      </LabelContainer>
-    </Container>
-  );
-});
+>(
+  (
+    {
+      children,
+      active,
+      icon,
+      labelText,
+      details,
+      ...props
+    }: Props & HTMLProps<HTMLDivElement>,
+    ref,
+  ) => {
+    const id = useId();
+    return (
+      <Container
+        ref={ref}
+        role="option"
+        id={id}
+        aria-selected={active}
+        $active={active}
+        {...props}
+      >
+        {icon}
+        <LabelContainer>
+          <Label>{labelText}</Label>
+          {details && <DetailsLabel>{details}</DetailsLabel>}
+        </LabelContainer>
+      </Container>
+    );
+  },
+);
 SuggestBoxItem.displayName = "SuggestBoxItem";
diff --git a/extensions/ql-vscode/src/view/common/SuggestBox/useEffectEvent.ts b/extensions/ql-vscode/src/view/common/SuggestBox/useEffectEvent.ts
index 13707487ad1..3bd2f92f4e0 100644
--- a/extensions/ql-vscode/src/view/common/SuggestBox/useEffectEvent.ts
+++ b/extensions/ql-vscode/src/view/common/SuggestBox/useEffectEvent.ts
@@ -18,6 +18,7 @@ export function useEffectEvent<T extends (...args: any[]) => any>(callback: T) {
   });
 
   return useCallback<(...args: Parameters<T>) => ReturnType<T>>(
+    // eslint-disable-next-line @typescript-eslint/no-unsafe-return
     (...args) => ref.current(...args),
     [],
   ) as T;
diff --git a/extensions/ql-vscode/src/view/common/SuggestBox/useOpenKey.ts b/extensions/ql-vscode/src/view/common/SuggestBox/useOpenKey.ts
index e0d158c8930..5e646286cd1 100644
--- a/extensions/ql-vscode/src/view/common/SuggestBox/useOpenKey.ts
+++ b/extensions/ql-vscode/src/view/common/SuggestBox/useOpenKey.ts
@@ -16,24 +16,22 @@ export const useOpenKey = <RT extends ReferenceType = ReferenceType>(
 ): ElementProps => {
   const { open, onOpenChange } = context;
 
-  const openOnOpenKey = useEffectEvent(
-    (event: KeyboardEvent<Element> | KeyboardEvent) => {
-      if (open) {
-        return;
-      }
+  const openOnOpenKey = useEffectEvent((event: KeyboardEvent<Element>) => {
+    if (open) {
+      return;
+    }
 
-      if (
-        event.key === " " &&
-        event.ctrlKey &&
-        !event.altKey &&
-        !event.metaKey &&
-        !event.shiftKey
-      ) {
-        event.preventDefault();
-        onOpenChange(true, isReactEvent(event) ? event.nativeEvent : event);
-      }
-    },
-  );
+    if (
+      event.key === " " &&
+      event.ctrlKey &&
+      !event.altKey &&
+      !event.metaKey &&
+      !event.shiftKey
+    ) {
+      event.preventDefault();
+      onOpenChange(true, isReactEvent(event) ? event.nativeEvent : event);
+    }
+  });
 
   return useMemo((): ElementProps => {
     return {
diff --git a/extensions/ql-vscode/src/view/common/Tag.tsx b/extensions/ql-vscode/src/view/common/Tag.tsx
new file mode 100644
index 00000000000..ca83c7c6bca
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/Tag.tsx
@@ -0,0 +1,14 @@
+import { styled } from "styled-components";
+
+export const Tag = styled.span`
+  background-color: var(--vscode-badge-background);
+  border: 1px solid var(--vscode-button-border, transparent);
+  border-radius: 2px;
+  color: var(--vscode-badge-foreground);
+  padding: 2px 4px;
+  text-transform: uppercase;
+  box-sizing: border-box;
+  font-family: var(--vscode-font-family);
+  font-size: 11px;
+  line-height: 16px;
+`;
diff --git a/extensions/ql-vscode/src/view/common/WarningBox.tsx b/extensions/ql-vscode/src/view/common/WarningBox.tsx
new file mode 100644
index 00000000000..b8003d83e57
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/WarningBox.tsx
@@ -0,0 +1,31 @@
+import { styled } from "styled-components";
+import { WarningIcon } from "./icon/WarningIcon";
+
+const WarningBoxDiv = styled.div`
+  max-width: 100em;
+  padding: 0.5em 1em;
+  border: 1px solid var(--vscode-widget-border);
+  box-shadow: var(--vscode-widget-shadow) 0px 3px 8px;
+  display: flex;
+`;
+
+const IconPane = styled.p`
+  width: 3em;
+  flex-shrink: 0;
+  text-align: center;
+`;
+
+export interface WarningBoxProps {
+  children: React.ReactNode;
+}
+
+export function WarningBox(props: WarningBoxProps) {
+  return (
+    <WarningBoxDiv>
+      <IconPane>
+        <WarningIcon />
+      </IconPane>
+      <p>{props.children}</p>
+    </WarningBoxDiv>
+  );
+}
diff --git a/extensions/ql-vscode/src/view/common/index.ts b/extensions/ql-vscode/src/view/common/index.ts
index 7d3564bed43..fe1f4a6ec63 100644
--- a/extensions/ql-vscode/src/view/common/index.ts
+++ b/extensions/ql-vscode/src/view/common/index.ts
@@ -6,3 +6,4 @@ export * from "./HorizontalSpace";
 export * from "./SectionTitle";
 export * from "./VerticalSpace";
 export * from "./ViewTitle";
+export * from "./WarningBox";
diff --git a/extensions/ql-vscode/src/view/common/useMessageFromExtension.ts b/extensions/ql-vscode/src/view/common/useMessageFromExtension.ts
new file mode 100644
index 00000000000..2ba13a99858
--- /dev/null
+++ b/extensions/ql-vscode/src/view/common/useMessageFromExtension.ts
@@ -0,0 +1,27 @@
+import { useEffect } from "react";
+
+/**
+ * Invokes the given callback when a message is received from the extension.
+ */
+export function useMessageFromExtension<T>(
+  onEvent: (event: T) => void,
+  onEventDependencies: unknown[],
+): void {
+  useEffect(() => {
+    const listener = (evt: MessageEvent) => {
+      if (evt.origin === window.origin) {
+        onEvent(evt.data as T);
+      } else {
+        // sanitize origin
+        const origin = evt.origin.replace(/\n|\r/g, "");
+        console.error(`Invalid event origin ${origin}`);
+      }
+    };
+    window.addEventListener("message", listener);
+
+    return () => {
+      window.removeEventListener("message", listener);
+    };
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+  }, onEventDependencies);
+}
diff --git a/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx b/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx
new file mode 100644
index 00000000000..c9fac0a09dc
--- /dev/null
+++ b/extensions/ql-vscode/src/view/compare-performance/ComparePerformance.tsx
@@ -0,0 +1,985 @@
+import type { ChangeEvent } from "react";
+import {
+  Fragment,
+  memo,
+  useDeferredValue,
+  useMemo,
+  useRef,
+  useState,
+} from "react";
+import type {
+  SetPerformanceComparisonQueries,
+  ToComparePerformanceViewMessage,
+} from "../../common/interface-types";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
+import type {
+  PerformanceComparisonDataFromLog,
+  PipelineSummary,
+} from "../../log-insights/performance-comparison";
+import { formatDecimal } from "../../common/number";
+import { styled } from "styled-components";
+import { Codicon, ViewTitle } from "../common";
+import { abbreviateRANames, abbreviateRASteps } from "./RAPrettyPrinter";
+import { Renaming, RenamingInput } from "./RenamingInput";
+
+const enum AbsentReason {
+  NotSeen = "NotSeen",
+  CacheHit = "CacheHit",
+  Sentinel = "Sentinel",
+}
+
+type Optional<T> = AbsentReason | T;
+
+function isPresent<T>(x: Optional<T>): x is T {
+  return typeof x !== "string";
+}
+
+interface PredicateInfo {
+  name: string;
+  raHash: string;
+  tuples: number;
+  evaluationCount: number;
+  iterationCount: number;
+  timeCost: number;
+  pipelines: Record<string, PipelineSummary>;
+}
+
+class ComparisonDataset {
+  /**
+   * Predicates indexed by a key consisting of the name and its pipeline hash.
+   * Unlike the RA hash, the pipeline hash only depends on the predicate's own pipeline.
+   */
+  public keyToIndex = new Map<string, number>();
+  public raToIndex = new Map<string, number>();
+  public nameToIndex = new Map<string, number>();
+  public cacheHitIndices: Set<number>;
+  public sentinelEmptyIndices: Set<number>;
+
+  constructor(private data: PerformanceComparisonDataFromLog) {
+    const { names, raHashes, pipelineSummaryList } = data;
+    const { keyToIndex, raToIndex, nameToIndex } = this;
+    for (let i = 0; i < names.length; i++) {
+      const name = names[i];
+      const pipelineHash = getPipelineSummaryHash(pipelineSummaryList[i]);
+      keyToIndex.set(`${name}@${pipelineHash}`, i);
+      nameToIndex.set(name, i);
+      raToIndex.set(raHashes[i], i);
+    }
+    this.cacheHitIndices = new Set(data.cacheHitIndices);
+    this.sentinelEmptyIndices = new Set(data.sentinelEmptyIndices);
+  }
+
+  keys() {
+    return Array.from(this.keyToIndex.keys());
+  }
+
+  getTupleCountInfo(key: string): Optional<PredicateInfo> {
+    const { data, keyToIndex, cacheHitIndices, sentinelEmptyIndices } = this;
+    const index = keyToIndex.get(key);
+    if (index == null) {
+      return AbsentReason.NotSeen;
+    }
+    const tupleCost = data.tupleCosts[index];
+    if (tupleCost === 0) {
+      if (sentinelEmptyIndices.has(index)) {
+        return AbsentReason.Sentinel;
+      } else if (cacheHitIndices.has(index)) {
+        return AbsentReason.CacheHit;
+      }
+    }
+    return {
+      name: data.names[index],
+      raHash: data.raHashes[index],
+      evaluationCount: data.evaluationCounts[index],
+      iterationCount: data.iterationCounts[index],
+      timeCost: data.timeCosts[index],
+      tuples: tupleCost,
+      pipelines: data.pipelineSummaryList[index],
+    };
+  }
+
+  /**
+   * Returns the RA hashes of all predicates that were evaluated in this data set, but not seen in `other`,
+   * because in `other` the dependency upon these predicates was cut off by a cache hit.
+   *
+   * For example, suppose predicate `A` depends on `B`, which depends on `C`, and the
+   * predicates were evaluated in the first log but not the second:
+   * ```
+   *                  first eval. log        second eval. log
+   * predicate A      seen evaluation        seen cache hit
+   *    |
+   *    V
+   * predicate B      seen evaluation        not seen
+   *    |
+   *    V
+   * predicate C      seen evaluation        not seen
+   * ```
+   *
+   * To ensure a meaningful comparison, we want to omit `predicate A` from the comparison view because of the cache hit.
+   *
+   * But predicates B and C did not have a recorded cache hit in the second log, because they were never scheduled for evaluation.
+   * Given the dependency graph, the most likely explanation is that they would have been evaluated if `A` had not been a cache hit.
+   * We therefore say that B and C are "shadowed" by the cache hit on A.
+   *
+   * The dependency graph is only visible in the first evaluation log, because `B` and `C` do not exist in the second log.
+   * So to compute this, we use the dependency graph from one log together with the set of cache hits in the other log.
+   */
+  getPredicatesShadowedByCacheHit(other: ComparisonDataset) {
+    const {
+      data: { dependencyLists, raHashes, names },
+      raToIndex,
+    } = this;
+    const cacheHits = new Set<string>();
+
+    function visit(index: number, raHash: string) {
+      if (cacheHits.has(raHash)) {
+        return;
+      }
+      cacheHits.add(raHash);
+      const dependencies = dependencyLists[index];
+      for (const dep of dependencies) {
+        const name = names[dep];
+        if (!other.nameToIndex.has(name)) {
+          visit(dep, raHashes[dep]);
+        }
+      }
+    }
+
+    for (const otherCacheHit of other.cacheHitIndices) {
+      {
+        // Look up by RA hash
+        const raHash = other.data.raHashes[otherCacheHit];
+        const ownIndex = raToIndex.get(raHash);
+        if (ownIndex != null) {
+          visit(ownIndex, raHash);
+        }
+      }
+      {
+        // Look up by name
+        const name = other.data.names[otherCacheHit];
+        const ownIndex = this.nameToIndex.get(name);
+        if (ownIndex != null) {
+          visit(ownIndex, raHashes[ownIndex]);
+        }
+      }
+    }
+
+    return cacheHits;
+  }
+}
+
+function renderOptionalValue(x: Optional<number>, unit: string | undefined) {
+  switch (x) {
+    case AbsentReason.NotSeen:
+      return <AbsentNumberCell>n/a</AbsentNumberCell>;
+    case AbsentReason.CacheHit:
+      return <AbsentNumberCell>cache hit</AbsentNumberCell>;
+    case AbsentReason.Sentinel:
+      return <AbsentNumberCell>sentinel empty</AbsentNumberCell>;
+    default:
+      return (
+        <NumberCell>
+          {formatDecimal(x)}
+          {renderUnit(unit)}
+        </NumberCell>
+      );
+  }
+}
+
+function renderPredicateMetric(
+  x: Optional<PredicateInfo>,
+  metric: Metric,
+  isPerEvaluation: boolean,
+) {
+  return renderOptionalValue(
+    metricGetOptional(metric, x, isPerEvaluation),
+    metric.unit,
+  );
+}
+
+function renderDelta(x: number, unit?: string) {
+  const sign = x > 0 ? "+" : "";
+  return (
+    <NumberCell className={x > 0 ? "bad-value" : x < 0 ? "good-value" : ""}>
+      {sign}
+      {formatDecimal(x)}
+      {renderUnit(unit)}
+    </NumberCell>
+  );
+}
+
+function renderUnit(unit: string | undefined) {
+  return unit == null ? "" : ` ${unit}`;
+}
+
+function orderBy<T>(fn: (x: T) => number | string) {
+  return (x: T, y: T) => {
+    const fx = fn(x);
+    const fy = fn(y);
+    return fx === fy ? 0 : fx < fy ? -1 : 1;
+  };
+}
+
+const ChevronCell = styled.td`
+  width: 1em !important;
+`;
+
+const NameHeader = styled.th`
+  text-align: left;
+`;
+
+const NumberHeader = styled.th`
+  text-align: right;
+  width: 10em !important;
+`;
+
+const NameCell = styled.td``;
+
+const NumberCell = styled.td`
+  text-align: right;
+  width: 10em !important;
+
+  &.bad-value {
+    color: var(--vscode-problemsErrorIcon-foreground);
+    tr.expanded & {
+      color: inherit;
+    }
+  }
+  &.good-value {
+    color: var(--vscode-problemsInfoIcon-foreground);
+    tr.expanded & {
+      color: inherit;
+    }
+  }
+`;
+
+const AbsentNumberCell = styled.td`
+  text-align: right;
+  color: var(--vscode-disabledForeground);
+
+  tr.expanded & {
+    color: inherit;
+  }
+  width: 10em !important;
+`;
+
+const Table = styled.table`
+  border-collapse: collapse;
+  width: 100%;
+  border-spacing: 0;
+  background-color: var(--vscode-background);
+  color: var(--vscode-foreground);
+  & td {
+    padding: 0.5em;
+  }
+  & th {
+    padding: 0.5em;
+  }
+  &.expanded {
+    border: 1px solid var(--vscode-list-activeSelectionBackground);
+    margin-bottom: 1em;
+  }
+  word-break: break-all;
+`;
+
+const PredicateTR = styled.tr`
+  cursor: pointer;
+
+  &.expanded {
+    background-color: var(--vscode-list-activeSelectionBackground);
+    color: var(--vscode-list-activeSelectionForeground);
+    position: sticky;
+    top: 0;
+  }
+
+  & .codicon-chevron-right {
+    visibility: hidden;
+  }
+
+  &:hover:not(.expanded) {
+    background-color: var(--vscode-list-hoverBackground);
+    & .codicon-chevron-right {
+      visibility: visible;
+    }
+  }
+`;
+
+const PipelineStepTR = styled.tr`
+  & td {
+    padding-top: 0.3em;
+    padding-bottom: 0.3em;
+  }
+`;
+
+const Dropdown = styled.select``;
+
+interface PipelineStepProps {
+  before: number | undefined;
+  after: number | undefined;
+  comparison: boolean;
+  step: React.ReactNode;
+}
+
+/**
+ * Row with details of a pipeline step, or one of the high-level stats appearing above the pipelines (evaluation/iteration counts).
+ */
+function PipelineStep(props: PipelineStepProps) {
+  let { before, after, comparison, step } = props;
+  if (before != null && before < 0) {
+    before = undefined;
+  }
+  if (after != null && after < 0) {
+    after = undefined;
+  }
+  const delta = before != null && after != null ? after - before : undefined;
+  return (
+    <PipelineStepTR>
+      <ChevronCell />
+      {comparison && (
+        <NumberCell>{before != null ? formatDecimal(before) : ""}</NumberCell>
+      )}
+      <NumberCell>{after != null ? formatDecimal(after) : ""}</NumberCell>
+      {comparison && (delta != null ? renderDelta(delta) : <td></td>)}
+      <NameCell>{step}</NameCell>
+    </PipelineStepTR>
+  );
+}
+
+const HeaderTR = styled.tr`
+  background-color: var(--vscode-sideBar-background);
+`;
+
+interface HeaderRowProps {
+  hasBefore?: boolean;
+  hasAfter?: boolean;
+  comparison: boolean;
+  title: React.ReactNode;
+}
+
+function HeaderRow(props: HeaderRowProps) {
+  const { comparison, hasBefore, hasAfter, title } = props;
+  return (
+    <HeaderTR>
+      <ChevronCell />
+      {comparison ? (
+        <>
+          <NumberHeader>{hasBefore ? "Before" : ""}</NumberHeader>
+          <NumberHeader>{hasAfter ? "After" : ""}</NumberHeader>
+          <NumberHeader>{hasBefore && hasAfter ? "Delta" : ""}</NumberHeader>
+        </>
+      ) : (
+        <NumberHeader>Value</NumberHeader>
+      )}
+      <NameHeader>{title}</NameHeader>
+    </HeaderTR>
+  );
+}
+
+interface HighLevelStatsProps {
+  before: Optional<PredicateInfo>;
+  after: Optional<PredicateInfo>;
+  comparison: boolean;
+}
+
+function HighLevelStats(props: HighLevelStatsProps) {
+  const { before, after, comparison } = props;
+  const hasBefore = isPresent(before);
+  const hasAfter = isPresent(after);
+  const showEvaluationCount =
+    (hasBefore && before.evaluationCount > 1) ||
+    (hasAfter && after.evaluationCount > 1);
+  return (
+    <>
+      <HeaderRow
+        hasBefore={hasBefore}
+        hasAfter={hasAfter}
+        title="Stats"
+        comparison={comparison}
+      />
+      {showEvaluationCount && (
+        <PipelineStep
+          before={hasBefore ? before.evaluationCount : undefined}
+          after={hasAfter ? after.evaluationCount : undefined}
+          comparison={comparison}
+          step="Number of evaluations"
+        />
+      )}
+      <PipelineStep
+        before={
+          hasBefore ? before.iterationCount / before.evaluationCount : undefined
+        }
+        after={
+          hasAfter ? after.iterationCount / after.evaluationCount : undefined
+        }
+        comparison={comparison}
+        step={
+          showEvaluationCount
+            ? "Number of iterations per evaluation"
+            : "Number of iterations"
+        }
+      />
+    </>
+  );
+}
+
+interface Row {
+  key: string;
+  name: string;
+  before: Optional<PredicateInfo>;
+  after: Optional<PredicateInfo>;
+  diff: number;
+}
+
+/**
+ * A set of predicates that have been grouped together because their names have the same fingerprint.
+ */
+interface RowGroup {
+  name: string;
+  rows: Row[];
+  before: Optional<number>;
+  after: Optional<number>;
+  diff: number;
+}
+
+function getSortOrder(sortOrder: "delta" | "absDelta") {
+  if (sortOrder === "absDelta") {
+    return orderBy((row: { diff: number }) => -Math.abs(row.diff));
+  }
+  return orderBy((row: { diff: number }) => row.diff);
+}
+
+interface Metric {
+  title: string;
+  get(info: PredicateInfo): number;
+  unit?: string;
+}
+
+const metrics: Record<string, Metric> = {
+  tuples: {
+    title: "Tuple count",
+    get: (info) => info.tuples,
+  },
+  time: {
+    title: "Time spent",
+    get: (info) => info.timeCost,
+    unit: "ms",
+  },
+  evaluations: {
+    title: "Evaluations",
+    get: (info) => info.evaluationCount,
+  },
+  iterationsTotal: {
+    title: "Iterations",
+    get: (info) => info.iterationCount,
+  },
+};
+
+function metricGetOptional(
+  metric: Metric,
+  info: Optional<PredicateInfo>,
+  isPerEvaluation: boolean,
+): Optional<number> {
+  if (!isPresent(info)) {
+    return info;
+  }
+  const value = metric.get(info);
+  return isPerEvaluation ? (value / info.evaluationCount) | 0 : value;
+}
+
+function addOptionals(a: Optional<number>, b: Optional<number>) {
+  if (isPresent(a) && isPresent(b)) {
+    return a + b;
+  }
+  if (isPresent(a)) {
+    return a;
+  }
+  if (isPresent(b)) {
+    return b;
+  }
+  if (a === b) {
+    return a; // If absent for the same reason, preserve that reason
+  }
+  return 0; // Otherwise collapse to zero
+}
+
+/**
+ * Returns a "fingerprint" from the given name, which is used to group together similar names.
+ */
+function getNameFingerprint(name: string, renamings: Renaming[]) {
+  for (const { patternRegexp, replacement } of renamings) {
+    if (patternRegexp != null) {
+      name = name.replace(patternRegexp, replacement);
+    }
+  }
+  return name;
+}
+
+function Chevron({ expanded }: { expanded: boolean }) {
+  return <Codicon name={expanded ? "chevron-down" : "chevron-right"} />;
+}
+
+function union<T>(a: Set<T> | T[], b: Set<T> | T[]) {
+  const result = new Set(a);
+  for (const x of b) {
+    result.add(x);
+  }
+  return result;
+}
+
+export function ComparePerformance(_: Record<string, never>) {
+  const [data, setData] = useState<
+    SetPerformanceComparisonQueries | undefined
+  >();
+
+  useMessageFromExtension<ToComparePerformanceViewMessage>(
+    (msg) => {
+      setData(msg);
+    },
+    [setData],
+  );
+
+  if (!data) {
+    return <div>Loading performance comparison...</div>;
+  }
+
+  return <ComparePerformanceWithData data={data} />;
+}
+
+function ComparePerformanceWithData(props: {
+  data: SetPerformanceComparisonQueries;
+}) {
+  const { data } = props;
+
+  const { from, to } = useMemo(
+    () => ({
+      from: new ComparisonDataset(data.from),
+      to: new ComparisonDataset(data.to),
+    }),
+    [data],
+  );
+
+  const comparison = data?.comparison;
+
+  const [hideCacheHits, setHideCacheHits] = useState(true);
+
+  const [sortOrder, setSortOrder] = useState<"delta" | "absDelta">("absDelta");
+
+  const [metric, setMetric] = useState<Metric>(metrics.tuples);
+
+  const [isPerEvaluation, setPerEvaluation] = useState(false);
+
+  const keySet = useMemo(() => union(from.keys(), to.keys()), [from, to]);
+
+  const hasCacheHitMismatch = useRef(false);
+
+  const shadowedCacheHitsFrom = useMemo(
+    () =>
+      hideCacheHits ? from.getPredicatesShadowedByCacheHit(to) : new Set(),
+    [from, to, hideCacheHits],
+  );
+  const shadowedCacheHitsTo = useMemo(
+    () =>
+      hideCacheHits ? to.getPredicatesShadowedByCacheHit(from) : new Set(),
+    [from, to, hideCacheHits],
+  );
+
+  const rows: Row[] = useMemo(() => {
+    hasCacheHitMismatch.current = false;
+    return Array.from(keySet)
+      .map((key) => {
+        const before = from.getTupleCountInfo(key);
+        const after = to.getTupleCountInfo(key);
+        const beforeValue = metricGetOptional(metric, before, isPerEvaluation);
+        const afterValue = metricGetOptional(metric, after, isPerEvaluation);
+        if (beforeValue === afterValue) {
+          return undefined!;
+        }
+        if (
+          before === AbsentReason.CacheHit ||
+          after === AbsentReason.CacheHit
+        ) {
+          hasCacheHitMismatch.current = true;
+          if (hideCacheHits) {
+            return undefined!;
+          }
+        }
+        if (
+          (isPresent(before) &&
+            !isPresent(after) &&
+            shadowedCacheHitsFrom.has(before.raHash)) ||
+          (isPresent(after) &&
+            !isPresent(before) &&
+            shadowedCacheHitsTo.has(after.raHash))
+        ) {
+          return undefined!;
+        }
+        const diff =
+          (isPresent(afterValue) ? afterValue : 0) -
+          (isPresent(beforeValue) ? beforeValue : 0);
+        const name = isPresent(before)
+          ? before.name
+          : isPresent(after)
+            ? after.name
+            : key;
+        return { key, name, before, after, diff } satisfies Row;
+      })
+      .filter((x) => !!x)
+      .sort(getSortOrder(sortOrder));
+  }, [
+    keySet,
+    from,
+    to,
+    metric,
+    hideCacheHits,
+    sortOrder,
+    isPerEvaluation,
+    shadowedCacheHitsFrom,
+    shadowedCacheHitsTo,
+  ]);
+
+  const { totalBefore, totalAfter, totalDiff } = useMemo(() => {
+    let totalBefore = 0;
+    let totalAfter = 0;
+    let totalDiff = 0;
+    for (const row of rows) {
+      totalBefore += isPresent(row.before) ? metric.get(row.before) : 0;
+      totalAfter += isPresent(row.after) ? metric.get(row.after) : 0;
+      totalDiff += row.diff;
+    }
+    return { totalBefore, totalAfter, totalDiff };
+  }, [rows, metric]);
+
+  const [renamings, setRenamings] = useState<Renaming[]>(() => [
+    new Renaming("#[0-9a-f]{8}(?![0-9a-f])", "#"),
+  ]);
+
+  // Use deferred value to avoid expensive re-rendering for every keypress in the renaming editor
+  const deferredRenamings = useDeferredValue(renamings);
+
+  const rowGroups = useMemo(() => {
+    const groupedRows = new Map<string, Row[]>();
+    for (const row of rows) {
+      const fingerprint = getNameFingerprint(row.name, deferredRenamings);
+      const rows = groupedRows.get(fingerprint);
+      if (rows) {
+        rows.push(row);
+      } else {
+        groupedRows.set(fingerprint, [row]);
+      }
+    }
+    return Array.from(groupedRows.entries())
+      .map(([fingerprint, rows]) => {
+        const before = rows
+          .map((row) => metricGetOptional(metric, row.before, isPerEvaluation))
+          .reduce(addOptionals);
+        const after = rows
+          .map((row) => metricGetOptional(metric, row.after, isPerEvaluation))
+          .reduce(addOptionals);
+        return {
+          name: rows.length === 1 ? rows[0].name : fingerprint,
+          before,
+          after,
+          diff:
+            (isPresent(after) ? after : 0) - (isPresent(before) ? before : 0),
+          rows,
+        } satisfies RowGroup;
+      })
+      .sort(getSortOrder(sortOrder));
+  }, [rows, metric, sortOrder, deferredRenamings, isPerEvaluation]);
+
+  const rowGroupNames = useMemo(
+    () => abbreviateRANames(rowGroups.map((group) => group.name)),
+    [rowGroups],
+  );
+
+  return (
+    <>
+      <ViewTitle>Performance comparison</ViewTitle>
+      {comparison && hasCacheHitMismatch.current && (
+        <label>
+          <input
+            type="checkbox"
+            checked={hideCacheHits}
+            onChange={() => setHideCacheHits(!hideCacheHits)}
+          />
+          Hide differences due to cache hits
+        </label>
+      )}
+      <RenamingInput renamings={renamings} setRenamings={setRenamings} />
+      Compare{" "}
+      <Dropdown
+        onChange={(e: ChangeEvent<HTMLSelectElement>) =>
+          setMetric(metrics[e.target.value])
+        }
+      >
+        {Object.entries(metrics).map(([key, value]) => (
+          <option key={key} value={key}>
+            {value.title}
+          </option>
+        ))}
+      </Dropdown>{" "}
+      <Dropdown
+        onChange={(e: ChangeEvent<HTMLSelectElement>) =>
+          setPerEvaluation(e.target.value === "per-evaluation")
+        }
+      >
+        <option value="total">Overall</option>
+        <option value="per-evaluation">Per evaluation</option>
+      </Dropdown>{" "}
+      {comparison && (
+        <>
+          sorted by{" "}
+          <Dropdown
+            onChange={(e: ChangeEvent<HTMLSelectElement>) =>
+              setSortOrder(e.target.value as "delta" | "absDelta")
+            }
+            value={sortOrder}
+          >
+            <option value="delta">Delta</option>
+            <option value="absDelta">Absolute delta</option>
+          </Dropdown>
+        </>
+      )}
+      <Table>
+        <thead>
+          <HeaderRow comparison={comparison} title="Predicate" />
+        </thead>
+        <tbody>
+          <tr key="total">
+            <ChevronCell />
+            {comparison && renderOptionalValue(totalBefore, metric.unit)}
+            {renderOptionalValue(totalAfter, metric.unit)}
+            {comparison && renderDelta(totalDiff, metric.unit)}
+            <NameCell>
+              <strong>TOTAL</strong>
+            </NameCell>
+          </tr>
+          <tr key="spacing">
+            <td colSpan={5} style={{ height: "1em" }}></td>
+          </tr>
+        </tbody>
+      </Table>
+      <PredicateTable
+        rowGroups={rowGroups}
+        rowGroupNames={rowGroupNames}
+        comparison={comparison}
+        metric={metric}
+        isPerEvaluation={isPerEvaluation}
+      />
+    </>
+  );
+}
+
+interface PredicateTableProps {
+  rowGroups: RowGroup[];
+  rowGroupNames: React.ReactNode[];
+  comparison: boolean;
+  metric: Metric;
+  isPerEvaluation: boolean;
+}
+
+function PredicateTableRaw(props: PredicateTableProps) {
+  const { comparison, metric, rowGroupNames, rowGroups, isPerEvaluation } =
+    props;
+  return rowGroups.map((rowGroup, rowGroupIndex) => (
+    <PredicateRowGroup
+      key={rowGroupIndex}
+      renderedName={rowGroupNames[rowGroupIndex]}
+      rowGroup={rowGroup}
+      comparison={comparison}
+      metric={metric}
+      isPerEvaluation={isPerEvaluation}
+    />
+  ));
+}
+
+const PredicateTable = memo(PredicateTableRaw);
+
+interface PredicateRowGroupProps {
+  renderedName: React.ReactNode;
+  rowGroup: RowGroup;
+  comparison: boolean;
+  metric: Metric;
+  isPerEvaluation: boolean;
+}
+
+function PredicateRowGroup(props: PredicateRowGroupProps) {
+  const { renderedName, rowGroup, comparison, metric, isPerEvaluation } = props;
+  const [isExpanded, setExpanded] = useState(false);
+  const rowNames = useMemo(
+    () => abbreviateRANames(rowGroup.rows.map((row) => row.name)),
+    [rowGroup],
+  );
+  if (rowGroup.rows.length === 1) {
+    return <PredicateRow row={rowGroup.rows[0]} {...props} />;
+  }
+  return (
+    <Table className={isExpanded ? "expanded" : ""}>
+      <tbody>
+        <PredicateTR
+          className={isExpanded ? "expanded" : ""}
+          key={"main"}
+          onClick={() => setExpanded(!isExpanded)}
+        >
+          <ChevronCell>
+            <Chevron expanded={isExpanded} />
+          </ChevronCell>
+          {comparison && renderOptionalValue(rowGroup.before, metric.unit)}
+          {renderOptionalValue(rowGroup.after, metric.unit)}
+          {comparison && renderDelta(rowGroup.diff, metric.unit)}
+          <NameCell>
+            {renderedName} ({rowGroup.rows.length} predicates)
+          </NameCell>
+        </PredicateTR>
+        {isExpanded &&
+          rowGroup.rows.map((row, rowIndex) => (
+            <tr key={rowIndex}>
+              <td colSpan={5}>
+                <PredicateRow
+                  renderedName={rowNames[rowIndex]}
+                  row={row}
+                  comparison={comparison}
+                  metric={metric}
+                  isPerEvaluation={isPerEvaluation}
+                />
+              </td>
+            </tr>
+          ))}
+      </tbody>
+    </Table>
+  );
+}
+
+interface PredicateRowProps {
+  renderedName: React.ReactNode;
+  row: Row;
+  comparison: boolean;
+  metric: Metric;
+  isPerEvaluation: boolean;
+}
+
+function PredicateRow(props: PredicateRowProps) {
+  const [isExpanded, setExpanded] = useState(false);
+  const { renderedName, row, comparison, metric, isPerEvaluation } = props;
+  const evaluationFactorBefore =
+    isPerEvaluation && isPresent(row.before) ? row.before.evaluationCount : 1;
+  const evaluationFactorAfter =
+    isPerEvaluation && isPresent(row.after) ? row.after.evaluationCount : 1;
+  return (
+    <Table className={isExpanded ? "expanded" : ""}>
+      <tbody>
+        <PredicateTR
+          className={isExpanded ? "expanded" : ""}
+          key={"main"}
+          onClick={() => setExpanded(!isExpanded)}
+        >
+          <ChevronCell>
+            <Chevron expanded={isExpanded} />
+          </ChevronCell>
+          {comparison &&
+            renderPredicateMetric(row.before, metric, isPerEvaluation)}
+          {renderPredicateMetric(row.after, metric, isPerEvaluation)}
+          {comparison && renderDelta(row.diff, metric.unit)}
+          <NameCell>{renderedName}</NameCell>
+        </PredicateTR>
+        {isExpanded && (
+          <>
+            <HighLevelStats
+              before={row.before}
+              after={row.after}
+              comparison={comparison}
+            />
+            {collatePipelines(
+              isPresent(row.before) ? row.before.pipelines : {},
+              isPresent(row.after) ? row.after.pipelines : {},
+            ).map(({ name, first, second }, pipelineIndex) => (
+              <Fragment key={pipelineIndex}>
+                <HeaderRow
+                  hasBefore={first != null}
+                  hasAfter={second != null}
+                  comparison={comparison}
+                  title={
+                    <>
+                      Tuple counts for &apos;{name}&apos; pipeline
+                      {comparison &&
+                        (first == null
+                          ? " (after)"
+                          : second == null
+                            ? " (before)"
+                            : "")}
+                    </>
+                  }
+                />
+                {abbreviateRASteps(first?.steps ?? second?.steps ?? []).map(
+                  (step, index) => (
+                    <PipelineStep
+                      key={index}
+                      before={
+                        first &&
+                        (first.counts[index] / evaluationFactorBefore) | 0
+                      }
+                      after={
+                        second &&
+                        (second.counts[index] / evaluationFactorAfter) | 0
+                      }
+                      comparison={comparison}
+                      step={step}
+                    />
+                  ),
+                )}
+              </Fragment>
+            ))}
+          </>
+        )}
+      </tbody>
+    </Table>
+  );
+}
+
+interface PipelinePair {
+  name: string;
+  first: PipelineSummary | undefined;
+  second: PipelineSummary | undefined;
+}
+
+function collatePipelines(
+  before: Record<string, PipelineSummary>,
+  after: Record<string, PipelineSummary>,
+): PipelinePair[] {
+  const result: PipelinePair[] = [];
+
+  for (const [name, first] of Object.entries(before)) {
+    const second = after[name];
+    if (second == null) {
+      result.push({ name, first, second: undefined });
+    } else if (samePipeline(first.steps, second.steps)) {
+      result.push({ name, first, second });
+    } else {
+      result.push({ name, first, second: undefined });
+      result.push({ name, first: undefined, second });
+    }
+  }
+
+  for (const [name, second] of Object.entries(after)) {
+    if (before[name] == null) {
+      result.push({ name, first: undefined, second });
+    }
+  }
+
+  return result;
+}
+
+function samePipeline(a: string[], b: string[]) {
+  return a.length === b.length && a.every((x, i) => x === b[i]);
+}
+
+function getPipelineSummaryHash(pipelines: Record<string, PipelineSummary>) {
+  // Note: we can't import "crypto" here because it is not available in the browser,
+  // so we just concatenate the hashes of the individual pipelines.
+  const keys = Object.keys(pipelines).sort();
+  let result = "";
+  for (const key of keys) {
+    result += `${pipelines[key].hash};`;
+  }
+  return result;
+}
diff --git a/extensions/ql-vscode/src/view/compare-performance/RAPrettyPrinter.tsx b/extensions/ql-vscode/src/view/compare-performance/RAPrettyPrinter.tsx
new file mode 100644
index 00000000000..b2595dd4c38
--- /dev/null
+++ b/extensions/ql-vscode/src/view/compare-performance/RAPrettyPrinter.tsx
@@ -0,0 +1,282 @@
+import { Fragment, useState } from "react";
+import { styled } from "styled-components";
+
+/**
+ * A set of names, for generating unambiguous abbreviations.
+ */
+class NameSet {
+  private readonly abbreviations = new Map<string, React.ReactNode>();
+
+  constructor(readonly names: string[]) {
+    const qnames = names.map(parseName);
+    const builder = new TrieBuilder();
+    qnames
+      .map((qname) => builder.visitQName(qname))
+      .forEach((r, index) => {
+        this.abbreviations.set(names[index], r.abbreviate(true));
+      });
+  }
+
+  public getAbbreviation(name: string): React.ReactNode {
+    return this.abbreviations.get(name) ?? name;
+  }
+}
+
+/** Name parsed into the form `prefix::name<args>` */
+interface QualifiedName {
+  prefix?: QualifiedName;
+  name: string;
+  args?: QualifiedName[];
+}
+
+function qnameToString(name: QualifiedName): string {
+  const parts: string[] = [];
+  if (name.prefix != null) {
+    parts.push(qnameToString(name.prefix));
+    parts.push("::");
+  }
+  parts.push(name.name);
+  if (name.args != null && name.args.length > 0) {
+    parts.push("<");
+    parts.push(name.args.map(qnameToString).join(","));
+    parts.push(">");
+  }
+  return parts.join("");
+}
+
+function tokeniseName(text: string) {
+  return Array.from(text.matchAll(/:+|<|>|,|"[^"]+"|`[^`]+`|[^:<>,"`]+/g));
+}
+
+function parseName(text: string): QualifiedName {
+  const tokens = tokeniseName(text);
+
+  function next() {
+    return tokens.pop()![0];
+  }
+  function peek() {
+    return tokens[tokens.length - 1][0];
+  }
+  function skipToken(token: string) {
+    if (tokens.length > 0 && peek() === token) {
+      tokens.pop();
+      return true;
+    } else {
+      return false;
+    }
+  }
+
+  function parseQName(): QualifiedName {
+    // Note that the tokens stream is parsed in reverse order. This is simpler, but may look confusing initially.
+    let args: QualifiedName[] | undefined;
+    if (skipToken(">")) {
+      args = [];
+      while (tokens.length > 0 && peek() !== "<") {
+        args.push(parseQName());
+        skipToken(",");
+      }
+      args.reverse();
+      skipToken("<");
+    }
+    const name = tokens.length === 0 ? "" : next();
+    const prefix = skipToken("::") ? parseQName() : undefined;
+    return {
+      prefix,
+      name,
+      args,
+    };
+  }
+
+  const result = parseQName();
+  if (tokens.length > 0) {
+    // It's a parse error if we did not consume all tokens.
+    // Just treat the whole text as the 'name'.
+    return { prefix: undefined, name: text, args: undefined };
+  }
+  return result;
+}
+
+class TrieNode {
+  children = new Map<string, TrieNode>();
+  constructor(readonly index: number) {}
+}
+
+interface VisitResult {
+  node: TrieNode;
+  abbreviate: (isRoot?: boolean) => React.ReactNode;
+}
+
+class TrieBuilder {
+  root = new TrieNode(0);
+  nextId = 1;
+
+  getOrCreate(trieNode: TrieNode, child: string) {
+    const { children } = trieNode;
+    let node = children.get(child);
+    if (node == null) {
+      node = new TrieNode(this.nextId++);
+      children.set(child, node);
+    }
+    return node;
+  }
+
+  visitQName(qname: QualifiedName): VisitResult {
+    const prefix =
+      qname.prefix != null ? this.visitQName(qname.prefix) : undefined;
+    const trieNodeBeforeArgs = this.getOrCreate(
+      prefix?.node ?? this.root,
+      qname.name,
+    );
+    let trieNode = trieNodeBeforeArgs;
+    const args = qname.args?.map((arg) => this.visitQName(arg));
+    if (args != null) {
+      const argKey = args.map((arg) => arg.node.index).join(",");
+      trieNode = this.getOrCreate(trieNodeBeforeArgs, argKey);
+    }
+    return {
+      node: trieNode,
+      abbreviate: (isRoot = false) => {
+        const result: React.ReactNode[] = [];
+        if (prefix != null) {
+          result.push(prefix.abbreviate());
+          result.push("::");
+        }
+        const { name } = qname;
+        const hash = name.indexOf("#");
+        if (hash !== -1 && isRoot) {
+          const shortName = name.substring(0, hash);
+          result.push(<IdentifierSpan>{shortName}</IdentifierSpan>);
+          result.push(name.substring(hash));
+        } else {
+          result.push(isRoot ? <IdentifierSpan>{name}</IdentifierSpan> : name);
+        }
+        if (args != null) {
+          result.push("<");
+          if (trieNodeBeforeArgs.children.size === 1) {
+            const argsText = qname
+              .args!.map((arg) => qnameToString(arg))
+              .join(",");
+            result.push(<ExpandableNamePart>{argsText}</ExpandableNamePart>);
+          } else {
+            let first = true;
+            for (const arg of args) {
+              result.push(arg.abbreviate());
+              if (first) {
+                first = false;
+              } else {
+                result.push(",");
+              }
+            }
+          }
+          result.push(">");
+        }
+        return result;
+      },
+    };
+  }
+}
+
+const ExpandableTextButton = styled.button`
+  background: none;
+  border: none;
+  cursor: pointer;
+  padding: 0;
+  color: inherit;
+  &:hover {
+    background-color: rgba(128, 128, 128, 0.2);
+  }
+`;
+
+interface ExpandableNamePartProps {
+  children: React.ReactNode;
+}
+
+function ExpandableNamePart(props: ExpandableNamePartProps) {
+  const [isExpanded, setExpanded] = useState(false);
+  return (
+    <ExpandableTextButton
+      onClick={(event: Event) => {
+        setExpanded(!isExpanded);
+        event.stopPropagation();
+      }}
+    >
+      {isExpanded ? props.children : "..."}
+    </ExpandableTextButton>
+  );
+}
+
+/**
+ * Span enclosing an entire qualified name.
+ *
+ * Can be used to gray out uninteresting parts of the name, though this looks worse than expected.
+ */
+const QNameSpan = styled.span`
+  /* color: var(--vscode-disabledForeground); */
+`;
+
+/** Span enclosing the innermost identifier, e.g. the `foo` in `A::B<X>::foo#abc` */
+const IdentifierSpan = styled.span`
+  font-weight: 600;
+`;
+
+/** Span enclosing keywords such as `JOIN` and `WITH`. */
+const KeywordSpan = styled.span`
+  font-weight: 500;
+`;
+
+const nameTokenRegex = /\b[^ (]+\b/g;
+
+function traverseMatches(
+  text: string,
+  regex: RegExp,
+  callbacks: {
+    onMatch: (match: RegExpMatchArray) => void;
+    onText: (text: string) => void;
+  },
+) {
+  const matches = Array.from(text.matchAll(regex));
+  let lastIndex = 0;
+  for (const match of matches) {
+    const before = text.substring(lastIndex, match.index);
+    if (before !== "") {
+      callbacks.onText(before);
+    }
+    callbacks.onMatch(match);
+    lastIndex = match.index + match[0].length;
+  }
+  const after = text.substring(lastIndex);
+  if (after !== "") {
+    callbacks.onText(after);
+  }
+}
+
+export function abbreviateRASteps(steps: string[]): React.ReactNode[] {
+  const nameTokens = steps.flatMap((step) =>
+    Array.from(step.matchAll(nameTokenRegex)).map((tok) => tok[0]),
+  );
+  const nameSet = new NameSet(nameTokens.filter((name) => name.includes("::")));
+  return steps.map((step, index) => {
+    const result: React.ReactNode[] = [];
+    traverseMatches(step, nameTokenRegex, {
+      onMatch(match) {
+        const text = match[0];
+        if (text.includes("::")) {
+          result.push(<QNameSpan>{nameSet.getAbbreviation(text)}</QNameSpan>);
+        } else if (/[A-Z]+/.test(text)) {
+          result.push(<KeywordSpan>{text}</KeywordSpan>);
+        } else {
+          result.push(match[0]);
+        }
+      },
+      onText(text) {
+        result.push(text);
+      },
+    });
+    return <Fragment key={index}>{result}</Fragment>;
+  });
+}
+
+export function abbreviateRANames(names: string[]): React.ReactNode[] {
+  const nameSet = new NameSet(names);
+  return names.map((name) => nameSet.getAbbreviation(name));
+}
diff --git a/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx b/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx
new file mode 100644
index 00000000000..c938cc6d1a4
--- /dev/null
+++ b/extensions/ql-vscode/src/view/compare-performance/RenamingInput.tsx
@@ -0,0 +1,103 @@
+import type { ChangeEvent } from "react";
+import { styled } from "styled-components";
+import { VscodeButton, VscodeTextfield } from "@vscode-elements/react-elements";
+import { Codicon } from "../common";
+
+export class Renaming {
+  patternRegexp: RegExp | undefined;
+
+  constructor(
+    public pattern: string,
+    public replacement: string,
+  ) {
+    this.patternRegexp = tryCompilePattern(pattern);
+  }
+}
+
+function tryCompilePattern(pattern: string): RegExp | undefined {
+  try {
+    return new RegExp(pattern, "i");
+  } catch {
+    return undefined;
+  }
+}
+
+const Input = styled(VscodeTextfield)`
+  width: 20em;
+`;
+
+const Row = styled.div`
+  display: flex;
+  padding-bottom: 0.25em;
+`;
+
+const Details = styled.details`
+  padding: 1em;
+`;
+
+interface RenamingInputProps {
+  renamings: Renaming[];
+  setRenamings: (renamings: Renaming[]) => void;
+}
+
+export function RenamingInput(props: RenamingInputProps) {
+  const { renamings, setRenamings } = props;
+  return (
+    <Details>
+      <summary>Predicate renaming</summary>
+      <p>
+        The following regexp replacements are applied to every predicate name on
+        both sides. Predicates whose names clash after renaming are grouped
+        together. Can be used to correlate predicates that were renamed between
+        the two runs.
+        <br />
+        Can also be used to group related predicates, for example, renaming{" "}
+        <code>.*ssa.*</code> to <code>SSA</code> will group all SSA-related
+        predicates together.
+      </p>
+      {renamings.map((renaming, index) => (
+        <Row key={index}>
+          <Input
+            value={renaming.pattern}
+            placeholder="Pattern"
+            onInput={(e: ChangeEvent<HTMLInputElement>) => {
+              const newRenamings = [...renamings];
+              newRenamings[index] = new Renaming(
+                e.target.value,
+                renaming.replacement,
+              );
+              setRenamings(newRenamings);
+            }}
+          >
+            <Codicon name="search" slot="start" />
+          </Input>
+          <Input
+            value={renaming.replacement}
+            placeholder="Replacement"
+            onInput={(e: ChangeEvent<HTMLInputElement>) => {
+              const newRenamings = [...renamings];
+              newRenamings[index] = new Renaming(
+                renaming.pattern,
+                e.target.value,
+              );
+              setRenamings(newRenamings);
+            }}
+          ></Input>
+          <VscodeButton
+            onClick={() =>
+              setRenamings(renamings.filter((_, i) => i !== index))
+            }
+          >
+            <Codicon name="trash" />
+          </VscodeButton>
+          <br />
+        </Row>
+      ))}
+      <VscodeButton
+        onClick={() => setRenamings([...renamings, new Renaming("", "")])}
+      >
+        Add renaming rule
+      </VscodeButton>
+    </Details>
+  );
+}
diff --git a/extensions/ql-vscode/src/view/compare-performance/index.tsx b/extensions/ql-vscode/src/view/compare-performance/index.tsx
new file mode 100644
index 00000000000..ad0bb8f889a
--- /dev/null
+++ b/extensions/ql-vscode/src/view/compare-performance/index.tsx
@@ -0,0 +1,8 @@
+import type { WebviewDefinition } from "../webview-definition";
+import { ComparePerformance } from "./ComparePerformance";
+
+const definition: WebviewDefinition = {
+  component: <ComparePerformance />,
+};
+
+export default definition;
diff --git a/extensions/ql-vscode/src/view/compare/Compare.tsx b/extensions/ql-vscode/src/view/compare/Compare.tsx
index f50e18fe99b..18412bac5f2 100644
--- a/extensions/ql-vscode/src/view/compare/Compare.tsx
+++ b/extensions/ql-vscode/src/view/compare/Compare.tsx
@@ -1,4 +1,4 @@
-import { useState, useEffect } from "react";
+import { useState, useRef } from "react";
 import { styled } from "styled-components";
 
 import type {
@@ -6,6 +6,8 @@ import type {
   SetComparisonsMessage,
   SetComparisonQueryInfoMessage,
   UserSettings,
+  StreamingComparisonSetupMessage,
+  QueryCompareResult,
 } from "../../common/interface-types";
 import { DEFAULT_USER_SETTINGS } from "../../common/interface-types";
 import CompareSelector from "./CompareSelector";
@@ -14,6 +16,7 @@ import CompareTable from "./CompareTable";
 
 import "../results/resultsView.css";
 import { assertNever } from "../../common/helpers-pure";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
 
 const Header = styled.div`
   display: flex;
@@ -37,39 +40,112 @@ export function Compare(_: Record<string, never>): React.JSX.Element {
     DEFAULT_USER_SETTINGS,
   );
 
