diff --git a/README.md b/README.md
index c7243033b..bcd9f85c8 100644
--- a/README.md
+++ b/README.md
@@ -726,12 +726,12 @@ The following sets of tools are available:
 - **issue_read** - Get issue details
   - `issue_number`: The number of the issue (number, required)
   - `method`: The read operation to perform on a single issue.
-Options are:
-1. get - Get details of a specific issue.
-2. get_comments - Get issue comments.
-3. get_sub_issues - Get sub-issues of the issue.
-4. get_labels - Get labels assigned to the issue.
- (string, required)
+    Options are:
+    1. get - Get details of a specific issue.
+    2. get_comments - Get issue comments.
+    3. get_sub_issues - Get sub-issues of the issue.
+    4. get_labels - Get labels assigned to the issue.
+     (string, required)
   - `owner`: The owner of the repository (string, required)
   - `page`: Page number for pagination (min 1) (number, optional)
   - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
@@ -744,10 +744,10 @@ Options are:
   - `issue_number`: Issue number to update (number, optional)
   - `labels`: Labels to apply to this issue (string[], optional)
   - `method`: Write operation to perform on a single issue.
-Options are:
-- 'create' - creates a new issue.
-- 'update' - updates an existing issue.
- (string, required)
+    Options are:
+    - 'create' - creates a new issue.
+    - 'update' - updates an existing issue.
+     (string, required)
   - `milestone`: Milestone number (number, optional)
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
@@ -784,11 +784,11 @@ Options are:
   - `before_id`: The ID of the sub-issue to be prioritized before (either after_id OR before_id should be specified) (number, optional)
   - `issue_number`: The number of the parent issue (number, required)
   - `method`: The action to perform on a single sub-issue
-Options are:
-- 'add' - add a sub-issue to a parent issue in a GitHub repository.
-- 'remove' - remove a sub-issue from a parent issue in a GitHub repository.
-- 'reprioritize' - change the order of sub-issues within a parent issue in a GitHub repository. Use either 'after_id' or 'before_id' to specify the new position.
-				 (string, required)
+    Options are:
+    - 'add' - add a sub-issue to a parent issue in a GitHub repository.
+    - 'remove' - remove a sub-issue from a parent issue in a GitHub repository.
+    - 'reprioritize' - change the order of sub-issues within a parent issue in a GitHub repository. Use either 'after_id' or 'before_id' to specify the new position.
+    				 (string, required)
   - `owner`: Repository owner (string, required)
   - `replace_parent`: When true, replaces the sub-issue's current parent issue. Use with 'add' method only. (boolean, optional)
   - `repo`: Repository name (string, required)
@@ -986,15 +986,15 @@ Options are:
 
 - **pull_request_read** - Get details for a single pull request
   - `method`: Action to specify what pull request data needs to be retrieved from GitHub. 
-Possible options: 
- 1. get - Get details of a specific pull request.
- 2. get_diff - Get the diff of a pull request.
- 3. get_status - Get status of a head commit in a pull request. This reflects status of builds and checks.
- 4. get_files - Get the list of files changed in a pull request. Use with pagination parameters to control the number of results returned.
- 5. get_review_comments - Get the review comments on a pull request. They are comments made on a portion of the unified diff during a pull request review. Use with pagination parameters to control the number of results returned.
- 6. get_reviews - Get the reviews on a pull request. When asked for review comments, use get_review_comments method.
- 7. get_comments - Get comments on a pull request. Use this if user doesn't specifically want review comments. Use with pagination parameters to control the number of results returned.
- (string, required)
+    Possible options: 
+     1. get - Get details of a specific pull request.
+     2. get_diff - Get the diff of a pull request.
+     3. get_status - Get status of a head commit in a pull request. This reflects status of builds and checks.
+     4. get_files - Get the list of files changed in a pull request. Use with pagination parameters to control the number of results returned.
+     5. get_review_comments - Get the review comments on a pull request. They are comments made on a portion of the unified diff during a pull request review. Use with pagination parameters to control the number of results returned.
+     6. get_reviews - Get the reviews on a pull request. When asked for review comments, use get_review_comments method.
+     7. get_comments - Get comments on a pull request. Use this if user doesn't specifically want review comments. Use with pagination parameters to control the number of results returned.
+     (string, required)
   - `owner`: Repository owner (string, required)
   - `page`: Page number for pagination (min 1) (number, optional)
   - `perPage`: Results per page for pagination (min 1, max 100) (number, optional)
diff --git a/cmd/github-mcp-server/generate_docs.go b/cmd/github-mcp-server/generate_docs.go
index 87c9c0514..61459d7f0 100644
--- a/cmd/github-mcp-server/generate_docs.go
+++ b/cmd/github-mcp-server/generate_docs.go
@@ -269,6 +269,9 @@ func generateToolDoc(tool mcp.Tool) string {
 