+  // This is a ref because we don't need to re-render when we get a new streaming comparison message
+  // and we don't want to change the listener every time we get a new message
+  const streamingComparisonRef = useRef<StreamingComparisonSetupMessage | null>(
+    null,
+  );
+
   const message = comparison?.message || "Empty comparison";
   const hasRows =
     comparison?.result &&
     (comparison.result.to.length || comparison.result.from.length);
 
-  useEffect(() => {
-    const listener = (evt: MessageEvent) => {
-      if (evt.origin === window.origin) {
-        const msg: ToCompareViewMessage = evt.data;
-        switch (msg.t) {
-          case "setComparisonQueryInfo":
-            setQueryInfo(msg);
-            break;
-          case "setComparisons":
-            setComparison(msg);
+  useMessageFromExtension<ToCompareViewMessage>((msg) => {
+    switch (msg.t) {
+      case "setComparisonQueryInfo":
+        setQueryInfo(msg);
+        break;
+      case "setComparisons":
+        setComparison(msg);
+        break;
+      case "streamingComparisonSetup":
+        setComparison(null);
+        streamingComparisonRef.current = msg;
+        break;
+      case "streamingComparisonAddResults": {
+        const prev = streamingComparisonRef.current;
+        if (prev === null) {
+          console.warn(
+            'Received "streamingComparisonAddResults" before "streamingComparisonSetup"',
+          );
+          break;
+        }
+
+        if (prev.id !== msg.id) {
+          console.warn(
+            'Received "streamingComparisonAddResults" with different id, ignoring',
+          );
+          break;
+        }
+
+        let result: QueryCompareResult;
+        switch (prev.result.kind) {
+          case "raw":
+            if (msg.result.kind !== "raw") {
+              throw new Error(
+                "Streaming comparison: expected raw results, got interpreted results",
+              );
+            }
+
+            result = {
+              ...prev.result,
+              from: [...prev.result.from, ...msg.result.from],
+              to: [...prev.result.to, ...msg.result.to],
+            };
             break;
-          case "setUserSettings":
-            setUserSettings(msg.userSettings);
+          case "interpreted":
+            if (msg.result.kind !== "interpreted") {
+              throw new Error(
+                "Streaming comparison: expected interpreted results, got raw results",
+              );
+            }
+
+            result = {
+              ...prev.result,
+              from: [...prev.result.from, ...msg.result.from],
+              to: [...prev.result.to, ...msg.result.to],
+            };
             break;
           default:
-            assertNever(msg);
+            throw new Error("Unexpected comparison result kind");
         }
-      } else {
-        // sanitize origin
-        const origin = evt.origin.replace(/\n|\r/g, "");
-        console.error(`Invalid event origin ${origin}`);
+
+        streamingComparisonRef.current = {
+          ...prev,
+          result,
+        };
+
+        break;
       }
-    };
-    window.addEventListener("message", listener);
+      case "streamingComparisonComplete":
+        if (streamingComparisonRef.current === null) {
+          console.warn(
+            'Received "streamingComparisonComplete" before "streamingComparisonSetup"',
+          );
+          setComparison(null);
+          break;
+        }
+
+        if (streamingComparisonRef.current.id !== msg.id) {
+          console.warn(
+            'Received "streamingComparisonComplete" with different id, ignoring',
+          );
+          break;
+        }
 
-    return () => {
-      window.removeEventListener("message", listener);
-    };
+        setComparison({
+          ...streamingComparisonRef.current,
+          t: "setComparisons",
+        });
+        streamingComparisonRef.current = null;
+        break;
+      case "setUserSettings":
+        setUserSettings(msg.userSettings);
+        break;
+      default:
+        assertNever(msg);
+    }
   }, []);
 
   if (!queryInfo || !comparison) {
diff --git a/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx b/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx
index 9267b81f053..6fc2b3b4ba7 100644
--- a/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx
+++ b/extensions/ql-vscode/src/view/data-flow-paths/DataFlowPathsView.tsx
@@ -1,7 +1,8 @@
-import { useEffect, useState } from "react";
+import { useState } from "react";
 import type { ToDataFlowPathsMessage } from "../../common/interface-types";
 import type { DataFlowPaths as DataFlowPathsDomainModel } from "../../variant-analysis/shared/data-flow-paths";
 import { DataFlowPaths } from "./DataFlowPaths";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
 
 export type DataFlowPathsViewProps = {
   dataFlowPaths?: DataFlowPathsDomainModel;
@@ -14,28 +15,12 @@ export function DataFlowPathsView({
     DataFlowPathsDomainModel | undefined
   >(initialDataFlowPaths);
 
-  useEffect(() => {
-    const listener = (evt: MessageEvent) => {
-      if (evt.origin === window.origin) {
-        const msg: ToDataFlowPathsMessage = evt.data;
-        if (msg.t === "setDataFlowPaths") {
-          setDataFlowPaths(msg.dataFlowPaths);
+  useMessageFromExtension<ToDataFlowPathsMessage>((msg) => {
+    setDataFlowPaths(msg.dataFlowPaths);
 
-          // Scroll to the top of the page when we're rendering
-          // new data flow paths.
-          window.scrollTo(0, 0);
-        }
-      } else {
-        // sanitize origin
-        const origin = evt.origin.replace(/\n|\r/g, "");
-        console.error(`Invalid event origin ${origin}`);
-      }
-    };
-    window.addEventListener("message", listener);
-
-    return () => {
-      window.removeEventListener("message", listener);
-    };
+    // Scroll to the top of the page when we're rendering
+    // new data flow paths.
+    window.scrollTo(0, 0);
   }, []);
 
   if (!dataFlowPaths) {
diff --git a/extensions/ql-vscode/src/view/jest-environment-jsdom.ts b/extensions/ql-vscode/src/view/jest-environment-jsdom.ts
new file mode 100644
index 00000000000..a43586ddbd3
--- /dev/null
+++ b/extensions/ql-vscode/src/view/jest-environment-jsdom.ts
@@ -0,0 +1,15 @@
+// eslint-disable-next-line import/no-namespace -- We need a type of JSDOM so we can't use named imports.
+import * as JSDOM from "jsdom";
+import type {
+  EnvironmentContext,
+  JestEnvironmentConfig,
+} from "@jest/environment";
+import BaseEnv from "@jest/environment-jsdom-abstract";
+
+export default class JSDOMEnvironment extends BaseEnv {
+  constructor(config: JestEnvironmentConfig, context: EnvironmentContext) {
+    super(config, context, JSDOM);
+  }
+}
+
+export const TestEnvironment = JSDOMEnvironment;
diff --git a/extensions/ql-vscode/src/view/jest.config.ts b/extensions/ql-vscode/src/view/jest.config.ts
index 441e0e970ca..c197b277e62 100644
--- a/extensions/ql-vscode/src/view/jest.config.ts
+++ b/extensions/ql-vscode/src/view/jest.config.ts
@@ -1,4 +1,5 @@
 import type { Config } from "jest";
+import { transformIgnorePatterns } from "../../test/jest-config";
 
 /*
  * For a detailed explanation regarding each configuration property and type check, visit:
@@ -141,7 +142,7 @@ const config: Config = {
   // snapshotSerializers: [],
 
   // The test environment that will be used for testing
-  testEnvironment: "jsdom",
+  testEnvironment: "<rootDir>/jest-environment-jsdom.ts",
 
   // Options that will be passed to the testEnvironment
   // testEnvironmentOptions: {},
@@ -184,10 +185,7 @@ const config: Config = {
   },
 
   // An array of regexp pattern strings that are matched against all source file paths, matched files will skip transformation
-  transformIgnorePatterns: [
-    // These use ES modules, so need to be transformed
-    "node_modules/(?!(?:@vscode/webview-ui-toolkit|@microsoft/.+|exenv-es6|d3|d3-(.*)|internmap|delaunator|robust-predicates)/.*)",
-  ],
+  transformIgnorePatterns,
 
   // An array of regexp pattern strings that are matched against all modules before the module loader will automatically return a mock for them
   // unmockedModulePathPatterns: undefined,
diff --git a/extensions/ql-vscode/src/view/jest.setup.ts b/extensions/ql-vscode/src/view/jest.setup.ts
index 23cb3e2f973..31dc6657d40 100644
--- a/extensions/ql-vscode/src/view/jest.setup.ts
+++ b/extensions/ql-vscode/src/view/jest.setup.ts
@@ -18,6 +18,20 @@ Object.defineProperty(window, "matchMedia", {
 // Used by Primer React
 window.CSS.supports = jest.fn().mockResolvedValue(false);
 
+// Functions that are not implemented in jsdom
+window.CSSStyleSheet.prototype.replaceSync = jest
+  .fn()
+  .mockReturnValue(undefined);
+window.ElementInternals.prototype.setFormValue = jest
+  .fn()
+  .mockReturnValue(undefined);
+window.ElementInternals.prototype.setValidity = jest
+  .fn()
+  .mockReturnValue(undefined);
+window.HTMLSlotElement.prototype.assignedElements = jest
+  .fn()
+  .mockReturnValue([]);
+
 // Store this on the window so we can mock it
 window.vsCodeApi = {
   postMessage: jest.fn(),
diff --git a/extensions/ql-vscode/src/view/method-modeling/MethodModeling.tsx b/extensions/ql-vscode/src/view/method-modeling/MethodModeling.tsx
index fcb3ed333c1..9e16ed67bb9 100644
--- a/extensions/ql-vscode/src/view/method-modeling/MethodModeling.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/MethodModeling.tsx
@@ -4,7 +4,7 @@ import { ModelingStatusIndicator } from "../model-editor/ModelingStatusIndicator
 import type { Method } from "../../model-editor/method";
 import { MethodName } from "../model-editor/MethodName";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
-import { VSCodeTag } from "@vscode/webview-ui-toolkit/react";
+import { Tag } from "../common/Tag";
 import { ReviewInEditorButton } from "./ReviewInEditorButton";
 import { MultipleModeledMethodsPanel } from "./MultipleModeledMethodsPanel";
 import type { QueryLanguage } from "../../common/query-language";
@@ -39,14 +39,12 @@ const DependencyContainer = styled.div`
   margin-bottom: 0.8rem;
 `;
 
-const StyledVSCodeTag = styled(VSCodeTag)<{ $visible: boolean }>`
+const StyledTag = styled(Tag)<{ $visible: boolean }>`
   visibility: ${(props) => (props.$visible ? "visible" : "hidden")};
 `;
 
 const UnsavedTag = ({ modelingStatus }: { modelingStatus: ModelingStatus }) => (
-  <StyledVSCodeTag $visible={modelingStatus === "unsaved"}>
-    Unsaved
-  </StyledVSCodeTag>
+  <StyledTag $visible={modelingStatus === "unsaved"}>Unsaved</StyledTag>
 );
 
 export type MethodModelingProps = {
@@ -55,8 +53,6 @@ export type MethodModelingProps = {
   modelingStatus: ModelingStatus;
   method: Method;
   modeledMethods: ModeledMethod[];
-  isModelingInProgress: boolean;
-  isProcessedByAutoModel: boolean;
   onChange: (methodSignature: string, modeledMethods: ModeledMethod[]) => void;
 };
 
@@ -66,8 +62,6 @@ export const MethodModeling = ({
   modelingStatus,
   modeledMethods,
   method,
-  isModelingInProgress,
-  isProcessedByAutoModel,
   onChange,
 }: MethodModelingProps): React.JSX.Element => {
   return (
@@ -86,9 +80,6 @@ export const MethodModeling = ({
         modelConfig={modelConfig}
         method={method}
         modeledMethods={modeledMethods}
-        isModelingInProgress={isModelingInProgress}
-        isProcessedByAutoModel={isProcessedByAutoModel}
-        modelingStatus={modelingStatus}
         onChange={onChange}
       />
       <ReviewInEditorButton method={method} />
diff --git a/extensions/ql-vscode/src/view/method-modeling/MethodModelingInputs.tsx b/extensions/ql-vscode/src/view/method-modeling/MethodModelingInputs.tsx
index 18b33ce6577..5db0705be44 100644
--- a/extensions/ql-vscode/src/view/method-modeling/MethodModelingInputs.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/MethodModelingInputs.tsx
@@ -5,7 +5,6 @@ import { ModelTypeDropdown } from "../model-editor/ModelTypeDropdown";
 import { ModelInputDropdown } from "../model-editor/ModelInputDropdown";
 import { ModelOutputDropdown } from "../model-editor/ModelOutputDropdown";
 import { ModelKindDropdown } from "../model-editor/ModelKindDropdown";
-import { InProgressDropdown } from "../model-editor/InProgressDropdown";
 import type { QueryLanguage } from "../../common/query-language";
 import type { ModelConfig } from "../../model-editor/languages";
 
@@ -28,8 +27,6 @@ export type MethodModelingInputsProps = {
   modelConfig: ModelConfig;
   method: Method;
   modeledMethod: ModeledMethod | undefined;
-  modelPending: boolean;
-  isModelingInProgress: boolean;
   onChange: (modeledMethod: ModeledMethod) => void;
 };
 
@@ -38,15 +35,12 @@ export const MethodModelingInputs = ({
   modelConfig,
   method,
   modeledMethod,
-  modelPending,
-  isModelingInProgress,
   onChange,
 }: MethodModelingInputsProps): React.JSX.Element => {
   const inputProps = {
     language,
     method,
     modeledMethod,
-    modelPending,
     onChange,
   };
 
@@ -55,41 +49,25 @@ export const MethodModelingInputs = ({
       <Container>
         <Input>
           <Name>Model Type</Name>
-          {isModelingInProgress ? (
-            <InProgressDropdown />
-          ) : (
-            <ModelTypeDropdown modelConfig={modelConfig} {...inputProps} />
-          )}
+          <ModelTypeDropdown modelConfig={modelConfig} {...inputProps} />
         </Input>
       </Container>
       <Container>
         <Input>
           <Name>Input</Name>
-          {isModelingInProgress ? (
-            <InProgressDropdown />
-          ) : (
-            <ModelInputDropdown {...inputProps} />
-          )}
+          <ModelInputDropdown {...inputProps} />
         </Input>
       </Container>
       <Container>
         <Input>
           <Name>Output</Name>
-          {isModelingInProgress ? (
-            <InProgressDropdown />
-          ) : (
-            <ModelOutputDropdown {...inputProps} />
-          )}
+          <ModelOutputDropdown {...inputProps} />
         </Input>
       </Container>
       <Container>
         <Input>
           <Name>Kind</Name>
-          {isModelingInProgress ? (
-            <InProgressDropdown />
-          ) : (
-            <ModelKindDropdown {...inputProps} />
-          )}
+          <ModelKindDropdown {...inputProps} />
         </Input>
       </Container>
     </>
diff --git a/extensions/ql-vscode/src/view/method-modeling/MethodModelingView.tsx b/extensions/ql-vscode/src/view/method-modeling/MethodModelingView.tsx
index 8e68a351be6..53ec8d1101a 100644
--- a/extensions/ql-vscode/src/view/method-modeling/MethodModelingView.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/MethodModelingView.tsx
@@ -1,4 +1,4 @@
-import { useEffect, useMemo, useState } from "react";
+import { useMemo, useState } from "react";
 import { MethodModeling } from "./MethodModeling";
 import { getModelingStatus } from "../../model-editor/shared/modeling-status";
 import type { Method } from "../../model-editor/method";
@@ -12,6 +12,7 @@ import { NoMethodSelected } from "./NoMethodSelected";
 import type { MethodModelingPanelViewState } from "../../model-editor/shared/view-state";
 import { MethodAlreadyModeled } from "./MethodAlreadyModeled";
 import { defaultModelConfig } from "../../model-editor/languages";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
 
 type Props = {
   initialViewState?: MethodModelingPanelViewState;
@@ -31,68 +32,38 @@ export function MethodModelingView({
 
   const [isMethodModified, setIsMethodModified] = useState<boolean>(false);
 
-  const [isModelingInProgress, setIsModelingInProgress] =
-    useState<boolean>(false);
-
-  const [isProcessedByAutoModel, setIsProcessedByAutoModel] =
-    useState<boolean>(false);
-
   const modelingStatus = useMemo(
     () => getModelingStatus(modeledMethods, isMethodModified),
     [modeledMethods, isMethodModified],
   );
 
-  useEffect(() => {
-    const listener = (evt: MessageEvent) => {
-      if (evt.origin === window.origin) {
-        const msg: ToMethodModelingMessage = evt.data;
-        switch (msg.t) {
-          case "setMethodModelingPanelViewState":
-            setViewState(msg.viewState);
-            break;
-          case "setInModelingMode":
-            setInModelingMode(msg.inModelingMode);
-            break;
-          case "setMultipleModeledMethods":
-            setModeledMethods(msg.modeledMethods);
-            break;
-          case "setMethodModified":
-            setIsMethodModified(msg.isModified);
-            break;
-          case "setNoMethodSelected":
-            setMethod(undefined);
-            setModeledMethods([]);
-            setIsMethodModified(false);
-            setIsModelingInProgress(false);
-            setIsProcessedByAutoModel(false);
-            break;
-          case "setSelectedMethod":
-            setMethod(msg.method);
-            setModeledMethods(msg.modeledMethods);
-            setIsMethodModified(msg.isModified);
-            setIsModelingInProgress(msg.isInProgress);
-            setIsProcessedByAutoModel(msg.processedByAutoModel);
-            break;
-          case "setInProgress":
-            setIsModelingInProgress(msg.inProgress);
-            break;
-          case "setProcessedByAutoModel":
-            setIsProcessedByAutoModel(msg.processedByAutoModel);
-            break;
-          default:
-            assertNever(msg);
-        }
-      } else {
-        // sanitize origin
-        const origin = evt.origin.replace(/\n|\r/g, "");
-        console.error(`Invalid event origin ${origin}`);
-      }
-    };
-    window.addEventListener("message", listener);
-
-    return () => {
-      window.removeEventListener("message", listener);
-    };
+  useMessageFromExtension<ToMethodModelingMessage>((msg) => {
+    switch (msg.t) {
+      case "setMethodModelingPanelViewState":
+        setViewState(msg.viewState);
+        break;
+      case "setInModelingMode":
+        setInModelingMode(msg.inModelingMode);
+        break;
+      case "setMultipleModeledMethods":
+        setModeledMethods(msg.modeledMethods);
+        break;
+      case "setMethodModified":
+        setIsMethodModified(msg.isModified);
+        break;
+      case "setNoMethodSelected":
+        setMethod(undefined);
+        setModeledMethods([]);
+        setIsMethodModified(false);
+        break;
+      case "setSelectedMethod":
+        setMethod(msg.method);
+        setModeledMethods(msg.modeledMethods);
+        setIsMethodModified(msg.isModified);
+        break;
+      default:
+        assertNever(msg);
+    }
   }, []);
 
   if (!inModelingMode || !viewState?.language) {
@@ -125,8 +96,6 @@ export function MethodModelingView({
       modelingStatus={modelingStatus}
       method={method}
       modeledMethods={modeledMethods}
-      isModelingInProgress={isModelingInProgress}
-      isProcessedByAutoModel={isProcessedByAutoModel}
       onChange={onChange}
     />
   );
diff --git a/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx b/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx
index dff8c55c8e7..ed55c497d71 100644
--- a/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/MultipleModeledMethodsPanel.tsx
@@ -1,31 +1,26 @@
 import { useCallback, useEffect, useMemo, useRef, useState } from "react";
 import type { Method } from "../../model-editor/method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
-import { isModelPending } from "../../model-editor/modeled-method";
 import {
   canAddNewModeledMethod,
   canRemoveModeledMethod,
 } from "../../model-editor/shared/multiple-modeled-methods";
 import { styled } from "styled-components";
 import { MethodModelingInputs } from "./MethodModelingInputs";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import { Codicon } from "../common";
 import { validateModeledMethods } from "../../model-editor/shared/validation";
 import { ModeledMethodAlert } from "./ModeledMethodAlert";
 import type { QueryLanguage } from "../../common/query-language";
 import { createEmptyModeledMethod } from "../../model-editor/modeled-method-empty";
 import { sendTelemetry } from "../common/telemetry";
-import type { ModelingStatus } from "../../model-editor/shared/modeling-status";
 import type { ModelConfig } from "../../model-editor/languages";
+import { ActionButton } from "../common/ActionButton/ActionButton";
 
 export type MultipleModeledMethodsPanelProps = {
   language: QueryLanguage;
   modelConfig: ModelConfig;
   method: Method;
   modeledMethods: ModeledMethod[];
-  modelingStatus: ModelingStatus;
-  isModelingInProgress: boolean;
-  isProcessedByAutoModel: boolean;
   onChange: (methodSignature: string, modeledMethods: ModeledMethod[]) => void;
 };
 
@@ -66,9 +61,6 @@ export const MultipleModeledMethodsPanel = ({
   modelConfig,
   method,
   modeledMethods,
-  modelingStatus,
-  isModelingInProgress,
-  isProcessedByAutoModel,
   onChange,
 }: MultipleModeledMethodsPanelProps) => {
   const [selectedIndex, setSelectedIndex] = useState<number>(0);
@@ -163,12 +155,6 @@ export const MultipleModeledMethodsPanel = ({
           modelConfig={modelConfig}
           method={method}
           modeledMethod={modeledMethods[selectedIndex]}
-          modelPending={isModelPending(
-            modeledMethods[selectedIndex],
-            modelingStatus,
-            isProcessedByAutoModel,
-          )}
-          isModelingInProgress={isModelingInProgress}
           onChange={handleChange}
         />
       ) : (
@@ -177,32 +163,24 @@ export const MultipleModeledMethodsPanel = ({
           modelConfig={modelConfig}
           method={method}
           modeledMethod={undefined}
-          modelPending={isModelPending(
-            modeledMethods[selectedIndex],
-            modelingStatus,
-            isProcessedByAutoModel,
-          )}
-          isModelingInProgress={isModelingInProgress}
           onChange={handleChange}
         />
       )}
       <Footer>
         <PaginationActions>
-          <VSCodeButton
-            appearance="icon"
+          <ActionButton
             aria-label="Previous modeling"
             onClick={handlePreviousClick}
             disabled={modeledMethods.length < 2 || selectedIndex === 0}
           >
             <Codicon name="chevron-left" />
-          </VSCodeButton>
+          </ActionButton>
           {modeledMethods.length > 1 && (
             <div>
               {selectedIndex + 1}/{modeledMethods.length}
             </div>
           )}
-          <VSCodeButton
-            appearance="icon"
+          <ActionButton
             aria-label="Next modeling"
             onClick={handleNextClick}
             disabled={
@@ -211,25 +189,23 @@ export const MultipleModeledMethodsPanel = ({
             }
           >
             <Codicon name="chevron-right" />
-          </VSCodeButton>
+          </ActionButton>
         </PaginationActions>
         <ModificationActions>
-          <VSCodeButton
-            appearance="icon"
+          <ActionButton
             aria-label="Delete modeling"
             onClick={handleRemoveClick}
             disabled={!canRemoveModeledMethod(modeledMethods)}
           >
             <Codicon name="trash" />
-          </VSCodeButton>
-          <VSCodeButton
-            appearance="icon"
+          </ActionButton>
+          <ActionButton
             aria-label="Add modeling"
             onClick={handleAddClick}
             disabled={!canAddNewModeledMethod(modeledMethods)}
           >
             <Codicon name="add" />
-          </VSCodeButton>
+          </ActionButton>
         </ModificationActions>
       </Footer>
     </Container>
diff --git a/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModeling.spec.tsx b/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModeling.spec.tsx
index 3c3325d41e1..9a6496aea20 100644
--- a/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModeling.spec.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModeling.spec.tsx
@@ -13,8 +13,6 @@ describe(MethodModeling.name, () => {
   it("renders method modeling panel", () => {
     const method = createMethod();
     const modeledMethod = createSinkModeledMethod();
-    const isModelingInProgress = false;
-    const isProcessedByAutoModel = false;
     const onChange = jest.fn();
 
     render({
@@ -23,8 +21,6 @@ describe(MethodModeling.name, () => {
       modelingStatus: "saved",
       method,
       modeledMethods: [modeledMethod],
-      isModelingInProgress,
-      isProcessedByAutoModel,
       onChange,
     });
 
diff --git a/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModelingInputs.spec.tsx b/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModelingInputs.spec.tsx
index e5dc9bb5bde..0734a7064e3 100644
--- a/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModelingInputs.spec.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/__tests__/MethodModelingInputs.spec.tsx
@@ -18,8 +18,6 @@ describe(MethodModelingInputs.name, () => {
   const language = QueryLanguage.Java;
   const method = createMethod();
   const modeledMethod = createSinkModeledMethod();
-  const modelPending = false;
-  const isModelingInProgress = false;
   const modelConfig = defaultModelConfig;
   const onChange = jest.fn();
 
@@ -28,8 +26,6 @@ describe(MethodModelingInputs.name, () => {
       language,
       method,
       modeledMethod,
-      modelPending,
-      isModelingInProgress,
       modelConfig,
       onChange,
     });
@@ -56,8 +52,6 @@ describe(MethodModelingInputs.name, () => {
       language,
       method,
       modeledMethod,
-      modelPending,
-      isModelingInProgress,
       modelConfig,
       onChange,
     });
@@ -80,8 +74,6 @@ describe(MethodModelingInputs.name, () => {
       language,
       method,
       modeledMethod,
-      modelPending,
-      isModelingInProgress,
       modelConfig,
       onChange,
     });
@@ -96,8 +88,6 @@ describe(MethodModelingInputs.name, () => {
         language={language}
         method={method}
         modeledMethod={updatedModeledMethod}
-        modelPending={modelPending}
-        isModelingInProgress={isModelingInProgress}
         modelConfig={modelConfig}
         onChange={onChange}
       />,
@@ -121,32 +111,4 @@ describe(MethodModelingInputs.name, () => {
     expect(modelOutputDropdown).toHaveValue("ReturnValue");
     expect(modelKindDropdown).toHaveValue("local");
   });
-
-  it("sets in progress dropdowns when modeling is in progress", () => {
-    render({
-      language,
-      method,
-      modeledMethod,
-      modelPending,
-      isModelingInProgress: true,
-      modelConfig,
-      onChange,
-    });
-
-    // Check that all the labels are rendered.
-    expect(screen.getByText("Model Type")).toBeInTheDocument();
-    expect(screen.getByText("Input")).toBeInTheDocument();
-    expect(screen.getByText("Output")).toBeInTheDocument();
-    expect(screen.getByText("Kind")).toBeInTheDocument();
-
-    // Check that all the dropdowns are rendered.
-    const dropdowns = screen.getAllByRole("combobox");
-    expect(dropdowns.length).toBe(4);
-
-    // Check that all the dropdowns are disabled and indicate have the value "Thinking...".
-    dropdowns.forEach((dropdown) => {
-      expect(dropdown).toBeDisabled();
-      expect(dropdown).toHaveValue("Thinking...");
-    });
-  });
 });
diff --git a/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx b/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx
index 87c220c7c05..27372287bfc 100644
--- a/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx
+++ b/extensions/ql-vscode/src/view/method-modeling/__tests__/MultipleModeledMethodsPanel.spec.tsx
@@ -10,25 +10,18 @@ import { MultipleModeledMethodsPanel } from "../MultipleModeledMethodsPanel";
 import { userEvent } from "@testing-library/user-event";
 import type { ModeledMethod } from "../../../model-editor/modeled-method";
 import { QueryLanguage } from "../../../common/query-language";
-import type { ModelingStatus } from "../../../model-editor/shared/modeling-status";
 import { defaultModelConfig } from "../../../model-editor/languages";
 
 describe(MultipleModeledMethodsPanel.name, () => {
   const language = QueryLanguage.Java;
   const method = createMethod();
-  const isModelingInProgress = false;
-  const isProcessedByAutoModel = false;
-  const modelingStatus: ModelingStatus = "unmodeled";
   const onChange = jest.fn<void, [string, ModeledMethod[]]>();
   const modelConfig = defaultModelConfig;
 
   const baseProps = {
     language,
     method,
-    modelingStatus,
-    isModelingInProgress,
     modelConfig,
-    isProcessedByAutoModel,
     onChange,
   };
 
@@ -59,32 +52,26 @@ describe(MultipleModeledMethodsPanel.name, () => {
       ).toHaveValue("none");
     });
 
-    it("disables all pagination", () => {
+    it("disables all pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.queryByText("0/0")).not.toBeInTheDocument();
       expect(screen.queryByText("1/0")).not.toBeInTheDocument();
     });
 
-    it("cannot add or delete modeling", () => {
+    it("cannot add or delete modeling", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Delete modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Add modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const deleteButton = await screen.findByLabelText("Delete modeling");
+      const addButton = await screen.findByLabelText("Add modeling");
+
+      expect(deleteButton).toBeDisabled();
+      expect(addButton).toBeDisabled();
     });
   });
 
@@ -111,28 +98,22 @@ describe(MultipleModeledMethodsPanel.name, () => {
       ).toHaveValue("sink");
     });
 
-    it("disables all pagination", () => {
+    it("disables all pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.queryByText("1/1")).not.toBeInTheDocument();
     });
 
-    it("cannot delete modeling", () => {
+    it("cannot delete modeling", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Delete modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      const deleteButton = await screen.findByLabelText("Delete modeling");
+      expect(deleteButton).toBeDisabled();
     });
 
     it("can add modeling", async () => {
@@ -206,37 +187,26 @@ describe(MultipleModeledMethodsPanel.name, () => {
     it("disables the correct pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeEnabled();
     });
 
     it("can use the pagination", async () => {
       render();
 
-      await userEvent.click(screen.getByLabelText("Next modeling"));
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
 
+      await userEvent.click(nextButton);
       await waitFor(() => {
-        expect(
-          screen
-            .getByLabelText("Previous modeling")
-            .getElementsByTagName("input")[0],
-        ).toBeEnabled();
+        expect(prevButton).toBeEnabled();
       });
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.getByText("2/2")).toBeInTheDocument();
 
       expect(
@@ -452,34 +422,20 @@ describe(MultipleModeledMethodsPanel.name, () => {
     it("can use the pagination", async () => {
       render();
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeDisabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      const prevButton = await screen.findByLabelText("Previous modeling");
+      const nextButton = await screen.findByLabelText("Next modeling");
+      expect(prevButton).toBeDisabled();
+      expect(nextButton).toBeEnabled();
       expect(screen.getByText("1/3")).toBeInTheDocument();
 
-      await userEvent.click(screen.getByLabelText("Next modeling"));
+      await userEvent.click(nextButton);
 
       await waitFor(() => {
-        expect(
-          screen
-            .getByLabelText("Previous modeling")
-            .getElementsByTagName("input")[0],
-        ).toBeEnabled();
+        expect(prevButton).toBeEnabled();
       });
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeEnabled();
       expect(screen.getByText("2/3")).toBeInTheDocument();
 
       expect(
@@ -488,16 +444,10 @@ describe(MultipleModeledMethodsPanel.name, () => {
         }),
       ).toHaveValue("source");
 
-      await userEvent.click(screen.getByLabelText("Next modeling"));
+      await userEvent.click(nextButton);
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeDisabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeDisabled();
       expect(screen.getByText("3/3")).toBeInTheDocument();
 
       expect(
@@ -506,24 +456,14 @@ describe(MultipleModeledMethodsPanel.name, () => {
         }),
       ).toHaveValue("local");
 
-      await userEvent.click(screen.getByLabelText("Previous modeling"));
+      await userEvent.click(prevButton);
 
       await waitFor(() => {
-        expect(
-          screen
-            .getByLabelText("Next modeling")
-            .getElementsByTagName("input")[0],
-        ).toBeEnabled();
+        expect(nextButton).toBeEnabled();
       });
 
-      expect(
-        screen
-          .getByLabelText("Previous modeling")
-          .getElementsByTagName("input")[0],
-      ).toBeEnabled();
-      expect(
-        screen.getByLabelText("Next modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(prevButton).toBeEnabled();
+      expect(nextButton).toBeEnabled();
       expect(screen.getByText("2/3")).toBeInTheDocument();
 
       expect(
@@ -581,12 +521,11 @@ describe(MultipleModeledMethodsPanel.name, () => {
 
     const render = createRender(modeledMethods);
 
-    it("can add modeling", () => {
+    it("can add modeling", async () => {
       render();
 
-      expect(
-        screen.getByLabelText("Add modeling").getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      const addButton = await screen.findByLabelText("Add modeling");
+      expect(addButton).toBeEnabled();
     });
 
     it("can delete first modeling", async () => {
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlerts.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlerts.tsx
index 6f065286336..70169f0a9f4 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlerts.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlerts.tsx
@@ -1,4 +1,4 @@
-import { useCallback, useEffect, useMemo, useState } from "react";
+import { useCallback, useMemo, useState } from "react";
 import { styled } from "styled-components";
 import { ModelAlertsHeader } from "./ModelAlertsHeader";
 import type { ModelAlertsViewState } from "../../model-editor/shared/view-state";
@@ -18,6 +18,7 @@ import {
 } from "../../model-editor/shared/model-alerts-filter-sort";
 import type { ModelAlertsFilterSortState } from "../../model-editor/shared/model-alerts-filter-sort";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
 
 type Props = {
   initialViewState?: ModelAlertsViewState;
@@ -67,47 +68,33 @@ export function ModelAlerts({
     null,
   );
 
-  useEffect(() => {
-    const listener = (evt: MessageEvent) => {
-      if (evt.origin === window.origin) {
-        const msg: ToModelAlertsMessage = evt.data;
-        switch (msg.t) {
-          case "setModelAlertsViewState": {
-            setViewState(msg.viewState);
-            break;
-          }
-          case "setVariantAnalysis": {
-            setVariantAnalysis(msg.variantAnalysis);
-            break;
-          }
-          case "setRepoResults": {
-            setRepoResults((oldRepoResults) => {
-              const newRepoIds = msg.repoResults.map((r) => r.repositoryId);
-              return [
-                ...oldRepoResults.filter(
-                  (v) => !newRepoIds.includes(v.repositoryId),
-                ),
-                ...msg.repoResults,
-              ];
-            });
-            break;
-          }
-          case "revealModel": {
-            setRevealedModel(msg.modeledMethod);
-            break;
-          }
-        }
-      } else {
-        // sanitize origin
-        const origin = evt.origin.replace(/\n|\r/g, "");
-        console.error(`Invalid event origin ${origin}`);
+  useMessageFromExtension<ToModelAlertsMessage>((msg) => {
+    switch (msg.t) {
+      case "setModelAlertsViewState": {
+        setViewState(msg.viewState);
+        break;
       }
-    };
-    window.addEventListener("message", listener);
-
-    return () => {
-      window.removeEventListener("message", listener);
-    };
+      case "setVariantAnalysis": {
+        setVariantAnalysis(msg.variantAnalysis);
+        break;
+      }
+      case "setRepoResults": {
+        setRepoResults((oldRepoResults) => {
+          const newRepoIds = msg.repoResults.map((r) => r.repositoryId);
+          return [
+            ...oldRepoResults.filter(
+              (v) => !newRepoIds.includes(v.repositoryId),
+            ),
+            ...msg.repoResults,
+          ];
+        });
+        break;
+      }
+      case "revealModel": {
+        setRevealedModel(msg.modeledMethod);
+        break;
+      }
+    }
   }, []);
 
   const modelAlerts = useMemo(() => {
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx
index e99689634d2..da73126d2fc 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsActions.tsx
@@ -1,6 +1,6 @@
 import { styled } from "styled-components";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-analysis";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 type ModelAlertsActionsProps = {
   variantAnalysisStatus: VariantAnalysisStatus;
@@ -14,7 +14,7 @@ const Container = styled.div`
   gap: 1em;
 `;
 
-const Button = styled(VSCodeButton)`
+const Button = styled(VscodeButton)`
   white-space: nowrap;
 `;
 
@@ -25,12 +25,12 @@ export const ModelAlertsActions = ({
   return (
     <Container>
       {variantAnalysisStatus === VariantAnalysisStatus.InProgress && (
-        <Button appearance="secondary" onClick={onStopRunClick}>
+        <Button secondary onClick={onStopRunClick}>
           Stop evaluation
         </Button>
       )}
       {variantAnalysisStatus === VariantAnalysisStatus.Canceling && (
-        <Button appearance="secondary" disabled={true}>
+        <Button secondary disabled={true}>
           Stopping evaluation
         </Button>
       )}
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx
index 51ea31ee88d..d10757e3748 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsResults.tsx
@@ -1,7 +1,6 @@
 import { styled } from "styled-components";
 import type { ModelAlerts } from "../../model-editor/model-alerts/model-alerts";
 import { Codicon } from "../common";
-import { VSCodeBadge, VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 import { useCallback, useEffect, useRef, useState } from "react";
 import { formatDecimal } from "../../common/number";
 import AnalysisAlertResult from "../variant-analysis/AnalysisAlertResult";
@@ -10,6 +9,8 @@ import { ModelDetails } from "./ModelDetails";
 import { vscode } from "../vscode-api";
 import { createModeledMethodKey } from "../../model-editor/modeled-method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
+import { Link } from "../common/Link";
+import { Badge } from "../common/Badge";
 
 // This will ensure that these icons have a className which we can use in the TitleContainer
 const ExpandCollapseCodicon = styled(Codicon)``;
@@ -39,7 +40,7 @@ const ModelTypeText = styled.span`
   color: var(--vscode-descriptionForeground);
 `;
 
-const ViewLink = styled(VSCodeLink)`
+const ViewLink = styled(Link)`
   white-space: nowrap;
   padding: 0 0 0.25em 1em;
 `;
@@ -102,7 +103,7 @@ export const ModelAlertsResults = ({
         {!isExpanded && (
           <ExpandCollapseCodicon name="chevron-right" label="Expand" />
         )}
-        <VSCodeBadge>{formatDecimal(modelAlerts.alerts.length)}</VSCodeBadge>
+        <Badge>{formatDecimal(modelAlerts.alerts.length)}</Badge>
         <MethodName {...modelAlerts.model}></MethodName>
         <ModelTypeText>{modelAlerts.model.type}</ModelTypeText>
         <ViewLink
diff --git a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx
index 043355a5782..e5d4e9f2eb6 100644
--- a/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx
+++ b/extensions/ql-vscode/src/view/model-alerts/ModelAlertsSort.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { SortKey } from "../../model-editor/shared/model-alerts-filter-sort";
 import { Codicon } from "../common";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -26,12 +29,12 @@ export const ModelAlertsSort = ({ value, onChange, className }: Props) => {
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="sort-precedence" label="Sort..." slot="indicator" />
-      <VSCodeOption value={SortKey.Alphabetically}>Alphabetically</VSCodeOption>
-      <VSCodeOption value={SortKey.NumberOfResults}>
+      <VscodeOption value={SortKey.Alphabetically}>Alphabetically</VscodeOption>
+      <VscodeOption value={SortKey.NumberOfResults}>
         Number of results
-      </VSCodeOption>
+      </VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/model-editor/InProgressDropdown.tsx b/extensions/ql-vscode/src/view/model-editor/InProgressDropdown.tsx
deleted file mode 100644
index ef4b7aae061..00000000000
--- a/extensions/ql-vscode/src/view/model-editor/InProgressDropdown.tsx
+++ /dev/null
@@ -1,17 +0,0 @@
-import { styled } from "styled-components";
-import { Dropdown } from "../common/Dropdown";
-
-const StyledDropdown = styled(Dropdown)`
-  font-style: italic;
-`;
-
-export const InProgressDropdown = () => {
-  return (
-    <StyledDropdown
-      value="Thinking..."
-      options={[]}
-      disabled={true}
-      disabledPlaceholder="Thinking..."
-    />
-  );
-};
diff --git a/extensions/ql-vscode/src/view/model-editor/InputDropdown.tsx b/extensions/ql-vscode/src/view/model-editor/InputDropdown.tsx
index df4e3d50e48..59811fc0c18 100644
--- a/extensions/ql-vscode/src/view/model-editor/InputDropdown.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/InputDropdown.tsx
@@ -1,6 +1,4 @@
 import { styled } from "styled-components";
 import { Dropdown } from "../common/Dropdown";
 
-export const InputDropdown = styled(Dropdown)<{ $pending: boolean }>`
-  font-style: ${(props) => (props.$pending ? "italic" : "normal")};
-`;
+export const InputDropdown = styled(Dropdown)``;
diff --git a/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx b/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx
index 0b4db064280..f2f1065b4d9 100644
--- a/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/LibraryRow.tsx
@@ -7,15 +7,12 @@ import { calculateModeledPercentage } from "../../model-editor/shared/modeled-pe
 import { percentFormatter } from "./formatters";
 import { Codicon } from "../common";
 import { Mode } from "../../model-editor/shared/mode";
-import {
-  VSCodeButton,
-  VSCodeDivider,
-  VSCodeTag,
-} from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton, VscodeDivider } from "@vscode-elements/react-elements";
 import type { ModelEditorViewState } from "../../model-editor/shared/view-state";
 import type { AccessPathSuggestionOptions } from "../../model-editor/suggestions";
-import { getCandidates } from "../../model-editor/shared/auto-model-candidates";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
+import { Tag } from "../common/Tag";
+import { ActionButton } from "../common/ActionButton/ActionButton";
 
 const LibraryContainer = styled.div`
   background-color: var(--vscode-peekViewResult-background);
@@ -38,9 +35,9 @@ const TitleContainer = styled.button`
   cursor: pointer;
 `;
 
-const SectionDivider = styled(VSCodeDivider)`
-  padding-top: 0.3rem;
-  padding-bottom: 0.3rem;
+const SectionDivider = styled(VscodeDivider)`
+  margin-top: 0.3rem;
+  margin-bottom: 0.8rem;
 `;
 
 const NameContainer = styled.div`
@@ -75,8 +72,6 @@ export type LibraryRowProps = {
   modeledMethodsMap: Record<string, ModeledMethod[]>;
   modifiedSignatures: Set<string>;
   selectedSignatures: Set<string>;
-  inProgressMethods: Set<string>;
-  processedByAutoModelMethods: Set<string>;
   viewState: ModelEditorViewState;
   hideModeledMethods: boolean;
   revealedMethodSignature: string | null;
@@ -85,11 +80,6 @@ export type LibraryRowProps = {
   onChange: (methodSignature: string, modeledMethods: ModeledMethod[]) => void;
   onMethodClick: (methodSignature: string) => void;
   onSaveModelClick: (methodSignatures: string[]) => void;
-  onGenerateFromLlmClick: (
-    dependencyName: string,
-    methodSignatures: string[],
-  ) => void;
-  onStopGenerateFromLlmClick: (dependencyName: string) => void;
   onGenerateFromSourceClick: () => void;
   onModelDependencyClick: () => void;
 };
@@ -101,8 +91,6 @@ export const LibraryRow = ({
   modeledMethodsMap,
   modifiedSignatures,
   selectedSignatures,
-  inProgressMethods,
-  processedByAutoModelMethods,
   viewState,
   hideModeledMethods,
   revealedMethodSignature,
@@ -111,8 +99,6 @@ export const LibraryRow = ({
   onChange,
   onMethodClick,
   onSaveModelClick,
-  onGenerateFromLlmClick,
-  onStopGenerateFromLlmClick,
   onGenerateFromSourceClick,
   onModelDependencyClick,
 }: LibraryRowProps) => {
@@ -134,27 +120,6 @@ export const LibraryRow = ({
     }
   }, [methods, revealedMethodSignature]);
 
-  const handleModelWithAI = useCallback(
-    async (e: React.MouseEvent) => {
-      onGenerateFromLlmClick(
-        title,
-        methods.map((m) => m.signature),
-      );
-      e.stopPropagation();
-      e.preventDefault();
-    },
-    [title, methods, onGenerateFromLlmClick],
-  );
-
-  const handleStopModelWithAI = useCallback(
-    async (e: React.MouseEvent) => {
-      onStopGenerateFromLlmClick(title);
-      e.stopPropagation();
-      e.preventDefault();
-    },
-    [title, onStopGenerateFromLlmClick],
-  );
-
   const handleModelFromSource = useCallback(
     async (e: React.MouseEvent) => {
       onGenerateFromSourceClick();
@@ -186,21 +151,6 @@ export const LibraryRow = ({
     return methods.some((method) => modifiedSignatures.has(method.signature));
   }, [methods, modifiedSignatures]);
 
-  const canStopAutoModeling = useMemo(() => {
-    return methods.some((method) => inProgressMethods.has(method.signature));
-  }, [methods, inProgressMethods]);
-
-  const modelWithAIDisabled = useMemo(() => {
-    return (
-      getCandidates(
-        viewState.mode,
-        methods,
-        modeledMethodsMap,
-        processedByAutoModelMethods,
-      ).length === 0
-    );
-  }, [methods, modeledMethodsMap, processedByAutoModelMethods, viewState.mode]);
-
   return (
     <LibraryContainer>
       <TitleContainer onClick={toggleExpanded} aria-expanded={isExpanded}>
@@ -217,36 +167,20 @@ export const LibraryRow = ({
           <ModeledPercentage>
             {percentFormatter.format(modeledPercentage / 100)} modeled
           </ModeledPercentage>
-          {hasUnsavedChanges ? <VSCodeTag>UNSAVED</VSCodeTag> : null}
+          {hasUnsavedChanges ? <Tag>UNSAVED</Tag> : null}
         </NameContainer>
-        {viewState.showLlmButton && !canStopAutoModeling && (
-          <VSCodeButton
-            appearance="icon"
-            disabled={modelWithAIDisabled}
-            onClick={handleModelWithAI}
-          >
-            <Codicon name="lightbulb-autofix" label="Model with AI" />
-            &nbsp;Model with AI
-          </VSCodeButton>
-        )}
-        {viewState.showLlmButton && canStopAutoModeling && (
-          <VSCodeButton appearance="icon" onClick={handleStopModelWithAI}>
-            <Codicon name="debug-stop" label="Stop model with AI" />
-            &nbsp;Stop
-          </VSCodeButton>
-        )}
         {viewState.showGenerateButton &&
           viewState.mode === Mode.Application && (
-            <VSCodeButton appearance="icon" onClick={handleModelFromSource}>
+            <ActionButton onClick={handleModelFromSource}>
               <Codicon name="code" label="Model from source" />
               &nbsp;Model from source
-            </VSCodeButton>
+            </ActionButton>
           )}
         {viewState.mode === Mode.Application && (
-          <VSCodeButton appearance="icon" onClick={handleModelDependency}>
+          <ActionButton onClick={handleModelDependency}>
             <Codicon name="references" label="Model dependency" />
             &nbsp;Model dependency
-          </VSCodeButton>
+          </ActionButton>
         )}
       </TitleContainer>
       {isExpanded && (
@@ -257,8 +191,6 @@ export const LibraryRow = ({
             modeledMethodsMap={modeledMethodsMap}
             modifiedSignatures={modifiedSignatures}
             selectedSignatures={selectedSignatures}
-            inProgressMethods={inProgressMethods}
-            processedByAutoModelMethods={processedByAutoModelMethods}
             viewState={viewState}
             hideModeledMethods={hideModeledMethods}
             revealedMethodSignature={revealedMethodSignature}
@@ -269,9 +201,9 @@ export const LibraryRow = ({
           />
           <SectionDivider />
           <ButtonsContainer>
-            <VSCodeButton onClick={handleSave} disabled={!hasUnsavedChanges}>
+            <VscodeButton onClick={handleSave} disabled={!hasUnsavedChanges}>
               {selectedSignatures.size === 0 ? "Save" : "Save selected"}
-            </VSCodeButton>
+            </VscodeButton>
           </ButtonsContainer>
         </>
       )}
diff --git a/extensions/ql-vscode/src/view/model-editor/MethodClassifications.tsx b/extensions/ql-vscode/src/view/model-editor/MethodClassifications.tsx
index 8acfea16d93..59f9b5ea2f9 100644
--- a/extensions/ql-vscode/src/view/model-editor/MethodClassifications.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/MethodClassifications.tsx
@@ -1,8 +1,8 @@
 import { useMemo } from "react";
 import type { Method } from "../../model-editor/method";
 import { CallClassification } from "../../model-editor/method";
-import { VSCodeTag } from "@vscode/webview-ui-toolkit/react";
 import { styled } from "styled-components";
+import { Tag } from "../common/Tag";
 
 const ClassificationsContainer = styled.div`
   display: inline-flex;
@@ -10,7 +10,7 @@ const ClassificationsContainer = styled.div`
   gap: 0.5rem;
 `;
 
-const ClassificationTag = styled(VSCodeTag)`
+const ClassificationTag = styled(Tag)`
   font-size: 0.75em;
   white-space: nowrap;
 `;
diff --git a/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx b/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx
index b0b0c428d08..6e753c3532d 100644
--- a/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/MethodRow.tsx
@@ -1,9 +1,3 @@
-import {
-  VSCodeBadge,
-  VSCodeButton,
-  VSCodeLink,
-  VSCodeProgressRing,
-} from "@vscode/webview-ui-toolkit/react";
 import {
   forwardRef,
   useCallback,
@@ -14,16 +8,16 @@ import {
 } from "react";
 import { styled } from "styled-components";
 import { vscode } from "../vscode-api";
+import { Link } from "../common/Link";
+import { ActionButton } from "../common/ActionButton/ActionButton";
 
 import type { Method } from "../../model-editor/method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
-import { isModelPending } from "../../model-editor/modeled-method";
 import { ModelKindDropdown } from "./ModelKindDropdown";
 import { Mode } from "../../model-editor/shared/mode";
 import { MethodClassifications } from "./MethodClassifications";
 import { getModelingStatus } from "../../model-editor/shared/modeling-status";
 import { ModelingStatusIndicator } from "./ModelingStatusIndicator";
-import { InProgressDropdown } from "./InProgressDropdown";
 import { MethodName } from "./MethodName";
 import { ModelTypeDropdown } from "./ModelTypeDropdown";
 import { ModelInputDropdown } from "./ModelInputDropdown";
@@ -41,6 +35,7 @@ import { ModelOutputSuggestBox } from "./ModelOutputSuggestBox";
 import { getModelsAsDataLanguage } from "../../model-editor/languages";
 import { ModelAlertsIndicator } from "./ModelAlertsIndicator";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
+import { Badge } from "../common/Badge";
 
 const ApiOrMethodRow = styled.div`
   min-height: calc(var(--input-height) * 1px);
@@ -58,21 +53,16 @@ const ModelButtonsContainer = styled.div`
   gap: 1em;
 `;
 
-const UsagesButton = styled(VSCodeBadge)`
+const UsagesButton = styled(Badge)`
   cursor: pointer;
+  display: table;
 `;
 
-const ViewLink = styled(VSCodeLink)`
+const ViewLink = styled(Link)`
   white-space: nowrap;
 `;
 
-const ProgressRing = styled(VSCodeProgressRing)`
-  width: 16px;
-  height: 16px;
-  margin-left: auto;
-`;
-
-const CodiconRow = styled(VSCodeButton)`
+const CodiconRow = styled(ActionButton)`
   min-height: calc(var(--input-height) * 1px);
   align-items: center;
 `;
@@ -83,8 +73,6 @@ export type MethodRowProps = {
   modeledMethods: ModeledMethod[];
   methodIsUnsaved: boolean;
   methodIsSelected: boolean;
-  modelingInProgress: boolean;
-  processedByAutoModel: boolean;
   viewState: ModelEditorViewState;
   revealedMethodSignature: string | null;
   inputAccessPathSuggestions?: AccessPathOption[];
@@ -116,13 +104,12 @@ export const MethodRow = (props: MethodRowProps) => {
 };
 
 const ModelableMethodRow = forwardRef<HTMLElement | undefined, MethodRowProps>(
-  (props, ref) => {
+  (props: MethodRowProps, ref) => {
     const {
       method,
       modeledMethods: modeledMethodsProp,
       methodIsUnsaved,
       methodIsSelected,
-      processedByAutoModel,
       viewState,
       revealedMethodSignature,
       inputAccessPathSuggestions,
@@ -269,140 +256,103 @@ const ModelableMethodRow = forwardRef<HTMLElement | undefined, MethodRowProps>(
             >
               View
             </ViewLink>
-            {props.modelingInProgress && <ProgressRing />}
           </ApiOrMethodRow>
         </DataGridCell>
-        {props.modelingInProgress && (
-          <>
-            <DataGridCell>
-              <InProgressDropdown />
-            </DataGridCell>
-            <DataGridCell>
-              <InProgressDropdown />
-            </DataGridCell>
-            <DataGridCell>
-              <InProgressDropdown />
-            </DataGridCell>
-            <DataGridCell>
-              <InProgressDropdown />
-            </DataGridCell>
-            <DataGridCell>
-              <CodiconRow appearance="icon" disabled={true}>
-                <Codicon name="add" label="Add new model" />
-              </CodiconRow>
-            </DataGridCell>
-          </>
-        )}
-        {!props.modelingInProgress && (
-          <>
-            {shownModeledMethods.map((modeledMethod, index) => {
-              const modelPending = isModelPending(
-                modeledMethod,
-                modelingStatus,
-                processedByAutoModel,
-              );
-
-              return (
-                <DataGridRow key={index} focused={focusedIndex === index}>
-                  <DataGridCell>
-                    <ModelTypeDropdown
-                      language={viewState.language}
-                      modelConfig={viewState.modelConfig}
-                      method={method}
-                      modeledMethod={modeledMethod}
-                      modelPending={modelPending}
-                      onChange={modeledMethodChangedHandlers[index]}
-                    />
-                  </DataGridCell>
-                  <DataGridCell>
-                    {inputAccessPathSuggestions === undefined ? (
-                      <ModelInputDropdown
-                        language={viewState.language}
-                        method={method}
-                        modeledMethod={modeledMethod}
-                        modelPending={modelPending}
-                        onChange={modeledMethodChangedHandlers[index]}
-                      />
-                    ) : (
-                      <ModelInputSuggestBox
-                        modeledMethod={modeledMethod}
-                        suggestions={inputAccessPathSuggestions}
-                        typePathSuggestions={outputAccessPathSuggestions ?? []}
-                        onChange={modeledMethodChangedHandlers[index]}
-                      />
-                    )}
-                  </DataGridCell>
-                  <DataGridCell>
-                    {outputAccessPathSuggestions === undefined ? (
-                      <ModelOutputDropdown
-                        language={viewState.language}
-                        method={method}
-                        modeledMethod={modeledMethod}
-                        modelPending={modelPending}
-                        onChange={modeledMethodChangedHandlers[index]}
-                      />
-                    ) : (
-                      <ModelOutputSuggestBox
-                        modeledMethod={modeledMethod}
-                        suggestions={outputAccessPathSuggestions}
-                        onChange={modeledMethodChangedHandlers[index]}
-                      />
-                    )}
-                  </DataGridCell>
-                  <DataGridCell>
-                    <ModelKindDropdown
-                      language={viewState.language}
-                      modeledMethod={modeledMethod}
-                      modelPending={modelPending}
-                      onChange={modeledMethodChangedHandlers[index]}
-                    />
-                  </DataGridCell>
-                  <DataGridCell>
-                    <ModelButtonsContainer>
-                      <ModelAlertsIndicator
-                        viewState={viewState}
-                        modeledMethod={modeledMethod}
-                        evaluationRun={evaluationRun}
-                      ></ModelAlertsIndicator>
-                      {index === 0 ? (
-                        <CodiconRow
-                          appearance="icon"
-                          aria-label="Add new model"
-                          onClick={(event: React.MouseEvent) => {
-                            event.stopPropagation();
-                            handleAddModelClick();
-                          }}
-                          disabled={addModelButtonDisabled}
-                        >
-                          <Codicon name="add" />
-                        </CodiconRow>
-                      ) : (
-                        <CodiconRow
-                          appearance="icon"
-                          aria-label="Remove model"
-                          onClick={(event: React.MouseEvent) => {
-                            event.stopPropagation();
-                            removeModelClickedHandlers[index]();
-                          }}
-                        >
-                          <Codicon name="trash" />
-                        </CodiconRow>
-                      )}
-                    </ModelButtonsContainer>
-                  </DataGridCell>
-                </DataGridRow>
-              );
-            })}
-            {validationErrors.map((error, index) => (
-              <DataGridCell gridColumn="span 5" key={index}>
-                <ModeledMethodAlert
-                  error={error}
-                  setSelectedIndex={setFocusedIndex}
+
+        {shownModeledMethods.map((modeledMethod, index) => {
+          return (
+            <DataGridRow key={index} focused={focusedIndex === index}>
+              <DataGridCell>
+                <ModelTypeDropdown
+                  language={viewState.language}
+                  modelConfig={viewState.modelConfig}
+                  method={method}
+                  modeledMethod={modeledMethod}
+                  onChange={modeledMethodChangedHandlers[index]}
                 />
               </DataGridCell>
-            ))}
-          </>
-        )}
+              <DataGridCell>
+                {inputAccessPathSuggestions === undefined ? (
+                  <ModelInputDropdown
+                    language={viewState.language}
+                    method={method}
+                    modeledMethod={modeledMethod}
+                    onChange={modeledMethodChangedHandlers[index]}
+                  />
+                ) : (
+                  <ModelInputSuggestBox
+                    modeledMethod={modeledMethod}
+                    suggestions={inputAccessPathSuggestions}
+                    typePathSuggestions={outputAccessPathSuggestions ?? []}
+                    onChange={modeledMethodChangedHandlers[index]}
+                  />
+                )}
+              </DataGridCell>
+              <DataGridCell>
+                {outputAccessPathSuggestions === undefined ? (
+                  <ModelOutputDropdown
+                    language={viewState.language}
+                    method={method}
+                    modeledMethod={modeledMethod}
+                    onChange={modeledMethodChangedHandlers[index]}
+                  />
+                ) : (
+                  <ModelOutputSuggestBox
+                    modeledMethod={modeledMethod}
+                    suggestions={outputAccessPathSuggestions}
+                    onChange={modeledMethodChangedHandlers[index]}
+                  />
+                )}
+              </DataGridCell>
+              <DataGridCell>
+                <ModelKindDropdown
+                  language={viewState.language}
+                  modeledMethod={modeledMethod}
+                  onChange={modeledMethodChangedHandlers[index]}
+                />
+              </DataGridCell>
+              <DataGridCell>
+                <ModelButtonsContainer>
+                  <ModelAlertsIndicator
+                    viewState={viewState}
+                    modeledMethod={modeledMethod}
+                    evaluationRun={evaluationRun}
+                  ></ModelAlertsIndicator>
+                  {index === 0 ? (
+                    <CodiconRow
+                      aria-label="Add new model"
+                      onClick={(event: React.MouseEvent) => {
+                        event.stopPropagation();
+                        handleAddModelClick();
+                      }}
+                      disabled={addModelButtonDisabled}
+                    >
+                      <Codicon name="add" />
+                    </CodiconRow>
+                  ) : (
+                    <CodiconRow
+                      aria-label="Remove model"
+                      onClick={(event: React.MouseEvent) => {
+                        event.stopPropagation();
+                        removeModelClickedHandlers[index]();
+                      }}
+                    >
+                      <Codicon name="trash" />
+                    </CodiconRow>
+                  )}
+                </ModelButtonsContainer>
+              </DataGridCell>
+            </DataGridRow>
+          );
+        })}
+        {validationErrors.map((error, index) => (
+          <DataGridCell gridColumn="span 5" key={index}>
+            <ModeledMethodAlert
+              error={error}
+              setSelectedIndex={setFocusedIndex}
+            />
+          </DataGridCell>
+        ))}
       </DataGridRow>
     );
   },
@@ -412,7 +362,7 @@ ModelableMethodRow.displayName = "ModelableMethodRow";
 const UnmodelableMethodRow = forwardRef<
   HTMLElement | undefined,
   MethodRowProps
->((props, ref) => {
+>((props: MethodRowProps, ref) => {
   const { method, viewState, revealedMethodSignature } = props;
 
   const jumpToMethod = useCallback(
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx b/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx
index 117d18903ca..a99bc815f1e 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelAlertsIndicator.tsx
@@ -2,10 +2,10 @@ import { styled } from "styled-components";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
 import type { ModelEditorViewState } from "../../model-editor/shared/view-state";
-import { VSCodeBadge } from "@vscode/webview-ui-toolkit/react";
 import { vscode } from "../vscode-api";
+import { Badge } from "../common/Badge";
 
-const ModelAlertsButton = styled(VSCodeBadge)`
+const ModelAlertsButton = styled(Badge)`
   cursor: pointer;
 `;
 
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx b/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx
index 6b478d84272..344a0d32d98 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelEditor.tsx
@@ -1,10 +1,6 @@
 import { useCallback, useEffect, useMemo, useState } from "react";
 import type { ToModelEditorMessage } from "../../common/interface-types";
-import {
-  VSCodeButton,
-  VSCodeCheckbox,
-  VSCodeTag,
-} from "@vscode/webview-ui-toolkit/react";
+import { VscodeButton, VscodeCheckbox } from "@vscode-elements/react-elements";
 import { styled } from "styled-components";
 import type { Method } from "../../model-editor/method";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
@@ -21,6 +17,8 @@ import { INITIAL_HIDE_MODELED_METHODS_VALUE } from "../../model-editor/shared/hi
 import type { AccessPathSuggestionOptions } from "../../model-editor/suggestions";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
 import { ModelEvaluation } from "./ModelEvaluation";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
+import { Tag } from "../common/Tag";
 
 const LoadingContainer = styled.div`
   text-align: center;
@@ -102,12 +100,6 @@ export function ModelEditor({
     new Set(),
   );
 
-  const [inProgressMethods, setInProgressMethods] = useState<Set<string>>(
-    new Set(),
-  );
-  const [processedByAutoModelMethods, setProcessedByAutoModelMethods] =
-    useState<Set<string>>(new Set());
-
   const [hideModeledMethods, setHideModeledMethods] = useState(
     initialHideModeledMethods,
   );
@@ -135,55 +127,33 @@ export function ModelEditor({
     AccessPathSuggestionOptions | undefined
   >(undefined);
 
-  useEffect(() => {
-    const listener = (evt: MessageEvent) => {
-      if (evt.origin === window.origin) {
-        const msg: ToModelEditorMessage = evt.data;
-        switch (msg.t) {
-          case "setModelEditorViewState":
-            setViewState(msg.viewState);
-            break;
-          case "setMethods":
-            setMethods(msg.methods);
-            break;
-          case "setModeledAndModifiedMethods":
-            setModeledMethods(msg.methods);
-            setModifiedSignatures(new Set(msg.modifiedMethodSignatures));
-            break;
-          case "setModifiedMethods":
-            setModifiedSignatures(new Set(msg.methodSignatures));
-            break;
-          case "setInProgressMethods": {
-            setInProgressMethods(new Set(msg.methods));
-            break;
-          }
-          case "setProcessedByAutoModelMethods": {
-            setProcessedByAutoModelMethods(new Set(msg.methods));
-            break;
-          }
-          case "revealMethod":
-            setRevealedMethodSignature(msg.methodSignature);
-            break;
-          case "setAccessPathSuggestions":
-            setAccessPathSuggestions(msg.accessPathSuggestions);
-            break;
-          case "setModelEvaluationRun":
-            setEvaluationRun(msg.run);
-            break;
-          default:
-            assertNever(msg);
-        }
-      } else {
-        // sanitize origin
-        const origin = evt.origin.replace(/\n|\r/g, "");
-        console.error(`Invalid event origin ${origin}`);
-      }
-    };
-    window.addEventListener("message", listener);
-
-    return () => {
-      window.removeEventListener("message", listener);
-    };
+  useMessageFromExtension<ToModelEditorMessage>((msg) => {
+    switch (msg.t) {
+      case "setModelEditorViewState":
+        setViewState(msg.viewState);
+        break;
+      case "setMethods":
+        setMethods(msg.methods);
+        break;
+      case "setModeledAndModifiedMethods":
+        setModeledMethods(msg.methods);
+        setModifiedSignatures(new Set(msg.modifiedMethodSignatures));
+        break;
+      case "setModifiedMethods":
+        setModifiedSignatures(new Set(msg.methodSignatures));
+        break;
+      case "revealMethod":
+        setRevealedMethodSignature(msg.methodSignature);
+        break;
+      case "setAccessPathSuggestions":
+        setAccessPathSuggestions(msg.accessPathSuggestions);
+        break;
+      case "setModelEvaluationRun":
+        setEvaluationRun(msg.run);
+        break;
+      default:
+        assertNever(msg);
+    }
   }, []);
 
   useEffect(() => {
@@ -294,24 +264,6 @@ export function ModelEditor({
     });
   }, []);
 
-  const onGenerateFromLlmClick = useCallback(
-    (packageName: string, methodSignatures: string[]) => {
-      vscode.postMessage({
-        t: "generateMethodsFromLlm",
-        packageName,
-        methodSignatures,
-      });
-    },
-    [],
-  );
-
-  const onStopGenerateFromLlmClick = useCallback((packageName: string) => {
-    vscode.postMessage({
-      t: "stopGeneratingMethodsFromLlm",
-      packageName,
-    });
-  }, []);
-
   const onOpenDatabaseClick = useCallback(() => {
     vscode.postMessage({
       t: "openDatabase",
@@ -350,9 +302,9 @@ export function ModelEditor({
             <ViewTitle>
               {getLanguageDisplayName(viewState.extensionPack.language)}
             </ViewTitle>
-            <VSCodeTag>
+            <Tag>
               {percentFormatter.format(modeledPercentage / 100)} modeled
-            </VSCodeTag>
+            </Tag>
           </HeaderRow>
           <HeaderRow>
             <>{viewState.extensionPack.name}</>
@@ -379,27 +331,27 @@ export function ModelEditor({
           </HeaderRow>
           <HeaderRow>
             <ButtonsContainer>
-              <VSCodeButton
+              <VscodeButton
                 onClick={onSaveAllClick}
                 disabled={modifiedSignatures.size === 0}
               >
                 {selectedSignatures.size === 0 ? "Save all" : "Save selected"}
-              </VSCodeButton>
-              <VSCodeButton
-                appearance="secondary"
+              </VscodeButton>
+              <VscodeButton
+                secondary
                 onClick={onDeselectAllClick}
                 disabled={selectedSignatures.size === 0}
               >
                 Deselect all
-              </VSCodeButton>
-              <VSCodeButton appearance="secondary" onClick={onRefreshClick}>
+              </VscodeButton>
+              <VscodeButton secondary onClick={onRefreshClick}>
                 Refresh
-              </VSCodeButton>
+              </VscodeButton>
               {viewState.showGenerateButton &&
                 viewState.mode === Mode.Framework && (
-                  <VSCodeButton onClick={onGenerateFromSourceClick}>
+                  <VscodeButton onClick={onGenerateFromSourceClick}>
                     Generate
-                  </VSCodeButton>
+                  </VscodeButton>
                 )}
               <ModelEvaluation
                 viewState={viewState}
@@ -415,12 +367,12 @@ export function ModelEditor({
         </HeaderColumn>
         <HeaderSpacer />
         <HeaderColumn>
-          <VSCodeCheckbox
+          <VscodeCheckbox
             checked={hideModeledMethods}
             onChange={onHideModeledMethods}
           >
             Hide modeled methods
-          </VSCodeCheckbox>
+          </VscodeCheckbox>
         </HeaderColumn>
       </HeaderContainer>
 
@@ -430,8 +382,6 @@ export function ModelEditor({
           modeledMethodsMap={modeledMethods}
           modifiedSignatures={modifiedSignatures}
           selectedSignatures={selectedSignatures}
-          inProgressMethods={inProgressMethods}
-          processedByAutoModelMethods={processedByAutoModelMethods}
           viewState={viewState}
           hideModeledMethods={hideModeledMethods}
           revealedMethodSignature={revealedMethodSignature}
@@ -440,8 +390,6 @@ export function ModelEditor({
           onChange={onChange}
           onMethodClick={onMethodClick}
           onSaveModelClick={onSaveModelClick}
-          onGenerateFromLlmClick={onGenerateFromLlmClick}
-          onStopGenerateFromLlmClick={onStopGenerateFromLlmClick}
           onGenerateFromSourceClick={onGenerateFromSourceClick}
           onModelDependencyClick={onModelDependencyClick}
         />
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx b/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx
index 3994caddf82..523e8fd32c8 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelEditorProgressRing.tsx
@@ -1,7 +1,7 @@
-import { VSCodeProgressRing } from "@vscode/webview-ui-toolkit/react";
+import { VscodeProgressRing } from "@vscode-elements/react-elements";
 import { styled } from "styled-components";
 
-export const ModelEditorProgressRing = styled(VSCodeProgressRing)`
+export const ModelEditorProgressRing = styled(VscodeProgressRing)`
   width: 16px;
   height: 16px;
   margin-right: 5px;
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx b/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx
index de87fc663eb..ba0266c083f 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelEvaluation.tsx
@@ -1,11 +1,12 @@
 import { styled } from "styled-components";
-import { VSCodeButton, VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 import type { ModeledMethod } from "../../model-editor/modeled-method";
 import type { ModelEditorViewState } from "../../model-editor/shared/view-state";
 import type { ModelEvaluationRunState } from "../../model-editor/shared/model-evaluation-run-state";
 import { modelEvaluationRunIsRunning } from "../../model-editor/shared/model-evaluation-run-state";
 import { ModelEditorProgressRing } from "./ModelEditorProgressRing";
 import { LinkIconButton } from "../common/LinkIconButton";
+import { Link } from "../common/Link";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 export type Props = {
   viewState: ModelEditorViewState;
@@ -17,7 +18,7 @@ export type Props = {
   evaluationRun: ModelEvaluationRunState | undefined;
 };
 
-const RunLink = styled(VSCodeLink)`
+const RunLink = styled(Link)`
   display: flex;
   align-items: center;
 `;
@@ -52,19 +53,19 @@ export const ModelEvaluation = ({
   return (
     <>
       {shouldShowEvaluateButton && (
-        <VSCodeButton
+        <VscodeButton
           onClick={onStartEvaluation}
-          appearance="secondary"
+          secondary
           disabled={!customModelsExist || unsavedChanges}
         >
           Evaluate
-        </VSCodeButton>
+        </VscodeButton>
       )}
       {shouldShowStopButton && (
-        <VSCodeButton onClick={onStopEvaluation} appearance="secondary">
+        <VscodeButton onClick={onStopEvaluation} secondary>
           <ModelEditorProgressRing />
           Stop evaluation
-        </VSCodeButton>
+        </VscodeButton>
       )}
       {shouldShowEvaluationRunLink && (
         <RunLink>
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelInputDropdown.tsx b/extensions/ql-vscode/src/view/model-editor/ModelInputDropdown.tsx
index a4604582438..a02d6d8346d 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelInputDropdown.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelInputDropdown.tsx
@@ -15,7 +15,6 @@ type Props = {
   language: QueryLanguage;
   method: Method;
   modeledMethod: ModeledMethod | undefined;
-  modelPending: boolean;
   onChange: (modeledMethod: ModeledMethod) => void;
 };
 
@@ -23,7 +22,6 @@ export const ModelInputDropdown = ({
   language,
   method,
   modeledMethod,
-  modelPending,
   onChange,
 }: Props): React.JSX.Element => {
   const options = useMemo(() => {
@@ -80,7 +78,6 @@ export const ModelInputDropdown = ({
       value={value}
       options={options}
       disabled={!enabled}
-      $pending={modelPending}
       onChange={handleChange}
       aria-label="Input"
     />
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelKindDropdown.tsx b/extensions/ql-vscode/src/view/model-editor/ModelKindDropdown.tsx
index 563463ec436..3f9ef6d3e7d 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelKindDropdown.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelKindDropdown.tsx
@@ -15,14 +15,12 @@ import { InputDropdown } from "./InputDropdown";
 type Props = {
   language: QueryLanguage;
   modeledMethod: ModeledMethod | undefined;
-  modelPending: boolean;
   onChange: (modeledMethod: ModeledMethod) => void;
 };
 
 export const ModelKindDropdown = ({
   language,
   modeledMethod,
-  modelPending,
   onChange,
 }: Props) => {
   const predicate = useMemo(() => {
@@ -92,7 +90,6 @@ export const ModelKindDropdown = ({
       value={value}
       options={options}
       disabled={disabled}
-      $pending={modelPending}
       onChange={handleChange}
       aria-label="Kind"
     />
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelOutputDropdown.tsx b/extensions/ql-vscode/src/view/model-editor/ModelOutputDropdown.tsx
index a04f82c582f..22a3ea8afd6 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelOutputDropdown.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelOutputDropdown.tsx
@@ -15,7 +15,6 @@ type Props = {
   language: QueryLanguage;
   method: Method;
   modeledMethod: ModeledMethod | undefined;
-  modelPending: boolean;
   onChange: (modeledMethod: ModeledMethod) => void;
 };
 
@@ -23,7 +22,6 @@ export const ModelOutputDropdown = ({
   language,
   method,
   modeledMethod,
-  modelPending,
   onChange,
 }: Props): React.JSX.Element => {
   const options = useMemo(() => {
@@ -81,7 +79,6 @@ export const ModelOutputDropdown = ({
       value={value}
       options={options}
       disabled={!enabled}
-      $pending={modelPending}
       onChange={handleChange}
       aria-label="Output"
     />
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelTypeDropdown.tsx b/extensions/ql-vscode/src/view/model-editor/ModelTypeDropdown.tsx
index 7ea0d83ef90..369851d98fd 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelTypeDropdown.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelTypeDropdown.tsx
@@ -22,7 +22,6 @@ type Props = {
   modelConfig: ModelConfig;
   method: Method;
   modeledMethod: ModeledMethod | undefined;
-  modelPending: boolean;
   onChange: (modeledMethod: ModeledMethod) => void;
 };
 
@@ -41,7 +40,6 @@ export const ModelTypeDropdown = ({
   modelConfig,
   method,
   modeledMethod,
-  modelPending,
   onChange,
 }: Props): React.JSX.Element => {
   const options = useMemo(() => {
@@ -126,7 +124,6 @@ export const ModelTypeDropdown = ({
     <InputDropdown
       value={modeledMethod?.type ?? "none"}
       options={options}
-      $pending={modelPending}
       onChange={handleChange}
       aria-label="Model type"
     />
diff --git a/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx b/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx
index d52ab1306bf..69f9a0829b9 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModelTypeTextbox.tsx
@@ -4,8 +4,8 @@ import type {
   ModeledMethod,
   TypeModeledMethod,
 } from "../../model-editor/modeled-method";
-import { VSCodeTextField } from "@vscode/webview-ui-toolkit/react";
 import { useDebounceCallback } from "../common/useDebounceCallback";
+import { VscodeTextfield } from "@vscode-elements/react-elements";
 
 type Props = {
   modeledMethod: TypeModeledMethod;
@@ -53,7 +53,7 @@ export const ModelTypeTextbox = ({
   );
 
   return (
-    <VSCodeTextField
+    <VscodeTextfield
       value={value}
       onInput={handleChange}
       onClick={stopClickPropagation}
diff --git a/extensions/ql-vscode/src/view/model-editor/ModeledMethodDataGrid.tsx b/extensions/ql-vscode/src/view/model-editor/ModeledMethodDataGrid.tsx
index 44cb7ec2e46..1e94b04283a 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModeledMethodDataGrid.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModeledMethodDataGrid.tsx
@@ -18,8 +18,6 @@ export type ModeledMethodDataGridProps = {
   modeledMethodsMap: Record<string, ModeledMethod[]>;
   modifiedSignatures: Set<string>;
   selectedSignatures: Set<string>;
-  inProgressMethods: Set<string>;
-  processedByAutoModelMethods: Set<string>;
   viewState: ModelEditorViewState;
   hideModeledMethods: boolean;
   revealedMethodSignature: string | null;
@@ -34,8 +32,6 @@ export const ModeledMethodDataGrid = ({
   modeledMethodsMap,
   modifiedSignatures,
   selectedSignatures,
-  inProgressMethods,
-  processedByAutoModelMethods,
   viewState,
   hideModeledMethods,
   revealedMethodSignature,
@@ -96,10 +92,6 @@ export const ModeledMethodDataGrid = ({
                 modeledMethods={modeledMethods}
                 methodIsUnsaved={modifiedSignatures.has(method.signature)}
                 methodIsSelected={selectedSignatures.has(method.signature)}
-                modelingInProgress={inProgressMethods.has(method.signature)}
-                processedByAutoModel={processedByAutoModelMethods.has(
-                  method.signature,
-                )}
                 viewState={viewState}
                 revealedMethodSignature={revealedMethodSignature}
                 inputAccessPathSuggestions={inputAccessPathSuggestions}
diff --git a/extensions/ql-vscode/src/view/model-editor/ModeledMethodsList.tsx b/extensions/ql-vscode/src/view/model-editor/ModeledMethodsList.tsx
index b6370ffc424..7d0a6c1b597 100644
--- a/extensions/ql-vscode/src/view/model-editor/ModeledMethodsList.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/ModeledMethodsList.tsx
@@ -16,8 +16,6 @@ export type ModeledMethodsListProps = {
   modeledMethodsMap: Record<string, ModeledMethod[]>;
   modifiedSignatures: Set<string>;
   selectedSignatures: Set<string>;
-  inProgressMethods: Set<string>;
-  processedByAutoModelMethods: Set<string>;
   revealedMethodSignature: string | null;
   accessPathSuggestions?: AccessPathSuggestionOptions;
   evaluationRun: ModelEvaluationRunState | undefined;
@@ -26,11 +24,6 @@ export type ModeledMethodsListProps = {
   onChange: (methodSignature: string, modeledMethods: ModeledMethod[]) => void;
   onMethodClick: (methodSignature: string) => void;
   onSaveModelClick: (methodSignatures: string[]) => void;
-  onGenerateFromLlmClick: (
-    packageName: string,
-    methodSignatures: string[],
-  ) => void;
-  onStopGenerateFromLlmClick: (packageName: string) => void;
   onGenerateFromSourceClick: () => void;
   onModelDependencyClick: () => void;
 };
@@ -44,8 +37,6 @@ export const ModeledMethodsList = ({
   modeledMethodsMap,
   modifiedSignatures,
   selectedSignatures,
-  inProgressMethods,
-  processedByAutoModelMethods,
   viewState,
   hideModeledMethods,
   revealedMethodSignature,
@@ -54,8 +45,6 @@ export const ModeledMethodsList = ({
   onChange,
   onMethodClick,
   onSaveModelClick,
-  onGenerateFromLlmClick,
-  onStopGenerateFromLlmClick,
   onGenerateFromSourceClick,
   onModelDependencyClick,
 }: ModeledMethodsListProps) => {
@@ -95,8 +84,6 @@ export const ModeledMethodsList = ({
           modeledMethodsMap={modeledMethodsMap}
           modifiedSignatures={modifiedSignatures}
           selectedSignatures={selectedSignatures}
-          inProgressMethods={inProgressMethods}
-          processedByAutoModelMethods={processedByAutoModelMethods}
           viewState={viewState}
           hideModeledMethods={hideModeledMethods}
           revealedMethodSignature={revealedMethodSignature}
@@ -105,8 +92,6 @@ export const ModeledMethodsList = ({
           onChange={onChange}
           onMethodClick={onMethodClick}
           onSaveModelClick={onSaveModelClick}
-          onGenerateFromLlmClick={onGenerateFromLlmClick}
-          onStopGenerateFromLlmClick={onStopGenerateFromLlmClick}
           onGenerateFromSourceClick={onGenerateFromSourceClick}
           onModelDependencyClick={onModelDependencyClick}
         />
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/LibraryRow.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/LibraryRow.spec.tsx
index 19caa8fd826..661c9f214c5 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/LibraryRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/LibraryRow.spec.tsx
@@ -10,8 +10,6 @@ describe(LibraryRow.name, () => {
   const onChange = jest.fn();
   const onMethodClick = jest.fn();
   const onSaveModelClick = jest.fn();
-  const onGenerateFromLlmClick = jest.fn();
-  const onStopGenerateFromLlmClick = jest.fn();
   const onModelDependencyClick = jest.fn();
 
   const viewState = createMockModelEditorViewState();
@@ -35,8 +33,6 @@ describe(LibraryRow.name, () => {
         }}
         modifiedSignatures={new Set([method.signature])}
         selectedSignatures={new Set()}
-        inProgressMethods={new Set()}
-        processedByAutoModelMethods={new Set()}
         evaluationRun={undefined}
         viewState={viewState}
         hideModeledMethods={false}
@@ -44,8 +40,6 @@ describe(LibraryRow.name, () => {
         onChange={onChange}
         onMethodClick={onMethodClick}
         onSaveModelClick={onSaveModelClick}
-        onGenerateFromLlmClick={onGenerateFromLlmClick}
-        onStopGenerateFromLlmClick={onStopGenerateFromLlmClick}
         onGenerateFromSourceClick={jest.fn()}
         onModelDependencyClick={onModelDependencyClick}
         {...props}
@@ -74,33 +68,6 @@ describe(LibraryRow.name, () => {
     expect(screen.queryByText("Model dependency")).toBeInTheDocument();
   });
 
-  it("renders the row when LLM is enabled", () => {
-    render({
-      viewState: {
-        ...viewState,
-        showLlmButton: true,
-      },
-    });
-
-    expect(screen.queryByText("Model from source")).not.toBeInTheDocument();
-    expect(screen.queryByText("Model with AI")).toBeInTheDocument();
-    expect(screen.queryByText("Model dependency")).toBeInTheDocument();
-  });
-
-  it("renders the row when generate button and LLM are enabled", () => {
-    render({
-      viewState: {
-        ...viewState,
-        showGenerateButton: true,
-        showLlmButton: true,
-      },
-    });
-
-    expect(screen.queryByText("Model from source")).toBeInTheDocument();
-    expect(screen.queryByText("Model with AI")).toBeInTheDocument();
-    expect(screen.queryByText("Model dependency")).toBeInTheDocument();
-  });
-
   it("can expand the row", async () => {
     render();
 
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx
index 5213dc15d3a..6ce364b4393 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/MethodRow.spec.tsx
@@ -42,8 +42,6 @@ describe(MethodRow.name, () => {
         modeledMethods={[modeledMethod]}
         methodIsUnsaved={false}
         methodIsSelected={false}
-        modelingInProgress={false}
-        processedByAutoModel={false}
         revealedMethodSignature={null}
         evaluationRun={undefined}
         viewState={viewState}
@@ -186,14 +184,6 @@ describe(MethodRow.name, () => {
     expect(screen.getByLabelText("Method not modeled")).toBeInTheDocument();
   });
 
-  it("shows the in progress indicator when in progress", () => {
-    render({
-      modelingInProgress: true,
-    });
-
-    expect(screen.getByLabelText("Loading")).toBeInTheDocument();
-  });
-
   it("can render multiple models", () => {
     render({
       modeledMethods: [
@@ -253,9 +243,9 @@ describe(MethodRow.name, () => {
       modeledMethods: [],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeDisabled();
+    expect(addButton).toBeDisabled();
 
     expect(screen.queryByLabelText("Remove model")).not.toBeInTheDocument();
   });
@@ -265,9 +255,9 @@ describe(MethodRow.name, () => {
       modeledMethods: [{ ...modeledMethod, type: "none" }],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeDisabled();
+    expect(addButton).toBeDisabled();
 
     expect(screen.queryByLabelText("Remove model")).not.toBeInTheDocument();
   });
@@ -277,9 +267,9 @@ describe(MethodRow.name, () => {
       modeledMethods: [modeledMethod],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(addButton).toBeEnabled();
 
     expect(screen.queryByLabelText("Remove model")).not.toBeInTheDocument();
   });
@@ -292,16 +282,16 @@ describe(MethodRow.name, () => {
       ],
     });
 
-    const addButton = screen.queryByLabelText("Add new model");
+    const addButton = await screen.findByLabelText("Add new model");
     expect(addButton).toBeInTheDocument();
-    expect(addButton?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(addButton).toBeEnabled();
 
-    const removeButton = screen.queryByLabelText("Remove model");
+    const removeButton = await screen.findByLabelText("Remove model");
     expect(removeButton).toBeInTheDocument();
-    expect(removeButton?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(removeButton).toBeEnabled();
   });
 
-  it("shows add model button on first row and remove model button on all other rows", async () => {
+  it("shows add model button on first row and remove model button on all other rows", () => {
     render({
       modeledMethods: [
         { ...modeledMethod, type: "source" },
@@ -313,12 +303,12 @@ describe(MethodRow.name, () => {
 
     const addButtons = screen.queryAllByLabelText("Add new model");
     expect(addButtons.length).toBe(1);
-    expect(addButtons[0]?.getElementsByTagName("input")[0]).toBeEnabled();
+    expect(addButtons[0]).toBeEnabled();
 
     const removeButtons = screen.queryAllByLabelText("Remove model");
     expect(removeButtons.length).toBe(3);
     for (const removeButton of removeButtons) {
-      expect(removeButton?.getElementsByTagName("input")[0]).toBeEnabled();
+      expect(removeButton).toBeEnabled();
     }
   });
 
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx
index 24897bfa098..150ace05b53 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelEvaluation.spec.tsx
@@ -1,4 +1,4 @@
-import { render as reactRender, screen } from "@testing-library/react";
+import { render as reactRender, screen, waitFor } from "@testing-library/react";
 import type { Props } from "../ModelEvaluation";
 import { ModelEvaluation } from "../ModelEvaluation";
 import { createMockModelEditorViewState } from "../../../../test/factories/model-editor/view-state";
@@ -39,47 +39,51 @@ describe(ModelEvaluation.name, () => {
   });
 
   describe("when showEvaluationUi is true", () => {
-    it("renders evaluation UI with 'Evaluate' button enabled", () => {
+    it("renders evaluation UI with 'Evaluate' button enabled", async () => {
       render();
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeEnabled();
+      expect(evaluateButton).toBeEnabled();
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
     });
 
-    it("disables 'Evaluate' button when there are no custom models", () => {
+    it("disables 'Evaluate' button when there are no custom models", async () => {
       render({
         modeledMethods: {},
       });
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeDisabled();
+      await waitFor(() => {
+        expect(evaluateButton).toBeDisabled();
+      });
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
     });
 
-    it("disables 'Evaluate' button when there are unsaved changes", () => {
+    it("disables 'Evaluate' button when there are unsaved changes", async () => {
       render({
         modifiedSignatures: new Set([method.signature]),
       });
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeDisabled();
+      await waitFor(() => {
+        expect(evaluateButton).toBeDisabled();
+      });
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
     });
 
-    it("renders 'Evaluate' button and 'Evaluation run' link when there is a completed evaluation", () => {
+    it("renders 'Evaluate' button and 'Evaluation run' link when there is a completed evaluation", async () => {
       render({
         evaluationRun: {
           isPreparing: false,
@@ -89,16 +93,16 @@ describe(ModelEvaluation.name, () => {
         },
       });
 
-      const evaluateButton = screen.queryByText("Evaluate");
+      const evaluateButton = await screen.findByText("Evaluate");
       expect(evaluateButton).toBeInTheDocument();
-      expect(evaluateButton?.getElementsByTagName("input")[0]).toBeEnabled();
+      expect(evaluateButton).toBeEnabled();
 
       expect(screen.queryByText("Evaluation run")).toBeInTheDocument();
 
       expect(screen.queryByText("Stop evaluation")).not.toBeInTheDocument();
     });
 
-    it("renders 'Stop evaluation' button when there is an in progress evaluation, but no variant analysis yet", () => {
+    it("renders 'Stop evaluation' button when there is an in progress evaluation, but no variant analysis yet", async () => {
       render({
         evaluationRun: {
           isPreparing: true,
@@ -106,18 +110,16 @@ describe(ModelEvaluation.name, () => {
         },
       });
 
-      const stopEvaluationButton = screen.queryByText("Stop evaluation");
+      const stopEvaluationButton = await screen.findByText("Stop evaluation");
       expect(stopEvaluationButton).toBeInTheDocument();
-      expect(
-        stopEvaluationButton?.getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(stopEvaluationButton).toBeEnabled();
 
       expect(screen.queryByText("Evaluation run")).not.toBeInTheDocument();
 
       expect(screen.queryByText("Evaluate")).not.toBeInTheDocument();
     });
 
-    it("renders 'Stop evaluation' button and 'Evaluation run' link when there is an in progress evaluation with variant analysis", () => {
+    it("renders 'Stop evaluation' button and 'Evaluation run' link when there is an in progress evaluation with variant analysis", async () => {
       render({
         evaluationRun: {
           isPreparing: false,
@@ -127,11 +129,9 @@ describe(ModelEvaluation.name, () => {
         },
       });
 
-      const stopEvaluationButton = screen.queryByText("Stop evaluation");
+      const stopEvaluationButton = await screen.findByText("Stop evaluation");
       expect(stopEvaluationButton).toBeInTheDocument();
-      expect(
-        stopEvaluationButton?.getElementsByTagName("input")[0],
-      ).toBeEnabled();
+      expect(stopEvaluationButton).toBeEnabled();
 
       expect(screen.queryByText("Evaluation run")).toBeInTheDocument();
 
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelKindDropdown.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelKindDropdown.spec.tsx
index 6fcc7848b64..22d4a3a65c7 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelKindDropdown.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelKindDropdown.spec.tsx
@@ -24,7 +24,6 @@ describe(ModelKindDropdown.name, () => {
       <ModelKindDropdown
         language={QueryLanguage.Java}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
       />,
     );
@@ -47,7 +46,6 @@ describe(ModelKindDropdown.name, () => {
       <ModelKindDropdown
         language={QueryLanguage.Java}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
       />,
     );
@@ -64,7 +62,6 @@ describe(ModelKindDropdown.name, () => {
       <ModelKindDropdown
         language={QueryLanguage.Java}
         modeledMethod={updatedModeledMethod}
-        modelPending={false}
         onChange={onChange}
       />,
     );
@@ -82,7 +79,6 @@ describe(ModelKindDropdown.name, () => {
       <ModelKindDropdown
         language={QueryLanguage.Java}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
       />,
     );
@@ -102,7 +98,6 @@ describe(ModelKindDropdown.name, () => {
       <ModelKindDropdown
         language={QueryLanguage.Java}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
       />,
     );
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelTypeDropdown.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelTypeDropdown.spec.tsx
index eb72f876b9f..f5ed858f3c1 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/ModelTypeDropdown.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/ModelTypeDropdown.spec.tsx
@@ -21,7 +21,6 @@ describe(ModelTypeDropdown.name, () => {
       <ModelTypeDropdown
         language={QueryLanguage.Java}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
         method={method}
         modelConfig={defaultModelConfig}
@@ -44,7 +43,6 @@ describe(ModelTypeDropdown.name, () => {
       <ModelTypeDropdown
         language={QueryLanguage.Ruby}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
         method={method}
         modelConfig={defaultModelConfig}
@@ -67,7 +65,6 @@ describe(ModelTypeDropdown.name, () => {
       <ModelTypeDropdown
         language={QueryLanguage.Java}
         modeledMethod={modeledMethod}
-        modelPending={false}
         onChange={onChange}
         method={method}
         modelConfig={defaultModelConfig}
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodDataGrid.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodDataGrid.spec.tsx
index 36af1f825b0..7a3645cca8f 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodDataGrid.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodDataGrid.spec.tsx
@@ -57,8 +57,6 @@ describe(ModeledMethodDataGrid.name, () => {
         }}
         modifiedSignatures={new Set([method1.signature])}
         selectedSignatures={new Set()}
-        inProgressMethods={new Set()}
-        processedByAutoModelMethods={new Set()}
         evaluationRun={undefined}
         viewState={viewState}
         hideModeledMethods={false}
diff --git a/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodsList.spec.tsx b/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodsList.spec.tsx
index 8136ee2df0f..6bf0078a3b7 100644
--- a/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodsList.spec.tsx
+++ b/extensions/ql-vscode/src/view/model-editor/__tests__/ModeledMethodsList.spec.tsx
@@ -35,8 +35,6 @@ describe(ModeledMethodsList.name, () => {
   const onChange = jest.fn();
   const onMethodClick = jest.fn();
   const onSaveModelClick = jest.fn();
-  const onGenerateFromLlmClick = jest.fn();
-  const onStopGenerateFromLlmClick = jest.fn();
   const onModelDependencyClick = jest.fn();
 
   const viewState = createMockModelEditorViewState();
@@ -58,8 +56,6 @@ describe(ModeledMethodsList.name, () => {
         }}
         modifiedSignatures={new Set([method1.signature])}
         selectedSignatures={new Set()}
-        inProgressMethods={new Set()}
-        processedByAutoModelMethods={new Set()}
         evaluationRun={undefined}
         viewState={viewState}
         hideModeledMethods={false}
@@ -67,8 +63,6 @@ describe(ModeledMethodsList.name, () => {
         onChange={onChange}
         onMethodClick={onMethodClick}
         onSaveModelClick={onSaveModelClick}
-        onGenerateFromLlmClick={onGenerateFromLlmClick}
-        onStopGenerateFromLlmClick={onStopGenerateFromLlmClick}
         onGenerateFromSourceClick={jest.fn()}
         onModelDependencyClick={onModelDependencyClick}
         {...props}
diff --git a/extensions/ql-vscode/src/view/results/AlertTablePathRow.tsx b/extensions/ql-vscode/src/view/results/AlertTablePathRow.tsx
index ab4faff74bb..db8af0efdb9 100644
--- a/extensions/ql-vscode/src/view/results/AlertTablePathRow.tsx
+++ b/extensions/ql-vscode/src/view/results/AlertTablePathRow.tsx
@@ -11,8 +11,9 @@ import { AlertTableDropdownIndicatorCell } from "./AlertTableDropdownIndicatorCe
 import { useCallback, useMemo } from "react";
 import { VerticalRule } from "../common/VerticalRule";
 import type { UserSettings } from "../../common/interface-types";
+import { pluralize } from "../../common/word";
 
-interface Props {
+export interface Props {
   path: ThreadFlow;
   pathIndex: number;
   resultIndex: number;
@@ -65,7 +66,7 @@ export function AlertTablePathRow(props: Props) {
           onClick={handleDropdownClick}
         />
         <td className="vscode-codeql__text-center" colSpan={4}>
-          Path
+          {`Path (${pluralize(path.locations.length, "step", "steps")})`}
         </td>
       </tr>
       {currentPathExpanded &&
diff --git a/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx b/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx
index c405f32006c..3ab31ed3f7f 100644
--- a/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx
+++ b/extensions/ql-vscode/src/view/results/AlertTableResultRow.tsx
@@ -13,8 +13,9 @@ import { SarifLocation } from "./locations/SarifLocation";
 import { SarifMessageWithLocations } from "./locations/SarifMessageWithLocations";
 import { AlertTablePathRow } from "./AlertTablePathRow";
 import type { UserSettings } from "../../common/interface-types";
+import { Badge } from "../common/Badge";
 
-interface Props {
+export interface Props {
   result: Result;
   resultIndex: number;
   expanded: Set<string>;
@@ -83,6 +84,11 @@ export function AlertTableResultRow(props: Props) {
       />
     );
 