 			description = prop.Description
 
+			// Indent any continuation lines in the description to maintain markdown formatting
+			description = indentMultilineDescription(description, "    ")
+
 			paramLine := fmt.Sprintf("  - `%s`: %s (%s, %s)", propName, description, typeStr, requiredStr)
 			lines = append(lines, paramLine)
 		}
@@ -288,6 +291,19 @@ func contains(slice []string, item string) bool {
 	return false
 }
 
+// indentMultilineDescription adds the specified indent to all lines after the first line.
+// This ensures that multi-line descriptions maintain proper markdown list formatting.
+func indentMultilineDescription(description, indent string) string {
+	lines := strings.Split(description, "\n")
+	if len(lines) <= 1 {
+		return description
+	}
+	for i := 1; i < len(lines); i++ {
+		lines[i] = indent + lines[i]
+	}
+	return strings.Join(lines, "\n")
+}
+
 func replaceSection(content, startMarker, endMarker, newContent string) string {
 	startPattern := fmt.Sprintf(`<!-- %s -->`, regexp.QuoteMeta(startMarker))
 	endPattern := fmt.Sprintf(`<!-- %s -->`, regexp.QuoteMeta(endMarker))
diff --git a/docs/remote-server.md b/docs/remote-server.md
index 1030911ef..e06d41a75 100644
--- a/docs/remote-server.md
+++ b/docs/remote-server.md
@@ -19,7 +19,7 @@ Below is a table of available toolsets for the remote GitHub MCP Server. Each to
 <!-- START AUTOMATED TOOLSETS -->
 | Name           | Description                                      | API URL                                               | 1-Click Install (VS Code)                                                                                                                                                                                                 | Read-only Link                                                                                                 | 1-Click Read-only Install (VS Code)                                                                                                                                                                                                 |
 |----------------|--------------------------------------------------|-------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Default            | ["Default" toolset](../README.md#default-toolset)                | https://api.githubcopilot.com/mcp/                    | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=github&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2F%22%7D)                                      | [read-only](https://api.githubcopilot.com/mcp/readonly)                                                      | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=github&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Freadonly%22%7D) |
+| all            | All available GitHub MCP tools                    | https://api.githubcopilot.com/mcp/                    | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=github&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2F%22%7D)                                      | [read-only](https://api.githubcopilot.com/mcp/readonly)                                                      | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=github&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Freadonly%22%7D) |
 | Actions        | GitHub Actions workflows and CI/CD operations    | https://api.githubcopilot.com/mcp/x/actions           | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-actions&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Factions%22%7D)                         | [read-only](https://api.githubcopilot.com/mcp/x/actions/readonly)                                              | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-actions&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Factions%2Freadonly%22%7D)                                                                          |
 | Code Security  | Code security related tools, such as GitHub Code Scanning | https://api.githubcopilot.com/mcp/x/code_security     | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-code_security&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcode_security%22%7D)             | [read-only](https://api.githubcopilot.com/mcp/x/code_security/readonly)                                        | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-code_security&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcode_security%2Freadonly%22%7D)                                                              |
 | Dependabot     | Dependabot tools                                 | https://api.githubcopilot.com/mcp/x/dependabot        | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-dependabot&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fdependabot%22%7D)                   | [read-only](https://api.githubcopilot.com/mcp/x/dependabot/readonly)                                           | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-dependabot&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fdependabot%2Freadonly%22%7D)                                                                    |
diff --git a/internal/ghmcp/server.go b/internal/ghmcp/server.go
index f4e67f264..41f9016a2 100644
--- a/internal/ghmcp/server.go
+++ b/internal/ghmcp/server.go
@@ -100,9 +100,10 @@ func NewMCPServer(cfg MCPServerConfig) (*mcp.Server, error) {
 
 	enabledToolsets := cfg.EnabledToolsets
 
-	// If dynamic toolsets are enabled, remove "all" from the enabled toolsets
+	// If dynamic toolsets are enabled, remove "all" and "default" from the enabled toolsets
 	if cfg.DynamicToolsets {
 		enabledToolsets = github.RemoveToolset(enabledToolsets, github.ToolsetMetadataAll.ID)
+		enabledToolsets = github.RemoveToolset(enabledToolsets, github.ToolsetMetadataDefault.ID)
 	}
 