+  const allPaths = getAllPaths(result);
+  const shortestPath = Math.min(
+    ...allPaths.map((path) => path.locations.length),
+  );
+
   const currentResultExpanded = expanded.has(keyToString(resultKey));
   return (
     <>
@@ -102,6 +108,9 @@ export function AlertTableResultRow(props: Props) {
               onClick={handleDropdownClick}
             />
             <td className="vscode-codeql__icon-cell">{listUnordered}</td>
+            <td className="vscode-codeql__icon-cell">
+              <Badge title="Shortest path">{shortestPath}</Badge>
+            </td>
             <td colSpan={3}>{msg}</td>
           </>
         )}
@@ -118,7 +127,7 @@ export function AlertTableResultRow(props: Props) {
       </tr>
       {currentResultExpanded &&
         result.codeFlows &&
-        getAllPaths(result).map((path, pathIndex) => (
+        allPaths.map((path, pathIndex) => (
           <AlertTablePathRow
             key={`${resultIndex}-${pathIndex}`}
             {...props}
diff --git a/extensions/ql-vscode/src/view/results/Graph.tsx b/extensions/ql-vscode/src/view/results/Graph.tsx
index 3f81f5d9b4f..0c82e41c008 100644
--- a/extensions/ql-vscode/src/view/results/Graph.tsx
+++ b/extensions/ql-vscode/src/view/results/Graph.tsx
@@ -48,7 +48,10 @@ export function Graph({ graphData, databaseUri }: GraphProps) {
             d.attributes["xlink:href"] = "#";
             d.attributes["href"] = "#";
             loc.uri = `file://${loc.uri}`;
-            select(this).on("click", () => jumpToLocation(loc, databaseUri));
+            select(this).on("click", (event: Event) => {
+              jumpToLocation(loc, databaseUri);
+              event.preventDefault(); // Avoid resetting scroll position
+            });
           }
         }
         if ("fill" in d.attributes) {
diff --git a/extensions/ql-vscode/src/view/results/ResultTables.tsx b/extensions/ql-vscode/src/view/results/ResultTables.tsx
index e84504462ea..3afcb170314 100644
--- a/extensions/ql-vscode/src/view/results/ResultTables.tsx
+++ b/extensions/ql-vscode/src/view/results/ResultTables.tsx
@@ -124,9 +124,11 @@ export function ResultTables(props: ResultTablesProps) {
     (evt: MessageEvent): void => {
       // sanitize origin
       const origin = evt.origin.replace(/\n|\r/g, "");
-      evt.origin === window.origin
-        ? handleMessage(evt.data as IntoResultsViewMsg)
-        : console.error(`Invalid event origin ${origin}`);
+      if (evt.origin === window.origin) {
+        handleMessage(evt.data as IntoResultsViewMsg);
+      } else {
+        console.error(`Invalid event origin ${origin}`);
+      }
     },
     [handleMessage],
   );
diff --git a/extensions/ql-vscode/src/view/results/ResultsApp.tsx b/extensions/ql-vscode/src/view/results/ResultsApp.tsx
index 394e10df0ad..f0ff4e2cd3c 100644
--- a/extensions/ql-vscode/src/view/results/ResultsApp.tsx
+++ b/extensions/ql-vscode/src/view/results/ResultsApp.tsx
@@ -16,11 +16,12 @@ import {
   DEFAULT_USER_SETTINGS,
   GRAPH_TABLE_NAME,
 } from "../../common/interface-types";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
 import { ResultTables } from "./ResultTables";
 import { onNavigation } from "./navigation";
 
 import "./resultsView.css";
-import { useCallback, useEffect, useState } from "react";
+import { useCallback, useState } from "react";
 
 /**
  * ResultsApp.tsx
@@ -113,8 +114,8 @@ export function ResultsApp() {
     [],
   );
 
-  const handleMessage = useCallback(
-    (msg: IntoResultsViewMsg): void => {
+  useMessageFromExtension<IntoResultsViewMsg>(
+    (msg) => {
       switch (msg.t) {
         case "setUserSettings":
           setUserSettings(msg.userSettings);
@@ -189,24 +190,6 @@ export function ResultsApp() {
     [updateStateWithNewResultsInfo],
   );
 
-  const vscodeMessageHandler = useCallback(
-    (evt: MessageEvent) => {
-      // sanitize origin
-      const origin = evt.origin.replace(/\n|\r/g, "");
-      evt.origin === window.origin
-        ? handleMessage(evt.data as IntoResultsViewMsg)
-        : console.error(`Invalid event origin ${origin}`);
-    },
-    [handleMessage],
-  );
-
-  useEffect(() => {
-    window.addEventListener("message", vscodeMessageHandler);
-    return () => {
-      window.removeEventListener("message", vscodeMessageHandler);
-    };
-  }, [vscodeMessageHandler]);
-
   const { displayedResults, nextResultsInfo, isExpectingResultsUpdate } = state;
   if (
     displayedResults.results !== null &&
diff --git a/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx b/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx
new file mode 100644
index 00000000000..001fa322a34
--- /dev/null
+++ b/extensions/ql-vscode/src/view/results/__tests__/AlertTablePathRow.spec.tsx
@@ -0,0 +1,40 @@
+import { render as reactRender, screen } from "@testing-library/react";
+import type { Props } from "../AlertTablePathRow";
+import { AlertTablePathRow } from "../AlertTablePathRow";
+import { createMockResults } from "../../../../test/factories/results/mockresults";
+
+describe(AlertTablePathRow.name, () => {
+  const render = (props?: Props) => {
+    const mockRef = { current: null } as React.RefObject<HTMLTableRowElement>;
+    const results = createMockResults();
+    const threadFlow = results[0]?.codeFlows?.[0]?.threadFlows?.[0];
+
+    if (!threadFlow) {
+      throw new Error("ThreadFlow is undefined");
+    }
+    reactRender(
+      <AlertTablePathRow
+        resultIndex={1}
+        selectedItem={undefined}
+        selectedItemRef={mockRef}
+        path={threadFlow}
+        pathIndex={0}
+        currentPathExpanded={true}
+        databaseUri={"dbUri"}
+        sourceLocationPrefix="src"
+        userSettings={{
+          shouldShowProvenance: false,
+        }}
+        updateSelectionCallback={jest.fn()}
+        toggleExpanded={jest.fn()}
+        {...props}
+      />,
+    );
+  };
+
+  it("renders number of steps", () => {
+    render();
+
+    expect(screen.getByText("Path (3 steps)")).toBeInTheDocument();
+  });
+});
diff --git a/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx b/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx
new file mode 100644
index 00000000000..9082384e9d2
--- /dev/null
+++ b/extensions/ql-vscode/src/view/results/__tests__/AlertTableResultRow.spec.tsx
@@ -0,0 +1,35 @@
+import { render as reactRender, screen } from "@testing-library/react";
+import { AlertTableResultRow } from "../AlertTableResultRow";
+import type { Props } from "../AlertTableResultRow";
+import { createMockResults } from "../../../../test/factories/results/mockresults";
+
+describe(AlertTableResultRow.name, () => {
+  const render = (props?: Props) => {
+    const mockRef = { current: null } as React.RefObject<HTMLTableRowElement>;
+    const results = createMockResults();
+
+    reactRender(
+      <AlertTableResultRow
+        result={results[0]}
+        expanded={new Set()}
+        resultIndex={1}
+        selectedItem={undefined}
+        selectedItemRef={mockRef}
+        databaseUri={"dbUri"}
+        sourceLocationPrefix="src"
+        userSettings={{
+          shouldShowProvenance: false,
+        }}
+        updateSelectionCallback={jest.fn()}
+        toggleExpanded={jest.fn()}
+        {...props}
+      />,
+    );
+  };
+
+  it("renders shortest path badge", () => {
+    render();
+
+    expect(screen.getByTitle("Shortest path")).toHaveTextContent("3");
+  });
+});
diff --git a/extensions/ql-vscode/src/view/tsconfig.json b/extensions/ql-vscode/src/view/tsconfig.json
index eceba57235f..d094c039d78 100644
--- a/extensions/ql-vscode/src/view/tsconfig.json
+++ b/extensions/ql-vscode/src/view/tsconfig.json
@@ -2,7 +2,7 @@
   "compilerOptions": {
     "module": "esnext",
     "moduleResolution": "node",
-    "target": "es6",
+    "target": "es2021",
     "outDir": "out",
     "lib": ["ES2021", "dom"],
     "jsx": "react-jsx",
@@ -14,7 +14,12 @@
     "noImplicitReturns": true,
     "noFallthroughCasesInSwitch": true,
     "experimentalDecorators": true,
-    "skipLibCheck": true
+    "skipLibCheck": true,
+    "plugins": [
+      {
+        "name": "typescript-plugin-css-modules"
+      }
+    ]
   },
   "exclude": ["node_modules"]
 }
diff --git a/extensions/ql-vscode/src/view/types.d.ts b/extensions/ql-vscode/src/view/types.d.ts
new file mode 100644
index 00000000000..1eabbb4297e
--- /dev/null
+++ b/extensions/ql-vscode/src/view/types.d.ts
@@ -0,0 +1 @@
+declare module "*.module.css";
diff --git a/extensions/ql-vscode/src/view/variant-analysis/FailureReasonAlert.tsx b/extensions/ql-vscode/src/view/variant-analysis/FailureReasonAlert.tsx
index d6d07400584..1b6c631dbb7 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/FailureReasonAlert.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/FailureReasonAlert.tsx
@@ -1,8 +1,8 @@
 import type { ReactNode } from "react";
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 import { Alert } from "../common";
 import { vscode } from "../vscode-api";
 import { VariantAnalysisFailureReason } from "../../variant-analysis/shared/variant-analysis";
+import { Link } from "../common/Link";
 
 type Props = {
   failureReason: VariantAnalysisFailureReason;
@@ -33,8 +33,8 @@ const getMessage = (failureReason: VariantAnalysisFailureReason): ReactNode => {
       return (
         <>
           The GitHub Actions workflow run has failed.{" "}
-          <VSCodeLink onClick={openLogs}>View actions logs</VSCodeLink> and try
-          running this query again.
+          <Link onClick={openLogs}>View actions logs</Link> and try running this
+          query again.
         </>
       );
     case VariantAnalysisFailureReason.InternalError:
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RawResultCell.tsx b/extensions/ql-vscode/src/view/variant-analysis/RawResultCell.tsx
index 0d7f589043e..7382d46f04b 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RawResultCell.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RawResultCell.tsx
@@ -1,10 +1,9 @@
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
-
 import type { CellValue } from "../../common/raw-result-types";
 import { sendTelemetry } from "../common/telemetry";
 import { convertNonPrintableChars } from "../../common/text-utils";
 import { tryGetRemoteLocation } from "../../common/bqrs-utils";
 import { RawNumberValue } from "../common/RawNumberValue";
+import { Link } from "../common/Link";
 
 type CellProps = {
   value: CellValue;
@@ -35,9 +34,9 @@ export const RawResultCell = ({
       const safeLabel = convertNonPrintableChars(value.value.label);
       if (url) {
         return (
-          <VSCodeLink onClick={sendRawResultsLinkTelemetry} href={url}>
+          <Link onClick={sendRawResultsLinkTelemetry} href={url}>
             {safeLabel}
-          </VSCodeLink>
+          </Link>
         );
       } else {
         return <span>{safeLabel}</span>;
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx
index fc381fe016f..19edad08cc2 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepoRow.tsx
@@ -1,7 +1,7 @@
 import type { ChangeEvent } from "react";
 import { useCallback, useEffect, useState } from "react";
 import { styled } from "styled-components";
-import { VSCodeBadge, VSCodeCheckbox } from "@vscode/webview-ui-toolkit/react";
+import { VscodeCheckbox } from "@vscode-elements/react-elements";
 import type { VariantAnalysisScannedRepositoryState } from "../../variant-analysis/shared/variant-analysis";
 import {
   isCompletedAnalysisRepoStatus,
@@ -27,6 +27,7 @@ import StarCount from "../common/StarCount";
 import { useTelemetryOnChange } from "../common/telemetry";
 import { DeterminateProgressRing } from "../common/DeterminateProgressRing";
 import { ResultFormat } from "../../variant-analysis/shared/variant-analysis-result-format";
+import { Badge } from "../common/Badge";
 
 // This will ensure that these icons have a className which we can use in the TitleContainer
 const ExpandCollapseCodicon = styled(Codicon)``;
@@ -61,6 +62,10 @@ const MetadataContainer = styled.div`
   margin-left: auto;
 `;
 
+const Checkbox = styled(VscodeCheckbox)`
+  margin-right: -9px; // VscodeCheckbox has 9px margin on the right by default
+`;
+
 type VisibilityProps = {
   isPrivate?: boolean;
 };
@@ -254,7 +259,7 @@ export const RepoRow = ({
         disabled={disabled}
         aria-expanded={isExpanded}
       >
-        <VSCodeCheckbox
+        <Checkbox
           onChange={onChangeCheckbox}
           onClick={onClickCheckbox}
           checked={selected}
@@ -269,9 +274,9 @@ export const RepoRow = ({
           <ExpandCollapseCodicon name="chevron-right" label="Expand" />
         )}
         {resultsLoading && <LoadingIcon label="Results are loading" />}
-        <VSCodeBadge>
+        <Badge>
           {resultCount === undefined ? "-" : formatDecimal(resultCount)}
-        </VSCodeBadge>
+        </Badge>
         <span>{repository.fullName}</span>
         <Visibility isPrivate={repository.private} />
         <span>
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx
index 56596b2ecbf..206b33586fb 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesFilter.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { Codicon } from "../common";
 import { FilterKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -26,10 +29,10 @@ export const RepositoriesFilter = ({ value, onChange, className }: Props) => {
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="list-filter" label="Filter..." slot="indicator" />
-      <VSCodeOption value={FilterKey.All}>All</VSCodeOption>
-      <VSCodeOption value={FilterKey.WithResults}>With results</VSCodeOption>
+      <VscodeOption value={FilterKey.All}>All</VscodeOption>
+      <VscodeOption value={FilterKey.WithResults}>With results</VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx
index 11ac814cc18..380599017eb 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesResultFormat.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { Codicon } from "../common";
 import { ResultFormat } from "../../variant-analysis/shared/variant-analysis-result-format";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -30,14 +33,14 @@ export const RepositoriesResultFormat = ({
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="table" label="Result format..." slot="indicator" />
-      <VSCodeOption value={ResultFormat.Alerts}>
+      <VscodeOption value={ResultFormat.Alerts}>
         {ResultFormat.Alerts}
-      </VSCodeOption>
-      <VSCodeOption value={ResultFormat.RawResults}>
+      </VscodeOption>
+      <VscodeOption value={ResultFormat.RawResults}>
         {ResultFormat.RawResults}
-      </VSCodeOption>
+      </VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx
index d4383a3e1ea..96ec4c43dd4 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/RepositoriesSort.tsx
@@ -1,10 +1,13 @@
 import { useCallback } from "react";
 import { styled } from "styled-components";
-import { VSCodeDropdown, VSCodeOption } from "@vscode/webview-ui-toolkit/react";
+import {
+  VscodeOption,
+  VscodeSingleSelect,
+} from "@vscode-elements/react-elements";
 import { SortKey } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { Codicon } from "../common";
 
-const Dropdown = styled(VSCodeDropdown)`
+const Dropdown = styled(VscodeSingleSelect)`
   width: 100%;
 `;
 
@@ -26,13 +29,13 @@ export const RepositoriesSort = ({ value, onChange, className }: Props) => {
   );
 
   return (
-    <Dropdown value={value} onInput={handleInput} className={className}>
+    <Dropdown value={value} onChange={handleInput} className={className}>
       <Codicon name="sort-precedence" label="Sort..." slot="indicator" />
-      <VSCodeOption value={SortKey.Alphabetically}>Alphabetically</VSCodeOption>
-      <VSCodeOption value={SortKey.NumberOfResults}>
+      <VscodeOption value={SortKey.Alphabetically}>Alphabetically</VscodeOption>
+      <VscodeOption value={SortKey.NumberOfResults}>
         Number of results
-      </VSCodeOption>
-      <VSCodeOption value={SortKey.Popularity}>Popularity</VSCodeOption>
+      </VscodeOption>
+      <VscodeOption value={SortKey.Popularity}>Popularity</VscodeOption>
     </Dropdown>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
index 3a72c3548cd..3ac0599ae6c 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysis.tsx
@@ -1,4 +1,4 @@
-import { useCallback, useEffect, useState } from "react";
+import { useCallback, useState } from "react";
 
 import type {
   VariantAnalysis as VariantAnalysisDomainModel,
@@ -9,10 +9,15 @@ import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-ana
 import { VariantAnalysisHeader } from "./VariantAnalysisHeader";
 import { VariantAnalysisOutcomePanels } from "./VariantAnalysisOutcomePanels";
 import { VariantAnalysisLoading } from "./VariantAnalysisLoading";
-import type { ToVariantAnalysisMessage } from "../../common/interface-types";
+import type {
+  ToVariantAnalysisMessage,
+  VariantAnalysisUserSettings,
+} from "../../common/interface-types";
 import { vscode } from "../vscode-api";
 import { defaultFilterSortState } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { sendTelemetry, useTelemetryOnChange } from "../common/telemetry";
+import { useMessageFromExtension } from "../common/useMessageFromExtension";
+import { DEFAULT_VARIANT_ANALYSIS_USER_SETTINGS } from "../../common/interface-types";
 
 export type VariantAnalysisProps = {
   variantAnalysis?: VariantAnalysisDomainModel;
@@ -76,52 +81,51 @@ export function VariantAnalysis({
   useTelemetryOnChange(filterSortState, "variant-analysis-filter-sort-state", {
     debounceTimeoutMillis: 1000,
   });
+  const [variantAnalysisUserSettings, setVariantAnalysisUserSettings] =
+    useState<VariantAnalysisUserSettings>(
+      DEFAULT_VARIANT_ANALYSIS_USER_SETTINGS,
+    );
 
-  useEffect(() => {
-    const listener = (evt: MessageEvent) => {
-      if (evt.origin === window.origin) {
-        const msg: ToVariantAnalysisMessage = evt.data;
-        if (msg.t === "setVariantAnalysis") {
-          setVariantAnalysis(msg.variantAnalysis);
-          vscode.setState({
-            variantAnalysisId: msg.variantAnalysis.id,
-          });
-        } else if (msg.t === "setFilterSortState") {
-          setFilterSortState(msg.filterSortState);
-        } else if (msg.t === "setRepoResults") {
-          setRepoResults((oldRepoResults) => {
-            const newRepoIds = msg.repoResults.map((r) => r.repositoryId);
-            return [
-              ...oldRepoResults.filter(
-                (v) => !newRepoIds.includes(v.repositoryId),
-              ),
-              ...msg.repoResults,
-            ];
-          });
-        } else if (msg.t === "setRepoStates") {
-          setRepoStates((oldRepoStates) => {
-            const newRepoIds = msg.repoStates.map((r) => r.repositoryId);
-            return [
-              ...oldRepoStates.filter(
-                (v) => !newRepoIds.includes(v.repositoryId),
-              ),
-              ...msg.repoStates,
-            ];
-          });
-        }
-      } else {
-        // sanitize origin
-        const origin = evt.origin.replace(/\n|\r/g, "");
-        console.error(`Invalid event origin ${origin}`);
-      }
-    };
-    window.addEventListener("message", listener);
-
-    return () => {
-      window.removeEventListener("message", listener);
-    };
+  useMessageFromExtension<ToVariantAnalysisMessage>((msg) => {
+    if (msg.t === "setVariantAnalysis") {
+      setVariantAnalysis(msg.variantAnalysis);
+      vscode.setState({
+        variantAnalysisId: msg.variantAnalysis.id,
+      });
+    } else if (msg.t === "setFilterSortState") {
+      setFilterSortState(msg.filterSortState);
+    } else if (msg.t === "setRepoResults") {
+      setRepoResults((oldRepoResults) => {
+        const newRepoIds = msg.repoResults.map((r) => r.repositoryId);
+        return [
+          ...oldRepoResults.filter((v) => !newRepoIds.includes(v.repositoryId)),
+          ...msg.repoResults,
+        ];
+      });
+    } else if (msg.t === "setRepoStates") {
+      setRepoStates((oldRepoStates) => {
+        const newRepoIds = msg.repoStates.map((r) => r.repositoryId);
+        return [
+          ...oldRepoStates.filter((v) => !newRepoIds.includes(v.repositoryId)),
+          ...msg.repoStates,
+        ];
+      });
+    } else if (msg.t === "setVariantAnalysisUserSettings") {
+      setVariantAnalysisUserSettings(msg.variantAnalysisUserSettings);
+    }
   }, []);
 
+  const viewAutofixes = useCallback(() => {
+    vscode.postMessage({
+      t: "viewAutofixes",
+      filterSort: {
+        ...filterSortState,
+        repositoryIds: selectedRepositoryIds,
+      },
+    });
+    sendTelemetry("variant-analysis-view-autofixes");
+  }, [filterSortState, selectedRepositoryIds]);
+
   const copyRepositoryList = useCallback(() => {
     vscode.postMessage({
       t: "copyRepositoryList",
@@ -165,9 +169,11 @@ export function VariantAnalysis({
         onOpenQueryFileClick={openQueryFile}
         onViewQueryTextClick={openQueryText}
         onStopQueryClick={stopQuery}
+        onViewAutofixesClick={viewAutofixes}
         onCopyRepositoryListClick={copyRepositoryList}
         onExportResultsClick={exportResults}
         onViewLogsClick={onViewLogsClick}
+        variantAnalysisUserSettings={variantAnalysisUserSettings}
       />
       <VariantAnalysisOutcomePanels
         variantAnalysis={variantAnalysis}
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx
index ed1b473c66a..abec9443946 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisActions.tsx
@@ -1,6 +1,6 @@
 import { styled } from "styled-components";
-import { VSCodeButton } from "@vscode/webview-ui-toolkit/react";
 import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-analysis";
+import { VscodeButton } from "@vscode-elements/react-elements";
 
 export type VariantAnalysisActionsProps = {
   variantAnalysisStatus: VariantAnalysisStatus;
@@ -9,13 +9,17 @@ export type VariantAnalysisActionsProps = {
   stopQueryDisabled?: boolean;
 
   showResultActions?: boolean;
+  onViewAutofixesClick: () => void;
   onCopyRepositoryListClick: () => void;
   onExportResultsClick: () => void;
+  viewAutofixesDisabled?: boolean;
   copyRepositoryListDisabled?: boolean;
   exportResultsDisabled?: boolean;
 
   hasSelectedRepositories?: boolean;
   hasFilteredRepositories?: boolean;
+
+  showViewAutofixesButton: boolean;
 };
 
 const Container = styled.div`
@@ -24,7 +28,7 @@ const Container = styled.div`
   gap: 1em;
 `;
 
-const Button = styled(VSCodeButton)`
+const Button = styled(VscodeButton)`
   white-space: nowrap;
 `;
 
@@ -55,19 +59,37 @@ export const VariantAnalysisActions = ({
   onStopQueryClick,
   stopQueryDisabled,
   showResultActions,
+  onViewAutofixesClick,
   onCopyRepositoryListClick,
   onExportResultsClick,
+  viewAutofixesDisabled,
   copyRepositoryListDisabled,
   exportResultsDisabled,
   hasSelectedRepositories,
   hasFilteredRepositories,
+  showViewAutofixesButton,
 }: VariantAnalysisActionsProps) => {
   return (
     <Container>
       {showResultActions && (
         <>
+          {showViewAutofixesButton && (
+            <Button
+              secondary
+              onClick={onViewAutofixesClick}
+              disabled={viewAutofixesDisabled}
+            >
+              {chooseText({
+                hasSelectedRepositories,
+                hasFilteredRepositories,
+                normalText: "View Autofixes",
+                selectedText: "View Autofixes for selected results",
+                filteredText: "View Autofixes for filtered results",
+              })}
+            </Button>
+          )}
           <Button
-            appearance="secondary"
+            secondary
             onClick={onCopyRepositoryListClick}
             disabled={copyRepositoryListDisabled}
           >
@@ -96,7 +118,7 @@ export const VariantAnalysisActions = ({
       )}
       {variantAnalysisStatus === VariantAnalysisStatus.InProgress && (
         <Button
-          appearance="secondary"
+          secondary
           onClick={onStopQueryClick}
           disabled={stopQueryDisabled}
         >
@@ -104,7 +126,7 @@ export const VariantAnalysisActions = ({
         </Button>
       )}
       {variantAnalysisStatus === VariantAnalysisStatus.Canceling && (
-        <Button appearance="secondary" disabled={true}>
+        <Button secondary disabled={true}>
           Stopping query
         </Button>
       )}
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx
index bdd9b5e11be..6f9ad00ad33 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisHeader.tsx
@@ -22,6 +22,7 @@ import {
   filterAndSortRepositoriesWithResults,
 } from "../../variant-analysis/shared/variant-analysis-filter-sort";
 import { ViewTitle } from "../common";
+import type { VariantAnalysisUserSettings } from "../../common/interface-types";
 
 type VariantAnalysisHeaderProps = {
   variantAnalysis: VariantAnalysis;
@@ -34,10 +35,13 @@ type VariantAnalysisHeaderProps = {
 
   onStopQueryClick: () => void;
 
+  onViewAutofixesClick: () => void;
   onCopyRepositoryListClick: () => void;
   onExportResultsClick: () => void;
 
   onViewLogsClick?: () => void;
+
+  variantAnalysisUserSettings: VariantAnalysisUserSettings;
 };
 
 const Container = styled.div`
@@ -82,9 +86,11 @@ export const VariantAnalysisHeader = ({
   onOpenQueryFileClick,
   onViewQueryTextClick,
   onStopQueryClick,
+  onViewAutofixesClick,
   onCopyRepositoryListClick,
   onExportResultsClick,
   onViewLogsClick,
+  variantAnalysisUserSettings,
 }: VariantAnalysisHeaderProps) => {
   const totalScannedRepositoryCount = useMemo(() => {
     return variantAnalysis.scannedRepos?.length ?? 0;
@@ -150,11 +156,13 @@ export const VariantAnalysisHeader = ({
           variantAnalysisStatus={variantAnalysis.status}
           showResultActions={(resultCount ?? 0) > 0}
           onStopQueryClick={onStopQueryClick}
+          onViewAutofixesClick={onViewAutofixesClick}
           onCopyRepositoryListClick={onCopyRepositoryListClick}
           onExportResultsClick={onExportResultsClick}
           stopQueryDisabled={!variantAnalysis.actionsWorkflowRunId}
           exportResultsDisabled={!hasDownloadedRepos}
           copyRepositoryListDisabled={!hasReposWithResults}
+          viewAutofixesDisabled={!hasReposWithResults}
           hasFilteredRepositories={
             variantAnalysis.scannedRepos?.length !==
             filteredRepositories?.length
@@ -162,6 +170,9 @@ export const VariantAnalysisHeader = ({
           hasSelectedRepositories={
             selectedRepositoryIds && selectedRepositoryIds.length > 0
           }
+          showViewAutofixesButton={
+            variantAnalysisUserSettings.shouldShowViewAutofixesButton
+          }
         />
       </Row>
       <VariantAnalysisStats
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx
index 469c7aa6d29..1f138ffd8cd 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisOutcomePanels.tsx
@@ -2,11 +2,10 @@ import type { Dispatch, SetStateAction } from "react";
 import { useState } from "react";
 import { styled } from "styled-components";
 import {
-  VSCodeBadge,
-  VSCodePanels,
-  VSCodePanelTab,
-  VSCodePanelView,
-} from "@vscode/webview-ui-toolkit/react";
+  VscodeTabHeader,
+  VscodeTabPanel,
+  VscodeTabs,
+} from "@vscode-elements/react-elements";
 import { formatDecimal } from "../../common/number";
 import type {
   VariantAnalysis,
@@ -21,6 +20,7 @@ import type { RepositoriesFilterSortState } from "../../variant-analysis/shared/
 import { RepositoriesSearchSortRow } from "./RepositoriesSearchSortRow";
 import { FailureReasonAlert } from "./FailureReasonAlert";
 import { ResultFormat } from "../../variant-analysis/shared/variant-analysis-result-format";
+import { Badge } from "../common/Badge";
 
 export type VariantAnalysisOutcomePanelProps = {
   variantAnalysis: VariantAnalysis;
@@ -34,8 +34,27 @@ export type VariantAnalysisOutcomePanelProps = {
   setFilterSortState: Dispatch<SetStateAction<RepositoriesFilterSortState>>;
 };
 
-const Tab = styled(VSCodePanelTab)`
+const Tabs = styled(VscodeTabs)`
+  column-gap: 32px;
+
+  > vscode-tab-header {
+    margin-right: 32px;
+  }
+`;
+
+const TabHeader = styled(VscodeTabHeader)`
   text-transform: uppercase;
+
+  > * {
+    // This copies the styles from @vscode/webview-ui-toolkit's VSCodePanelTab
+    &:last-child {
+      margin-left: 8px;
+    }
+  }
+`;
+
+const TabPanel = styled(VscodeTabPanel)`
+  padding: 10px 6px;
 `;
 
 const WarningsContainer = styled.div`
@@ -154,33 +173,31 @@ export const VariantAnalysisOutcomePanels = ({
         onResultFormatChange={setResultFormat}
         variantAnalysisQueryKind={variantAnalysis.query.kind}
       />
-      <VSCodePanels>
+      <Tabs>
         {scannedReposCount > 0 && (
-          <Tab>
+          <TabHeader>
             Analyzed
-            <VSCodeBadge appearance="secondary">
+            <Badge>
               {formatDecimal(variantAnalysis.scannedRepos?.length ?? 0)}
-            </VSCodeBadge>
-          </Tab>
-        )}
-        {notFoundRepos?.repositoryCount && (
-          <Tab>
-            No access
-            <VSCodeBadge appearance="secondary">
-              {formatDecimal(notFoundRepos.repositoryCount)}
-            </VSCodeBadge>
-          </Tab>
-        )}
-        {noCodeqlDbRepos?.repositoryCount && (
-          <Tab>
-            No database
-            <VSCodeBadge appearance="secondary">
-              {formatDecimal(noCodeqlDbRepos.repositoryCount)}
-            </VSCodeBadge>
-          </Tab>
+            </Badge>
+          </TabHeader>
         )}
+        {notFoundRepos?.repositoryCount !== undefined &&
+          notFoundRepos?.repositoryCount > 0 && (
+            <TabHeader>
+              No access
+              <Badge>{formatDecimal(notFoundRepos.repositoryCount)}</Badge>
+            </TabHeader>
+          )}
+        {noCodeqlDbRepos?.repositoryCount !== undefined &&
+          noCodeqlDbRepos?.repositoryCount > 0 && (
+            <TabHeader>
+              No database
+              <Badge>{formatDecimal(noCodeqlDbRepos.repositoryCount)}</Badge>
+            </TabHeader>
+          )}
         {scannedReposCount > 0 && (
-          <VSCodePanelView>
+          <TabPanel>
             <VariantAnalysisAnalyzedRepos
               variantAnalysis={variantAnalysis}
               repositoryStates={repositoryStates}
@@ -190,29 +207,31 @@ export const VariantAnalysisOutcomePanels = ({
               selectedRepositoryIds={selectedRepositoryIds}
               setSelectedRepositoryIds={setSelectedRepositoryIds}
             />
-          </VSCodePanelView>
-        )}
-        {notFoundRepos?.repositoryCount && (
-          <VSCodePanelView>
-            <VariantAnalysisSkippedRepositoriesTab
-              alertTitle="No access"
-              alertMessage="The following repositories can't be analyzed because they don’t exist or you don’t have access."
-              skippedRepositoryGroup={notFoundRepos}
-              filterSortState={filterSortState}
-            />
-          </VSCodePanelView>
-        )}
-        {noCodeqlDbRepos?.repositoryCount && (
-          <VSCodePanelView>
-            <VariantAnalysisSkippedRepositoriesTab
-              alertTitle="No CodeQL database"
-              alertMessage="The following repositories can't be analyzed because they don't currently have a CodeQL database available for the selected language."
-              skippedRepositoryGroup={noCodeqlDbRepos}
-              filterSortState={filterSortState}
-            />
-          </VSCodePanelView>
+          </TabPanel>
         )}
-      </VSCodePanels>
+        {notFoundRepos?.repositoryCount !== undefined &&
+          notFoundRepos?.repositoryCount > 0 && (
+            <TabPanel>
+              <VariantAnalysisSkippedRepositoriesTab
+                alertTitle="No access"
+                alertMessage="The following repositories can't be analyzed because they don’t exist or you don’t have access."
+                skippedRepositoryGroup={notFoundRepos}
+                filterSortState={filterSortState}
+              />
+            </TabPanel>
+          )}
+        {noCodeqlDbRepos?.repositoryCount !== undefined &&
+          noCodeqlDbRepos?.repositoryCount > 0 && (
+            <TabPanel>
+              <VariantAnalysisSkippedRepositoriesTab
+                alertTitle="No CodeQL database"
+                alertMessage="The following repositories can't be analyzed because they don't currently have a CodeQL database available for the selected language."
+                skippedRepositoryGroup={noCodeqlDbRepos}
+                filterSortState={filterSortState}
+              />
+            </TabPanel>
+          )}
+      </Tabs>
     </>
   );
 };
diff --git a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisStatusStats.tsx b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisStatusStats.tsx
index 3969fd7951e..5f937b74682 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisStatusStats.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/VariantAnalysisStatusStats.tsx
@@ -1,7 +1,7 @@
 import { styled } from "styled-components";
-import { VSCodeLink } from "@vscode/webview-ui-toolkit/react";
 import { formatDate } from "../../common/date";
 import { VariantAnalysisStatus } from "../../variant-analysis/shared/variant-analysis";
+import { Link } from "../common/Link";
 
 export type VariantAnalysisStatusStatsProps = {
   variantAnalysisStatus: VariantAnalysisStatus;
@@ -37,7 +37,7 @@ export const VariantAnalysisStatusStats = ({
         <span>{completedAt !== undefined ? formatDate(completedAt) : "-"}</span>
       )}
       {onViewLogsClick && (
-        <VSCodeLink onClick={onViewLogsClick}>View actions logs</VSCodeLink>
+        <Link onClick={onViewLogsClick}>View actions logs</Link>
       )}
     </Container>
   );
diff --git a/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx b/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx
index b1f4df59a71..1c89400615d 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/__tests__/RepoRow.spec.tsx
@@ -1,9 +1,4 @@
-import {
-  act,
-  render as reactRender,
-  screen,
-  waitFor,
-} from "@testing-library/react";
+import { act, render as reactRender, screen } from "@testing-library/react";
 import {
   VariantAnalysisRepoStatus,
   VariantAnalysisScannedRepositoryDownloadStatus,
@@ -403,7 +398,8 @@ describe(RepoRow.name, () => {
       status: VariantAnalysisRepoStatus.InProgress,
     });
 
-    expect(screen.getByRole("checkbox")).toBeDisabled();
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeDisabled();
   });
 
   it("does not allow selecting the item if the item has not been downloaded", async () => {
@@ -411,7 +407,8 @@ describe(RepoRow.name, () => {
       status: VariantAnalysisRepoStatus.Succeeded,
     });
 
-    expect(screen.getByRole("checkbox")).toBeDisabled();
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeDisabled();
   });
 
   it("does not allow selecting the item if the item has not been downloaded successfully", async () => {
@@ -423,11 +420,8 @@ describe(RepoRow.name, () => {
       },
     });
 
-    // It seems like sometimes the first render doesn't have the checkbox disabled
-    // Might be related to https://github.com/microsoft/vscode-webview-ui-toolkit/issues/404
-    await waitFor(() => {
-      expect(screen.getByRole("checkbox")).toBeDisabled();
-    });
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeDisabled();
   });
 
   it("allows selecting the item if the item has been downloaded", async () => {
@@ -440,6 +434,7 @@ describe(RepoRow.name, () => {
       },
     });
 
-    expect(screen.getByRole("checkbox")).toBeEnabled();
+    const checkbox = await screen.findByRole("checkbox");
+    expect(checkbox).toBeEnabled();
   });
 });
diff --git a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx
index b8a7bfcd539..3279ed446d2 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysis.spec.tsx
@@ -1,4 +1,4 @@
-import { render as reactRender, screen, waitFor } from "@testing-library/react";
+import { render as reactRender, screen } from "@testing-library/react";
 import {
   VariantAnalysisFailureReason,
   VariantAnalysisStatus,
@@ -57,9 +57,6 @@ describe(VariantAnalysis.name, () => {
     const variantAnalysis = createMockVariantAnalysis({});
     render({ variantAnalysis });
 
-    await waitFor(() => screen.getByDisplayValue("All"));
-    await waitFor(() => screen.getByDisplayValue("Number of results"));
-
     await postMessage<ToVariantAnalysisMessage>({
       t: "setFilterSortState",
       filterSortState: {
@@ -69,8 +66,11 @@ describe(VariantAnalysis.name, () => {
       },
     });
 
-    expect(screen.getByDisplayValue("With results")).toBeInTheDocument();
-    expect(screen.getByDisplayValue("Alphabetically")).toBeInTheDocument();
+    const withResults = await screen.findByText("With results");
+    expect(withResults).toBeInTheDocument();
+
+    const alphabetically = await screen.findByText("Alphabetically");
+    expect(alphabetically).toBeInTheDocument();
 
     expect(screen.queryByDisplayValue("All")).not.toBeInTheDocument();
     expect(
diff --git a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx
index de19458646e..08d3fe84b54 100644
--- a/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx
+++ b/extensions/ql-vscode/src/view/variant-analysis/__tests__/VariantAnalysisActions.spec.tsx
@@ -6,11 +6,13 @@ import { VariantAnalysisActions } from "../VariantAnalysisActions";
 
 describe(VariantAnalysisActions.name, () => {
   const onStopQueryClick = jest.fn();
+  const onViewAutofixesClick = jest.fn();
   const onCopyRepositoryListClick = jest.fn();
   const onExportResultsClick = jest.fn();
 
   afterEach(() => {
     onStopQueryClick.mockReset();
+    onViewAutofixesClick.mockReset();
     onCopyRepositoryListClick.mockReset();
     onExportResultsClick.mockReset();
   });
@@ -22,8 +24,10 @@ describe(VariantAnalysisActions.name, () => {
     reactRender(
       <VariantAnalysisActions
         onStopQueryClick={onStopQueryClick}
+        onViewAutofixesClick={onViewAutofixesClick}
         onCopyRepositoryListClick={onCopyRepositoryListClick}
         onExportResultsClick={onExportResultsClick}
+        showViewAutofixesButton={false}
         {...props}
       />,
     );
@@ -50,9 +54,9 @@ describe(VariantAnalysisActions.name, () => {
       variantAnalysisStatus: VariantAnalysisStatus.Canceling,
     });
 
-    const button = screen.getByText("Stopping query");
+    const button = await screen.findByText("Stopping query");
     expect(button).toBeInTheDocument();
-    expect(button.getElementsByTagName("input")[0]).toBeDisabled();
+    expect(button).toBeDisabled();
   });
 
   it("does not render a stop query button when canceling", async () => {
diff --git a/extensions/ql-vscode/src/view/webview.tsx b/extensions/ql-vscode/src/view/webview.tsx
index d3adadf74a1..5081dbaffe3 100644
--- a/extensions/ql-vscode/src/view/webview.tsx
+++ b/extensions/ql-vscode/src/view/webview.tsx
@@ -6,6 +6,7 @@ import { registerUnhandledErrorListener } from "./common/errors";
 import type { WebviewDefinition } from "./webview-definition";
 
 import compareView from "./compare";
+import comparePerformance from "./compare-performance";
 import dataFlowPathsView from "./data-flow-paths";
 import methodModelingView from "./method-modeling";
 import modelEditorView from "./model-editor";
@@ -18,6 +19,7 @@ import "@vscode/codicons/dist/codicon.css";
 
 const views: Record<string, WebviewDefinition> = {
   compare: compareView,
+  "compare-performance": comparePerformance,
   "data-flow-paths": dataFlowPathsView,
   "method-modeling": methodModelingView,
   "model-editor": modelEditorView,
diff --git a/extensions/ql-vscode/supported_cli_versions.json b/extensions/ql-vscode/supported_cli_versions.json
index 31666d596d4..2a5361eb498 100644
--- a/extensions/ql-vscode/supported_cli_versions.json
+++ b/extensions/ql-vscode/supported_cli_versions.json
@@ -1,7 +1,7 @@
 [
-  "v2.18.1",
-  "v2.17.6",
-  "v2.16.6",
-  "v2.15.5",
+  "v2.23.3",
+  "v2.22.4",
+  "v2.21.4",
+  "v2.20.7",
   "nightly"
 ]
diff --git a/extensions/ql-vscode/syntaxes/ql.tmLanguage.yml b/extensions/ql-vscode/syntaxes/ql.tmLanguage.yml
index fe10a86d03d..9348f74f763 100644
--- a/extensions/ql-vscode/syntaxes/ql.tmLanguage.yml
+++ b/extensions/ql-vscode/syntaxes/ql.tmLanguage.yml
@@ -1065,7 +1065,7 @@ repository:
     beginPattern: '#as'
     # Ends after the first identifier we encounter.
     # REVIEW: Make similar to import-as-clause.
-    end: '(?<=(?#id-character)(?#end-of-id))'
+    end: '(?<=(?#id-character))(?#end-of-id)'
     match: meta.block.select-as-clause.ql
     patterns:
     - include: '#non-context-sensitive'
diff --git a/extensions/ql-vscode/test/benchmarks/jsonl-reader.bench.ts b/extensions/ql-vscode/test/benchmarks/jsonl-reader.bench.ts
new file mode 100644
index 00000000000..a5a3b64b0b2
--- /dev/null
+++ b/extensions/ql-vscode/test/benchmarks/jsonl-reader.bench.ts
@@ -0,0 +1,87 @@
+/**
+ * Benchmarks the jsonl-parser against a reference implementation and checks that it generates
+ * the same output.
+ *
+ * Usage:
+ *
+ *   ts-node json-reader.bench.ts [evaluator-log.summary.jsonl] [count]
+ *
+ * The log file defaults to a small checked-in log and count defaults to 100
+ * (and should be lowered significantly for large files).
+ *
+ * At the time of writing it is about as fast as the synchronous reference implementation,
+ * but doesn't run out of memory for large files.
+ */
+import { readFile } from "fs-extra";
+import { readJsonlFile } from "../../src/common/jsonl-reader";
+import { performance } from "perf_hooks";
+import { join } from "path";
+
+/** An "obviously correct" implementation to test against. */
+async function readJsonlReferenceImpl<T>(
+  path: string,
+  handler: (value: T) => Promise<void>,
+): Promise<void> {
+  const logSummary = await readFile(path, "utf-8");
+
+  // Remove newline delimiters because summary is in .jsonl format.
+  const jsonSummaryObjects: string[] = logSummary.split(/\r?\n\r?\n/g);
+
+  for (const obj of jsonSummaryObjects) {
+    const jsonObj = JSON.parse(obj) as T;
+    await handler(jsonObj);
+  }
+}
+
+type ParserFn = (
+  text: string,
+  callback: (v: unknown) => Promise<void>,
+) => Promise<void>;
+
+const parsers: Record<string, ParserFn> = {
+  readJsonlReferenceImpl,
+  readJsonlFile,
+};
+
+async function main() {
+  const args = process.argv.slice(2);
+  const file =
+    args.length > 0
+      ? args[0]
+      : join(
+          __dirname,
+          "../unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl",
+        );
+  const numTrials = args.length > 1 ? Number(args[1]) : 100;
+  const referenceValues: any[] = [];
+  await readJsonlReferenceImpl(file, async (event) => {
+    referenceValues.push(event);
+  });
+  const referenceValueString = JSON.stringify(referenceValues);
+  // Do warm-up runs and check against reference implementation
+  for (const [name, parser] of Object.entries(parsers)) {
+    const values: unknown[] = [];
+    await parser(file, async (event) => {
+      values.push(event);
+    });
+    if (JSON.stringify(values) !== referenceValueString) {
+      console.error(`${name}: failed to match reference implementation`);
+    }
+  }
+  for (const [name, parser] of Object.entries(parsers)) {
+    const startTime = performance.now();
+    for (let i = 0; i < numTrials; ++i) {
+      await Promise.all([
+        parser(file, async () => {}),
+        parser(file, async () => {}),
+      ]);
+    }
+    const duration = performance.now() - startTime;
+    const durationPerTrial = duration / numTrials;
+    console.log(`${name}: ${durationPerTrial.toFixed(1)} ms`);
+  }
+}
+
+main().catch((err: unknown) => {
+  console.error(err);
+});
diff --git a/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts b/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
index 0df03c32ea3..ad835dda77e 100644
--- a/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
+++ b/extensions/ql-vscode/test/common/logging/output-channel-logger.test.ts
@@ -50,7 +50,7 @@ describe("OutputChannelLogger tests", function () {
     tempFolders.storagePath.removeCallback();
   });
 
-  // eslint-disable-next-line @typescript-eslint/no-var-requires
+  // eslint-disable-next-line @typescript-eslint/no-require-imports
   const mockOutputChannel = require("vscode").mockOutputChannel;
 
   it("should log to the output channel", async () => {
diff --git a/extensions/ql-vscode/test/data-extensions/pack-using-extensions/codeql-pack.lock.yml b/extensions/ql-vscode/test/data-extensions/pack-using-extensions/codeql-pack.lock.yml
new file mode 100644
index 00000000000..61121d6d0cf
--- /dev/null
+++ b/extensions/ql-vscode/test/data-extensions/pack-using-extensions/codeql-pack.lock.yml
@@ -0,0 +1,26 @@
+---
+lockVersion: 1.0.0
+dependencies:
+  codeql/dataflow:
+    version: 2.0.7
+  codeql/javascript-all:
+    version: 2.6.3
+  codeql/mad:
+    version: 1.0.23
+  codeql/regex:
+    version: 1.0.23
+  codeql/ssa:
+    version: 1.1.2
+  codeql/threat-models:
+    version: 1.0.23
+  codeql/tutorial:
+    version: 1.0.23
+  codeql/typetracking:
+    version: 2.0.7
+  codeql/util:
+    version: 2.0.10
+  codeql/xml:
+    version: 1.0.23
+  codeql/yaml:
+    version: 1.0.23
+compiled: false
diff --git a/extensions/ql-vscode/test/data/debugger/QuickEvalBigIntQuery.ql b/extensions/ql-vscode/test/data/debugger/QuickEvalBigIntQuery.ql
new file mode 100644
index 00000000000..e17e9e0b614
--- /dev/null
+++ b/extensions/ql-vscode/test/data/debugger/QuickEvalBigIntQuery.ql
@@ -0,0 +1,31 @@
+import QuickEvalLib
+
+class InterestingBigInt instanceof InterestingNumber
+{
+    QlBuiltins::BigInt getBigIntValue() {
+        result = super.getValue().toBigInt().pow(10)
+    }
+
+    string toString() {
+        result = super.toString()
+    }
+}
+
+class PrimeNumber extends InterestingNumber {
+    PrimeNumber() {
+        exists(int n | this = MkNumber(n) |
+            n in [
+                2,
+                3,
+                5,
+                7,
+                11,
+                13,
+                17,
+                19
+            ])
+    }
+}
+
+from InterestingNumber n
+select n.toString()
diff --git a/extensions/ql-vscode/test/e2e/README.md b/extensions/ql-vscode/test/e2e/README.md
index c91c802835f..824c76535ee 100644
--- a/extensions/ql-vscode/test/e2e/README.md
+++ b/extensions/ql-vscode/test/e2e/README.md
@@ -9,12 +9,12 @@ Setup
 - install playwright if you haven't yet (`npx playwright install`)
 - go to the e2e test folder on your terminal
 - make sure docker is running
-- run `docker-compose build`
-- run `docker-compose up`
+- run `docker compose build`
+- run `docker compose up`
 
 Run tests
 
-- run  `npx playwright test --ui` from the e2e test folder to follow the test while it's running. This UI has a 'locator' tool with which elements on the test screen can be found
+- run `npx playwright test --ui` from the e2e test folder to follow the test while it's running. This UI has a 'locator' tool with which elements on the test screen can be found
 - use `npx playwright test --debug` to follow the test in real time and interact with the interface, e.g. press enter or input into fields, stop and start
 
 During the test elements are created in the docker volume, e.g. the downloaded database or query data. This might interfer with other tests or when running a test twice. If that happens restart your docker volume by using `docker-compose down -v` and `docker-compose up`. Sometimes already existing queries from former runs change the input the extension needs.
diff --git a/extensions/ql-vscode/test/e2e/docker-compose.yml b/extensions/ql-vscode/test/e2e/docker-compose.yml
index 76a3f265f89..1afb2090e94 100644
--- a/extensions/ql-vscode/test/e2e/docker-compose.yml
+++ b/extensions/ql-vscode/test/e2e/docker-compose.yml
@@ -1,5 +1,3 @@
-version: "3.8"
-
 services:
   code-server:
     build:
@@ -38,7 +36,7 @@ services:
     depends_on:
       - files-init
   files-init:
-    image: alpine:3.19.1
+    image: alpine:3.21.0
     restart: "no"
     # Since we're not running the code-server container using the same user as our host user,
     # we need to set the permissions on the mounted volumes to match the user inside the container.
diff --git a/extensions/ql-vscode/test/e2e/docker/Dockerfile b/extensions/ql-vscode/test/e2e/docker/Dockerfile
index c27d3a3cd62..7f7b22e1a57 100644
--- a/extensions/ql-vscode/test/e2e/docker/Dockerfile
+++ b/extensions/ql-vscode/test/e2e/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM codercom/code-server:4.23.1
+FROM codercom/code-server:4.104.1
 
 USER root
 
diff --git a/extensions/ql-vscode/test/e2e/docker/User/settings.json b/extensions/ql-vscode/test/e2e/docker/User/settings.json
index 8dfd44b281c..bd40904834a 100644
--- a/extensions/ql-vscode/test/e2e/docker/User/settings.json
+++ b/extensions/ql-vscode/test/e2e/docker/User/settings.json
@@ -1,6 +1,5 @@
 {
   "workbench.startupEditor": "none",
   "security.workspace.trust.enabled": false,
-  "codeQL.cli.executablePath": "/opt/codeql/codeql",
-  "codeQL.telemetry.enableTelemetry": false
+  "codeQL.cli.executablePath": "/opt/codeql/codeql"
 }
diff --git a/extensions/ql-vscode/test/e2e/run-query.spec.ts b/extensions/ql-vscode/test/e2e/run-query.spec.ts
index 6007a279fd6..1bec2591355 100644
--- a/extensions/ql-vscode/test/e2e/run-query.spec.ts
+++ b/extensions/ql-vscode/test/e2e/run-query.spec.ts
@@ -5,11 +5,6 @@ test("run query and open it from history", async ({ page }) => {
 
   await page.getByRole("tab", { name: "CodeQL" }).locator("a").click();
 
-  // decline extension telemetry
-  await page.getByRole("button", { name: "No", exact: true }).click({
-    timeout: 60000,
-  });
-
   await page.keyboard.press("Control+Shift+P");
   await page.keyboard.type("Create Query");
   await page.keyboard.press("Enter");
diff --git a/extensions/ql-vscode/test/factories/model-editor/extension-pack.ts b/extensions/ql-vscode/test/factories/model-editor/extension-pack.ts
index cca396c85bd..a3459694ba6 100644
--- a/extensions/ql-vscode/test/factories/model-editor/extension-pack.ts
+++ b/extensions/ql-vscode/test/factories/model-editor/extension-pack.ts
@@ -1,5 +1,4 @@
 import type { ExtensionPack } from "../../../src/model-editor/shared/extension-pack";
-import { join } from "path";
 
 export function createMockExtensionPack({
   path = "/path/to/extension-pack",
@@ -7,7 +6,7 @@ export function createMockExtensionPack({
 }: Partial<ExtensionPack> = {}): ExtensionPack {
   return {
     path,
-    yamlPath: join(path, "codeql-pack.yml"),
+    yamlPath: `${path}/codeql-pack.yml`,
     name: "sql2o",
     version: "0.0.0",
     language: "java",
diff --git a/extensions/ql-vscode/test/factories/model-editor/view-state.ts b/extensions/ql-vscode/test/factories/model-editor/view-state.ts
index f7d338a19cd..62c42f98ca6 100644
--- a/extensions/ql-vscode/test/factories/model-editor/view-state.ts
+++ b/extensions/ql-vscode/test/factories/model-editor/view-state.ts
@@ -11,7 +11,6 @@ export function createMockModelEditorViewState(
     language: QueryLanguage.Java,
     mode: Mode.Application,
     showGenerateButton: false,
-    showLlmButton: false,
     showEvaluationUi: false,
     showModeSwitchButton: true,
     extensionPack: createMockExtensionPack(),
diff --git a/extensions/ql-vscode/test/factories/results/mockresults.ts b/extensions/ql-vscode/test/factories/results/mockresults.ts
new file mode 100644
index 00000000000..368c05bb312
--- /dev/null
+++ b/extensions/ql-vscode/test/factories/results/mockresults.ts
@@ -0,0 +1,104 @@
+import type { Result } from "sarif";
+
+export function createMockResults(): Result[] {
+  return [
+    {
+      ruleId: "java/sql-injection",
+      ruleIndex: 0,
+      rule: { id: "java/sql-injection", index: 0 },
+      message: {
+        text: "This query depends on a [user-provided value](1).",
+      },
+      locations: [
+        {
+          physicalLocation: {
+            artifactLocation: {
+              uri: "src/main/java/org/example/HelloController.java",
+              uriBaseId: "%SRCROOT%",
+              index: 0,
+            },
+            region: { startLine: 15, startColumn: 29, endColumn: 56 },
+          },
+        },
+      ],
+      partialFingerprints: {
+        primaryLocationLineHash: "87e2d3cc5b365094:1",
+        primaryLocationStartColumnFingerprint: "16",
+      },
+      codeFlows: [
+        {
+          threadFlows: [
+            {
+              locations: [
+                {
+                  location: {
+                    physicalLocation: {
+                      artifactLocation: {
+                        uri: "src/main/java/org/example/HelloController.java",
+                        uriBaseId: "%SRCROOT%",
+                        index: 0,
+                      },
+                      region: {
+                        startLine: 13,
+                        startColumn: 25,
+                        endColumn: 54,
+                      },
+                    },
+                    message: { text: "id : String" },
+                  },
+                },
+                {
+                  location: {
+                    physicalLocation: {
+                      artifactLocation: {
+                        uri: "file:/",
+                        index: 5,
+                      },
+                      region: {
+                        startLine: 13,
+                        startColumn: 25,
+                        endColumn: 54,
+                      },
+                    },
+                    message: { text: "id : String" },
+                  },
+                },
+                {
+                  location: {
+                    physicalLocation: {
+                      artifactLocation: {
+                        uri: "src/main/java/org/example/HelloController.java",
+                        uriBaseId: "%SRCROOT%",
+                        index: 0,
+                      },
+                      region: {
+                        startLine: 15,
+                        startColumn: 29,
+                        endColumn: 56,
+                      },
+                    },
+                    message: { text: "... + ..." },
+                  },
+                },
+              ],
+            },
+          ],
+        },
+      ],
+      relatedLocations: [
+        {
+          id: 1,
+          physicalLocation: {
+            artifactLocation: {
+              uri: "src/main/java/org/example/HelloController.java",
+              uriBaseId: "%SRCROOT%",
+              index: 0,
+            },
+            region: { startLine: 13, startColumn: 25, endColumn: 54 },
+          },
+          message: { text: "user-provided value" },
+        },
+      ],
+    },
+  ];
+}
diff --git a/extensions/ql-vscode/test/factories/variant-analysis/gh-api/variant-analysis-repo-task.ts b/extensions/ql-vscode/test/factories/variant-analysis/gh-api/variant-analysis-repo-task.ts
index cbfa5369e13..23e46b8b104 100644
--- a/extensions/ql-vscode/test/factories/variant-analysis/gh-api/variant-analysis-repo-task.ts
+++ b/extensions/ql-vscode/test/factories/variant-analysis/gh-api/variant-analysis-repo-task.ts
@@ -3,7 +3,8 @@ import type { VariantAnalysisRepoTask } from "../../../../src/variant-analysis/g
 import { VariantAnalysisRepoStatus } from "../../../../src/variant-analysis/shared/variant-analysis";
 import { createMockRepository } from "./repository";
 
-export function createMockVariantAnalysisRepoTask(): VariantAnalysisRepoTask {
+export function createMockVariantAnalysisRepoTask(): VariantAnalysisRepoTask &
+  Required<Pick<VariantAnalysisRepoTask, "artifact_url">> {
   return {
     repository: {
       ...createMockRepository(),
@@ -12,6 +13,6 @@ export function createMockVariantAnalysisRepoTask(): VariantAnalysisRepoTask {
     analysis_status: VariantAnalysisRepoStatus.Succeeded,
     result_count: faker.number.int(),
     artifact_size_in_bytes: faker.number.int(),
-    artifact_url: "https://www.pickles.com/",
+    artifact_url: faker.internet.url(),
   };
 }
diff --git a/extensions/ql-vscode/test/factories/variant-analysis/shared/variant-analysis-repo-tasks.ts b/extensions/ql-vscode/test/factories/variant-analysis/shared/variant-analysis-repo-tasks.ts
index a9f230cb390..e33500657b8 100644
--- a/extensions/ql-vscode/test/factories/variant-analysis/shared/variant-analysis-repo-tasks.ts
+++ b/extensions/ql-vscode/test/factories/variant-analysis/shared/variant-analysis-repo-tasks.ts
@@ -5,7 +5,8 @@ import { createMockRepositoryWithMetadata } from "./repository";
 
 export function createMockVariantAnalysisRepositoryTask(
   data?: Partial<VariantAnalysisRepositoryTask>,
-): VariantAnalysisRepositoryTask {
+): VariantAnalysisRepositoryTask &
+  Required<Pick<VariantAnalysisRepositoryTask, "artifactUrl">> {
   return {
     repository: createMockRepositoryWithMetadata(),
     analysisStatus: VariantAnalysisRepoStatus.Pending,
diff --git a/extensions/ql-vscode/test/jest-config.ts b/extensions/ql-vscode/test/jest-config.ts
new file mode 100644
index 00000000000..3270067df7a
--- /dev/null
+++ b/extensions/ql-vscode/test/jest-config.ts
@@ -0,0 +1,35 @@
+// These are all the packages that DO need to be transformed. All other packages will be ignored.
+// These pacakges all use ES modules, so need to be transformed
+const transformScopes = [
+  "@microsoft",
+  "@octokit",
+  "@vscode-elements",
+  "@lit",
+  "@lit-labs",
+];
+const transformPackages = [
+  "before-after-hook",
+  "d3",
+  "data-uri-to-buffer",
+  "delaunator",
+  "exenv-es6",
+  "fetch-blob",
+  "formdata-polyfill",
+  "internmap",
+  "lit",
+  "nanoid",
+  "p-queue",
+  "p-timeout",
+  "robust-predicates",
+  "universal-user-agent",
+];
+const transformWildcards = ["d3-(.*)", "lit-(.*)"];
+const transformPatterns = [
+  ...transformScopes.map((scope) => `${scope}/.+`),
+  ...transformPackages,
+  ...transformWildcards,
+];
+
+export const transformIgnorePatterns = [
+  `node_modules/(?!(?:${transformPatterns.join("|")})/.*)`,
+];
diff --git a/extensions/ql-vscode/test/mock-memento.ts b/extensions/ql-vscode/test/mock-memento.ts
index d5f12ec5c38..8d2a036ff81 100644
--- a/extensions/ql-vscode/test/mock-memento.ts
+++ b/extensions/ql-vscode/test/mock-memento.ts
@@ -17,7 +17,7 @@ class MockMemento<T> implements Memento {
 
   public get<T>(key: string): T | undefined;
   public get<T>(key: string, defaultValue: T): T;
-  public get(key: any, defaultValue?: any): T | T | undefined {
+  public get(key: any, defaultValue?: T): T | undefined {
     return this.map.get(key) || defaultValue;
   }
 
diff --git a/extensions/ql-vscode/test/mocked-object.ts b/extensions/ql-vscode/test/mocked-object.ts
index e20caba295b..bd4374a843b 100644
--- a/extensions/ql-vscode/test/mocked-object.ts
+++ b/extensions/ql-vscode/test/mocked-object.ts
@@ -25,9 +25,11 @@ export function mockedObject<T extends object>(
   return new Proxy<T>({} as unknown as T, {
     get: (_target, prop) => {
       if (prop in props) {
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-return
         return (props as any)[prop];
       }
       if (dynamicProperties && prop in dynamicProperties) {
+        // eslint-disable-next-line @typescript-eslint/no-unsafe-return
         return (dynamicProperties as any)[prop]();
       }
 
diff --git a/extensions/ql-vscode/test/unit-tests/codeql-cli/distribution/releases-api-consumer.test.ts b/extensions/ql-vscode/test/unit-tests/codeql-cli/distribution/releases-api-consumer.test.ts
index d1d238c3431..a8d4bb40674 100644
--- a/extensions/ql-vscode/test/unit-tests/codeql-cli/distribution/releases-api-consumer.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/codeql-cli/distribution/releases-api-consumer.test.ts
@@ -1,4 +1,3 @@
-import { Response } from "node-fetch";
 import { Range } from "semver";
 
 import type { GithubRelease } from "../../../../src/codeql-cli/distribution/releases-api-consumer";
diff --git a/extensions/ql-vscode/test/unit-tests/common/disposable-object.test.ts b/extensions/ql-vscode/test/unit-tests/common/disposable-object.test.ts
index b211141e39c..381bf838d2c 100644
--- a/extensions/ql-vscode/test/unit-tests/common/disposable-object.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/common/disposable-object.test.ts
@@ -77,10 +77,10 @@ describe("DisposableObject and DisposeHandler", () => {
     expect(disposable1.dispose).toHaveBeenCalled();
   });
 
-  it("ahould use a dispose handler", () => {
+  it("should use a dispose handler", () => {
     const handler = (d: any) =>
       d === disposable1 || d === disposable3 || d === nestedDisposableObject
-        ? d.dispose(handler)
+        ? void d.dispose(handler)
         : void 0;
 
     disposableObject.push(disposable1);
diff --git a/extensions/ql-vscode/test/unit-tests/common/errors.test.ts b/extensions/ql-vscode/test/unit-tests/common/errors.test.ts
index ca9e01de37e..0f9cabf5c37 100644
--- a/extensions/ql-vscode/test/unit-tests/common/errors.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/common/errors.test.ts
@@ -37,7 +37,7 @@ describe("errorMessage", () => {
       myRealFunction();
 
       fail("Expected an error to be thrown");
-    } catch (e: unknown) {
+    } catch (e) {
       if (!(e instanceof Error)) {
         throw new Error("Expected an Error to be thrown");
       }
diff --git a/extensions/ql-vscode/test/unit-tests/common/files.test.ts b/extensions/ql-vscode/test/unit-tests/common/files.test.ts
index 9c435a3b4c6..b9b90136ee9 100644
--- a/extensions/ql-vscode/test/unit-tests/common/files.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/common/files.test.ts
@@ -66,18 +66,19 @@ describe("files", () => {
 
     it("should scan a directory", async () => {
       const file1 = join(dataDir, "compute-default-strings.ql");
-      const file2 = join(dataDir, "debugger", "QuickEvalQuery.ql");
-      const file3 = join(dataDir, "debugger", "simple-query.ql");
-      const file4 = join(dataDir, "multiple-result-sets.ql");
-      const file5 = join(dataDir, "query.ql");
+      const file2 = join(dataDir, "debugger", "QuickEvalBigIntQuery.ql");
+      const file3 = join(dataDir, "debugger", "QuickEvalQuery.ql");
+      const file4 = join(dataDir, "debugger", "simple-query.ql");
+      const file5 = join(dataDir, "multiple-result-sets.ql");
+      const file6 = join(dataDir, "query.ql");
 
       const vaDir = join(dataDir, "variant-analysis-query-packs");
-      const file6 = join(vaDir, "workspace1", "dir1", "query1.ql");
-      const file7 = join(vaDir, "workspace1", "pack1", "query1.ql");
-      const file8 = join(vaDir, "workspace1", "pack1", "query2.ql");
-      const file9 = join(vaDir, "workspace1", "pack2", "query1.ql");
-      const file10 = join(vaDir, "workspace1", "query1.ql");
-      const file11 = join(vaDir, "workspace2", "query1.ql");
+      const file7 = join(vaDir, "workspace1", "dir1", "query1.ql");
+      const file8 = join(vaDir, "workspace1", "pack1", "query1.ql");
+      const file9 = join(vaDir, "workspace1", "pack1", "query2.ql");
+      const file10 = join(vaDir, "workspace1", "pack2", "query1.ql");
+      const file11 = join(vaDir, "workspace1", "query1.ql");
+      const file12 = join(vaDir, "workspace2", "query1.ql");
 
       const result = await gatherQlFiles([dataDir]);
       expect(result.sort()).toEqual([
@@ -93,6 +94,7 @@ describe("files", () => {
           file9,
           file10,
           file11,
+          file12,
         ],
         true,
       ]);
@@ -112,18 +114,19 @@ describe("files", () => {
 
     it("should avoid duplicates", async () => {
       const file1 = join(dataDir, "compute-default-strings.ql");
-      const file2 = join(dataDir, "debugger", "QuickEvalQuery.ql");
-      const file3 = join(dataDir, "debugger", "simple-query.ql");
-      const file4 = join(dataDir, "multiple-result-sets.ql");
-      const file5 = join(dataDir, "query.ql");
+      const file2 = join(dataDir, "debugger", "QuickEvalBigIntQuery.ql");
+      const file3 = join(dataDir, "debugger", "QuickEvalQuery.ql");
+      const file4 = join(dataDir, "debugger", "simple-query.ql");
+      const file5 = join(dataDir, "multiple-result-sets.ql");
+      const file6 = join(dataDir, "query.ql");
 
       const vaDir = join(dataDir, "variant-analysis-query-packs");
-      const file6 = join(vaDir, "workspace1", "dir1", "query1.ql");
-      const file7 = join(vaDir, "workspace1", "pack1", "query1.ql");
-      const file8 = join(vaDir, "workspace1", "pack1", "query2.ql");
-      const file9 = join(vaDir, "workspace1", "pack2", "query1.ql");
-      const file10 = join(vaDir, "workspace1", "query1.ql");
-      const file11 = join(vaDir, "workspace2", "query1.ql");
+      const file7 = join(vaDir, "workspace1", "dir1", "query1.ql");
+      const file8 = join(vaDir, "workspace1", "pack1", "query1.ql");
+      const file9 = join(vaDir, "workspace1", "pack1", "query2.ql");
+      const file10 = join(vaDir, "workspace1", "pack2", "query1.ql");
+      const file11 = join(vaDir, "workspace1", "query1.ql");
+      const file12 = join(vaDir, "workspace2", "query1.ql");
 
       const result = await gatherQlFiles([file1, dataDir, file3, file4, file5]);
       result[0].sort();
@@ -140,6 +143,7 @@ describe("files", () => {
           file9,
           file10,
           file11,
+          file12,
         ],
         true,
       ]);
diff --git a/extensions/ql-vscode/test/unit-tests/common/invocation-rate-limiter.test.ts b/extensions/ql-vscode/test/unit-tests/common/invocation-rate-limiter.test.ts
index 4623c62a523..d29b60261b8 100644
--- a/extensions/ql-vscode/test/unit-tests/common/invocation-rate-limiter.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/common/invocation-rate-limiter.test.ts
@@ -39,8 +39,8 @@ describe("Invocation rate limiter", () => {
      * value (`undefined`) with the given key.
      * @return The stored value or the defaultValue.
      */
-    get<T>(key: string, defaultValue?: T): T {
-      return this.map.has(key) ? this.map.get(key) : defaultValue;
+    get<T>(key: string, defaultValue?: T): T | undefined {
+      return this.map.has(key) ? (this.map.get(key) as T) : defaultValue;
     }
 
     /**
diff --git a/extensions/ql-vscode/test/unit-tests/compare/differentPathsDifferentSourceSink.json b/extensions/ql-vscode/test/unit-tests/compare/differentPathsDifferentSourceSink.json
new file mode 100644
index 00000000000..9188cde5156
--- /dev/null
+++ b/extensions/ql-vscode/test/unit-tests/compare/differentPathsDifferentSourceSink.json
@@ -0,0 +1,23905 @@
+{
+  "result1": {
+    "ruleId": "java/polynomial-redos",
+    "ruleIndex": 0,
+    "rule": {
+      "id": "java/polynomial-redos",
+      "index": 0
+    },
+    "message": {
+      "text": "This [regular expression](1) that depends on a [user-provided value](2) may run slow on strings with many repetitions of '\\\\t'."
+    },
+    "locations": [
+      {
+        "physicalLocation": {
+          "artifactLocation": {
+            "uri": "src/java.base/share/classes/java/lang/String.java",
+            "uriBaseId": "%SRCROOT%",
+            "index": 0
+          },
+          "region": {
+            "startLine": 2855,
+            "startColumn": 39,
+            "endColumn": 43
+          }
+        }
+      }
+    ],
+    "partialFingerprints": {
+      "primaryLocationLineHash": "5270db7557dfd174:1",
+      "primaryLocationStartColumnFingerprint": "30"
+    },
+    "codeFlows": [
+      {
+        "threadFlows": [
+          {
+            "locations": [
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 142,
+                      "startColumn": 43,
+                      "endColumn": 73
+                    }
+                  },
+                  "message": {
+                    "text": "getInputStream(...) : InputStream"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 0,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "source"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 147,
+                      "startColumn": 32,
+                      "endColumn": 43
+                    }
+                  },
+                  "message": {
+                    "text": "inputStream : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 147,
+                      "startColumn": 49,
+                      "endColumn": 52
+                    }
+                  },
+                  "message": {
+                    "text": "buf [post update] : byte[]"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 9,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 148,
+                      "startColumn": 32,
+                      "endColumn": 35
+                    }
+                  },
+                  "message": {
+                    "text": "buf : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 148,
+                      "startColumn": 21,
+                      "endColumn": 25
+                    }
+                  },
+                  "message": {
+                    "text": "baos [post update] : ByteArrayOutputStream"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 10,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 154,
+                      "startColumn": 66,
+                      "endColumn": 70
+                    }
+                  },
+                  "message": {
+                    "text": "baos : ByteArrayOutputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 154,
+                      "startColumn": 66,
+                      "endColumn": 84
+                    }
+                  },
+                  "message": {
+                    "text": "toByteArray(...) : byte[]"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 11,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 126,
+                      "startColumn": 30,
+                      "endColumn": 48
+                    }
+                  },
+                  "message": {
+                    "text": "inputOctets : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 128,
+                      "startColumn": 22,
+                      "endColumn": 33
+                    }
+                  },
+                  "message": {
+                    "text": "inputOctets : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 128,
+                      "startColumn": 9,
+                      "endColumn": 13
+                    }
+                  },
+                  "message": {
+                    "text": "this [post update] : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 154,
+                      "startColumn": 44,
+                      "endColumn": 85
+                    }
+                  },
+                  "message": {
+                    "text": "new XMLSignatureInput(...) : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/implementations/ResolverDirectHTTP.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 160,
+                      "startColumn": 24,
+                      "endColumn": 30
+                    }
+                  },
+                  "message": {
+                    "text": "result : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/utils/resolver/ResourceResolver.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 47
+                    },
+                    "region": {
+                      "startLine": 162,
+                      "startColumn": 24,
+                      "endColumn": 58
+                    }
+                  },
+                  "message": {
+                    "text": "engineResolveURI(...) : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/DOMURIDereferencer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 48
+                    },
+                    "region": {
+                      "startLine": 144,
+                      "startColumn": 36,
+                      "endColumn": 72
+                    }
+                  },
+                  "message": {
+                    "text": "resolve(...) : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/DOMURIDereferencer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 48
+                    },
+                    "region": {
+                      "startLine": 146,
+                      "startColumn": 50,
+                      "endColumn": 52
+                    }
+                  },
+                  "message": {
+                    "text": "in : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/ApacheOctetStreamData.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 49
+                    },
+                    "region": {
+                      "startLine": 37,
+                      "startColumn": 34,
+                      "endColumn": 54
+                    }
+                  },
+                  "message": {
+                    "text": "xi : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/ApacheOctetStreamData.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 49
+                    },
+                    "region": {
+                      "startLine": 40,
+                      "startColumn": 15,
+                      "endColumn": 17
+                    }
+                  },
+                  "message": {
+                    "text": "xi : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 243,
+                      "startColumn": 24,
+                      "endColumn": 38
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 249,
+                      "startColumn": 62,
+                      "endColumn": 67
+                    }
+                  },
+                  "message": {
+                    "text": "this <.field> : XMLSignatureInput [bytes] : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 249,
+                      "startColumn": 62,
+                      "endColumn": 67
+                    }
+                  },
+                  "message": {
+                    "text": "bytes : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 249,
+                      "startColumn": 37,
+                      "endColumn": 68
+                    }
+                  },
+                  "message": {
+                    "text": "new ByteArrayInputStream(...) : ByteArrayInputStream"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 12,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/com/sun/org/apache/xml/internal/security/signature/XMLSignatureInput.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 46
+                    },
+                    "region": {
+                      "startLine": 250,
+                      "startColumn": 20,
+                      "endColumn": 41
+                    }
+                  },
+                  "message": {
+                    "text": "inputOctetStreamProxy : ByteArrayInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/ApacheOctetStreamData.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 49
+                    },
+                    "region": {
+                      "startLine": 40,
+                      "startColumn": 15,
+                      "endColumn": 34
+                    }
+                  },
+                  "message": {
+                    "text": "getOctetStream(...) : ByteArrayInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/ApacheOctetStreamData.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 49
+                    },
+                    "region": {
+                      "startLine": 40,
+                      "startColumn": 9,
+                      "endColumn": 73
+                    }
+                  },
+                  "message": {
+                    "text": "this <constr(this)> [post update] : ApacheOctetStreamData"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 13,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/DOMURIDereferencer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 48
+                    },
+                    "region": {
+                      "startLine": 146,
+                      "startColumn": 24,
+                      "endColumn": 53
+                    }
+                  },
+                  "message": {
+                    "text": "new ApacheOctetStreamData(...) : ApacheOctetStreamData"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/DOMReference.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 50
+                    },
+                    "region": {
+                      "startLine": 416,
+                      "startColumn": 20,
+                      "endColumn": 52
+                    }
+                  },
+                  "message": {
+                    "text": "dereference(...) : ApacheOctetStreamData"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml.crypto/share/classes/org/jcp/xml/dsig/internal/dom/DOMReference.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 50
+                    },
+                    "region": {
+                      "startLine": 423,
+                      "startColumn": 16,
+                      "endColumn": 20
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+                    "artifactLocation": {
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+                      "uriBaseId": "%SRCROOT%",
+                      "index": 2
+                    },
+                    "region": {
+                      "startLine": 1310,
+                      "startColumn": 43,
+                      "endColumn": 49
+                    }
+                  },
+                  "message": {
+                    "text": "this <.field> : PrivilegedOperation [params, []] : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management.rmi/share/classes/javax/management/remote/rmi/RMIConnectionImpl.java",
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+                      "index": 2
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+                    "region": {
+                      "startLine": 1310,
+                      "startColumn": 43,
+                      "endColumn": 49
+                    }
+                  },
+                  "message": {
+                    "text": "params : Object[] [[]] : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management.rmi/share/classes/javax/management/remote/rmi/RMIConnectionImpl.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 2
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+                    "region": {
+                      "startLine": 1421,
+                      "startColumn": 47,
+                      "endColumn": 62
+                    }
+                  },
+                  "message": {
+                    "text": "params : Object[] [[]] : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management.rmi/share/classes/javax/management/remote/rmi/RMIConnectionImpl.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 2
+                    },
+                    "region": {
+                      "startLine": 1431,
+                      "startColumn": 52,
+                      "endColumn": 58
+                    }
+                  },
+                  "message": {
+                    "text": "params : Object[] [[]] : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management.rmi/share/classes/javax/management/remote/rmi/RMIConnectionImpl.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 2
+                    },
+                    "region": {
+                      "startLine": 1431,
+                      "startColumn": 52,
+                      "endColumn": 61
+                    }
+                  },
+                  "message": {
+                    "text": "...[...] : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management.rmi/share/classes/javax/management/remote/rmi/RMIConnectionImpl.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 2
+                    },
+                    "region": {
+                      "startLine": 1431,
+                      "startColumn": 44,
+                      "endColumn": 61
+                    }
+                  },
+                  "message": {
+                    "text": "(...)... : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 3
+                    },
+                    "region": {
+                      "startLine": 220,
+                      "startColumn": 39,
+                      "endColumn": 55
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
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+                    },
+                    "region": {
+                      "startLine": 230,
+                      "startColumn": 21,
+                      "endColumn": 30
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 247,
+                      "startColumn": 29,
+                      "endColumn": 45
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 248,
+                      "startColumn": 40,
+                      "endColumn": 49
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 303,
+                      "startColumn": 70,
+                      "endColumn": 80
+                    }
+                  },
+                  "message": {
+                    "text": "arg : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 333,
+                      "startColumn": 56,
+                      "endColumn": 59
+                    }
+                  },
+                  "message": {
+                    "text": "arg : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 360,
+                      "startColumn": 61,
+                      "endColumn": 77
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 362,
+                      "startColumn": 50,
+                      "endColumn": 59
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 368,
+                      "startColumn": 59,
+                      "endColumn": 75
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.management/share/classes/com/sun/jmx/remote/security/MBeanServerFileAccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 4
+                    },
+                    "region": {
+                      "startLine": 387,
+                      "startColumn": 16,
+                      "endColumn": 25
+                    }
+                  },
+                  "message": {
+                    "text": "className : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/String.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 0
+                    },
+                    "region": {
+                      "startLine": 2854,
+                      "startColumn": 20,
+                      "endColumn": 27
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/String.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 0
+                    },
+                    "region": {
+                      "startLine": 2855,
+                      "startColumn": 39,
+                      "endColumn": 43
+                    }
+                  },
+                  "message": {
+                    "text": "this"
+                  }
+                }
+              }
+            ]
+          }
+        ]
+      }
+    ],
+    "relatedLocations": [
+      {
+        "id": 1,
+        "physicalLocation": {
+          "artifactLocation": {
+            "uri": "src/jdk.compiler/share/classes/com/sun/tools/javac/main/Main.java",
+            "uriBaseId": "%SRCROOT%",
+            "index": 1
+          },
+          "region": {
+            "startLine": 379,
+            "startColumn": 42,
+            "endColumn": 46
+          }
+        },
+        "message": {
+          "text": "regular expression"
+        }
+      },
+      {
+        "id": 2,
+        "physicalLocation": {
+          "artifactLocation": {
+            "uri": "src/java.base/share/classes/java/net/URLClassLoader.java",
+            "uriBaseId": "%SRCROOT%",
+            "index": 31
+          },
+          "region": {
+            "startLine": 296,
+            "startColumn": 30,
+            "endColumn": 51
+          }
+        },
+        "message": {
+          "text": "user-provided value"
+        }
+      }
+    ]
+  }
+}
diff --git a/extensions/ql-vscode/test/unit-tests/compare/differentPathsSameSourceSink.json b/extensions/ql-vscode/test/unit-tests/compare/differentPathsSameSourceSink.json
new file mode 100644
index 00000000000..fe5a756f62a
--- /dev/null
+++ b/extensions/ql-vscode/test/unit-tests/compare/differentPathsSameSourceSink.json
@@ -0,0 +1,13390 @@
+{
+  "result1": {
+    "ruleId": "java/polynomial-redos",
+    "ruleIndex": 0,
+    "rule": {
+      "id": "java/polynomial-redos",
+      "index": 0
+    },
+    "message": {
+      "text": "This [regular expression](1) that depends on a [user-provided value](2) may run slow on strings with many repetitions of '\\\\t'."
+    },
+    "locations": [
+      {
+        "physicalLocation": {
+          "artifactLocation": {
+            "uri": "src/java.base/share/classes/java/lang/String.java",
+            "uriBaseId": "%SRCROOT%",
+            "index": 0
+          },
+          "region": {
+            "startLine": 2855,
+            "startColumn": 39,
+            "endColumn": 43
+          }
+        }
+      }
+    ],
+    "partialFingerprints": {
+      "primaryLocationLineHash": "5270db7557dfd174:1",
+      "primaryLocationStartColumnFingerprint": "30"
+    },
+    "codeFlows": [
+      {
+        "threadFlows": [
+          {
+            "locations": [
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 654,
+                      "startColumn": 30,
+                      "endColumn": 54
+                    }
+                  },
+                  "message": {
+                    "text": "getInputStream(...) : InputStream"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 0,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "source"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 697,
+                      "startColumn": 80,
+                      "endColumn": 86
+                    }
+                  },
+                  "message": {
+                    "text": "stream : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 3003,
+                      "startColumn": 38,
+                      "endColumn": 52
+                    }
+                  },
+                  "message": {
+                    "text": "is : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 3005,
+                      "startColumn": 28,
+                      "endColumn": 30
+                    }
+                  },
+                  "message": {
+                    "text": "is : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 3005,
+                      "startColumn": 13,
+                      "endColumn": 25
+                    }
+                  },
+                  "message": {
+                    "text": "this <.field> [post update] : RewindableInputStream [fInputStream] : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 697,
+                      "startColumn": 54,
+                      "endColumn": 87
+                    }
+                  },
+                  "message": {
+                    "text": "new RewindableInputStream(...) : RewindableInputStream [fInputStream] : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 720,
+                      "startColumn": 29,
+                      "endColumn": 35
+                    }
+                  },
+                  "message": {
+                    "text": "stream : RewindableInputStream [fInputStream] : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 3089,
+                      "startColumn": 21,
+                      "endColumn": 25
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : RewindableInputStream [fInputStream] : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 3099,
+                      "startColumn": 24,
+                      "endColumn": 36
+                    }
+                  },
+                  "message": {
+                    "text": "this <.field> : RewindableInputStream [fInputStream] : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 9
+                    },
+                    "region": {
+                      "startLine": 3099,
+                      "startColumn": 24,
+                      "endColumn": 36
+                    }
+                  },
+                  "message": {
+                    "text": "fInputStream : InputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 3687,
+                      "startColumn": 21,
+                      "endColumn": 25
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 3701,
+                      "startColumn": 22,
+                      "endLine": 3702,
+                      "endColumn": 71
+                    }
+                  },
+                  "message": {
+                    "text": "this <.method> : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 3649,
+                      "startColumn": 20,
+                      "endColumn": 24
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 3652,
+                      "startColumn": 30,
+                      "endColumn": 35
+                    }
+                  },
+                  "message": {
+                    "text": "super : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 3652,
+                      "startColumn": 41,
+                      "endColumn": 42
+                    }
+                  },
+                  "message": {
+                    "text": "b [post update] : byte[]"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 1,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 1964,
+                      "startColumn": 47,
+                      "endColumn": 93
+                    }
+                  },
+                  "message": {
+                    "text": "new HttpInputStream(...) : HttpInputStream"
+                  }
+                },
+                "taxa": [
+                  {
+                    "id": "AdditionalTaintStep",
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 1985,
+                      "startColumn": 24,
+                      "endColumn": 35
+                    }
+                  },
+                  "message": {
+                    "text": "inputStream : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/sun/net/www/protocol/http/HttpURLConnection.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 10
+                    },
+                    "region": {
+                      "startLine": 1573,
+                      "startColumn": 44,
+                      "endColumn": 61
+                    }
+                  },
+                  "message": {
+                    "text": "getInputStream0(...) : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/security/AccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 5
+                    },
+                    "region": {
+                      "startLine": 809,
+                      "startColumn": 20,
+                      "endColumn": 32
+                    }
+                  },
+                  "message": {
+                    "text": "run(...) : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/security/AccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 5
+                    },
+                    "region": {
+                      "startLine": 816,
+                      "startColumn": 16,
+                      "endColumn": 22
+                    }
+                  },
+                  "message": {
+                    "text": "result : HttpInputStream"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/security/AccessController.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 5
+                    },
+                    "region": {
+                      "startLine": 571,
+                      "startColumn": 20,
+                      "endColumn": 62
+                    }
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+                      "uri": "src/java.desktop/share/classes/javax/swing/text/rtf/MockAttributeSet.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 14
+                    },
+                    "region": {
+                      "startLine": 67,
+                      "startColumn": 16,
+                      "endColumn": 33
+                    }
+                  },
+                  "message": {
+                    "text": "get(...) : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/text/StyleContext.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 40
+                    },
+                    "region": {
+                      "startLine": 1496,
+                      "startColumn": 20,
+                      "endColumn": 53
+                    }
+                  },
+                  "message": {
+                    "text": "getAttribute(...) : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/text/SimpleAttributeSet.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 15
+                    },
+                    "region": {
+                      "startLine": 151,
+                      "startColumn": 25,
+                      "endColumn": 50
+                    }
+                  },
+                  "message": {
+                    "text": "getAttribute(...) : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/text/SimpleAttributeSet.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 15
+                    },
+                    "region": {
+                      "startLine": 154,
+                      "startColumn": 16,
+                      "endColumn": 21
+                    }
+                  },
+                  "message": {
+                    "text": "value : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/text/html/StyleSheet.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 41
+                    },
+                    "region": {
+                      "startLine": 845,
+                      "startColumn": 20,
+                      "endColumn": 43
+                    }
+                  },
+                  "message": {
+                    "text": "getAttribute(...) : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/text/SimpleAttributeSet.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 15
+                    },
+                    "region": {
+                      "startLine": 328,
+                      "startColumn": 28,
+                      "endColumn": 45
+                    }
+                  },
+                  "message": {
+                    "text": "getAttribute(...) : byte[]"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/text/SimpleAttributeSet.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 15
+                    },
+                    "region": {
+                      "startLine": 336,
+                      "startColumn": 16,
+                      "endColumn": 17
+                    }
+                  },
+                  "message": {
+                    "text": "s : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.desktop/share/classes/javax/swing/tree/DefaultMutableTreeNode.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 42
+                    },
+                    "region": {
+                      "startLine": 1264,
+                      "startColumn": 20,
+                      "endColumn": 41
+                    }
+                  },
+                  "message": {
+                    "text": "toString(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/MessageFormat.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 16
+                    },
+                    "region": {
+                      "startLine": 1304,
+                      "startColumn": 27,
+                      "endColumn": 41
+                    }
+                  },
+                  "message": {
+                    "text": "toString(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/MessageFormat.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 16
+                    },
+                    "region": {
+                      "startLine": 1349,
+                      "startColumn": 35,
+                      "endColumn": 38
+                    }
+                  },
+                  "message": {
+                    "text": "arg : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 311,
+                      "startColumn": 45,
+                      "endColumn": 55
+                    }
+                  },
+                  "message": {
+                    "text": "str : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 313,
+                      "startColumn": 22,
+                      "endColumn": 25
+                    }
+                  },
+                  "message": {
+                    "text": "str : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 313,
+                      "startColumn": 9,
+                      "endColumn": 14
+                    }
+                  },
+                  "message": {
+                    "text": "super [post update] : StringBuffer"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 5,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/MessageFormat.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 16
+                    },
+                    "region": {
+                      "startLine": 1349,
+                      "startColumn": 21,
+                      "endColumn": 27
+                    }
+                  },
+                  "message": {
+                    "text": "result [post update] : StringBuffer"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/MessageFormat.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 16
+                    },
+                    "region": {
+                      "startLine": 1364,
+                      "startColumn": 16,
+                      "endColumn": 22
+                    }
+                  },
+                  "message": {
+                    "text": "result : StringBuffer"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/MessageFormat.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 16
+                    },
+                    "region": {
+                      "startLine": 885,
+                      "startColumn": 16,
+                      "endColumn": 66
+                    }
+                  },
+                  "message": {
+                    "text": "subformat(...) : StringBuffer"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/Format.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 18
+                    },
+                    "region": {
+                      "startLine": 159,
+                      "startColumn": 16,
+                      "endColumn": 69
+                    }
+                  },
+                  "message": {
+                    "text": "format(...) : StringBuffer"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 713,
+                      "startColumn": 32,
+                      "endColumn": 40
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : StringBuffer"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 715,
+                      "startColumn": 47,
+                      "endColumn": 51
+                    }
+                  },
+                  "message": {
+                    "text": "this : StringBuffer"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 715,
+                      "startColumn": 36,
+                      "endColumn": 58
+                    }
+                  },
+                  "message": {
+                    "text": "new String(...) : String"
+                  }
+                },
+                "taxa": [
+                  {
+                    "index": 6,
+                    "toolComponent": {
+                      "index": 13
+                    },
+                    "properties": {
+                      "CodeQL/DataflowRole": "step"
+                    }
+                  }
+                ]
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/StringBuffer.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 17
+                    },
+                    "region": {
+                      "startLine": 715,
+                      "startColumn": 20,
+                      "endColumn": 58
+                    }
+                  },
+                  "message": {
+                    "text": "...=... : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/text/Format.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 18
+                    },
+                    "region": {
+                      "startLine": 159,
+                      "startColumn": 16,
+                      "endColumn": 80
+                    }
+                  },
+                  "message": {
+                    "text": "toString(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/jdk.internal.opt/share/classes/jdk/internal/joptsimple/internal/Messages.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 43
+                    },
+                    "region": {
+                      "startLine": 75,
+                      "startColumn": 16,
+                      "endColumn": 37
+                    }
+                  },
+                  "message": {
+                    "text": "format(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/jdk.internal.opt/share/classes/jdk/internal/joptsimple/OptionException.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 44
+                    },
+                    "region": {
+                      "startLine": 152,
+                      "startColumn": 16,
+                      "endColumn": 121
+                    }
+                  },
+                  "message": {
+                    "text": "message(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/jdk.internal.opt/share/classes/jdk/internal/joptsimple/OptionException.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 44
+                    },
+                    "region": {
+                      "startLine": 148,
+                      "startColumn": 16,
+                      "endColumn": 42
+                    }
+                  },
+                  "message": {
+                    "text": "formattedMessage(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/jdk.internal.opt/share/classes/jdk/internal/joptsimple/OptionException.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 44
+                    },
+                    "region": {
+                      "startLine": 144,
+                      "startColumn": 16,
+                      "endColumn": 55
+                    }
+                  },
+                  "message": {
+                    "text": "localizedMessage(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.xml/share/classes/javax/xml/transform/TransformerFactoryConfigurationError.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 45
+                    },
+                    "region": {
+                      "startLine": 110,
+                      "startColumn": 20,
+                      "endColumn": 42
+                    }
+                  },
+                  "message": {
+                    "text": "getMessage(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "make/jdk/src/classes/build/tools/module/ModuleInfoExtraTest.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 21
+                    },
+                    "region": {
+                      "startLine": 254,
+                      "startColumn": 18,
+                      "endColumn": 32
+                    }
+                  },
+                  "message": {
+                    "text": "getMessage(...) : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/String.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 0
+                    },
+                    "region": {
+                      "startLine": 2854,
+                      "startColumn": 20,
+                      "endColumn": 27
+                    }
+                  },
+                  "message": {
+                    "text": "parameter this : String"
+                  }
+                }
+              },
+              {
+                "location": {
+                  "physicalLocation": {
+                    "artifactLocation": {
+                      "uri": "src/java.base/share/classes/java/lang/String.java",
+                      "uriBaseId": "%SRCROOT%",
+                      "index": 0
+                    },
+                    "region": {
+                      "startLine": 2855,
+                      "startColumn": 39,
+                      "endColumn": 43
+                    }
+                  },
+                  "message": {
+                    "text": "this"
+                  }
+                }
+              }
+            ]
+          }
+        ]
+      }
+    ],
+    "relatedLocations": [
+      {
+        "id": 1,
+        "physicalLocation": {
+          "artifactLocation": {
+            "uri": "src/jdk.compiler/share/classes/com/sun/tools/javac/main/Main.java",
+            "uriBaseId": "%SRCROOT%",
+            "index": 1
+          },
+          "region": {
+            "startLine": 379,
+            "startColumn": 42,
+            "endColumn": 46
+          }
+        },
+        "message": {
+          "text": "regular expression"
+        }
+      },
+      {
+        "id": 2,
+        "physicalLocation": {
+          "artifactLocation": {
+            "uri": "src/java.xml/share/classes/com/sun/org/apache/xerces/internal/impl/XMLEntityManager.java",
+            "uriBaseId": "%SRCROOT%",
+            "index": 9
+          },
+          "region": {
+            "startLine": 654,
+            "startColumn": 30,
+            "endColumn": 54
+          }
+        },
+        "message": {
+          "text": "user-provided value"
+        }
+      }
+    ]
+  }
+}
diff --git a/extensions/ql-vscode/test/unit-tests/compare/sarif-diff.test.ts b/extensions/ql-vscode/test/unit-tests/compare/sarif-diff.test.ts
index 15d5df07a48..5785866fd35 100644
--- a/extensions/ql-vscode/test/unit-tests/compare/sarif-diff.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/compare/sarif-diff.test.ts
@@ -1,5 +1,7 @@
 import type { Result } from "sarif";
 import { sarifDiff } from "../../../src/compare/sarif-diff";
+import { readJson } from "fs-extra";
+import { resolve } from "path";
 
 describe("sarifDiff", () => {
   const result1: Result = {
@@ -496,6 +498,28 @@ describe("sarifDiff", () => {
     });
   });
 
+  it("only compares the source and sink of a result", async () => {
+    const { result1, result2 } = (await readJson(
+      resolve(__dirname, "differentPathsSameSourceSink.json"),
+    )) as { result1: Result; result2: Result };
+
+    expect(sarifDiff([result1], [result2])).toEqual({
+      from: [],
+      to: [],
+    });
+  });
+
+  it("gives a diff when the source and sink of a result differ", async () => {
+    const { result1, result2 } = (await readJson(
+      resolve(__dirname, "differentPathsDifferentSourceSink.json"),
+    )) as { result1: Result; result2: Result };
+
+    expect(sarifDiff([result1, result2], [result2])).toEqual({
+      from: [result1],
+      to: [],
+    });
+  });
+
   it("does not modify the input", () => {
     const result1: Result = {
       message: {
diff --git a/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl b/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl
index 8d366067387..59d6e67f64a 100644
--- a/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl
+++ b/extensions/ql-vscode/test/unit-tests/data/evaluator-log-summaries/bad-join-order.jsonl
@@ -11458,7 +11458,7 @@
     "duplicationPercentages" : [ 0, -1, 1, 0, -1, 0, -1, 0, 0, -1, 1, 0, 1, -1, 1, 0 ]
   }, {
     "raReference" : "order_500000",
-    "counts" : [ 0, -1, 0, -1, 3138, -1, 3138, 3138, -1, 0, -1, 0, 0, -1, 0, -1, 133, 133, -1, 0, 0, -1, 133, 133, 3271, 3271, 3271 ],
+    "counts" : [ 0, -1, 0, -1, 31380000, -1, 3138, 3138, -1, 0, -1, 0, 0, -1, 0, -1, 133, 133, -1, 0, 0, -1, 133, 133, 3271, 3271, 3271 ],
     "duplicationPercentages" : [ 0, -1, 0, -1, 0, -1, 0, 0, -1, 0, -1, 0, 0, -1, 0, -1, 0, 0, -1, 0, 0, -1, 0, 0, 0, 0, 1 ]
   }, {
     "raReference" : "order_500000",
diff --git a/extensions/ql-vscode/test/unit-tests/jest.config.ts b/extensions/ql-vscode/test/unit-tests/jest.config.ts
index 74c207b2715..21f0a38b2ea 100644
--- a/extensions/ql-vscode/test/unit-tests/jest.config.ts
+++ b/extensions/ql-vscode/test/unit-tests/jest.config.ts
@@ -1,4 +1,5 @@
 import type { Config } from "jest";
+import { transformIgnorePatterns } from "../jest-config";
 
 /*
  * For a detailed explanation regarding each configuration property and type check, visit:
@@ -180,10 +181,7 @@ const config: Config = {
   },
 
   // An array of regexp pattern strings that are matched against all source file paths, matched files will skip transformation
-  transformIgnorePatterns: [
-    // These use ES modules, so need to be transformed
-    "node_modules/(?!(?:@vscode/webview-ui-toolkit|@microsoft/.+|exenv-es6|nanoid|p-queue|p-timeout)/.*)",
-  ],
+  transformIgnorePatterns,
 
   // An array of regexp pattern strings that are matched against all modules before the module loader will automatically return a mock for them
   // unmockedModulePathPatterns: undefined,
diff --git a/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts b/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts
index 3d49f3362a1..0012cecda23 100644
--- a/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/log-scanner.test.ts
@@ -1,28 +1,39 @@
+import { scanAndReportJoinOrderProblems } from "../../src/log-insights/join-order";
 import type { EvaluationLogProblemReporter } from "../../src/log-insights/log-scanner";
-import { EvaluationLogScannerSet } from "../../src/log-insights/log-scanner";
-import { JoinOrderScannerProvider } from "../../src/log-insights/join-order";
 import { join } from "path";
 
 interface TestProblem {
   predicateName: string;
   raHash: string;
-  iteration: number;
+  order: string | undefined;
   message: string;
 }
 
 class TestProblemReporter implements EvaluationLogProblemReporter {
   public readonly problems: TestProblem[] = [];
 
-  public reportProblem(
+  public reportProblemNonRecursive(
     predicateName: string,
     raHash: string,
-    iteration: number,
     message: string,
   ): void {
     this.problems.push({
       predicateName,
       raHash,
-      iteration,
+      order: undefined,
+      message,
+    });
+  }
+  public reportProblemForRecursionSummary(
+    predicateName: string,
+    raHash: string,
+    order: string,
+    message: string,
+  ): void {
+    this.problems.push({
+      predicateName,
+      raHash,
+      order,
       message,
     });
   }
@@ -34,23 +45,33 @@ class TestProblemReporter implements EvaluationLogProblemReporter {
 
 describe("log scanners", () => {
   it("should detect bad join orders", async () => {
-    const scanners = new EvaluationLogScannerSet();
-    scanners.registerLogScannerProvider(new JoinOrderScannerProvider(() => 50));
     const summaryPath = join(
       __dirname,
       "data/evaluator-log-summaries/bad-join-order.jsonl",
     );
     const problemReporter = new TestProblemReporter();
-    await scanners.scanLog(summaryPath, problemReporter);
+    await scanAndReportJoinOrderProblems(summaryPath, problemReporter, 50);
+
+    expect(problemReporter.problems.length).toBe(2);
 