 	// Clean up the passed toolsets
@@ -176,8 +177,8 @@ func NewMCPServer(cfg MCPServerConfig) (*mcp.Server, error) {
 
 	// Register specific tools if configured
 	if len(cfg.EnabledTools) > 0 {
-		// Clean and validate tool names
 		enabledTools := github.CleanTools(cfg.EnabledTools)
+		enabledTools, _ = tsg.ResolveToolAliases(enabledTools)
 
 		// Register the specified tools (additive to any toolsets already enabled)
 		err = tsg.RegisterSpecificTools(ghServer, enabledTools, cfg.ReadOnly)
diff --git a/pkg/github/deprecated_tool_aliases.go b/pkg/github/deprecated_tool_aliases.go
new file mode 100644
index 000000000..4abdca14d
--- /dev/null
+++ b/pkg/github/deprecated_tool_aliases.go
@@ -0,0 +1,14 @@
+// deprecated_tool_aliases.go
+package github
+
+// DeprecatedToolAliases maps old tool names to their new canonical names.
+// When tools are renamed, add an entry here to maintain backward compatibility.
+// Users referencing the old name will receive the new tool with a deprecation warning.
+//
+// Example:
+//
+//	"get_issue": "issue_read",
+//	"create_pr": "pull_request_create",
+var DeprecatedToolAliases = map[string]string{
+	// Add entries as tools are renamed
+}
diff --git a/pkg/github/issues.go b/pkg/github/issues.go
index 46111a4d6..ec83e4efa 100644
--- a/pkg/github/issues.go
+++ b/pkg/github/issues.go
@@ -1381,11 +1381,14 @@ func ListIssues(getGQLClient GetGQLClientFn, t translations.TranslationHelperFun
 				return utils.NewToolResultError(err.Error()), nil, nil
 			}
 
-			// If the state has a value, cast into an array of strings
+			// Normalize and filter by state
+			state = strings.ToUpper(state)
 			var states []githubv4.IssueState
-			if state != "" {
-				states = append(states, githubv4.IssueState(state))
-			} else {
+
+			switch state {
+			case "OPEN", "CLOSED":
+				states = []githubv4.IssueState{githubv4.IssueState(state)}
+			default:
 				states = []githubv4.IssueState{githubv4.IssueStateOpen, githubv4.IssueStateClosed}
 			}
 
@@ -1405,13 +1408,21 @@ func ListIssues(getGQLClient GetGQLClientFn, t translations.TranslationHelperFun
 				return utils.NewToolResultError(err.Error()), nil, nil
 			}
 
-			// These variables are required for the GraphQL query to be set by default
-			// If orderBy is empty, default to CREATED_AT
-			if orderBy == "" {
+			// Normalize and validate orderBy
+			orderBy = strings.ToUpper(orderBy)
+			switch orderBy {
+			case "CREATED_AT", "UPDATED_AT", "COMMENTS":
+				// Valid, keep as is
+			default:
 				orderBy = "CREATED_AT"
 			}
-			// If direction is empty, default to DESC
-			if direction == "" {
+
+			// Normalize and validate direction
+			direction = strings.ToUpper(direction)
+			switch direction {
+			case "ASC", "DESC":
+				// Valid, keep as is
+			default:
 				direction = "DESC"
 			}
 