-    expect(problemReporter.problems.length).toBe(1);
-    expect(problemReporter.problems[0].predicateName).toBe("#select#ff");
+    expect(problemReporter.problems[0].predicateName).toBe(
+      "Enclosing::exprEnclosingElement#c50c5fbf#ff",
+    );
     expect(problemReporter.problems[0].raHash).toBe(
-      "1bb43c97jpmuh8r2v0f9hktim63",
+      "7cc60wtoigvl1lheqqa12d8fmi4",
     );
-    expect(problemReporter.problems[0].iteration).toBe(0);
+    expect(problemReporter.problems[0].order).toBe("order_500000");
     expect(problemReporter.problems[0].message).toBe(
-      "Relation '#select#ff' has an inefficient join order. Its join order metric is 4961.83, which is larger than the threshold of 50.00.",
+      "The order_500000 pipeline for 'Enclosing::exprEnclosingElement#c50c5fbf#ff@7cc60wto' has an inefficient join order. Its join order metric is 98.07, which is larger than the threshold of 50.00.",
+    );
+
+    expect(problemReporter.problems[1].predicateName).toBe("#select#ff");
+    expect(problemReporter.problems[1].raHash).toBe(
+      "1bb43c97jpmuh8r2v0f9hktim63",
+    );
+    expect(problemReporter.problems[1].order).toBeUndefined();
+    expect(problemReporter.problems[1].message).toBe(
+      "'#select#ff@1bb43c97' has an inefficient join order. Its join order metric is 4961.83, which is larger than the threshold of 50.00.",
     );
   });
 });
diff --git a/extensions/ql-vscode/test/unit-tests/model-editor/auto-model.test.ts b/extensions/ql-vscode/test/unit-tests/model-editor/auto-model.test.ts
deleted file mode 100644
index 50e67fffdc8..00000000000
--- a/extensions/ql-vscode/test/unit-tests/model-editor/auto-model.test.ts
+++ /dev/null
@@ -1,82 +0,0 @@
-import {
-  createAutoModelRequest,
-  encodeSarif,
-} from "../../../src/model-editor/auto-model";
-import { Mode } from "../../../src/model-editor/shared/mode";
-import { AutomodelMode } from "../../../src/model-editor/auto-model-api";
-import type { AutoModelQueriesResult } from "../../../src/model-editor/auto-model-codeml-queries";
-import type { Log } from "sarif";
-import { gzipDecode } from "../../../src/common/zlib";
-
-describe("createAutoModelRequest", () => {
-  const createSarifLog = (queryId: string): Log => {
-    return {
-      version: "2.1.0",
-      $schema: "http://json.schemastore.org/sarif-2.1.0-rtm.4",
-      runs: [
-        {
-          tool: {
-            driver: {
-              name: "CodeQL",
-              rules: [
-                {
-                  id: queryId,
-                },
-              ],
-            },
-          },
-          results: [
-            {
-              message: {
-                text: "msg",
-              },
-              locations: [
-                {
-                  physicalLocation: {
-                    contextRegion: {
-                      startLine: 10,
-                      endLine: 12,
-                      snippet: {
-                        text: "Foo",
-                      },
-                    },
-                    region: {
-                      startLine: 10,
-                      startColumn: 1,
-                      endColumn: 3,
-                    },
-                    artifactLocation: {
-                      uri: "foo.js",
-                    },
-                  },
-                },
-              ],
-            },
-          ],
-        },
-      ],
-    };
-  };
-
-  const result: AutoModelQueriesResult = {
-    candidates: createSarifLog(
-      "java/ml/extract-automodel-application-candidates",
-    ),
-  };
-
-  it("creates a matching request", async () => {
-    expect(await createAutoModelRequest(Mode.Application, result)).toEqual({
-      mode: AutomodelMode.Application,
-      candidates: await encodeSarif(result.candidates),
-    });
-  });
-
-  it("can decode the SARIF", async () => {
-    const request = await createAutoModelRequest(Mode.Application, result);
-    const decoded = Buffer.from(request.candidates, "base64");
-    const decompressed = await gzipDecode(decoded);
-    const json = decompressed.toString("utf-8");
-    const parsed = JSON.parse(json);
-    expect(parsed).toEqual(result.candidates);
-  });
-});
diff --git a/extensions/ql-vscode/test/unit-tests/model-editor/shared/auto-model-candidates.test.ts b/extensions/ql-vscode/test/unit-tests/model-editor/shared/auto-model-candidates.test.ts
deleted file mode 100644
index c89e604c53f..00000000000
--- a/extensions/ql-vscode/test/unit-tests/model-editor/shared/auto-model-candidates.test.ts
+++ /dev/null
@@ -1,120 +0,0 @@
-import type { Method } from "../../../../src/model-editor/method";
-import { EndpointType } from "../../../../src/model-editor/method";
-import type { ModeledMethod } from "../../../../src/model-editor/modeled-method";
-import { getCandidates } from "../../../../src/model-editor/shared/auto-model-candidates";
-import { Mode } from "../../../../src/model-editor/shared/mode";
-
-describe("getCandidates", () => {
-  it("doesn't return methods that are already modelled", () => {
-    const methods: Method[] = [
-      {
-        library: "my.jar",
-        signature: "org.my.A#x()",
-        endpointType: EndpointType.Method,
-        packageName: "org.my",
-        typeName: "A",
-        methodName: "x",
-        methodParameters: "()",
-        supported: false,
-        supportedType: "none",
-        usages: [],
-      },
-    ];
-    const modeledMethods: Record<string, ModeledMethod[]> = {
-      "org.my.A#x()": [
-        {
-          type: "neutral",
-          kind: "sink",
-          provenance: "manual",
-          signature: "org.my.A#x()",
-          endpointType: EndpointType.Method,
-          packageName: "org.my",
-          typeName: "A",
-          methodName: "x",
-          methodParameters: "()",
-        },
-      ],
-    };
-    const candidates = getCandidates(
-      Mode.Application,
-      methods,
-      modeledMethods,
-      new Set(),
-    );
-    expect(candidates.length).toEqual(0);
-  });
-
-  it("doesn't return methods that are supported from other sources", () => {
-    const methods: Method[] = [
-      {
-        library: "my.jar",
-        signature: "org.my.A#x()",
-        endpointType: EndpointType.Method,
-        packageName: "org.my",
-        typeName: "A",
-        methodName: "x",
-        methodParameters: "()",
-        supported: true,
-        supportedType: "none",
-        usages: [],
-      },
-    ];
-    const modeledMethods = {};
-    const candidates = getCandidates(
-      Mode.Application,
-      methods,
-      modeledMethods,
-      new Set(),
-    );
-    expect(candidates.length).toEqual(0);
-  });
-
-  it("doesn't return methods that are already processed by auto model", () => {
-    const methods: Method[] = [
-      {
-        library: "my.jar",
-        signature: "org.my.A#x()",
-        endpointType: EndpointType.Method,
-        packageName: "org.my",
-        typeName: "A",
-        methodName: "x",
-        methodParameters: "()",
-        supported: false,
-        supportedType: "none",
-        usages: [],
-      },
-    ];
-    const modeledMethods = {};
-    const candidates = getCandidates(
-      Mode.Application,
-      methods,
-      modeledMethods,
-      new Set(["org.my.A#x()"]),
-    );
-    expect(candidates.length).toEqual(0);
-  });
-
-  it("returns methods that are neither modeled nor supported from other sources", () => {
-    const methods: Method[] = [];
-    methods.push({
-      library: "my.jar",
-      signature: "org.my.A#x()",
-      endpointType: EndpointType.Method,
-      packageName: "org.my",
-      typeName: "A",
-      methodName: "x",
-      methodParameters: "()",
-      supported: false,
-      supportedType: "none",
-      usages: [],
-    });
-    const modeledMethods = {};
-    const candidates = getCandidates(
-      Mode.Application,
-      methods,
-      modeledMethods,
-      new Set(),
-    );
-    expect(candidates.length).toEqual(1);
-  });
-});
diff --git a/extensions/ql-vscode/test/unit-tests/model-editor/shared/sorting.test.ts b/extensions/ql-vscode/test/unit-tests/model-editor/shared/sorting.test.ts
index 47320e13114..4d4f2624f11 100644
--- a/extensions/ql-vscode/test/unit-tests/model-editor/shared/sorting.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/model-editor/shared/sorting.test.ts
@@ -10,16 +10,8 @@ import { shuffle } from "../../../vscode-tests/utils/list-helpers";
 
 describe("sortMethods", () => {
   it("uses primary sort order", () => {
-    const unsavedPositiveAutoModelPrediction = createMethod({
-      signature: "org.sql2o.Sql2o#unsavedPositiveAutoModelPrediction()",
-      supported: false,
-    });
-    const negativeAutoModelPrediction = createMethod({
-      signature: "org.sql2o.Sql2o#negativeAutoModelPrediction()",
-      supported: false,
-    });
-    const unsavedManualModel = createMethod({
-      signature: "org.sql2o.Sql2o#unsavedManualModel()",
+    const unsavedModel = createMethod({
+      signature: "org.sql2o.Sql2o#unsavedModel()",
       supported: false,
     });
     const unmodeledMethodWithEarlierSignature = createMethod({
@@ -30,12 +22,8 @@ describe("sortMethods", () => {
       signature: "org.sql2o.Sql2o#zzz_unmodeledMethodWithLaterSignature()",
       supported: false,
     });
-    const savedAutoModelPrediction = createMethod({
-      signature: "org.sql2o.Sql2o#savedAutoModelPrediction()",
-      supported: false,
-    });
-    const savedManualModel = createMethod({
-      signature: "org.sql2o.Sql2o#savedManualModel()",
+    const savedModel = createMethod({
+      signature: "org.sql2o.Sql2o#savedModel()",
       supported: false,
     });
     const supportedMethod = createMethod({
@@ -44,65 +32,31 @@ describe("sortMethods", () => {
     });
 
     const methods: Method[] = shuffle([
-      unsavedPositiveAutoModelPrediction,
-      negativeAutoModelPrediction,
-      unsavedManualModel,
+      unsavedModel,
       unmodeledMethodWithEarlierSignature,
       unmodeledMethodWithLaterSignature,
-      savedAutoModelPrediction,
-      savedManualModel,
+      savedModel,
       supportedMethod,
     ]);
 
     const modeledMethodsMap: Record<string, readonly ModeledMethod[]> = {};
-    modeledMethodsMap[unsavedPositiveAutoModelPrediction.signature] = [
-      createSinkModeledMethod(),
-    ];
-    modeledMethodsMap[unsavedManualModel.signature] = [
-      createSinkModeledMethod(),
-    ];
-    modeledMethodsMap[savedAutoModelPrediction.signature] = [
-      createSinkModeledMethod(),
-    ];
-    modeledMethodsMap[savedManualModel.signature] = [createSinkModeledMethod()];
+    modeledMethodsMap[unsavedModel.signature] = [createSinkModeledMethod()];
+    modeledMethodsMap[savedModel.signature] = [createSinkModeledMethod()];
 
-    const modifiedSignatures: Set<string> = new Set([
-      unsavedPositiveAutoModelPrediction.signature,
-      unsavedManualModel.signature,
-    ]);
-
-    const processedByAutoModelMethods: Set<string> = new Set([
-      unsavedPositiveAutoModelPrediction.signature,
-      negativeAutoModelPrediction.signature,
-      savedAutoModelPrediction.signature,
-    ]);
+    const modifiedSignatures: Set<string> = new Set([unsavedModel.signature]);
 
-    expect(
-      sortMethods(
-        methods,
-        modeledMethodsMap,
-        modifiedSignatures,
-        processedByAutoModelMethods,
-      ),
-    ).toEqual([
-      unsavedPositiveAutoModelPrediction,
-      negativeAutoModelPrediction,
-      unmodeledMethodWithEarlierSignature,
-      unsavedManualModel,
-      unmodeledMethodWithLaterSignature,
-      savedAutoModelPrediction,
-      savedManualModel,
-      supportedMethod,
-    ]);
+    expect(sortMethods(methods, modeledMethodsMap, modifiedSignatures)).toEqual(
+      [
+        unmodeledMethodWithEarlierSignature,
+        unsavedModel,
+        unmodeledMethodWithLaterSignature,
+        savedModel,
+        supportedMethod,
+      ],
+    );
   });
 
   it("uses secondary sort order based on usages and signature", () => {
-    const negativeAutoModelPrediction = createMethod({
-      signature: "org.sql2o.Sql2o#negativeAutoModelPrediction()",
-      supported: false,
-      usages: [],
-    });
-
     const unmodeledMethodWithTwoUsages = createMethod({
       signature: "org.sql2o.Sql2o#unmodeledMethodWithTwoUsages()",
       supported: false,
@@ -126,7 +80,6 @@ describe("sortMethods", () => {
     });
 
     const methods: Method[] = shuffle([
-      negativeAutoModelPrediction,
       unmodeledMethodWithTwoUsages,
       unmodeledMethodWithOneUsage,
       unmodeledMethodWithEarlierSignature,
@@ -137,23 +90,13 @@ describe("sortMethods", () => {
 
     const modifiedSignatures: Set<string> = new Set([]);
 
-    const processedByAutoModelMethods: Set<string> = new Set([
-      negativeAutoModelPrediction.signature,
-    ]);
-
-    expect(
-      sortMethods(
-        methods,
-        modeledMethodsMap,
-        modifiedSignatures,
-        processedByAutoModelMethods,
-      ),
-    ).toEqual([
-      negativeAutoModelPrediction,
-      unmodeledMethodWithTwoUsages,
-      unmodeledMethodWithOneUsage,
-      unmodeledMethodWithEarlierSignature,
-      unmodeledMethodWithLaterSignature,
-    ]);
+    expect(sortMethods(methods, modeledMethodsMap, modifiedSignatures)).toEqual(
+      [
+        unmodeledMethodWithTwoUsages,
+        unmodeledMethodWithOneUsage,
+        unmodeledMethodWithEarlierSignature,
+        unmodeledMethodWithLaterSignature,
+      ],
+    );
   });
 });
diff --git a/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts b/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts
index 31dda880376..820855d7ad4 100644
--- a/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/packages/commands/CommandManager.test.ts
@@ -15,15 +15,11 @@ describe("CommandManager", () => {
   });
 
   it("can register typed commands", async () => {
-    const commands = {
-      "codeQL.openVariantAnalysisLogs": async (variantAnalysisId: number) => {
-        return variantAnalysisId * 10;
-      },
-    };
-    const commandManager = new CommandManager<typeof commands>(
-      jest.fn(),
-      jest.fn(),
-    );
+    const commandManager = new CommandManager<{
+      "codeQL.openVariantAnalysisLogs": (
+        variantAnalysisId: number,
+      ) => Promise<number>;
+    }>(jest.fn(), jest.fn());
 
     // @ts-expect-error wrong command name should give a type error
     commandManager.register("abc", jest.fn());
@@ -81,15 +77,11 @@ describe("CommandManager", () => {
   });
 
   it("can execute typed commands", async () => {
-    const commands = {
-      "codeQL.openVariantAnalysisLogs": async (variantAnalysisId: number) => {
-        return variantAnalysisId * 10;
-      },
-    };
-    const commandManager = new CommandManager<typeof commands>(
-      jest.fn(),
-      jest.fn(),
-    );
+    const commandManager = new CommandManager<{
+      "codeQL.openVariantAnalysisLogs": (
+        variantAnalysisId: number,
+      ) => Promise<number>;
+    }>(jest.fn(), jest.fn());
 
     // @ts-expect-error wrong command name should give a type error
     await commandManager.execute("abc", 4);
diff --git a/extensions/ql-vscode/test/unit-tests/sarif-processing.test.ts b/extensions/ql-vscode/test/unit-tests/sarif-processing.test.ts
index 987e21e03fa..39ebf8a2c83 100644
--- a/extensions/ql-vscode/test/unit-tests/sarif-processing.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/sarif-processing.test.ts
@@ -89,7 +89,7 @@ describe("SARIF processing", () => {
         const rule = tryGetRule(sarifRun, result);
 
         expect(rule).toBeTruthy();
-        expect(rule!.id).toBe(result!.rule!.id);
+        expect(rule!.id).toBe(result.rule!.id);
       });
     });
 
@@ -455,7 +455,7 @@ describe("SARIF processing", () => {
 
     it("should return errors for results that have no message", () => {
       const sarif = buildValidSarifLog();
-      sarif.runs![0]!.results![0]!.message.text = undefined;
+      sarif.runs[0].results![0].message.text = undefined;
 
       const result = extractAnalysisAlerts(sarif, fakefileLinkPrefix);
 
@@ -466,7 +466,7 @@ describe("SARIF processing", () => {
 
     it("should not return errors for result locations with no snippet", () => {
       const sarif = buildValidSarifLog();
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.contextRegion!.snippet =
+      sarif.runs[0].results![0].locations![0].physicalLocation!.contextRegion!.snippet =
         undefined;
 
       const result = extractAnalysisAlerts(sarif, fakefileLinkPrefix);
@@ -486,7 +486,7 @@ describe("SARIF processing", () => {
 
     it("should use highlightedRegion for result locations with no contextRegion", () => {
       const sarif = buildValidSarifLog();
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.contextRegion =
+      sarif.runs[0].results![0].locations![0].physicalLocation!.contextRegion =
         undefined;
 
       const result = extractAnalysisAlerts(sarif, fakefileLinkPrefix);
@@ -506,7 +506,7 @@ describe("SARIF processing", () => {
 
     it("should not return errors for result locations with no region", () => {
       const sarif = buildValidSarifLog();
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.region =
+      sarif.runs[0].results![0].locations![0].physicalLocation!.region =
         undefined;
 
       const result = extractAnalysisAlerts(sarif, fakefileLinkPrefix);
@@ -518,7 +518,7 @@ describe("SARIF processing", () => {
 
     it("should return errors for result locations with no physical location", () => {
       const sarif = buildValidSarifLog();
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.artifactLocation =
+      sarif.runs[0].results![0].locations![0].physicalLocation!.artifactLocation =
         undefined;
 
       const result = extractAnalysisAlerts(sarif, fakefileLinkPrefix);
@@ -642,8 +642,8 @@ describe("SARIF processing", () => {
       const sarif = buildValidSarifLog();
       const messageText =
         "This shell command depends on an uncontrolled [absolute path](1).";
-      sarif.runs![0]!.results![0]!.message!.text = messageText;
-      sarif.runs![0]!.results![0].relatedLocations = [
+      sarif.runs[0].results![0].message.text = messageText;
+      sarif.runs[0].results![0].relatedLocations = [
         {
           id: 1,
           physicalLocation: {
@@ -694,7 +694,7 @@ describe("SARIF processing", () => {
       const sarif = buildValidSarifLog();
       // Build string of 10 kilobytes
       const snippet = new Array(10 * 1024).fill("a").join("");
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.contextRegion!.snippet =
+      sarif.runs[0].results![0].locations![0].physicalLocation!.contextRegion!.snippet =
         {
           text: snippet,
         };
@@ -712,11 +712,11 @@ describe("SARIF processing", () => {
       const sarif = buildValidSarifLog();
       // Build string of 10 kilobytes
       const snippet = new Array(10 * 1024).fill("a").join("");
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.contextRegion!.snippet =
+      sarif.runs[0].results![0].locations![0].physicalLocation!.contextRegion!.snippet =
         {
           text: snippet,
         };
-      sarif.runs![0]!.results![0]!.locations![0]!.physicalLocation!.region!.endColumn = 1000;
+      sarif.runs[0].results![0].locations![0].physicalLocation!.region!.endColumn = 1000;
 
       const result = extractAnalysisAlerts(sarif, fakefileLinkPrefix);
 
@@ -729,8 +729,8 @@ describe("SARIF processing", () => {
 
     it("should be able to handle when a location has no uri", () => {
       const sarif = buildValidSarifLog();
-      sarif.runs![0].results![0].message.text = "message [String](1)";
-      sarif.runs![0].results![0].relatedLocations = [
+      sarif.runs[0].results![0].message.text = "message [String](1)";
+      sarif.runs[0].results![0].relatedLocations = [
         {
           id: 1,
           physicalLocation: {
diff --git a/extensions/ql-vscode/test/unit-tests/variant-analysis/custom-errors.test.ts b/extensions/ql-vscode/test/unit-tests/variant-analysis/custom-errors.test.ts
index 91bb4331126..e35442480df 100644
--- a/extensions/ql-vscode/test/unit-tests/variant-analysis/custom-errors.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/variant-analysis/custom-errors.test.ts
@@ -32,9 +32,6 @@ describe("handleRequestError", () => {
 
   it("returns false when handling an error without response", () => {
     const e = new RequestError("Timeout", 500, {
-      headers: {
-        "Content-Type": "application/json",
-      },
       request: {
         method: "POST",
         url: faker.internet.url(),
@@ -176,8 +173,9 @@ function toErrorMessage(data: any) {
     if (Array.isArray(data.errors)) {
       return `${data.message}: ${data.errors.map(JSON.stringify).join(", ")}`;
     }
-
-    return data.message;
+    if (typeof data.message === "string") {
+      return data.message as string;
+    }
   }
 
   // istanbul ignore next - just in case
diff --git a/extensions/ql-vscode/test/unit-tests/variant-analysis/gh-api/gh-api-client.test.ts b/extensions/ql-vscode/test/unit-tests/variant-analysis/gh-api/gh-api-client.test.ts
index b03b107cb93..85a956a5e8c 100644
--- a/extensions/ql-vscode/test/unit-tests/variant-analysis/gh-api/gh-api-client.test.ts
+++ b/extensions/ql-vscode/test/unit-tests/variant-analysis/gh-api/gh-api-client.test.ts
@@ -13,7 +13,7 @@ import { response as variantAnalysisRepoJson_response } from "../../../../src/co
 import { testCredentialsWithRealOctokit } from "../../../factories/authentication";
 
 const mockServer = new MockGitHubApiServer();
-beforeAll(() => mockServer.startServer());
+beforeAll(() => mockServer.startServer("error"));
 afterEach(() => mockServer.unloadScenario());
 afterAll(() => mockServer.stopServer());
 
diff --git a/extensions/ql-vscode/test/vscode-tests/activated-extension/jest.setup.ts b/extensions/ql-vscode/test/vscode-tests/activated-extension/jest.setup.ts
index 6ffa38a398b..ac7f5b361ec 100644
--- a/extensions/ql-vscode/test/vscode-tests/activated-extension/jest.setup.ts
+++ b/extensions/ql-vscode/test/vscode-tests/activated-extension/jest.setup.ts
@@ -6,7 +6,7 @@ import {
 
 beforeAll(async () => {
   await beforeAllAction();
-});
+}, 20_000);
 
 beforeEach(async () => {
   await beforeEachAction();
diff --git a/extensions/ql-vscode/test/vscode-tests/activated-extension/model-editor/model-evaluator.test.ts b/extensions/ql-vscode/test/vscode-tests/activated-extension/model-editor/model-evaluator.test.ts
index 6853c25f600..51e0fb6286d 100644
--- a/extensions/ql-vscode/test/vscode-tests/activated-extension/model-editor/model-evaluator.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/activated-extension/model-editor/model-evaluator.test.ts
@@ -14,6 +14,8 @@ import { createMockLogger } from "../../../__mocks__/loggerMock";
 import { createMockModelingStore } from "../../../__mocks__/model-editor/modelingStoreMock";
 import { mockedObject } from "../../../mocked-object";
 
+const SETUP_TIMEOUT = 20_000;
+
 describe("Model Evaluator", () => {
   let modelEvaluator: ModelEvaluator;
   let logger: NotificationLogger;
@@ -56,7 +58,7 @@ describe("Model Evaluator", () => {
       extensionPack,
       updateView,
     );
-  });
+  }, SETUP_TIMEOUT);
 
   describe("stopping evaluation", () => {
     it("should just log a message if it never started", async () => {
diff --git a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts
index 1374787104e..850e221d84f 100644
--- a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-manager.test.ts
@@ -12,9 +12,6 @@ import {
   remove,
 } from "fs-extra";
 import { join } from "path";
-import { Readable } from "stream";
-import * as fetchModule from "node-fetch";
-import { Response } from "node-fetch";
 
 import { VariantAnalysisManager } from "../../../../src/variant-analysis/variant-analysis-manager";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
@@ -50,10 +47,36 @@ import {
 } from "../../../../src/variant-analysis/repo-states-store";
 import { permissiveFilterSortState } from "../../../unit-tests/variant-analysis-filter-sort.test";
 import { createMockVariantAnalysisConfig } from "../../../factories/config";
+import { setupServer } from "msw/node";
+import type { RequestHandler } from "msw";
+import { http } from "msw";
+import { getErrorMessage } from "../../../../src/common/helpers-pure";
 
 // up to 3 minutes per test
 jest.setTimeout(3 * 60 * 1000);
 
+const server = setupServer();
+
+beforeAll(() =>
+  server.listen({
+    onUnhandledRequest: "error",
+  }),
+);
+afterEach(() => server.resetHandlers());
+afterAll(() => server.close());
+
+let requests: Request[] = [];
+
+beforeAll(() => {
+  server.events.on("request:start", ({ request }) => {
+    requests.push(request);
+  });
+});
+
+beforeEach(() => {
+  requests = [];
+});
+
 describe("Variant Analysis Manager", () => {
   let app: App;
   let variantAnalysisManager: VariantAnalysisManager;
@@ -176,9 +199,6 @@ describe("Variant Analysis Manager", () => {
     let getVariantAnalysisRepoStub: jest.SpiedFunction<
       typeof ghApiClient.getVariantAnalysisRepo
     >;
-    let getVariantAnalysisRepoResultStub: jest.SpiedFunction<
-      typeof fetchModule.default
-    >;
 
     let repoStatesPath: string;
 
@@ -187,7 +207,6 @@ describe("Variant Analysis Manager", () => {
         ghApiClient,
         "getVariantAnalysisRepo",
       );
-      getVariantAnalysisRepoResultStub = jest.spyOn(fetchModule, "default");
 
       repoStatesPath = join(
         storagePath,
@@ -198,7 +217,8 @@ describe("Variant Analysis Manager", () => {
 
     describe("when the artifact_url is missing", () => {
       beforeEach(async () => {
-        const dummyRepoTask = createMockVariantAnalysisRepoTask();
+        const dummyRepoTask: VariantAnalysisRepoTask =
+          createMockVariantAnalysisRepoTask();
         delete dummyRepoTask.artifact_url;
 
         getVariantAnalysisRepoStub.mockResolvedValue(dummyRepoTask);
@@ -210,26 +230,30 @@ describe("Variant Analysis Manager", () => {
           variantAnalysis,
         );
 
-        expect(getVariantAnalysisRepoResultStub).not.toHaveBeenCalled();
+        expect(requests).toEqual([]);
       });
     });
 
     describe("when the artifact_url is present", () => {
-      let dummyRepoTask: VariantAnalysisRepoTask;
+      let dummyRepoTask: ReturnType<typeof createMockVariantAnalysisRepoTask>;
+      let handlers: RequestHandler[];
 
       beforeEach(async () => {
         dummyRepoTask = createMockVariantAnalysisRepoTask();
 
         getVariantAnalysisRepoStub.mockResolvedValue(dummyRepoTask);
 
-        const sourceFilePath = join(
-          __dirname,
-          "data/variant-analysis-results.zip",
-        );
-        const fileContents = await readFile(sourceFilePath);
-        const response = new Response(Readable.from(fileContents));
-        response.size = fileContents.length;
-        getVariantAnalysisRepoResultStub.mockResolvedValue(response);
+        handlers = [
+          http.get(dummyRepoTask.artifact_url, async () => {
+            const sourceFilePath = join(
+              __dirname,
+              "data/variant-analysis-results.zip",
+            );
+            const fileContents = await readFile(sourceFilePath);
+            return new Response(fileContents);
+          }),
+        ];
+        server.resetHandlers(...handlers);
       });
 
       it("should fetch a repo task", async () => {
@@ -247,7 +271,7 @@ describe("Variant Analysis Manager", () => {
           variantAnalysis,
         );
 
-        expect(getVariantAnalysisRepoResultStub).toHaveBeenCalled();
+        expect(requests).toHaveLength(1);
       });
 
       it("should skip the download if the repository has already been downloaded", async () => {
@@ -283,8 +307,10 @@ describe("Variant Analysis Manager", () => {
       });
 
       it("should not write the repo state when the download fails", async () => {
-        getVariantAnalysisRepoResultStub.mockRejectedValue(
-          new Error("Failed to download"),
+        server.resetHandlers(
+          http.get(dummyRepoTask.artifact_url, async () => {
+            return new Response(JSON.stringify({}), { status: 500 });
+          }),
         );
 
         await expect(
@@ -331,8 +357,10 @@ describe("Variant Analysis Manager", () => {
       });
 
       it("should have a failed repo state when the download fails", async () => {
-        getVariantAnalysisRepoResultStub.mockRejectedValueOnce(
-          new Error("Failed to download"),
+        server.resetHandlers(
+          http.get(dummyRepoTask.artifact_url, async () => {
+            return new Response(JSON.stringify({}), { status: 500 });
+          }),
         );
 
         await expect(
@@ -344,6 +372,8 @@ describe("Variant Analysis Manager", () => {
 
         await expect(pathExists(repoStatesPath)).resolves.toBe(false);
 
+        server.resetHandlers(...handlers);
+
         await variantAnalysisManager.autoDownloadVariantAnalysisResult(
           scannedRepos[1],
           variantAnalysis,
@@ -593,8 +623,8 @@ describe("Variant Analysis Manager", () => {
         await variantAnalysisManager.cancelVariantAnalysis(
           variantAnalysis.id + 100,
         );
-      } catch (error: any) {
-        expect(error.message).toBe(
+      } catch (error) {
+        expect(getErrorMessage(error)).toBe(
           `No variant analysis with id: ${variantAnalysis.id + 100}`,
         );
       }
@@ -608,8 +638,8 @@ describe("Variant Analysis Manager", () => {
 
       try {
         await variantAnalysisManager.cancelVariantAnalysis(variantAnalysis.id);
-      } catch (error: any) {
-        expect(error.message).toBe(
+      } catch (error) {
+        expect(getErrorMessage(error)).toBe(
           `No workflow run id for variant analysis with id: ${variantAnalysis.id}`,
         );
       }
diff --git a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-results-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-results-manager.test.ts
index 9fa66973e97..842dbaa29e0 100644
--- a/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-results-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/activated-extension/variant-analysis/variant-analysis-results-manager.test.ts
@@ -1,10 +1,6 @@
 import { extLogger } from "../../../../src/common/logging/vscode";
-import { readFile, pathExists, remove, outputJson, readJson } from "fs-extra";
+import { outputJson, pathExists, readFile, readJson, remove } from "fs-extra";
 import { join, resolve } from "path";
-import { Readable } from "stream";
-import * as fetchModule from "node-fetch";
-import type { RequestInfo, RequestInit } from "node-fetch";
-import { Response } from "node-fetch";
 
 import { VariantAnalysisResultsManager } from "../../../../src/variant-analysis/variant-analysis-results-manager";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
@@ -17,9 +13,21 @@ import type {
 } from "../../../../src/variant-analysis/shared/variant-analysis";
 import { mockedObject } from "../../utils/mocking.helpers";
 import { createMockVariantAnalysisConfig } from "../../../factories/config";
+import { setupServer } from "msw/node";
+import { http } from "msw";
 
 jest.setTimeout(10_000);
 
+const server = setupServer();
+
+beforeAll(() =>
+  server.listen({
+    onUnhandledRequest: "error",
+  }),
+);
+afterEach(() => server.resetHandlers());
+afterAll(() => server.close());
+
 describe(VariantAnalysisResultsManager.name, () => {
   let variantAnalysisId: number;
   let variantAnalysisResultsManager: VariantAnalysisResultsManager;
@@ -37,7 +45,9 @@ describe(VariantAnalysisResultsManager.name, () => {
   });
 
   describe("download", () => {
-    let dummyRepoTask: VariantAnalysisRepositoryTask;
+    let dummyRepoTask: ReturnType<
+      typeof createMockVariantAnalysisRepositoryTask
+    >;
     let variantAnalysisStoragePath: string;
     let repoTaskStorageDirectory: string;
 
@@ -76,7 +86,8 @@ describe(VariantAnalysisResultsManager.name, () => {
 
     describe("when the artifact_url is missing", () => {
       it("should not try to download the result", async () => {
-        const dummyRepoTask = createMockVariantAnalysisRepositoryTask();
+        const dummyRepoTask: VariantAnalysisRepositoryTask =
+          createMockVariantAnalysisRepositoryTask();
         delete dummyRepoTask.artifactUrl;
 
         await expect(
@@ -91,10 +102,8 @@ describe(VariantAnalysisResultsManager.name, () => {
     });
 
     describe("when the artifact_url is present", () => {
-      let getVariantAnalysisRepoResultStub: jest.SpiedFunction<
-        typeof fetchModule.default
-      >;
       let fileContents: Buffer;
+      let artifactRequest: Request | undefined;
 
       beforeEach(async () => {
         const sourceFilePath = join(
@@ -103,14 +112,19 @@ describe(VariantAnalysisResultsManager.name, () => {
         );
         fileContents = await readFile(sourceFilePath);
 
-        getVariantAnalysisRepoResultStub = jest
-          .spyOn(fetchModule, "default")
-          .mockImplementation((url: RequestInfo, _init?: RequestInit) => {
-            if (url === dummyRepoTask.artifactUrl) {
-              return Promise.resolve(new Response(Readable.from(fileContents)));
+        artifactRequest = undefined;
+
+        server.resetHandlers(
+          http.get(dummyRepoTask.artifactUrl, ({ request }) => {
+            if (artifactRequest) {
+              throw new Error("Unexpected artifact request");
             }
-            return Promise.reject(new Error("Unexpected artifact URL"));
-          });
+
+            artifactRequest = request;
+
+            return new Response(fileContents);
+          }),
+        );
       });
 
       it("should call the API to download the results", async () => {
@@ -121,7 +135,7 @@ describe(VariantAnalysisResultsManager.name, () => {
           () => Promise.resolve(),
         );
 
-        expect(getVariantAnalysisRepoResultStub).toHaveBeenCalledTimes(1);
+        expect(artifactRequest).not.toBeUndefined();
       });
 
       it("should save the results zip file to disk", async () => {
@@ -151,28 +165,29 @@ describe(VariantAnalysisResultsManager.name, () => {
       });
 
       it("should report download progress", async () => {
-        // This generates a "fake" stream which "downloads" the file in 5 chunks,
-        // rather than in 1 chunk. This is used for testing that we actually get
-        // multiple progress reports.
-        async function* generateInParts() {
-          const partLength = fileContents.length / 5;
-          for (let i = 0; i < 5; i++) {
-            yield fileContents.subarray(i * partLength, (i + 1) * partLength);
-          }
-        }
-
-        getVariantAnalysisRepoResultStub.mockImplementation(
-          (url: RequestInfo, _init?: RequestInit) => {
-            if (url === dummyRepoTask.artifactUrl) {
-              const response = new Response(Readable.from(generateInParts()));
-              response.headers.set(
-                "Content-Length",
-                fileContents.length.toString(),
-              );
-              return Promise.resolve(response);
-            }
-            return Promise.reject(new Error("Unexpected artifact URL"));
-          },
+        server.resetHandlers(
+          http.get(dummyRepoTask.artifactUrl, () => {
+            // This generates a "fake" stream which "downloads" the file in 5 chunks,
+            // rather than in 1 chunk. This is used for testing that we actually get
+            // multiple progress reports.
+            const stream = new ReadableStream({
+              start(controller) {
+                const partLength = fileContents.length / 5;
+                for (let i = 0; i < 5; i++) {
+                  controller.enqueue(
+                    fileContents.subarray(i * partLength, (i + 1) * partLength),
+                  );
+                }
+                controller.close();
+              },
+            });
+
+            return new Response(stream, {
+              headers: {
+                "Content-Length": fileContents.length.toString(),
+              },
+            });
+          }),
         );
 
         const downloadPercentageChanged = jest
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts
index 35435b1a797..86da827d88d 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debug-controller.ts
@@ -83,14 +83,17 @@ class Tracker implements DebugAdapterTracker {
           kind: "evaluationCompleted",
           started: this.started!,
           results: {
-            ...this.started!,
-            ...this.completed!,
+            id: this.started!.id,
+            results: new Map([[this.queryPath!, this.completed]]),
             outputDir: new QueryOutputDir(this.started!.outputDir),
-            queryTarget: {
-              queryPath: this.queryPath!,
-              quickEvalPosition:
-                this.started!.quickEvalContext?.quickEvalPosition,
-            },
+            queryTargets: [
+              {
+                queryPath: this.queryPath!,
+                outputBaseName: "results",
+                quickEvalPosition:
+                  this.started!.quickEvalContext?.quickEvalPosition,
+              },
+            ],
             dbPath: this.database!,
           },
         });
@@ -350,15 +353,19 @@ class DebugController
 
   public async expectSucceeded(): Promise<EvaluationCompletedEvent> {
     const event = await this.expectCompleted();
-    if (event.results.resultType !== QueryResultType.SUCCESS) {
-      expect(event.results.message).toBe("success");
+    const results = Array.from(event.results.results.values());
+    expect(results.length).toBe(1);
+    if (results[0].resultType !== QueryResultType.SUCCESS) {
+      expect(results[0].message).toBe("success");
     }
     return event;
   }
 
   public async expectFailed(): Promise<EvaluationCompletedEvent> {
     const event = await this.expectCompleted();
-    expect(event.results.resultType).not.toEqual(QueryResultType.SUCCESS);
+    const results = Array.from(event.results.results.values());
+    expect(results.length).toBe(1);
+    expect(results[0].resultType).not.toEqual(QueryResultType.SUCCESS);
     return event;
   }
 
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts
index 3ced5bead5a..0230bf996f0 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/debugger/debugger.test.ts
@@ -10,10 +10,10 @@ import {
 import { describeWithCodeQL } from "../../cli";
 import { withDebugController } from "./debug-controller";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
-import type { QueryOutputDir } from "../../../../src/local-queries/query-output-dir";
 import { createVSCodeCommandManager } from "../../../../src/common/vscode/commands";
 import type { AllCommands } from "../../../../src/common/commands";
 import { getDataFolderFilePath } from "../utils";
+import type { CoreCompletedQuery } from "../../../../src/query-server";
 
 async function selectForQuickEval(
   path: string,
@@ -30,10 +30,15 @@ async function selectForQuickEval(
 }
 
 async function getResultCount(
-  outputDir: QueryOutputDir,
+  completedQuery: CoreCompletedQuery,
   cli: CodeQLCliServer,
 ): Promise<number> {
-  const info = await cli.bqrsInfo(outputDir.bqrsPath, 100);
+  const results = Array.from(completedQuery.results.values());
+  expect(results.length).toBe(1);
+  const info = await cli.bqrsInfo(
+    completedQuery.outputDir.getBqrsPath(results[0].outputBaseName),
+    100,
+  );
   const resultSet = info["result-sets"][0];
   return resultSet.rows;
 }
@@ -49,6 +54,9 @@ describeWithCodeQL()("Debugger", () => {
   const quickEvalQueryPath = getDataFolderFilePath(
     "debugger/QuickEvalQuery.ql",
   );
+  const quickEvalBigIntQueryPath = getDataFolderFilePath(
+    "debugger/QuickEvalBigIntQuery.ql",
+  );
   const quickEvalLibPath = getDataFolderFilePath("debugger/QuickEvalLib.qll");
 
   beforeEach(async () => {
@@ -101,8 +109,9 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "InterestingNumber",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(8);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(8);
       await controller.expectStopped();
     });
   });
@@ -119,8 +128,9 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "InterestingNumber",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(0);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(0);
       await controller.expectStopped();
     });
   });
@@ -138,8 +148,28 @@ describeWithCodeQL()("Debugger", () => {
       expect(result.started.quickEvalContext!.quickEvalText).toBe(
         "InterestingNumber",
       );
-      expect(result.results.queryTarget.quickEvalPosition).toBeDefined();
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(8);
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(8);
+      await controller.expectStopped();
+    });
+  });
+
+  it("should run a quick evaluation with a bigint-valued result column", async () => {
+    await withDebugController(appCommands, async (controller) => {
+      await selectForQuickEval(quickEvalBigIntQueryPath, 4, 23, 4, 37);
+
+      // Don't specify a query path, so we'll default to the active document ("QuickEvalBigIntQuery.ql")
+      await controller.startDebuggingSelection({});
+      await controller.expectLaunched();
+      const result = await controller.expectSucceeded();
+      expect(result.started.quickEvalContext).toBeDefined();
+      expect(result.started.quickEvalContext!.quickEvalText).toBe(
+        "getBigIntValue",
+      );
+      expect(result.results.queryTargets.length).toBe(1);
+      expect(result.results.queryTargets[0].quickEvalPosition).toBeDefined();
+      expect(await getResultCount(result.results, cli)).toBe(8);
       await controller.expectStopped();
     });
   });
@@ -191,7 +221,7 @@ describeWithCodeQL()("Debugger", () => {
       await controller.expectSessionClosed();
 
       // Expect the number of results to be the same as if we had run the simple query, not the quick eval query.
-      expect(await getResultCount(result.results.outputDir, cli)).toBe(2);
+      expect(await getResultCount(result.results, cli)).toBe(2);
     });
   });
 });
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/jest.setup.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/jest.setup.ts
index c3990282a7a..af6b5a99573 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/jest.setup.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/jest.setup.ts
@@ -8,7 +8,6 @@ import {
 import { createWriteStream, existsSync, mkdirpSync } from "fs-extra";
 import { dirname, join } from "path";
 import { DB_URL, dbLoc, testprojLoc } from "../global.helper";
-import fetch from "node-fetch";
 import { renameSync } from "fs";
 import { unzipToDirectoryConcurrently } from "../../../src/common/unzip-concurrently";
 import { platform } from "os";
@@ -21,18 +20,42 @@ beforeAll(async () => {
   if (!existsSync(dbLoc)) {
     console.log(`Downloading test database to ${dbLoc}`);
 
-    await new Promise((resolve, reject) => {
-      return fetch(DB_URL).then((response) => {
-        const dest = createWriteStream(dbLoc);
-        response.body.pipe(dest);
+    const response = await fetch(DB_URL);
+    if (!response.body) {
+      throw new Error("No response body found");
+    }
+    if (!response.ok) {
+      throw new Error(`Failed to download test database: ${response.status}`);
+    }
+
+    const dest = createWriteStream(dbLoc);
+
+    const reader = response.body.getReader();
+    for (;;) {
+      const { done, value } = await reader.read();
 
-        response.body.on("error", reject);
-        dest.on("error", reject);
-        dest.on("close", () => {
-          resolve(dbLoc);
+      if (done) {
+        break;
+      }
+
+      await new Promise((resolve, reject) => {
+        dest.write(value, (err) => {
+          if (err) {
+            reject(err);
+          }
+          resolve(undefined);
         });
       });
-    });
+    }
+
+    await new Promise((resolve, reject) =>
+      dest.close((err) => {
+        if (err) {
+          reject(err);
+        }
+        resolve(undefined);
+      }),
+    );
   }
 
   // unzip the database from dbLoc to testprojLoc
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
index 9076ec9bed4..4e5c9489869 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/local-queries/skeleton-query-wizard.test.ts
@@ -78,7 +78,9 @@ describe("SkeletonQueryWizard", () => {
       getSupportedLanguages: jest
         .fn()
         .mockResolvedValue([
+          "actions",
           "ruby",
+          "rust",
           "javascript",
           "go",
           "java",
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts
index b3bd56a2371..239b1ca0435 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/queries.test.ts
@@ -162,7 +162,7 @@ describeWithCodeQL()("Queries", () => {
 
     async function runQueryWithExtensions() {
       console.log("Calling compileAndRunQuery");
-      const result = await compileAndRunQuery(
+      const completedQuery = await compileAndRunQuery(
         mode,
         appCommandManager,
         localQueries,
@@ -176,12 +176,14 @@ describeWithCodeQL()("Queries", () => {
       console.log("Completed compileAndRunQuery");
 
       // Check that query was successful
-      expect(result.resultType).toBe(QueryResultType.SUCCESS);
+      const results = Array.from(completedQuery.results.values());
+      expect(results.length).toBe(1);
+      expect(results[0].resultType).toBe(QueryResultType.SUCCESS);
 
       console.log("Loading query results");
       // Load query results
       const chunk = await qs.cliServer.bqrsDecode(
-        result.outputDir.bqrsPath,
+        completedQuery.outputDir.getBqrsPath(results[0].outputBaseName),
         SELECT_QUERY_NAME,
         {
           // there should only be one result
@@ -198,7 +200,7 @@ describeWithCodeQL()("Queries", () => {
 
   describe.each(MODES)("running queries (%s)", (mode) => {
     it("should run a query", async () => {
-      const result = await compileAndRunQuery(
+      const completedQuery = await compileAndRunQuery(
         mode,
         appCommandManager,
         localQueries,
@@ -211,13 +213,15 @@ describeWithCodeQL()("Queries", () => {
       );
 
       // just check that the query was successful
-      expect(result.resultType).toBe(QueryResultType.SUCCESS);
+      const results = Array.from(completedQuery.results.values());
+      expect(results.length).toBe(1);
+      expect(results[0].resultType).toBe(QueryResultType.SUCCESS);
     });
 
     // Asserts a fix for bug https://github.com/github/vscode-codeql/issues/733
     it("should restart the database and run a query", async () => {
       await appCommandManager.execute("codeQL.restartQueryServer");
-      const result = await compileAndRunQuery(
+      const completedQuery = await compileAndRunQuery(
         mode,
         appCommandManager,
         localQueries,
@@ -229,7 +233,9 @@ describeWithCodeQL()("Queries", () => {
         undefined,
       );
 
-      expect(result.resultType).toBe(QueryResultType.SUCCESS);
+      const results = Array.from(completedQuery.results.values());
+      expect(results.length).toBe(1);
+      expect(results[0].resultType).toBe(QueryResultType.SUCCESS);
     });
   });
 
@@ -278,7 +284,7 @@ describeWithCodeQL()("Queries", () => {
   function safeDel(file: string) {
     try {
       unlinkSync(file);
-    } catch (e) {
+    } catch {
       // ignore
     }
   }
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
index c986e69ae62..3fe7c6fadfb 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/query-server/query-server-client.test.ts
@@ -3,9 +3,12 @@ import { dirSync } from "tmp";
 import { CancellationTokenSource } from "vscode-jsonrpc";
 import type { RunQueryParams } from "../../../../src/query-server/messages";
 import {
+  clearCache,
   QueryResultType,
   registerDatabases,
   runQuery,
+  trimCache,
+  trimCacheWithMode,
 } from "../../../../src/query-server/messages";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
 import type { BqrsCellValue } from "../../../../src/common/bqrs-cli-types";
@@ -189,14 +192,67 @@ describeWithCodeQL()("using the query server", () => {
     it(`should have correct results for query ${queryName}`, async () => {
       await parsedResults.done();
       expect(actualResultSets).not.toEqual({});
-      expect(Object.keys(actualResultSets!).sort()).toEqual(
+      expect(Object.keys(actualResultSets).sort()).toEqual(
         Object.keys(queryTestCase.expectedResultSets).sort(),
       );
       for (const name in queryTestCase.expectedResultSets) {
-        expect(actualResultSets![name]).toEqual(
+        expect(actualResultSets[name]).toEqual(
           queryTestCase.expectedResultSets[name],
         );
       }
     });
+
+    it("should invoke codeQL.trimOverlayBaseCache command when queryServerTrimCacheWithMode is enabled", async () => {
+      const features = (await cliServer.getFeatures()) as {
+        [feature: string]: boolean | undefined;
+      };
+
+      // Register the database first (if not already done)
+      await qs.sendRequest(registerDatabases, { databases: [db] });
+
+      try {
+        // Send the trimCacheWithMode request
+        const params = {
+          db,
+          mode: "overlay",
+        };
+        const result = await qs.sendRequest(
+          trimCacheWithMode,
+          params,
+          token,
+          () => {},
+        );
+
+        // The result should contain a deletionMessage string
+        expect(result).toHaveProperty("deletionMessage");
+        expect(typeof result.deletionMessage).toBe("string");
+        expect(features.queryServerTrimCacheWithMode).toBeTruthy();
+      } catch (e) {
+        expect(features.queryServerTrimCacheWithMode).toBeFalsy();
+        expect((e as Error).message).toContain(
+          "Unsupported request method: evaluation/trimCacheWithMode",
+        );
+      }
+    });
+
+    it("should invoke trimCache command and receive a deletionMessage", async () => {
+      // Register the database first (if not already done)
+      await qs.sendRequest(registerDatabases, { databases: [db] });
+
+      const params = { db };
+      const result = await qs.sendRequest(trimCache, params, token, () => {});
+      expect(result).toHaveProperty("deletionMessage");
+      expect(typeof result.deletionMessage).toBe("string");
+    });
+
+    it("should invoke clearCache command and receive a deletionMessage", async () => {
+      // Register the database first (if not already done)
+      await qs.sendRequest(registerDatabases, { databases: [db] });
+
+      const params = { db, dryRun: false };
+      const result = await qs.sendRequest(clearCache, params, token, () => {});
+      expect(result).toHaveProperty("deletionMessage");
+      expect(typeof result.deletionMessage).toBe("string");
+    });
   }
 });
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts
index ef92ee39e06..326cfdf4892 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/run-cli.test.ts
@@ -16,7 +16,7 @@ import { faker } from "@faker-js/faker";
 import { getActivatedExtension } from "../global.helper";
 import type { BaseLogger } from "../../../src/common/logging";
 import { getQlPackForDbscheme } from "../../../src/databases/qlpack";
-import { dbSchemeToLanguage } from "../../../src/common/query-language";
+import { languageToDbScheme } from "../../../src/common/query-language";
 
 /**
  * Perform proper integration tests by running the CLI
@@ -27,14 +27,6 @@ describe("Use cli", () => {
 
   let logSpy: jest.SpiedFunction<BaseLogger["log"]>;
 
-  const languageToDbScheme = Object.entries(dbSchemeToLanguage).reduce(
-    (acc, [k, v]) => {
-      acc[v] = k;
-      return acc;
-    },
-    {} as { [k: string]: string },
-  );
-
   beforeEach(async () => {
     const extension = await getActivatedExtension();
     cli = extension.cliServer;
@@ -107,12 +99,17 @@ describe("Use cli", () => {
   itWithCodeQL()(
     "should resolve printAST queries for supported languages",
     async () => {
-      for (const lang of supportedLanguages) {
+      for (let lang of supportedLanguages) {
         if (lang === "go") {
           // The codeql-go submodule is not available in the integration tests.
           return;
         }
 
+        if (lang === "actions") {
+          // The actions queries use the javascript dbscheme.
+          lang = "javascript";
+        }
+
         console.log(`resolving printAST queries for ${lang}`);
         const pack = await getQlPackForDbscheme(cli, languageToDbScheme[lang]);
         expect(pack.dbschemePack).toContain(lang);
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts
index 1f770162533..62a8af2b61f 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-manager.test.ts
@@ -15,7 +15,6 @@ import { isAbsolute, join } from "path";
 
 import { VariantAnalysisManager } from "../../../../src/variant-analysis/variant-analysis-manager";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
-import { CliVersionConstraint } from "../../../../src/codeql-cli/cli";
 import { getActivatedExtension, storagePath } from "../../global.helper";
 import { VariantAnalysisResultsManager } from "../../../../src/variant-analysis/variant-analysis-results-manager";
 import type { VariantAnalysisSubmission } from "../../../../src/variant-analysis/shared/variant-analysis";
@@ -347,13 +346,6 @@ describe("Variant Analysis Manager", () => {
       const queryToRun =
         "Security/CWE/CWE-020/ExternalAPIsUsedWithUntrustedData.ql";
 
-      // Recent versions of the CLI don't preserve queries with extensible predicates in MRVA packs,
-      // because all the necessary info is in the `.packinfo` file.
-      const extraQueries =
-        (await cli.cliConstraints.preservesExtensiblePredicatesInMrvaPack())
-          ? ["Telemetry/ExtractorInformation.ql"]
-          : [];
-
       const qlPackRootPath = join(process.env.TEST_CODEQL_PATH, "java/ql/src");
       const queryPath = join(qlPackRootPath, queryToRun);
       const qlPackFilePath = join(qlPackRootPath, "qlpack.yml");
@@ -362,7 +354,7 @@ describe("Variant Analysis Manager", () => {
         qlPackRootPath,
         qlPackFilePath,
         expectedPackName: "codeql/java-queries",
-        filesThatExist: [queryToRun, ...extraQueries],
+        filesThatExist: [queryToRun],
         filesThatDoNotExist: [],
         qlxFilesThatExist: [],
         dependenciesToCheck: ["codeql/java-all"],
@@ -372,13 +364,6 @@ describe("Variant Analysis Manager", () => {
     });
 
     it("should run multiple queries that are part of the same pack", async () => {
-      if (!(await cli.cliConstraints.supportsPackCreateWithMultipleQueries())) {
-        console.log(
-          `Skipping test because MRVA with multiple queries is only suppported in CLI version ${CliVersionConstraint.CLI_VERSION_WITH_MULTI_QUERY_PACK_CREATE} or later.`,
-        );
-        return;
-      }
-
       await doVariantAnalysisTest({
         queryPaths: [
           "data-qlpack-multiple-queries/query1.ql",
diff --git a/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-submission-integration.test.ts b/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-submission-integration.test.ts
index 04e555fd1e9..928371856a8 100644
--- a/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-submission-integration.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/cli-integration/variant-analysis/variant-analysis-submission-integration.test.ts
@@ -3,26 +3,21 @@ import { resolve } from "path";
 import type { TextDocument } from "vscode";
 import { authentication, commands, window, workspace } from "vscode";
 
-import { MockGitHubApiServer } from "../../../../src/common/mock-gh-api/mock-gh-api-server";
 import { mockedQuickPickItem } from "../../utils/mocking.helpers";
 import { setRemoteControllerRepo } from "../../../../src/config";
 import { getActivatedExtension } from "../../global.helper";
 import { createVSCodeCommandManager } from "../../../../src/common/vscode/commands";
 import type { AllCommands } from "../../../../src/common/commands";
 
-const mockServer = new MockGitHubApiServer();
-beforeAll(() => mockServer.startServer());
-afterEach(() => mockServer.unloadScenario());
-afterAll(() => mockServer.stopServer());
-
 async function showQlDocument(name: string): Promise<TextDocument> {
   const folderPath = workspace.workspaceFolders![0].uri.fsPath;
   const documentPath = resolve(folderPath, name);
   const document = await workspace.openTextDocument(documentPath);
-  await window.showTextDocument(document!);
+  await window.showTextDocument(document);
   return document;
 }
 
+// MSW can't intercept fetch requests made in VS Code, so we are skipping these tests for now
 describe("Variant Analysis Submission Integration", () => {
   const commandManager = createVSCodeCommandManager<AllCommands>();
   let quickPickSpy: jest.SpiedFunction<typeof window.showQuickPick>;
@@ -53,9 +48,16 @@ describe("Variant Analysis Submission Integration", () => {
     await getActivatedExtension();
   });
 
+  afterAll(async () => {
+    await commandManager.execute("codeQL.mockGitHubApiServer.unloadScenario");
+  });
+
   describe("Successful scenario", () => {
     beforeEach(async () => {
-      await mockServer.loadScenario("mrva-problem-query-success");
+      await commandManager.execute(
+        "codeQL.mockGitHubApiServer.loadScenario",
+        "mrva-problem-query-success",
+      );
     });
 
     it("opens the variant analysis view", async () => {
@@ -80,7 +82,10 @@ describe("Variant Analysis Submission Integration", () => {
 
   describe("Missing controller repo", () => {
     beforeEach(async () => {
-      await mockServer.loadScenario("mrva-missing-controller-repo");
+      await commandManager.execute(
+        "codeQL.mockGitHubApiServer.loadScenario",
+        "mrva-missing-controller-repo",
+      );
     });
 
     it("shows the error message", async () => {
@@ -107,7 +112,10 @@ describe("Variant Analysis Submission Integration", () => {
 
   describe("Submission failure", () => {
     beforeEach(async () => {
-      await mockServer.loadScenario("mrva-submission-failure");
+      await commandManager.execute(
+        "codeQL.mockGitHubApiServer.loadScenario",
+        "mrva-submission-failure",
+      );
     });
 
     it("shows the error message", async () => {
diff --git a/extensions/ql-vscode/test/vscode-tests/ensureCli.ts b/extensions/ql-vscode/test/vscode-tests/ensureCli.ts
index 15e88c284ce..4c090a10910 100644
--- a/extensions/ql-vscode/test/vscode-tests/ensureCli.ts
+++ b/extensions/ql-vscode/test/vscode-tests/ensureCli.ts
@@ -5,7 +5,6 @@ import {
   codeQlLauncherName,
 } from "../../src/common/distribution";
 import { unzipToDirectorySequentially } from "../../src/common/unzip";
-import fetch from "node-fetch";
 import supportedCliVersions from "../../supported_cli_versions.json";
 
 /**
@@ -112,26 +111,32 @@ async function downloadWithProgress(url: string, filePath: string) {
   const contentLength = Number(assetStream.headers.get("content-length") || 0);
   console.log("Total content size", Math.round(contentLength / _1MB), "MB");
   const archiveFile = createWriteStream(filePath);
-  const body = assetStream.body;
-  await new Promise<void>((resolve, reject) => {
-    let numBytesDownloaded = 0;
-    let lastMessage = 0;
-    body.on("data", (data) => {
-      numBytesDownloaded += data.length;
-      if (numBytesDownloaded - lastMessage > _10MB) {
-        console.log("Downloaded", Math.round(numBytesDownloaded / _1MB), "MB");
-        lastMessage = numBytesDownloaded;
-      }
-      archiveFile.write(data);
-    });
-    body.on("finish", () => {
-      archiveFile.end(() => {
-        console.log("Finished download into", filePath);
-        resolve();
+  const body = assetStream.body?.getReader();
+  if (!body) {
+    throw new Error("No response body found");
+  }
+
+  let numBytesDownloaded = 0;
+  let lastMessage = 0;
+
+  while (true) {
+    const { done, value } = await body.read();
+    if (done) {
+      return new Promise((resolve) => {
+        archiveFile.end(() => {
+          console.log("Finished download into", filePath);
+          resolve(undefined);
+        });
       });
-    });
-    body.on("error", reject);
-  });
+    }
+
+    numBytesDownloaded += value.length;
+    if (numBytesDownloaded - lastMessage > _10MB) {
+      console.log("Downloaded", Math.round(numBytesDownloaded / _1MB), "MB");
+      lastMessage = numBytesDownloaded;
+    }
+    archiveFile.write(value);
+  }
 }
 
 async function unzipWithProgress(
diff --git a/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts b/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts
index 5085fc19460..dc47c409111 100644
--- a/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts
+++ b/extensions/ql-vscode/test/vscode-tests/jest.activated-extension.setup.ts
@@ -8,6 +8,7 @@ import {
   setStoragePath,
   storagePath,
 } from "./global.helper";
+import { getErrorMessage } from "../../src/common/helpers-pure";
 
 if (process.env.CI) {
   jest.retryTimes(3, {
@@ -50,6 +51,8 @@ export async function afterAllAction() {
   } catch (e) {
     // we are exiting anyway so don't worry about it.
     // most likely the directory this is a test on Windows and some files are locked.
-    console.warn(`Failed to remove storage directory '${storagePath}': ${e}`);
+    console.warn(
+      `Failed to remove storage directory '${storagePath}': ${getErrorMessage(e)}`,
+    );
   }
 }
diff --git a/extensions/ql-vscode/test/vscode-tests/jest.config.base.ts b/extensions/ql-vscode/test/vscode-tests/jest.config.base.ts
index 1af4f866146..4b2d69a28d1 100644
--- a/extensions/ql-vscode/test/vscode-tests/jest.config.base.ts
+++ b/extensions/ql-vscode/test/vscode-tests/jest.config.base.ts
@@ -1,5 +1,6 @@
 import type { Config } from "jest";
 import { resolve } from "path";
+import { transformIgnorePatterns } from "../jest-config";
 
 /*
  * For a detailed explanation regarding each configuration property and type check, visit:
@@ -181,10 +182,7 @@ const config: Config = {
   },
 
   // An array of regexp pattern strings that are matched against all source file paths, matched files will skip transformation
-  transformIgnorePatterns: [
-    // These use ES modules, so need to be transformed
-    "node_modules/(?!(?:@vscode/webview-ui-toolkit|@microsoft/.+|exenv-es6|nanoid|p-queue|p-timeout)/.*)",
-  ],
+  transformIgnorePatterns,
 
   // An array of regexp pattern strings that are matched against all modules before the module loader will automatically return a mock for them
   // unmockedModulePathPatterns: undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/determining-selected-query-test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/determining-selected-query-test.ts
index f05786680b6..c6c07c161da 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/determining-selected-query-test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/local-queries/determining-selected-query-test.ts
@@ -10,7 +10,7 @@ async function showQlDocument(name: string): Promise<TextDocument> {
   const folderPath = workspace.workspaceFolders![0].uri.fsPath;
   const documentPath = resolve(folderPath, name);
   const document = await workspace.openTextDocument(documentPath);
-  await window.showTextDocument(document!);
+  await window.showTextDocument(document);
   return document;
 }
 
diff --git a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/query-testing/qltest-discovery.test.ts b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/query-testing/qltest-discovery.test.ts
index 7e538bb1111..e2329031ed0 100644
--- a/extensions/ql-vscode/test/vscode-tests/minimal-workspace/query-testing/qltest-discovery.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/minimal-workspace/query-testing/qltest-discovery.test.ts
@@ -3,6 +3,7 @@ import { Uri } from "vscode";
 import { remove } from "fs-extra";
 import { join } from "path";
 
+import { isIOError } from "../../../../src/common/files";
 import { QLTestDiscovery } from "../../../../src/query-testing/qltest-discovery";
 import type { DirectoryResult } from "tmp-promise";
 import { dir } from "tmp-promise";
@@ -49,7 +50,15 @@ describe("qltest-discovery", () => {
     });
 
     afterEach(async () => {
-      await directory.cleanup();
+      try {
+        await directory.cleanup();
+      } catch (e) {
+        if (isIOError(e) && e.code === "ENOENT") {
+          // This is fine, the directory was already removed
+        } else {
+          throw e;
+        }
+      }
     });
 
     it("should run discovery", async () => {
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution.test.ts
index 189e1b12b0c..965aebb1d21 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution.test.ts
@@ -1,21 +1,44 @@
 import * as log from "../../../../src/common/logging/notifications";
 import { extLogger } from "../../../../src/common/logging/vscode";
-import { writeFile } from "fs-extra";
+import {
+  outputFile,
+  outputJson,
+  readFile,
+  readJson,
+  writeFile,
+} from "fs-extra";
 import { join } from "path";
 import * as os from "os";
 import type { DirectoryResult } from "tmp-promise";
 import { dir } from "tmp-promise";
+import type { DistributionState } from "../../../../src/codeql-cli/distribution";
 import {
+  DEFAULT_DISTRIBUTION_VERSION_RANGE,
   DistributionManager,
+  DistributionUpdateCheckResultKind,
   getExecutableFromDirectory,
 } from "../../../../src/codeql-cli/distribution";
 import type {
   showAndLogErrorMessage,
   showAndLogWarningMessage,
 } from "../../../../src/common/logging";
+import { createMockLogger } from "../../../__mocks__/loggerMock";
+import { mockedObject } from "../../../mocked-object";
+import type { DistributionConfig } from "../../../../src/config";
+import type { ExtensionContext } from "vscode";
+import { Uri } from "vscode";
+import { setupServer } from "msw/node";
+import { http, HttpResponse } from "msw";
+import {
+  codeQlLauncherName,
+  getRequiredAssetName,
+} from "../../../../src/common/distribution";
+import type { GithubRelease } from "../../../../src/codeql-cli/distribution/releases-api-consumer";
+import type { Release } from "../../../../src/codeql-cli/distribution/release";
+import { zip } from "zip-a-folder";
 
 jest.mock("os", () => {
-  const original = jest.requireActual("os");
+  const original: typeof os = jest.requireActual("os");
   return {
     ...original,
     platform: jest.fn(),
@@ -108,6 +131,7 @@ describe("Launcher path", () => {
       { customCodeQlPath: pathToCmd } as any,
       {} as any,
       {} as any,
+      createMockLogger(),
     );
 
     const result = await manager.getCodeQlPathWithoutVersionCheck();
@@ -126,6 +150,7 @@ describe("Launcher path", () => {
       { customCodeQlPath: pathToCmd } as any,
       {} as any,
       {} as any,
+      createMockLogger(),
     );
 
     const result = await manager.getCodeQlPathWithoutVersionCheck();
@@ -141,6 +166,7 @@ describe("Launcher path", () => {
       { customCodeQlPath: pathToCmd } as any,
       {} as any,
       {} as any,
+      createMockLogger(),
     );
 
     const result = await manager.getCodeQlPathWithoutVersionCheck();
@@ -151,3 +177,344 @@ describe("Launcher path", () => {
     expect(errorSpy).toHaveBeenCalledTimes(1);
   });
 });
+
+describe("Distribution updates", () => {
+  const server = setupServer();
+  beforeAll(() =>
+    server.listen({
+      onUnhandledRequest: "error",
+    }),
+  );
+  afterEach(() => server.resetHandlers());
+  afterAll(() => server.close());
+
+  let manager: DistributionManager;
+
+  let globalStorageDirectory: DirectoryResult;
+
+  beforeEach(async () => {
+    globalStorageDirectory = await dir({
+      unsafeCleanup: true,
+    });
+
+    manager = new DistributionManager(
+      mockedObject<DistributionConfig>({
+        customCodeQlPath: undefined,
+        channel: "stable",
+        includePrerelease: false,
+        personalAccessToken: undefined,
+        downloadTimeout: 100,
+        onDidChangeConfiguration: () => {},
+      }),
+      DEFAULT_DISTRIBUTION_VERSION_RANGE,
+      mockedObject<ExtensionContext>({
+        globalState: {
+          get: () => {},
+          update: () => {},
+        },
+        globalStorageUri: Uri.file(globalStorageDirectory.path),
+      }),
+      createMockLogger(),
+    );
+
+    await manager.initialize();
+  });
+
+  afterEach(async () => {
+    await globalStorageDirectory.cleanup();
+  });
+
+  it("should have an empty distribution.json file after initialization", async () => {
+    expect(
+      await readJson(join(globalStorageDirectory.path, "distribution.json")),
+    ).toEqual({
+      folderIndex: 0,
+      release: null,
+    } satisfies DistributionState);
+  });
+
+  describe("checkForUpdatesToDistribution", () => {
+    beforeEach(() => {
+      server.resetHandlers(
+        http.get(
+          "https://api.github.com/repos/github/codeql-cli-binaries/releases",
+          async () => {
+            return HttpResponse.json([
+              {
+                id: 1335,
+                name: "v2.2.0",
+                tag_name: "v2.2.0",
+                created_at: "2024-02-02T02:02:02Z",
+                prerelease: false,
+                assets: [
+                  {
+                    id: 783,
+                    name: getRequiredAssetName(),
+                    size: 2378,
+                  },
+                ],
+              },
+              {
+                id: 1,
+                name: "v2.1.0",
+                tag_name: "v2.1.0",
+                created_at: "2022-02-02T02:02:02Z",
+                prerelease: false,
+                assets: [
+                  {
+                    id: 1,
+                    name: getRequiredAssetName(),
+                    size: 100,
+                  },
+                ],
+              },
+            ] satisfies GithubRelease[]);
+          },
+        ),
+      );
+    });
+
+    it("should have an update when no distribution is installed", async () => {
+      expect(
+        await manager.checkForUpdatesToExtensionManagedDistribution(0),
+      ).toEqual({
+        kind: DistributionUpdateCheckResultKind.UpdateAvailable,
+        updatedRelease: {
+          id: 1335,
+          name: "v2.2.0",
+          createdAt: "2024-02-02T02:02:02Z",
+          assets: [
+            {
+              id: 783,
+              name: getRequiredAssetName(),
+              size: 2378,
+            },
+          ],
+        },
+      } satisfies Awaited<
+        ReturnType<typeof manager.checkForUpdatesToExtensionManagedDistribution>
+      >);
+    });
+
+    it("should not have an update when the latest distribution is installed", async () => {
+      await outputJson(join(globalStorageDirectory.path, "distribution.json"), {
+        folderIndex: 1,
+        release: {
+          id: 1335,
+          name: "v2.2.0",
+          createdAt: "2024-02-02T02:02:02Z",
+          assets: [
+            {
+              id: 783,
+              name: getRequiredAssetName(),
+              size: 2378,
+            },
+          ],
+        },
+      } satisfies DistributionState);
+      await outputFile(
+        join(
+          globalStorageDirectory.path,
+          "distribution1",
+          "codeql",
+          codeQlLauncherName(),
+        ),
+        "",
+      );
+
+      // Re-initialize manager to read the state from the file
+      await manager.initialize();
+
+      expect(
+        await manager.checkForUpdatesToExtensionManagedDistribution(0),
+      ).toEqual({
+        kind: DistributionUpdateCheckResultKind.AlreadyUpToDate,
+      } satisfies Awaited<
+        ReturnType<typeof manager.checkForUpdatesToExtensionManagedDistribution>
+      >);
+    });
+
+    it("should have an update when an older distribution is installed", async () => {
+      await outputJson(join(globalStorageDirectory.path, "distribution.json"), {
+        folderIndex: 1,
+        release: {
+          id: 1,
+          name: "v2.1.0",
+          createdAt: "2022-02-02T02:02:02Z",
+          assets: [
+            {
+              id: 1,
+              name: getRequiredAssetName(),
+              size: 100,
+            },
+          ],
+        },
+      } satisfies DistributionState);
+      await outputFile(
+        join(
+          globalStorageDirectory.path,
+          "distribution1",
+          "codeql",
+          codeQlLauncherName(),
+        ),
+        "",
+      );
+
+      // Re-initialize manager to read the state from the file
+      await manager.initialize();
+
+      expect(
+        await manager.checkForUpdatesToExtensionManagedDistribution(0),
+      ).toEqual({
+        kind: DistributionUpdateCheckResultKind.UpdateAvailable,
+        updatedRelease: {
+          id: 1335,
+          name: "v2.2.0",
+          createdAt: "2024-02-02T02:02:02Z",
+          assets: [
+            {
+              id: 783,
+              name: getRequiredAssetName(),
+              size: 2378,
+            },
+          ],
+        },
+      } satisfies Awaited<
+        ReturnType<typeof manager.checkForUpdatesToExtensionManagedDistribution>
+      >);
+    });
+  });
+
+  describe("installExtensionManagedDistributionRelease", () => {
+    const release: Release = {
+      id: 1335,
+      name: "v2.2.0",
+      createdAt: "2024-02-02T02:02:02Z",
+      assets: [
+        {
+          id: 783,
+          name: getRequiredAssetName(),
+          size: 2378,
+        },
+      ],
+    };
+
+    let codeqlReleaseZipTempDir: DirectoryResult;
+    let codeqlReleaseZipPath: string;
+
+    beforeAll(async () => {
+      codeqlReleaseZipTempDir = await dir({
+        unsafeCleanup: true,
+      });
+
+      await outputFile(
+        join(
+          codeqlReleaseZipTempDir.path,
+          "distribution",
+          "codeql",
+          codeQlLauncherName(),
+        ),
+        "launcher!",
+      );
+      codeqlReleaseZipPath = join(codeqlReleaseZipTempDir.path, "codeql.zip");
+
+      await zip(
+        join(codeqlReleaseZipTempDir.path, "distribution"),
+        codeqlReleaseZipPath,
+      );
+
+      server.resetHandlers(
+        http.get(
+          "https://api.github.com/repos/github/codeql-cli-binaries/releases/assets/783",
+          async () => {
+            const file = await readFile(codeqlReleaseZipPath);
+
+            return HttpResponse.arrayBuffer(file.buffer, {
+              headers: {
+                "Content-Type": "application/octet-stream",
+              },
+            });
+          },
+        ),
+      );
+    });
+
+    afterAll(async () => {
+      await codeqlReleaseZipTempDir?.cleanup();
+    });
+
+    it("installs a distribution when no distribution exists", async () => {
+      await manager.installExtensionManagedDistributionRelease(release);
+
+      expect(
+        await readJson(join(globalStorageDirectory.path, "distribution.json")),
+      ).toEqual({
+        folderIndex: 1,
+        release,
+      } satisfies DistributionState);
+
+      expect(
+        await readFile(
+          join(
+            globalStorageDirectory.path,
+            "distribution1",
+            "codeql",
+            codeQlLauncherName(),
+          ),
+          "utf-8",
+        ),
+      ).toEqual("launcher!");
+    });
+
+    it("installs a distribution when a distribution already exists", async () => {
+      await outputJson(join(globalStorageDirectory.path, "distribution.json"), {
+        folderIndex: 78,
+        release: {
+          id: 1,
+          name: "v2.1.0",
+          createdAt: "2022-02-02T02:02:02Z",
+          assets: [
+            {
+              id: 1,
+              name: getRequiredAssetName(),
+              size: 100,
+            },
+          ],
+        },
+      } satisfies DistributionState);
+      await outputFile(
+        join(
+          globalStorageDirectory.path,
+          "distribution78",
+          "codeql",
+          codeQlLauncherName(),
+        ),
+        "",
+      );
+
+      // Re-initialize manager to read the state from the file
+      await manager.initialize();
+
+      await manager.installExtensionManagedDistributionRelease(release);
+
+      expect(
+        await readJson(join(globalStorageDirectory.path, "distribution.json")),
+      ).toEqual({
+        folderIndex: 79,
+        release,
+      } satisfies DistributionState);
+
+      expect(
+        await readFile(
+          join(
+            globalStorageDirectory.path,
+            "distribution79",
+            "codeql",
+            codeQlLauncherName(),
+          ),
+          "utf-8",
+        ),
+      ).toEqual("launcher!");
+    });
+  });
+});
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution/cleaner.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution/cleaner.test.ts
new file mode 100644
index 00000000000..20a7a71c318
--- /dev/null
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/codeql-cli/distribution/cleaner.test.ts
@@ -0,0 +1,146 @@
+import { ExtensionManagedDistributionCleaner } from "../../../../../src/codeql-cli/distribution/cleaner";
+import { mockedObject } from "../../../../mocked-object";
+import type { ExtensionContext } from "vscode";
+import { Uri } from "vscode";
+import { createMockLogger } from "../../../../__mocks__/loggerMock";
+import type { DirectoryResult } from "tmp-promise";
+import { dir } from "tmp-promise";
+import { outputFile, pathExists } from "fs-extra";
+import { join } from "path";
+import { codeQlLauncherName } from "../../../../../src/common/distribution";
+import { getDirectoryNamesInsidePath } from "../../../../../src/common/files";
+
+describe("ExtensionManagedDistributionCleaner", () => {
+  let globalStorageDirectory: DirectoryResult;
+
+  let manager: ExtensionManagedDistributionCleaner;
+
+  beforeEach(async () => {
+    globalStorageDirectory = await dir({
+      unsafeCleanup: true,
+    });
+
+    manager = new ExtensionManagedDistributionCleaner(
+      mockedObject<ExtensionContext>({
+        globalStorageUri: Uri.file(globalStorageDirectory.path),
+      }),
+      createMockLogger(),
+      {
+        folderIndex: 768,
+        distributionFolderPrefix: "distribution",
+      },
+    );
+
+    // Mock setTimeout to call the callback immediately
+    jest.spyOn(global, "setTimeout").mockImplementation((callback) => {
+      callback();
+      return 0 as unknown as ReturnType<typeof setTimeout>;
+    });
+  });
+
+  afterEach(async () => {
+    await globalStorageDirectory.cleanup();
+  });
+
+  it("does nothing when no distributions exist", async () => {
+    await manager.cleanup();
+  });
+
+  it("does nothing when only the current distribution exists", async () => {
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution768",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+
+    await manager.cleanup();
+
+    expect(
+      await pathExists(
+        join(
+          globalStorageDirectory.path,
+          "distribution768",
+          "codeql",
+          "bin",
+          codeQlLauncherName(),
+        ),
+      ),
+    ).toBe(true);
+  });
+
+  it("removes old distributions", async () => {
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution12",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution244",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution637",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution768",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+    await outputFile(
+      join(
+        globalStorageDirectory.path,
+        "distribution890",
+        "codeql",
+        "bin",
+        codeQlLauncherName(),
+      ),
+      "launcher!",
+    );
+
+    const promise = manager.cleanup();
+
+    await promise;
+
+    expect(
+      (await getDirectoryNamesInsidePath(globalStorageDirectory.path)).sort(),
+    ).toEqual(["distribution768", "distribution890"]);
+  });
+});
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/dialog.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/dialog.test.ts
index 895928b6368..c843787dda8 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/dialog.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/dialog.test.ts
@@ -1,7 +1,6 @@
 import { window } from "vscode";
 import {
   showBinaryChoiceDialog,
-  showBinaryChoiceWithUrlDialog,
   showInformationMessageWithAction,
   showNeverAskAgainDialog,
 } from "../../../../../src/common/vscode/dialog";
@@ -68,57 +67,6 @@ describe("showInformationMessageWithAction", () => {
   });
 });
 
-describe("showBinaryChoiceWithUrlDialog", () => {
-  let showInformationMessageSpy: jest.SpiedFunction<
-    typeof window.showInformationMessage
-  >;
-
-  beforeEach(() => {
-    showInformationMessageSpy = jest
-      .spyOn(window, "showInformationMessage")
-      .mockResolvedValue(undefined);
-  });
-
-  const resolveArg =
-    (index: number) =>
-    (...args: any[]) =>
-      Promise.resolve(args[index]);
-
-  it("should show a binary choice dialog with a url and return `yes`", async () => {
-    // pretend user clicks on the url twice and then clicks 'yes'
-    showInformationMessageSpy
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(3));
-    const val = await showBinaryChoiceWithUrlDialog("xxx", "invalid:url");
-    expect(val).toBe(true);
-  });
-
-  it("should show a binary choice dialog with a url and return `no`", async () => {
-    // pretend user clicks on the url twice and then clicks 'no'
-    showInformationMessageSpy
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(4));
-    const val = await showBinaryChoiceWithUrlDialog("xxx", "invalid:url");
-    expect(val).toBe(false);
-  });
-
-  it("should show a binary choice dialog and exit after clcking `more info` 5 times", async () => {
-    // pretend user clicks on the url twice and then clicks 'no'
-    showInformationMessageSpy
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(2))
-      .mockImplementation(resolveArg(2));
-    const val = await showBinaryChoiceWithUrlDialog("xxx", "invalid:url");
-    // No choice was made
-    expect(val).toBeUndefined();
-    expect(showInformationMessageSpy).toHaveBeenCalledTimes(5);
-  });
-});
-
 describe("showNeverAskAgainDialog", () => {
   let showInformationMessageSpy: jest.SpiedFunction<
     typeof window.showInformationMessage
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/progress.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/progress.test.ts
index 3dad02cfb4b..c6f49ac144a 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/progress.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/common/vscode/progress.test.ts
@@ -3,19 +3,15 @@ import { reportStreamProgress } from "../../../../../src/common/vscode/progress"
 describe("helpers", () => {
   it("should report stream progress", () => {
     const progressSpy = jest.fn();
-    const mockReadable = {
-      on: jest.fn(),
-    };
     const max = 1024 * 1024 * 4;
     const firstStep = 1024 * 1024 + 1024 * 600;
     const secondStep = 1024 * 1024 * 2;
 
-    (reportStreamProgress as any)(mockReadable, "My prefix", max, progressSpy);
+    const reportProgress = reportStreamProgress("My prefix", max, progressSpy);
 
     // now pretend that we have received some messages
-    const listener = mockReadable.on.mock.calls[0][1] as (data: any) => void;
-    listener({ length: firstStep });
-    listener({ length: secondStep });
+    reportProgress(firstStep);
+    reportProgress(secondStep);
 
     expect(progressSpy).toHaveBeenCalledTimes(3);
     expect(progressSpy).toHaveBeenCalledWith({
@@ -37,18 +33,14 @@ describe("helpers", () => {
 
   it("should report stream progress when total bytes unknown", () => {
     const progressSpy = jest.fn();
-    const mockReadable = {
-      on: jest.fn(),
-    };
-    (reportStreamProgress as any)(
-      mockReadable,
+    const reportProgress = reportStreamProgress(
       "My prefix",
       undefined,
       progressSpy,
     );
 
-    // There are no listeners registered to this readable
-    expect(mockReadable.on).not.toHaveBeenCalled();
+    // It should not report progress when calling the callback
+    reportProgress(100);
 
     expect(progressSpy).toHaveBeenCalledTimes(1);
     expect(progressSpy).toHaveBeenCalledWith({
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/index.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/index.ts
index 50f2deeccea..8e0e4764a4a 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/index.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/index.ts
@@ -3,15 +3,13 @@ import type { ExtensionContext } from "vscode";
 export function createMockExtensionContext(): ExtensionContext {
   return {
     globalState: {
-      _state: {
-        "telemetry-request-viewed": true,
-      } as Record<string, any>,
-      get(key: string) {
-        return this._state[key];
+      _state: {} as Record<string, any>,
+      get<T>(key: string): T | undefined {
+        return this._state[key] as T | undefined;
       },
       update(key: string, val: any) {
         this._state[key] = val;
       },
     },
-  } as any;
+  } as unknown as ExtensionContext;
 }
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts
index fd033de5f06..df108005c21 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/language-support/ast-viewer/ast-builder.test.ts
@@ -2,10 +2,10 @@ import { readFileSync } from "fs-extra";
 
 import type { CodeQLCliServer } from "../../../../../src/codeql-cli/cli";
 import { Uri } from "vscode";
-import { QueryOutputDir } from "../../../../../src/local-queries/query-output-dir";
 import { mockDatabaseItem, mockedObject } from "../../../utils/mocking.helpers";
 import path from "path";
 import { AstBuilder } from "../../../../../src/language-support";
+import type { DecodedBqrsChunk } from "../../../../../src/common/bqrs-cli-types";
 
 /**
  *
@@ -30,7 +30,7 @@ int disable_interrupts(void)
 
 describe("AstBuilder", () => {
   let mockCli: CodeQLCliServer;
-  let overrides: Record<string, Record<string, unknown> | undefined>;
+  let overrides: Record<string, DecodedBqrsChunk | undefined>;
 
   beforeEach(() => {
     mockCli = mockedObject<CodeQLCliServer>({
@@ -133,6 +133,7 @@ describe("AstBuilder", () => {
   it("should fail when graphProperties are not correct", async () => {
     overrides.graphProperties = {
       tuples: [["semmle.graphKind", "hucairz"]],
+      columns: [],
     };
 
     const astBuilder = createAstBuilder();
@@ -141,7 +142,7 @@ describe("AstBuilder", () => {
 
   function createAstBuilder() {
     return new AstBuilder(
-      new QueryOutputDir("/a/b/c"),
+      path.normalize("/a/b/c/results.bqrs"),
       mockCli,
       mockDatabaseItem({
         resolveSourceFile: undefined,
@@ -150,7 +151,9 @@ describe("AstBuilder", () => {
     );
   }
 
-  function mockDecode(resultSet: "nodes" | "edges" | "graphProperties") {
+  async function mockDecode(
+    resultSet: "nodes" | "edges" | "graphProperties",
+  ): Promise<DecodedBqrsChunk> {
     if (overrides[resultSet]) {
       return overrides[resultSet];
     }
@@ -160,14 +163,14 @@ describe("AstBuilder", () => {
       edges: 1,
       graphProperties: 2,
     };
-    const index = mapper[resultSet] as number;
+    const index = mapper[resultSet];
     if (index >= 0 && index <= 2) {
       return JSON.parse(
         readFileSync(
           `${__dirname}/../../data/language-support/ast-viewer/ast-builder.json`,
           "utf8",
         ),
-      )[index];
+      )[index] as DecodedBqrsChunk;
     } else {
       throw new Error(`Invalid resultSet: ${resultSet}`);
     }
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/auto-model-codeml-queries.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/auto-model-codeml-queries.test.ts
deleted file mode 100644
index ed310b15b01..00000000000
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/auto-model-codeml-queries.test.ts
+++ /dev/null
@@ -1,207 +0,0 @@
-import { createMockLogger } from "../../../__mocks__/loggerMock";
-import type { DatabaseItem } from "../../../../src/databases/local-databases";
-import { DatabaseKind } from "../../../../src/databases/local-databases";
-import { file } from "tmp-promise";
-import { QueryResultType } from "../../../../src/query-server/messages";
-import {
-  generateCandidateFilterPack,
-  runAutoModelQueries,
-} from "../../../../src/model-editor/auto-model-codeml-queries";
-import { Mode } from "../../../../src/model-editor/shared/mode";
-import { mockedObject, mockedUri } from "../../utils/mocking.helpers";
-import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
-import type { QueryRunner } from "../../../../src/query-server";
-import * as queryResolver from "../../../../src/local-queries/query-resolver";
-import type { MethodSignature } from "../../../../src/model-editor/method";
-import { EndpointType } from "../../../../src/model-editor/method";
-import { join } from "path";
-import { pathExists, readFile } from "fs-extra";
-import { load as loadYaml } from "js-yaml";
-import { CancellationTokenSource } from "vscode-jsonrpc";
-import { QueryOutputDir } from "../../../../src/local-queries/query-output-dir";
-import type { ModelExtensionFile } from "../../../../src/model-editor/model-extension-file";
-
-describe("runAutoModelQueries", () => {
-  let resolveQueriesSpy: jest.SpiedFunction<
-    typeof queryResolver.resolveQueries
-  >;
-  beforeEach(() => {
-    resolveQueriesSpy = jest
-      .spyOn(queryResolver, "resolveQueries")
-      .mockImplementation(
-        async (_cliServer, _packsToSearch, _name, constraints) => {
-          if (constraints["tags contain all"]?.includes("candidates")) {
-            return ["/a/b/c/ql/candidates.ql"];
-          }
-          if (constraints["tags contain all"]?.includes("positive")) {
-            return ["/a/b/c/ql/positive-examples.ql"];
-          }
-          if (constraints["tags contain all"]?.includes("negative")) {
-            return ["/a/b/c/ql/negative-examples.ql"];
-          }
-
-          return [];
-        },
-      );
-  });
-
-  it("should run the query and return the results", async () => {
-    const queryStorageDir = (await file()).path;
-    const outputDir = new QueryOutputDir(join(queryStorageDir, "1"));
-
-    const options = {
-      mode: Mode.Application,
-      candidateMethods: [],
-      cliServer: mockedObject<CodeQLCliServer>({
-        resolveQlpacks: jest.fn().mockResolvedValue({
-          "/a/b/c/my-extension-pack": {},
-        }),
-        resolveMetadata: jest.fn().mockResolvedValue({
-          kind: "problem",
-        }),
-        interpretBqrsSarif: jest.fn().mockResolvedValue({
-          version: "2.1.0",
-          $schema: "http://json.schemastore.org/sarif-2.1.0-rtm.4",
-          runs: [
-            {
-              tool: {
-                driver: {
-                  name: "CodeQL",
-                },
-              },
-              results: [
-                {
-                  message: {
-                    text: "msg",
-                  },
-                  locations: [
-                    {
-                      physicalLocation: {
-                        contextRegion: {
-                          startLine: 10,
-                          endLine: 12,
-                          snippet: {
-                            text: "Foo",
-                          },
-                        },
-                        region: {
-                          startLine: 10,
-                          startColumn: 1,
-                          endColumn: 3,
-                        },
-                        artifactLocation: {
-                          uri: "foo.js",
-                        },
-                      },
-                    },
-                  ],
-                },
-              ],
-            },
-          ],
-        }),
-      }),
-      queryRunner: mockedObject<QueryRunner>({
-        createQueryRun: jest.fn().mockReturnValue({
-          evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.SUCCESS,
-            outputDir,
-          }),
-          outputDir,
-        }),
-        logger: createMockLogger(),
-      }),
-      databaseItem: mockedObject<DatabaseItem>({
-        databaseUri: mockedUri("/a/b/c/src.zip"),
-        contents: {
-          kind: DatabaseKind.Database,
-          name: "foo",
-          datasetUri: mockedUri(),
-        },
-        language: "java",
-        getSourceLocationPrefix: jest
-          .fn()
-          .mockResolvedValue("/home/runner/work/my-repo/my-repo"),
-        sourceArchive: mockedUri("/a/b/c/src.zip"),
-      }),
-      queryStorageDir: "/tmp/queries",
-      progress: jest.fn(),
-      cancellationTokenSource: new CancellationTokenSource(),
-    };
-
-    const result = await runAutoModelQueries(options);
-    expect(result).not.toBeUndefined();
-
-    expect(options.cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
-    expect(options.cliServer.resolveQlpacks).toHaveBeenCalledWith(
-      expect.arrayContaining([expect.stringContaining("tmp")]),
-      true,
-    );
-    expect(resolveQueriesSpy).toHaveBeenCalledTimes(1);
-    expect(resolveQueriesSpy).toHaveBeenCalledWith(
-      options.cliServer,
-      ["codeql/java-automodel-queries"],
-      "Extract automodel candidates",
-      {
-        kind: "problem",
-        "tags contain all": ["automodel", "application-mode", "candidates"],
-      },
-    );
-    expect(options.queryRunner.createQueryRun).toHaveBeenCalledTimes(1);
-    expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
-      "/a/b/c/src.zip",
-      {
-        queryPath: "/a/b/c/ql/candidates.ql",
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
-      false,
-      expect.arrayContaining([expect.stringContaining("tmp")]),
-      ["/a/b/c/my-extension-pack"],
-      {},
-      "/tmp/queries",
-      undefined,
-      undefined,
-    );
-  });
-});
-
-describe("generateCandidateFilterPack", () => {
-  it("should create a temp pack containing the candidate filters", async () => {
-    const candidateMethods: MethodSignature[] = [
-      {
-        signature: "org.my.A#x()",
-        endpointType: EndpointType.Method,
-        packageName: "org.my",
-        typeName: "A",
-        methodName: "x",
-        methodParameters: "()",
-      },
-    ];
-    const { packDir, cleanup } = await generateCandidateFilterPack(
-      "java",
-      candidateMethods,
-    );
-    expect(packDir).not.toBeUndefined();
-    const qlpackFile = join(packDir, "codeql-pack.yml");
-    expect(await pathExists(qlpackFile)).toBe(true);
-    const filterFile = join(packDir, "filter.yml");
-    expect(await pathExists(filterFile)).toBe(true);
-    // Read the contents of filterFile and parse as yaml
-    const yaml = (await loadYaml(
-      await readFile(filterFile, "utf8"),
-    )) as ModelExtensionFile;
-    const extensions = yaml.extensions;
-    expect(extensions).toBeInstanceOf(Array);
-    expect(extensions).toHaveLength(1);
-    const extension = extensions[0];
-    expect(extension.addsTo.pack).toEqual("codeql/java-automodel-queries");
-    expect(extension.addsTo.extensible).toEqual("automodelCandidateFilter");
-    expect(extension.data).toBeInstanceOf(Array);
-    expect(extension.data).toHaveLength(1);
-    expect(extension.data[0]).toEqual(["org.my", "A", "x", "()"]);
-
-    await cleanup();
-    expect(await pathExists(packDir)).toBe(false);
-  });
-});
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts
index 8bbda315a42..bdc407502cb 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/external-api-usage-query.test.ts
@@ -30,15 +30,13 @@ describe("runModelEditorQueries", () => {
     > = jest.spyOn(log, "showAndLogExceptionWithTelemetry");
 
     const outputDir = new QueryOutputDir(join((await file()).path, "1"));
-
+    const queryPath = "/a/b/c/ApplicationModeEndpoints.ql";
     const options = {
       cliServer: mockedObject<CodeQLCliServer>({
         resolveQlpacks: jest.fn().mockResolvedValue({
           "my/extensions": "/a/b/c/",
         }),
-        resolveQueriesInSuite: jest
-          .fn()
-          .mockResolvedValue(["/a/b/c/ApplicationModeEndpoints.ql"]),
+        resolveQueriesInSuite: jest.fn().mockResolvedValue([queryPath]),
         packPacklist: jest
           .fn()
           .mockResolvedValue([
@@ -50,7 +48,9 @@ describe("runModelEditorQueries", () => {
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.CANCELLATION,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.CANCELLATION }],
+            ]),
           }),
           outputDir,
         }),
@@ -88,15 +88,13 @@ describe("runModelEditorQueries", () => {
 
   it("should run query for random language", async () => {
     const outputDir = new QueryOutputDir(join((await file()).path, "1"));
-
+    const queryPath = "/a/b/c/ApplicationModeEndpoints.ql";
     const options = {
       cliServer: mockedObject<CodeQLCliServer>({
         resolveQlpacks: jest.fn().mockResolvedValue({
           "my/extensions": "/a/b/c/",
         }),
-        resolveQueriesInSuite: jest
-          .fn()
-          .mockResolvedValue(["/a/b/c/ApplicationModeEndpoints.ql"]),
+        resolveQueriesInSuite: jest.fn().mockResolvedValue([queryPath]),
         packPacklist: jest
           .fn()
           .mockResolvedValue([
@@ -105,13 +103,26 @@ describe("runModelEditorQueries", () => {
             "/a/b/c/qlpack2.yml",
           ]),
         bqrsInfo: jest.fn().mockResolvedValue({
-          "result-sets": [],
+          "result-sets": [
+            {
+              name: "results",
+              rows: 45,
+              columns: [],
+            },
+          ],
+        }),
+        bqrsDecode: jest.fn().mockResolvedValue({
+          tuples: [],
+          columns: [],
         }),
       }),
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
             resultType: QueryResultType.SUCCESS,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.SUCCESS }],
+            ]),
             outputDir,
           }),
           outputDir,
@@ -140,23 +151,26 @@ describe("runModelEditorQueries", () => {
 
     const result = await runModelEditorQueries(Mode.Framework, options);
 
-    expect(result).not.toBeUndefined;
+    expect(result).not.toBeUndefined();
 
     expect(options.cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
     expect(options.cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
       "/a/b/c/src.zip",
-      {
-        queryPath: expect.stringMatching(/\S*ModeEndpoints\.ql/),
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
+      [
+        {
+          outputBaseName: "results",
+          queryPath: expect.stringMatching(/\S*ModeEndpoints\.ql/),
+          quickEvalPosition: undefined,
+          quickEvalCountOnly: false,
+        },
+      ],
       false,
       [],
       ["my/extensions"],
       {},
       "/tmp/queries",
-      undefined,
+      "ApplicationModeEndpoints.ql",
       undefined,
     );
   });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts
index 173f901a7ee..7686e66d912 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/generate.test.ts
@@ -28,12 +28,10 @@ describe("runGenerateQueries", () => {
     const outputDir = new QueryOutputDir(join(queryStorageDir, "1"));
 
     const onResults = jest.fn();
-
+    const queryPath = "/a/b/c/GenerateModel.ql";
     const options = {
       cliServer: mockedObject<CodeQLCliServer>({
-        resolveQueriesInSuite: jest
-          .fn()
-          .mockResolvedValue(["/a/b/c/GenerateModel.ql"]),
+        resolveQueriesInSuite: jest.fn().mockResolvedValue([queryPath]),
         bqrsDecodeAll: jest.fn().mockResolvedValue({
           sourceModel: {
             columns: [
@@ -101,7 +99,9 @@ describe("runGenerateQueries", () => {
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.SUCCESS,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.SUCCESS }],
+            ]),
             outputDir,
           }),
           outputDir,
@@ -221,17 +221,20 @@ describe("runGenerateQueries", () => {
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledTimes(1);
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
       "/a/b/c/src.zip",
-      {
-        queryPath: "/a/b/c/GenerateModel.ql",
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
+      [
+        {
+          outputBaseName: "results",
+          queryPath: "/a/b/c/GenerateModel.ql",
+          quickEvalPosition: undefined,
+          quickEvalCountOnly: false,
+        },
+      ],
       false,
       [],
       undefined,
       {},
       "/tmp/queries",
-      undefined,
+      "GenerateModel.ql",
       undefined,
     );
   });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/method-modeling/method-modeling-view-provider.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/method-modeling/method-modeling-view-provider.test.ts
index e1113911727..1604b992b7e 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/method-modeling/method-modeling-view-provider.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/method-modeling/method-modeling-view-provider.test.ts
@@ -153,8 +153,6 @@ describe("method modeling view provider", () => {
       usage: createUsage(),
       modeledMethods: [],
       isModified: false,
-      isInProgress: false,
-      processedByAutoModel: false,
     };
     getSelectedMethodDetails.mockReturnValue(selectedMethodDetails);
 
@@ -191,8 +189,6 @@ describe("method modeling view provider", () => {
       method: selectedMethodDetails.method,
       modeledMethods: selectedMethodDetails.modeledMethods,
       isModified: selectedMethodDetails.isModified,
-      isInProgress: selectedMethodDetails.isInProgress,
-      processedByAutoModel: selectedMethodDetails.processedByAutoModel,
     });
   });
 });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-data-provider.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-data-provider.test.ts
index b049aa672fa..c5936e3ec1c 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-data-provider.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-data-provider.test.ts
@@ -402,11 +402,7 @@ describe("MethodsUsageDataProvider", () => {
             modifiedMethodSignatures,
           );
           expect(
-            dataProvider
-              .getChildren()
-              .map(
-                (item) => (item as MethodsUsageTreeViewItem).method.signature,
-              ),
+            dataProvider.getChildren().map((item) => item.method.signature),
           ).toEqual(["b.a.C.a()", "b.a.C.b()", "b.a.C.d()", "a.b.C.d()"]);
         });
       });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-panel.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-panel.test.ts
index a09600e0432..3dbb8ca4a7d 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-panel.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/methods-usage/methods-usage-panel.test.ts
@@ -104,8 +104,6 @@ describe("MethodsUsagePanel", () => {
         usage,
         modeledMethods[method.signature],
         modifiedMethodSignatures.has(method.signature),
-        false,
-        false,
       );
 
       expect(mockTreeView.reveal).toHaveBeenCalledWith(
@@ -139,8 +137,6 @@ describe("MethodsUsagePanel", () => {
         usage,
         modeledMethods[method.signature],
         modifiedMethodSignatures.has(method.signature),
-        false,
-        false,
       );
 
       expect(mockTreeView.reveal).not.toHaveBeenCalled();
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/model-editor-queries.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/model-editor-queries.test.ts
index 733d6e61c8b..a66d49899f0 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/model-editor-queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/model-editor-queries.test.ts
@@ -8,7 +8,6 @@ import type { QueryLanguage } from "../../../../src/common/query-language";
 import { Mode } from "../../../../src/model-editor/shared/mode";
 import { mockedObject } from "../../utils/mocking.helpers";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
-import type { ModelConfig } from "../../../../src/config";
 import { createMockLogger } from "../../../__mocks__/loggerMock";
 
 describe("setUpPack", () => {
@@ -44,18 +43,8 @@ describe("setUpPack", () => {
         resolveQueriesInSuite: jest.fn().mockResolvedValue([]),
       });
       const logger = createMockLogger();
-      const modelConfig = mockedObject<ModelConfig>({
-        llmGeneration: false,
-      });
 
-      await setUpPack(
-        cliServer,
-        logger,
-        queryDir,
-        language,
-        modelConfig,
-        Mode.Application,
-      );
+      await setUpPack(cliServer, logger, queryDir, language, Mode.Application);
 
       const queryFiles = await readdir(queryDir);
       expect(queryFiles).toEqual(
@@ -109,18 +98,8 @@ describe("setUpPack", () => {
           .mockResolvedValue(["/a/b/c/ApplicationModeEndpoints.ql"]),
       });
       const logger = createMockLogger();
-      const modelConfig = mockedObject<ModelConfig>({
-        llmGeneration: false,
-      });
 
-      await setUpPack(
-        cliServer,
-        logger,
-        queryDir,
-        language,
-        modelConfig,
-        Mode.Application,
-      );
+      await setUpPack(cliServer, logger, queryDir, language, Mode.Application);
 
       const queryFiles = await readdir(queryDir);
       expect(queryFiles.sort()).toEqual(["codeql-pack.yml"].sort());
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts
index f3ebc013b1f..eeb41f869e1 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/model-editor/suggestion-queries.test.ts
@@ -146,9 +146,8 @@ describe("runSuggestionsQuery", () => {
       .mockResolvedValueOnce(mockInputSuggestions)
       .mockResolvedValueOnce(mockOutputSuggestions);
 
-    const resolveQueriesInSuite = jest
-      .fn()
-      .mockResolvedValue(["/a/b/c/FrameworkModeAccessPathSuggestions.ql"]);
+    const queryPath = "/a/b/c/FrameworkModeAccessPathSuggestions.ql";
+    const resolveQueriesInSuite = jest.fn().mockResolvedValue([queryPath]);
 
     const options = {
       parseResults,
@@ -173,7 +172,9 @@ describe("runSuggestionsQuery", () => {
       queryRunner: mockedObject<QueryRunner>({
         createQueryRun: jest.fn().mockReturnValue({
           evaluate: jest.fn().mockResolvedValue({
-            resultType: QueryResultType.SUCCESS,
+            results: new Map([
+              [queryPath, { resultType: QueryResultType.SUCCESS }],
+            ]),
             outputDir,
           }),
           outputDir,
@@ -200,23 +201,26 @@ describe("runSuggestionsQuery", () => {
 
     const result = await runSuggestionsQuery(Mode.Framework, options);
 
-    expect(result).not.toBeUndefined;
+    expect(result).not.toBeUndefined();
 
     expect(options.cliServer.resolveQlpacks).toHaveBeenCalledTimes(1);
     expect(options.cliServer.resolveQlpacks).toHaveBeenCalledWith([], true);
     expect(options.queryRunner.createQueryRun).toHaveBeenCalledWith(
       "/a/b/c/src.zip",
-      {
-        queryPath: expect.stringMatching(/\S*AccessPathSuggestions\.ql/),
-        quickEvalPosition: undefined,
-        quickEvalCountOnly: false,
-      },
+      [
+        {
+          queryPath: expect.stringMatching(/\S*AccessPathSuggestions\.ql/),
+          outputBaseName: "results",
+          quickEvalPosition: undefined,
+          quickEvalCountOnly: false,
+        },
+      ],
       false,
       [],
       ["my/extensions"],
       {},
       "/tmp/queries",
-      undefined,
+      "FrameworkModeAccessPathSuggestions.ql",
       undefined,
     );
     expect(options.cliServer.resolveQueriesInSuite).toHaveBeenCalledTimes(1);
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-item-label-provider.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-item-label-provider.test.ts
index 0cd2b346313..3ed0a7ee621 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-item-label-provider.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-item-label-provider.test.ts
@@ -21,241 +21,489 @@ describe("HistoryItemLabelProvider", () => {
 
   beforeEach(() => {
     config = {
-      format: "xxx %q xxx",
+      format: "xxx ${queryName} xxx",
       ttlInMillis: 0,
       onDidChangeConfiguration: jest.fn(),
     };
     labelProvider = new HistoryItemLabelProvider(config);
   });
 
-  describe("local queries", () => {
-    it("should interpolate query when user specified", () => {
-      const fqi = createMockLocalQueryInfo({
-        startTime: date,
-        userSpecifiedLabel,
-        resultCount: 456,
-        hasMetadata: true,
-      });
-
-      expect(labelProvider.getLabel(fqi)).toBe("user-specified-name");
+  describe("modern format", () => {
+    describe("local queries", () => {
+      it("should interpolate query when user specified", () => {
+        const fqi = createMockLocalQueryInfo({
+          startTime: date,
+          userSpecifiedLabel,
+          resultCount: 456,
+          hasMetadata: true,
+        });
 
-      fqi.userSpecifiedLabel = "%t %q %d %s %f %r %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
-      );
+        expect(labelProvider.getLabel(fqi)).toBe("user-specified-name");
 
-      fqi.userSpecifiedLabel = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %::${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
-      );
-    });
+        fqi.userSpecifiedLabel =
+          "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
+        );
 
-    it("should interpolate query when not user specified", () => {
-      const fqi = createMockLocalQueryInfo({
-        startTime: date,
-        resultCount: 456,
-        hasMetadata: true,
+        fqi.userSpecifiedLabel = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %::${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
+        );
       });
 
-      expect(labelProvider.getLabel(fqi)).toBe("xxx query-name xxx");
+      it("should interpolate query when not user specified", () => {
+        const fqi = createMockLocalQueryInfo({
+          startTime: date,
+          resultCount: 456,
+          hasMetadata: true,
+        });
 
-      config.format = "%t %q %d %s %f %r %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
-      );
+        expect(labelProvider.getLabel(fqi)).toBe("xxx query-name xxx");
 
-      config.format = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %::${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
-      );
-    });
+        config.format =
+          "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
+        );
 
-    it("should get query short label", () => {
-      const fqi = createMockLocalQueryInfo({
-        startTime: date,
-        userSpecifiedLabel,
-        hasMetadata: true,
-        resultCount: 456,
+        config.format =
+          "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %::${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %::${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
+        );
       });
 
-      // fall back on user specified if one exists.
-      expect(labelProvider.getShortLabel(fqi)).toBe("user-specified-name");
+      it("should get query short label", () => {
+        const fqi = createMockLocalQueryInfo({
+          startTime: date,
+          userSpecifiedLabel,
+          hasMetadata: true,
+          resultCount: 456,
+        });
 
-      // use query name if no user-specified label exists
-      fqi.userSpecifiedLabel = undefined;
-      expect(labelProvider.getShortLabel(fqi)).toBe("query-name");
+        // fall back on user specified if one exists.
+        expect(labelProvider.getShortLabel(fqi)).toBe("user-specified-name");
 
-      // use file name if no user-specified label exists and the query is not yet completed (meaning it has no results)
-      const fqi2 = createMockLocalQueryInfo({
-        startTime: date,
-        hasMetadata: true,
+        // use query name if no user-specified label exists
+        fqi.userSpecifiedLabel = undefined;
+        expect(labelProvider.getShortLabel(fqi)).toBe("query-name");
+
+        // use file name if no user-specified label exists and the query is not yet completed (meaning it has no results)
+        const fqi2 = createMockLocalQueryInfo({
+          startTime: date,
+          hasMetadata: true,
+        });
+        expect(labelProvider.getShortLabel(fqi2)).toBe("query-file.ql");
       });
-      expect(labelProvider.getShortLabel(fqi2)).toBe("query-file.ql");
     });
-  });
 
-  describe("variant analyses", () => {
-    it("should interpolate query when user specified", () => {
-      const fqi = createMockVariantAnalysisHistoryItem({
-        userSpecifiedLabel,
-        executionStartTime,
+    describe("variant analyses", () => {
+      it("should interpolate query when user specified", () => {
+        const fqi = createMockVariantAnalysisHistoryItem({
+          userSpecifiedLabel,
+          executionStartTime,
+        });
+
+        expect(labelProvider.getLabel(fqi)).toBe(userSpecifiedLabel);
+
+        fqi.userSpecifiedLabel =
+          "${startTime} ${queryName} ${databaseName} ${status} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} a-query-name (javascript) 1/3 repositories in progress %`,
+        );
+
+        fqi.userSpecifiedLabel =
+          "${startTime} ${queryName} ${databaseName} ${status} %::${startTime} ${queryName} ${databaseName} ${status} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} a-query-name (javascript) 1/3 repositories in progress %::${dateStr} a-query-name (javascript) 1/3 repositories in progress %`,
+        );
       });
 
-      expect(labelProvider.getLabel(fqi)).toBe(userSpecifiedLabel);
+      it("should interpolate query when not user-specified", () => {
+        const fqi = createMockVariantAnalysisHistoryItem({
+          historyItemStatus: QueryStatus.Completed,
+          variantAnalysisStatus: VariantAnalysisStatus.Succeeded,
+          executionStartTime,
+          resultCount: 16,
+        });
 
-      fqi.userSpecifiedLabel = "%t %q %d %s %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} a-query-name (javascript) 1/3 repositories in progress %`,
-      );
+        expect(labelProvider.getLabel(fqi)).toBe(
+          "xxx a-query-name (javascript) xxx",
+        );
 
-      fqi.userSpecifiedLabel = "%t %q %d %s %%::%t %q %d %s %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} a-query-name (javascript) 1/3 repositories in progress %::${dateStr} a-query-name (javascript) 1/3 repositories in progress %`,
-      );
-    });
+        config.format =
+          "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %`,
+        );
 
-    it("should interpolate query when not user-specified", () => {
-      const fqi = createMockVariantAnalysisHistoryItem({
-        historyItemStatus: QueryStatus.Completed,
-        variantAnalysisStatus: VariantAnalysisStatus.Succeeded,
-        executionStartTime,
-        resultCount: 16,
+        config.format =
+          "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %::${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %::${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %`,
+        );
       });
 
-      expect(labelProvider.getLabel(fqi)).toBe(
-        "xxx a-query-name (javascript) xxx",
-      );
+      it("should get query short label", () => {
+        const fqi = createMockVariantAnalysisHistoryItem({
+          historyItemStatus: QueryStatus.Completed,
+          variantAnalysisStatus: VariantAnalysisStatus.Succeeded,
+          executionStartTime,
+          userSpecifiedLabel,
+        });
 
-      config.format = "%t %q %d %s %f %r %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %`,
-      );
+        // fall back on user specified if one exists.
+        expect(labelProvider.getShortLabel(fqi)).toBe("user-specified-name");
 
-      config.format = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
-      expect(labelProvider.getLabel(fqi)).toBe(
-        `${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %::${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %`,
-      );
-    });
+        // use query name if no user-specified label exists
+        const fqi2 = createMockVariantAnalysisHistoryItem({});
 
-    it("should get query short label", () => {
-      const fqi = createMockVariantAnalysisHistoryItem({
-        historyItemStatus: QueryStatus.Completed,
-        variantAnalysisStatus: VariantAnalysisStatus.Succeeded,
-        executionStartTime,
-        userSpecifiedLabel,
+        expect(labelProvider.getShortLabel(fqi2)).toBe("a-query-name");
       });
 
-      // fall back on user specified if one exists.
-      expect(labelProvider.getShortLabel(fqi)).toBe("user-specified-name");
+      describe("when results are present", () => {
+        it("should display results if there are any", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 16,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format =
+            "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path (16 results) %`,
+          );
+        });
+      });
 
-      // use query name if no user-specified label exists
-      const fqi2 = createMockVariantAnalysisHistoryItem({});
+      describe("when results are not present", () => {
+        it("should skip displaying them", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format =
+            "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          );
+        });
+      });
+
+      describe("when extra whitespace is present in the middle of the label", () => {
+        it("should squash it down to a single whitespace", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format =
+            "${startTime}   ${queryName}        ${databaseName} ${status}   ${queryFileBasename}   ${resultCount} %";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          );
+        });
+      });
+
+      describe("when extra whitespace is present at the start of the label", () => {
+        it("should squash it down to a single whitespace", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format =
+            "   ${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            ` ${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          );
+        });
+      });
 
-      expect(labelProvider.getShortLabel(fqi2)).toBe("a-query-name");
+      describe("when extra whitespace is present at the end of the label", () => {
+        it("should squash it down to a single whitespace", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format =
+            "${startTime} ${queryName} ${databaseName} ${status} ${queryFileBasename} ${resultCount} %   ";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path % `,
+          );
+        });
+      });
     });
+  });
 
-    describe("when results are present", () => {
-      it("should display results if there are any", () => {
-        const fqi = createMockVariantAnalysisHistoryItem({
-          historyItemStatus: QueryStatus.Completed,
-          resultCount: 16,
-          variantAnalysis: createMockVariantAnalysis({
-            status: VariantAnalysisStatus.Succeeded,
-            executionStartTime,
-            scannedRepos: createMockScannedRepos([
-              VariantAnalysisRepoStatus.Succeeded,
-              VariantAnalysisRepoStatus.Succeeded,
-            ]),
-          }),
+  describe("legacy format", () => {
+    describe("local queries", () => {
+      it("should interpolate query when user specified", () => {
+        const fqi = createMockLocalQueryInfo({
+          startTime: date,
+          userSpecifiedLabel,
+          resultCount: 456,
+          hasMetadata: true,
         });
-        config.format = "%t %q %d %s %f %r %%";
+
+        expect(labelProvider.getLabel(fqi)).toBe("user-specified-name");
+
+        fqi.userSpecifiedLabel = "%t %q %d %s %f %r %%";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
+        );
+
+        fqi.userSpecifiedLabel = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
         expect(labelProvider.getLabel(fqi)).toBe(
-          `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path (16 results) %`,
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %::${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
         );
       });
-    });
 
-    describe("when results are not present", () => {
-      it("should skip displaying them", () => {
-        const fqi = createMockVariantAnalysisHistoryItem({
-          historyItemStatus: QueryStatus.Completed,
-          resultCount: 0,
-          variantAnalysis: createMockVariantAnalysis({
-            status: VariantAnalysisStatus.Succeeded,
-            executionStartTime,
-            scannedRepos: createMockScannedRepos([
-              VariantAnalysisRepoStatus.Succeeded,
-              VariantAnalysisRepoStatus.Succeeded,
-            ]),
-          }),
+      it("should interpolate query when not user specified", () => {
+        const fqi = createMockLocalQueryInfo({
+          startTime: date,
+          resultCount: 456,
+          hasMetadata: true,
         });
+
+        expect(labelProvider.getLabel(fqi)).toBe("xxx query-name xxx");
+
         config.format = "%t %q %d %s %f %r %%";
         expect(labelProvider.getLabel(fqi)).toBe(
-          `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
+        );
+
+        config.format = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %::${dateStr} query-name db-name finished in 0 seconds query-file.ql (456 results) %`,
         );
       });
+
+      it("should get query short label", () => {
+        const fqi = createMockLocalQueryInfo({
+          startTime: date,
+          userSpecifiedLabel,
+          hasMetadata: true,
+          resultCount: 456,
+        });
+
+        // fall back on user specified if one exists.
+        expect(labelProvider.getShortLabel(fqi)).toBe("user-specified-name");
+
+        // use query name if no user-specified label exists
+        fqi.userSpecifiedLabel = undefined;
+        expect(labelProvider.getShortLabel(fqi)).toBe("query-name");
+
+        // use file name if no user-specified label exists and the query is not yet completed (meaning it has no results)
+        const fqi2 = createMockLocalQueryInfo({
+          startTime: date,
+          hasMetadata: true,
+        });
+        expect(labelProvider.getShortLabel(fqi2)).toBe("query-file.ql");
+      });
     });
 
-    describe("when extra whitespace is present in the middle of the label", () => {
-      it("should squash it down to a single whitespace", () => {
+    describe("variant analyses", () => {
+      it("should interpolate query when user specified", () => {
         const fqi = createMockVariantAnalysisHistoryItem({
-          historyItemStatus: QueryStatus.Completed,
-          resultCount: 0,
-          variantAnalysis: createMockVariantAnalysis({
-            status: VariantAnalysisStatus.Succeeded,
-            executionStartTime,
-            scannedRepos: createMockScannedRepos([
-              VariantAnalysisRepoStatus.Succeeded,
-              VariantAnalysisRepoStatus.Succeeded,
-            ]),
-          }),
+          userSpecifiedLabel,
+          executionStartTime,
         });
-        config.format = "%t   %q        %d %s   %f   %r %%";
+
+        expect(labelProvider.getLabel(fqi)).toBe(userSpecifiedLabel);
+
+        fqi.userSpecifiedLabel = "%t %q %d %s %%";
         expect(labelProvider.getLabel(fqi)).toBe(
-          `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          `${dateStr} a-query-name (javascript) 1/3 repositories in progress %`,
+        );
+
+        fqi.userSpecifiedLabel = "%t %q %d %s %%::%t %q %d %s %%";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} a-query-name (javascript) 1/3 repositories in progress %::${dateStr} a-query-name (javascript) 1/3 repositories in progress %`,
         );
       });
-    });
 
-    describe("when extra whitespace is present at the start of the label", () => {
-      it("should squash it down to a single whitespace", () => {
+      it("should interpolate query when not user-specified", () => {
         const fqi = createMockVariantAnalysisHistoryItem({
           historyItemStatus: QueryStatus.Completed,
-          resultCount: 0,
-          variantAnalysis: createMockVariantAnalysis({
-            status: VariantAnalysisStatus.Succeeded,
-            executionStartTime,
-            scannedRepos: createMockScannedRepos([
-              VariantAnalysisRepoStatus.Succeeded,
-              VariantAnalysisRepoStatus.Succeeded,
-            ]),
-          }),
+          variantAnalysisStatus: VariantAnalysisStatus.Succeeded,
+          executionStartTime,
+          resultCount: 16,
         });
-        config.format = "   %t %q %d %s %f %r %%";
+
+        expect(labelProvider.getLabel(fqi)).toBe(
+          "xxx a-query-name (javascript) xxx",
+        );
+
+        config.format = "%t %q %d %s %f %r %%";
+        expect(labelProvider.getLabel(fqi)).toBe(
+          `${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %`,
+        );
+
+        config.format = "%t %q %d %s %f %r %%::%t %q %d %s %f %r %%";
         expect(labelProvider.getLabel(fqi)).toBe(
-          ` ${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          `${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %::${dateStr} a-query-name (javascript) 1/3 repositories completed a-query-file-path (16 results) %`,
         );
       });
-    });
 
-    describe("when extra whitespace is present at the end of the label", () => {
-      it("should squash it down to a single whitespace", () => {
+      it("should get query short label", () => {
         const fqi = createMockVariantAnalysisHistoryItem({
           historyItemStatus: QueryStatus.Completed,
-          resultCount: 0,
-          variantAnalysis: createMockVariantAnalysis({
-            status: VariantAnalysisStatus.Succeeded,
-            executionStartTime,
-            scannedRepos: createMockScannedRepos([
-              VariantAnalysisRepoStatus.Succeeded,
-              VariantAnalysisRepoStatus.Succeeded,
-            ]),
-          }),
+          variantAnalysisStatus: VariantAnalysisStatus.Succeeded,
+          executionStartTime,
+          userSpecifiedLabel,
+        });
+
+        // fall back on user specified if one exists.
+        expect(labelProvider.getShortLabel(fqi)).toBe("user-specified-name");
+
+        // use query name if no user-specified label exists
+        const fqi2 = createMockVariantAnalysisHistoryItem({});
+
+        expect(labelProvider.getShortLabel(fqi2)).toBe("a-query-name");
+      });
+
+      describe("when results are present", () => {
+        it("should display results if there are any", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 16,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format = "%t %q %d %s %f %r %%";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path (16 results) %`,
+          );
+        });
+      });
+
+      describe("when results are not present", () => {
+        it("should skip displaying them", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format = "%t %q %d %s %f %r %%";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          );
+        });
+      });
+
+      describe("when extra whitespace is present in the middle of the label", () => {
+        it("should squash it down to a single whitespace", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format = "%t   %q        %d %s   %f   %r %%";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          );
+        });
+      });
+
+      describe("when extra whitespace is present at the start of the label", () => {
+        it("should squash it down to a single whitespace", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format = "   %t %q %d %s %f %r %%";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            ` ${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path %`,
+          );
+        });
+      });
+
+      describe("when extra whitespace is present at the end of the label", () => {
+        it("should squash it down to a single whitespace", () => {
+          const fqi = createMockVariantAnalysisHistoryItem({
+            historyItemStatus: QueryStatus.Completed,
+            resultCount: 0,
+            variantAnalysis: createMockVariantAnalysis({
+              status: VariantAnalysisStatus.Succeeded,
+              executionStartTime,
+              scannedRepos: createMockScannedRepos([
+                VariantAnalysisRepoStatus.Succeeded,
+                VariantAnalysisRepoStatus.Succeeded,
+              ]),
+            }),
+          });
+          config.format = "%t %q %d %s %f %r %%   ";
+          expect(labelProvider.getLabel(fqi)).toBe(
+            `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path % `,
+          );
         });
-        config.format = "%t %q %d %s %f %r %%   ";
-        expect(labelProvider.getLabel(fqi)).toBe(
-          `${dateStr} a-query-name (javascript) 2/2 repositories completed a-query-file-path % `,
-        );
       });
     });
   });
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts
index 7026e6c6684..a0305761e91 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/history-tree-data-provider.test.ts
@@ -38,6 +38,7 @@ describe("HistoryTreeDataProvider", () => {
   let app: App;
   let configListener: QueryHistoryConfigListener;
   const doCompareCallback = jest.fn();
+  const doComparePerformanceCallback = jest.fn();
 
   let queryHistoryManager: QueryHistoryManager;
 
@@ -506,6 +507,7 @@ describe("HistoryTreeDataProvider", () => {
       }),
       languageContext,
       doCompareCallback,
+      doComparePerformanceCallback,
     );
     (qhm.treeDataProvider as any).history = [...allHistory];
     await workspace.saveAll();
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts
index b5176590822..38eb471c918 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/query-history-manager.test.ts
@@ -40,6 +40,7 @@ describe("QueryHistoryManager", () => {
     typeof variantAnalysisManagerStub.cancelVariantAnalysis
   >;
   const doCompareCallback = jest.fn();
+  const doComparePerformanceCallback = jest.fn();
 
   let executeCommand: jest.MockedFn<
     (commandName: string, ...args: any[]) => Promise<any>
@@ -939,6 +940,7 @@ describe("QueryHistoryManager", () => {
       }),
       new LanguageContextStore(mockApp),
       doCompareCallback,
+      doComparePerformanceCallback,
     );
     (qhm.treeDataProvider as any).history = [...allHistory];
     await workspace.saveAll();
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
index 34c092987cc..e8ae5a82975 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/store/query-history-store.test.ts
@@ -237,12 +237,12 @@ describe("write and read", () => {
     dbPath = "/a/b/c",
   ): QueryWithResults {
     // pretend that the results path exists
-    const resultsPath = join(queryPath, "results.bqrs");
     mkdirpSync(queryPath);
-    writeFileSync(resultsPath, "", "utf8");
+    writeFileSync(join(queryPath, "results.bqrs"), "", "utf8");
 
     const queryEvalInfo = new QueryEvaluationInfo(
       queryPath,
+      "results",
       Uri.file(dbPath).fsPath,
       true,
       undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts
index 1719ee00971..5442d5e2c38 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-history/variant-analysis-history.test.ts
@@ -105,6 +105,7 @@ describe("Variant Analyses and QueryHistoryManager", () => {
       }),
       new LanguageContextStore(app),
       asyncNoop,
+      asyncNoop,
     );
     disposables.push(qhm);
 
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts
index b4e27f60fdf..fc31fc909e3 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-results.test.ts
@@ -127,7 +127,7 @@ describe("query-results", () => {
       const expectedResultsPath = join(queryPath, "results.bqrs");
       const expectedSortedResultsPath = join(
         queryPath,
-        "sortedResults-cc8589f226adc134f87f2438e10075e0667571c72342068e2281e0b3b65e1092.bqrs",
+        "results-sorted-cc8589f226adc134f87f2438e10075e0667571c72342068e2281e0b3b65e1092.bqrs",
       );
       expect(spy).toHaveBeenCalledWith(
         expectedResultsPath,
@@ -291,7 +291,7 @@ describe("query-results", () => {
         });
 
         const finished = new Promise((res, rej) => {
-          validSarifStream.addListener("close", res);
+          validSarifStream.addListener("close", () => res(undefined));
           validSarifStream.addListener("error", rej);
         });
 
@@ -357,7 +357,7 @@ describe("query-results", () => {
         });
 
         const finished = new Promise((res, rej) => {
-          invalidSarifStream.addListener("close", res);
+          invalidSarifStream.addListener("close", () => res(undefined));
           invalidSarifStream.addListener("error", rej);
         });
 
@@ -408,7 +408,7 @@ describe("query-results", () => {
   function safeDel(file: string) {
     try {
       unlinkSync(file);
-    } catch (e) {
+    } catch {
       // ignore
     }
   }
@@ -419,12 +419,12 @@ describe("query-results", () => {
     dbPath = "/a/b/c",
   ): QueryWithResults {
     // pretend that the results path exists
-    const resultsPath = join(queryPath, "results.bqrs");
     mkdirpSync(queryPath);
-    writeFileSync(resultsPath, "", "utf8");
+    writeFileSync(join(queryPath, "results.bqrs"), "", "utf8");
 
     const queryEvalInfo = new QueryEvaluationInfo(
       queryPath,
+      "results",
       Uri.file(dbPath).fsPath,
       true,
       undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-testing/test-runner.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-testing/test-runner.test.ts
index ea33088f87a..62d5a98dc64 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/query-testing/test-runner.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/query-testing/test-runner.test.ts
@@ -1,4 +1,5 @@
 import { CancellationTokenSource, Uri } from "vscode";
+import type * as fsExtra from "fs-extra";
 import type { CodeQLCliServer } from "../../../../src/codeql-cli/cli";
 import type {
   DatabaseItem,
@@ -15,7 +16,7 @@ import {
 } from "./test-runner-helpers";
 
 jest.mock("fs-extra", () => {
-  const original = jest.requireActual("fs-extra");
+  const original: typeof fsExtra = jest.requireActual("fs-extra");
   return {
     ...original,
     access: jest.fn(),
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts
index 45e0063b1bb..8437249e815 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/run-queries.test.ts
@@ -28,12 +28,10 @@ describe("run-queries", () => {
     const saveDir = "query-save-dir";
     const queryEvalInfo = createMockQueryEvaluationInfo(true, saveDir);
 
-    expect(queryEvalInfo.dilPath).toBe(join(saveDir, "results.dil"));
-    expect(queryEvalInfo.resultsPaths.resultsPath).toBe(
-      join(saveDir, "results.bqrs"),
-    );
-    expect(queryEvalInfo.resultsPaths.interpretedResultsPath).toBe(
-      join(saveDir, "interpretedResults.sarif"),
+    expect(queryEvalInfo.dilPath).toBe(join(saveDir, "foo.dil"));
+    expect(queryEvalInfo.resultsPath).toBe(join(saveDir, "foo.bqrs"));
+    expect(queryEvalInfo.interpretedResultsPath).toBe(
+      join(saveDir, "foo-interpreted.sarif"),
     );
     expect(queryEvalInfo.dbItemPath).toBe(Uri.file("/abc").fsPath);
   });
@@ -215,6 +213,7 @@ describe("run-queries", () => {
   ) {
     return new QueryEvaluationInfo(
       saveDir,
+      "foo",
       Uri.parse("file:///abc").fsPath,
       databaseHasMetadataFile,
       undefined,
diff --git a/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts b/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts
index 5d797b78918..d1f6f525019 100644
--- a/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts
+++ b/extensions/ql-vscode/test/vscode-tests/no-workspace/telemetry.test.ts
@@ -1,14 +1,10 @@
 import TelemetryReporter from "vscode-extension-telemetry";
-import type { ExtensionContext } from "vscode";
-import { workspace, ConfigurationTarget, window, env } from "vscode";
+import { workspace, env } from "vscode";
 import {
   ExtensionTelemetryListener,
   telemetryListener as globalTelemetryListener,
 } from "../../../src/common/vscode/telemetry";
 import { UserCancellationException } from "../../../src/common/vscode/progress";
-import { ENABLE_TELEMETRY } from "../../../src/config";
-import { createMockExtensionContext } from "./index";
-import { vscodeGetConfigurationMock } from "../test-config";
 import { redactableError } from "../../../src/common/errors";
 import { SemVer } from "semver";
 
@@ -17,10 +13,7 @@ import { SemVer } from "semver";
 jest.setTimeout(10000);
 
 describe("telemetry reporting", () => {
-  let originalTelemetryExtension: boolean | undefined;
-  let originalTelemetryGlobal: string | undefined;
   let isCanary: string;
-  let ctx: ExtensionContext;
   let telemetryListener: ExtensionTelemetryListener;
 
   let sendTelemetryEventSpy: jest.SpiedFunction<
@@ -29,22 +22,8 @@ describe("telemetry reporting", () => {
   let sendTelemetryErrorEventSpy: jest.SpiedFunction<
     typeof TelemetryReporter.prototype.sendTelemetryErrorEvent
   >;
-  let disposeSpy: jest.SpiedFunction<
-    typeof TelemetryReporter.prototype.dispose
-  >;
-
-  let isTelemetryEnabledSpy: jest.SpyInstance<
-    typeof env.isTelemetryEnabled,
-    []
-  >;
-
-  let showInformationMessageSpy: jest.SpiedFunction<
-    typeof window.showInformationMessage
-  >;
 
   beforeEach(async () => {
-    vscodeGetConfigurationMock.mockRestore();
-
     try {
       // in case a previous test has accidentally activated this extension,
       // need to disable it first.
@@ -52,44 +31,24 @@ describe("telemetry reporting", () => {
       // specified in the package.json.
       globalTelemetryListener?.dispose();
 
-      ctx = createMockExtensionContext();
-
       sendTelemetryEventSpy = jest
         .spyOn(TelemetryReporter.prototype, "sendTelemetryEvent")
         .mockReturnValue(undefined);
       sendTelemetryErrorEventSpy = jest
         .spyOn(TelemetryReporter.prototype, "sendTelemetryErrorEvent")
         .mockReturnValue(undefined);
-      disposeSpy = jest
-        .spyOn(TelemetryReporter.prototype, "dispose")
-        .mockResolvedValue(undefined);
 
-      showInformationMessageSpy = jest
-        .spyOn(window, "showInformationMessage")
-        .mockResolvedValue(undefined);
-
-      originalTelemetryExtension = workspace
-        .getConfiguration()
-        .get<boolean>("codeQL.telemetry.enableTelemetry");
-      originalTelemetryGlobal = workspace
-        .getConfiguration()
-        .get<string>("telemetry.telemetryLevel");
       isCanary = (!!workspace
         .getConfiguration()
         .get<boolean>("codeQL.canary")).toString();
 
       // each test will default to telemetry being enabled
-      isTelemetryEnabledSpy = jest
-        .spyOn(env, "isTelemetryEnabled", "get")
-        .mockReturnValue(true);
-      await setTelemetryLevel("telemetry", "all");
-      await enableTelemetry("codeQL.telemetry", true);
+      jest.spyOn(env, "isTelemetryEnabled", "get").mockReturnValue(true);
 
       telemetryListener = new ExtensionTelemetryListener(
         "my-id",
         "1.2.3",
         "fake-key",
-        ctx,
       );
       await wait(100);
     } catch (e) {
@@ -99,18 +58,9 @@ describe("telemetry reporting", () => {
 
   afterEach(async () => {
     telemetryListener?.dispose();
-    // await wait(100);
-    try {
-      await setTelemetryLevel("telemetry", originalTelemetryGlobal);
-      await enableTelemetry("codeQL.telemetry", originalTelemetryExtension);
-    } catch (e) {
-      console.error(e);
-    }
   });
 
-  it("should initialize telemetry when 'codeQL.telemetry.enableTelemetry' is enabled and global 'telemetry.telemetryLevel' is 'all'", async () => {
-    await telemetryListener.initialize();
-
+  it("should initialize telemetry", async () => {
     expect(telemetryListener._reporter).toBeDefined();
     const reporter: any = telemetryListener._reporter;
     expect(reporter.extensionId).toBe("my-id");
@@ -118,80 +68,7 @@ describe("telemetry reporting", () => {
     expect(reporter.userOptIn).toBe(true); // enabled
   });
 
-  it("should initialize telemetry when global 'telemetry.telemetryLevel' is 'off'", async () => {
-    isTelemetryEnabledSpy.mockReturnValue(false);
-    await setTelemetryLevel("telemetry", "off");
-    await telemetryListener.initialize();
-    expect(telemetryListener._reporter).toBeDefined();
-
-    const reporter: any = telemetryListener._reporter;
-    expect(reporter.userOptIn).toBe(false); // disabled
-  });
-
-  it("should not initialize telemetry when extension option disabled", async () => {
-    await enableTelemetry("codeQL.telemetry", false);
-    await telemetryListener.initialize();
-
-    expect(telemetryListener._reporter).toBeUndefined();
-  });
-
-  it("should not initialize telemetry when both options disabled", async () => {
-    await enableTelemetry("codeQL.telemetry", false);
-    isTelemetryEnabledSpy.mockReturnValue(false);
-    await setTelemetryLevel("telemetry", "off");
-    await telemetryListener.initialize();
-    expect(telemetryListener._reporter).toBeUndefined();
-  });
-
-  it("should dispose telemetry object when re-initializing and should not add multiple", async () => {
-    await telemetryListener.initialize();
-    expect(telemetryListener._reporter).toBeDefined();
-    const firstReporter = telemetryListener._reporter;
-    await telemetryListener.initialize();
-    expect(telemetryListener._reporter).toBeDefined();
-    expect(telemetryListener._reporter).not.toBe(firstReporter);
-
-    expect(disposeSpy).toHaveBeenCalledTimes(1);
-
-    // initializing a third time continues to dispose
-    await telemetryListener.initialize();
-    expect(disposeSpy).toHaveBeenCalledTimes(2);
-  });
-
-  it("should reinitialize reporter when extension setting changes", async () => {
-    await telemetryListener.initialize();
-
-    expect(disposeSpy).not.toHaveBeenCalled();
-    expect(telemetryListener._reporter).toBeDefined();
-
-    // this disables the reporter
-    await enableTelemetry("codeQL.telemetry", false);
-
-    expect(telemetryListener._reporter).toBeUndefined();
-
-    expect(disposeSpy).toHaveBeenCalledTimes(1);
-
-    // creates a new reporter, but does not dispose again
-    await enableTelemetry("codeQL.telemetry", true);
-
-    expect(telemetryListener._reporter).toBeDefined();
-    expect(disposeSpy).toHaveBeenCalledTimes(1);
-  });
-
-  it("should set userOptIn to false when global setting changes", async () => {
-    await telemetryListener.initialize();
-
-    const reporter: any = telemetryListener._reporter;
-    expect(reporter.userOptIn).toBe(true); // enabled
-
-    isTelemetryEnabledSpy.mockReturnValue(false);
-    await setTelemetryLevel("telemetry", "off");
-    expect(reporter.userOptIn).toBe(false); // disabled
-  });
-
   it("should send an event", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.sendCommandUsage("command-id", 1234, undefined);
 
     expect(sendTelemetryEventSpy).toHaveBeenCalledWith(
@@ -208,8 +85,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should send a command usage event with an error", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.sendCommandUsage(
       "command-id",
       1234,
@@ -230,7 +105,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should send a command usage event with a cli version", async () => {
-    await telemetryListener.initialize();
     telemetryListener.cliVersion = new SemVer("1.2.3");
 
     telemetryListener.sendCommandUsage(
@@ -274,39 +148,7 @@ describe("telemetry reporting", () => {
     expect(sendTelemetryErrorEventSpy).not.toHaveBeenCalled();
   });
 
-  it("should avoid sending an event when telemetry is disabled", async () => {
-    await telemetryListener.initialize();
-    await enableTelemetry("codeQL.telemetry", false);
-
-    telemetryListener.sendCommandUsage("command-id", 1234, undefined);
-    telemetryListener.sendCommandUsage("command-id", 1234, new Error());
-
-    expect(sendTelemetryEventSpy).not.toHaveBeenCalled();
-    expect(sendTelemetryErrorEventSpy).not.toHaveBeenCalled();
-  });
-
-  it("should send an event when telemetry is re-enabled", async () => {
-    await telemetryListener.initialize();
-    await enableTelemetry("codeQL.telemetry", false);
-    await enableTelemetry("codeQL.telemetry", true);
-
-    telemetryListener.sendCommandUsage("command-id", 1234, undefined);
-
-    expect(sendTelemetryEventSpy).toHaveBeenCalledWith(
-      "command-usage",
-      {
-        name: "command-id",
-        status: "Success",
-        isCanary,
-        cliVersion: "not-set",
-      },
-      { executionTime: 1234 },
-    );
-    expect(sendTelemetryErrorEventSpy).not.toHaveBeenCalled();
-  });
-
   it("should filter undesired properties from telemetry payload", async () => {
-    await telemetryListener.initialize();
     // Reach into the internal appInsights client to grab our telemetry processor.
     const telemetryProcessor: Function = (telemetryListener._reporter as any)
       .appInsightsClient._telemetryProcessors[0];
@@ -340,118 +182,7 @@ describe("telemetry reporting", () => {
     });
   });
 
-  const resolveArg =
-    (index: number) =>
-    (...args: any[]) =>
-      Promise.resolve(args[index]);
-
-  it("should request permission if popup has never been seen before", async () => {
-    showInformationMessageSpy.mockImplementation(
-      resolveArg(3 /* "yes" item */),
-    );
-    await ctx.globalState.update("telemetry-request-viewed", false);
-    expect(env.isTelemetryEnabled).toBe(true);
-
-    await enableTelemetry("codeQL.telemetry", false);
-
-    await telemetryListener.initialize();
-
-    // Wait for user's selection to propagate in settings.
-    await wait(500);
-
-    // Dialog opened, user clicks "yes" and telemetry enabled
-    expect(showInformationMessageSpy).toHaveBeenCalledTimes(1);
-    expect(ENABLE_TELEMETRY.getValue()).toBe(true);
-    expect(ctx.globalState.get("telemetry-request-viewed")).toBe(true);
-  });
-
-  it("should prevent telemetry if permission is denied", async () => {
-    showInformationMessageSpy.mockImplementation(resolveArg(4 /* "no" item */));
-    await ctx.globalState.update("telemetry-request-viewed", false);
-    await enableTelemetry("codeQL.telemetry", true);
-
-    await telemetryListener.initialize();
-
-    // Dialog opened, user clicks "no" and telemetry disabled
-    expect(showInformationMessageSpy).toHaveBeenCalledTimes(1);
-    expect(ENABLE_TELEMETRY.getValue()).toBe(false);
-    expect(ctx.globalState.get("telemetry-request-viewed")).toBe(true);
-  });
-
-  it("should unchange telemetry if permission dialog is dismissed", async () => {
-    showInformationMessageSpy.mockResolvedValue(undefined /* cancelled */);
-    await ctx.globalState.update("telemetry-request-viewed", false);
-
-    // this causes requestTelemetryPermission to be called
-    await enableTelemetry("codeQL.telemetry", false);
-
-    // Dialog opened, and user closes without interacting with it
-    expect(showInformationMessageSpy).toHaveBeenCalledTimes(1);
-    expect(ENABLE_TELEMETRY.getValue()).toBe(false);
-    // dialog was canceled, so should not have marked as viewed
-    expect(ctx.globalState.get("telemetry-request-viewed")).toBe(false);
-  });
-
-  it("should unchange telemetry if permission dialog is cancelled if starting as true", async () => {
-    await enableTelemetry("codeQL.telemetry", false);
-
-    // as before, except start with telemetry enabled. It should _stay_ enabled if the
-    // dialog is canceled.
-    showInformationMessageSpy.mockResolvedValue(undefined /* cancelled */);
-    await ctx.globalState.update("telemetry-request-viewed", false);
-
-    // this causes requestTelemetryPermission to be called
-    await enableTelemetry("codeQL.telemetry", true);
-
-    // Dialog opened, and user closes without interacting with it
-    // Telemetry state should not have changed
-    expect(showInformationMessageSpy).toHaveBeenCalledTimes(1);
-    expect(ENABLE_TELEMETRY.getValue()).toBe(true);
-    // dialog was canceled, so should not have marked as viewed
-    expect(ctx.globalState.get("telemetry-request-viewed")).toBe(false);
-  });
-
-  it("should avoid showing dialog if global telemetry is disabled", async () => {
-    // when telemetry is disabled globally, we never want to show the
-    // opt in/out dialog. We just assume that codeql telemetry should
-    // remain disabled as well.
-    // If the user ever turns global telemetry back on, then we can
-    // show the dialog.
-
-    isTelemetryEnabledSpy.mockReturnValue(false);
-    await setTelemetryLevel("telemetry", "off");
-    await ctx.globalState.update("telemetry-request-viewed", false);
-
-    await telemetryListener.initialize();
-
-    // popup should not be shown even though we have initialized telemetry
-    expect(showInformationMessageSpy).not.toHaveBeenCalled();
-  });
-
-  // This test is failing because codeQL.canary is not a registered configuration.
-  // We do not want to have it registered because we don't want this item
-  // appearing in the settings page. It needs to only be set by users we tell
-  // about it to.
-  // At this point, I see no other way of testing re-requesting permission.
-  xit("should request permission again when user changes canary setting", async () => {
-    // initially, both canary and telemetry are false
-    await workspace.getConfiguration().update("codeQL.canary", false);
-    await enableTelemetry("codeQL.telemetry", false);
-    await ctx.globalState.update("telemetry-request-viewed", true);
-    await telemetryListener.initialize();
-    showInformationMessageSpy.mockResolvedValue(undefined /* cancelled */);
-
-    // set canary to true
-    await workspace.getConfiguration().update("codeQL.canary", true);
-
-    // now, we should have to click through the telemetry requestor again
-    expect(ctx.globalState.get("telemetry-request-viewed")).toBe(false);
-    expect(showInformationMessageSpy).toHaveBeenCalledTimes(1);
-  });
-
   it("should send a ui-interaction telemetry event", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.sendUIInteraction("test");
 
     expect(sendTelemetryEventSpy).toHaveBeenCalledWith(
@@ -467,8 +198,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should send a ui-interaction telemetry event with a cli version", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.cliVersion = new SemVer("1.2.3");
     telemetryListener.sendUIInteraction("test");
 
@@ -485,8 +214,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should send an error telemetry event", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.sendError(redactableError`test`);
 
     expect(sendTelemetryEventSpy).not.toHaveBeenCalled();
@@ -503,7 +230,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should send an error telemetry event with a cli version", async () => {
-    await telemetryListener.initialize();
     telemetryListener.cliVersion = new SemVer("1.2.3");
 
     telemetryListener.sendError(redactableError`test`);
@@ -522,8 +248,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should redact error message contents", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.sendError(
       redactableError`test message with secret information: ${42} and more ${"secret"} parts`,
     );
@@ -543,8 +267,6 @@ describe("telemetry reporting", () => {
   });
 
   it("should send config telemetry event", async () => {
-    await telemetryListener.initialize();
-
     telemetryListener.sendConfigInformation({
       testKey: "testValue",
       testKey2: "42",
@@ -563,26 +285,6 @@ describe("telemetry reporting", () => {
     expect(sendTelemetryErrorEventSpy).not.toHaveBeenCalled();
   });
 
-  async function enableTelemetry(section: string, value: boolean | undefined) {
-    await workspace
-      .getConfiguration(section)
-      .update("enableTelemetry", value, ConfigurationTarget.Global);
-
-    // Need to wait some time since the onDidChangeConfiguration listeners fire
-    // asynchronously. Must ensure they to complete in order to have a successful test.
-    await wait(100);
-  }
-
-  async function setTelemetryLevel(section: string, value: string | undefined) {
-    await workspace
-      .getConfiguration(section)
-      .update("telemetryLevel", value, ConfigurationTarget.Global);
-
-    // Need to wait some time since the onDidChangeConfiguration listeners fire
-    // asynchronously. Must ensure they to complete in order to have a successful test.
-    await wait(100);
-  }
-
   async function wait(ms = 0) {
     return new Promise((resolve) => setTimeout(resolve, ms));
   }
diff --git a/extensions/ql-vscode/test/vscode-tests/test-dispose-handler.ts b/extensions/ql-vscode/test/vscode-tests/test-dispose-handler.ts
index 94f490dafe1..1ecc6c7aa83 100644
--- a/extensions/ql-vscode/test/vscode-tests/test-dispose-handler.ts
+++ b/extensions/ql-vscode/test/vscode-tests/test-dispose-handler.ts
@@ -1,13 +1,19 @@
-import type { Disposable } from "vscode";
+import type { Disposable, TreeView } from "vscode";
 import { DisposableObject } from "../../src/common/disposable-object";
 
-export function testDisposeHandler(disposable: any & Disposable) {
-  if (
-    disposable.onDidExpandElement &&
-    disposable.onDidCollapseElement &&
-    disposable.reveal
-  ) {
-    // This looks like a treeViewer. Don't dispose
+function isTreeView(obj: unknown): obj is TreeView<unknown> {
+  return (
+    typeof obj === "object" &&
+    obj !== null &&
+    "onDidExpandElement" in obj &&
+    "onDidCollapseElement" in obj &&
+    "reveal" in obj
+  );
+}
+
+export function testDisposeHandler(disposable: Disposable) {
+  if (isTreeView(disposable)) {
+    // This looks like a TreeView. Don't dispose
     return;
   }
   if (disposable instanceof DisposableObject) {
diff --git a/scripts/replace-cli-version.sh b/scripts/replace-cli-version.sh
deleted file mode 100755
index 03db7fec03c..00000000000
--- a/scripts/replace-cli-version.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/bin/bash
-
-VERSIONS=$(gh api -H "Accept: application/vnd.github+json" /repos/github/codeql-cli-binaries/releases | jq -r '.[].tag_name' | head -2)
-
-# we are exporting these variables so that we can access these variables in the workflow
-LATEST_VERSION=$(echo $VERSIONS | awk '{ print $1 }')
-PREVIOUS_VERSION=$(echo $VERSIONS | awk '{ print $2 }')
-
-echo "LATEST_VERSION=$LATEST_VERSION" >> $GITHUB_ENV
-echo "PREVIOUS_VERSION=$PREVIOUS_VERSION" >> $GITHUB_ENV
-
-sed -i "s/$PREVIOUS_VERSION/$LATEST_VERSION/g" extensions/ql-vscode/supported_cli_versions.json
diff --git a/syntaxes/ql.tmLanguage.json b/syntaxes/ql.tmLanguage.json
index a8b5c3909a2..1269433c127 100644
--- a/syntaxes/ql.tmLanguage.json
+++ b/syntaxes/ql.tmLanguage.json
@@ -675,9 +675,6 @@
               "begin": "(?x)(?<=/\\*\\*)([^*]|\\*(?!/))*$",
               "while": "(?x)(^|\\G)\\s*([^*]|\\*(?!/))(?=([^*]|[*](?!/))*$)",
               "patterns": [
-
-
-
                 {
                   "match": "(?x)\\G\\s* (@\\S+)",
                   "name": "keyword.tag.ql"
@@ -1469,7 +1466,7 @@
       }
     },
     "select-as-clause": {
-      "end": "(?x)(?<=(?:[0-9A-Za-z_])(?:(?!(?:[0-9A-Za-z_]))))",
+      "end": "(?x)(?<=(?:[0-9A-Za-z_]))(?:(?!(?:[0-9A-Za-z_])))",
       "match": "(?x)meta.block.select-as-clause.ql",
       "patterns": [
         {
@@ -1540,4 +1537,4 @@
       "name": "constant.character.escape.ql"
     }
   }
-}
+}
\ No newline at end of file