diff --git a/pkg/github/issues_test.go b/pkg/github/issues_test.go
index 48901ccdc..c4454624b 100644
--- a/pkg/github/issues_test.go
+++ b/pkg/github/issues_test.go
@@ -1183,6 +1183,16 @@ func Test_ListIssues(t *testing.T) {
 			expectError:   false,
 			expectedCount: 2,
 		},
+		{
+			name: "filter by open state - lc",
+			reqParams: map[string]interface{}{
+				"owner": "owner",
+				"repo":  "repo",
+				"state": "open",
+			},
+			expectError:   false,
+			expectedCount: 2,
+		},
 		{
 			name: "filter by closed state",
 			reqParams: map[string]interface{}{
@@ -1229,6 +1239,9 @@ func Test_ListIssues(t *testing.T) {
 			case "filter by open state":
 				matcher := githubv4mock.NewQueryMatcher(qBasicNoLabels, varsOpenOnly, mockResponseOpenOnly)
 				httpClient = githubv4mock.NewMockedHTTPClient(matcher)
+			case "filter by open state - lc":
+				matcher := githubv4mock.NewQueryMatcher(qBasicNoLabels, varsOpenOnly, mockResponseOpenOnly)
+				httpClient = githubv4mock.NewMockedHTTPClient(matcher)
 			case "filter by closed state":
 				matcher := githubv4mock.NewQueryMatcher(qBasicNoLabels, varsClosedOnly, mockResponseClosedOnly)
 				httpClient = githubv4mock.NewMockedHTTPClient(matcher)
diff --git a/pkg/github/repositories.go b/pkg/github/repositories.go
index dbf24e8e3..ff81484f2 100644
--- a/pkg/github/repositories.go
+++ b/pkg/github/repositories.go
@@ -402,6 +402,8 @@ func CreateOrUpdateFile(getClient GetClientFn, t translations.TranslationHelperF
 		if err != nil {
 			return nil, nil, fmt.Errorf("failed to get GitHub client: %w", err)
 		}
+
+		path = strings.TrimPrefix(path, "/")
 		fileContent, resp, err := client.Repositories.CreateFile(ctx, owner, repo, path, opts)
 		if err != nil {
 			return ghErrors.NewGitHubAPIErrorResponse(ctx,
diff --git a/pkg/github/tools.go b/pkg/github/tools.go
index d37af98b8..f21a9ae5b 100644
--- a/pkg/github/tools.go
+++ b/pkg/github/tools.go
@@ -378,6 +378,8 @@ func DefaultToolsetGroup(readOnly bool, getClient GetClientFn, getGQLClient GetG
 	tsg.AddToolset(stargazers)
 	tsg.AddToolset(labels)
 
+	tsg.AddDeprecatedToolAliases(DeprecatedToolAliases)
+
 	return tsg
 }
 
diff --git a/pkg/toolsets/toolsets.go b/pkg/toolsets/toolsets.go
index d4964ee5f..d96b5fb50 100644
--- a/pkg/toolsets/toolsets.go
+++ b/pkg/toolsets/toolsets.go
@@ -192,16 +192,24 @@ func (t *Toolset) AddReadTools(tools ...ServerTool) *Toolset {
 }
 
 type ToolsetGroup struct {
-	Toolsets     map[string]*Toolset
-	everythingOn bool
-	readOnly     bool
+	Toolsets          map[string]*Toolset
+	deprecatedAliases map[string]string
+	everythingOn      bool
+	readOnly          bool
 }
 
 func NewToolsetGroup(readOnly bool) *ToolsetGroup {
 	return &ToolsetGroup{
-		Toolsets:     make(map[string]*Toolset),
-		everythingOn: false,
-		readOnly:     readOnly,
+		Toolsets:          make(map[string]*Toolset),
+		deprecatedAliases: make(map[string]string),
+		everythingOn:      false,
+		readOnly:          readOnly,
+	}
+}
+
+func (tg *ToolsetGroup) AddDeprecatedToolAliases(aliases map[string]string) {
+	for oldName, newName := range aliases {
+		tg.deprecatedAliases[oldName] = newName
 	}
 }
 
@@ -307,6 +315,26 @@ func NewToolDoesNotExistError(name string) *ToolDoesNotExistError {
 	return &ToolDoesNotExistError{Name: name}
 }
 
+// ResolveToolAliases resolves deprecated tool aliases to their canonical names.
+// It logs a warning to stderr for each deprecated alias that is resolved.
+// Returns:
+//   - resolved: tool names with aliases replaced by canonical names
+//   - aliasesUsed: map of oldName → newName for each alias that was resolved
+func (tg *ToolsetGroup) ResolveToolAliases(toolNames []string) (resolved []string, aliasesUsed map[string]string) {
+	resolved = make([]string, 0, len(toolNames))
+	aliasesUsed = make(map[string]string)
+	for _, toolName := range toolNames {
+		if canonicalName, isAlias := tg.deprecatedAliases[toolName]; isAlias {
+			fmt.Fprintf(os.Stderr, "Warning: tool %q is deprecated, use %q instead\n", toolName, canonicalName)
+			aliasesUsed[toolName] = canonicalName
+			resolved = append(resolved, canonicalName)
+		} else {
+			resolved = append(resolved, toolName)
+		}
+	}
+	return resolved, aliasesUsed
+}
+
 // FindToolByName searches all toolsets (enabled or disabled) for a tool by name.
 // Returns the tool, its parent toolset name, and an error if not found.
 func (tg *ToolsetGroup) FindToolByName(toolName string) (*ServerTool, string, error) {
diff --git a/pkg/toolsets/toolsets_test.go b/pkg/toolsets/toolsets_test.go
index 3f4581f34..6362aad0e 100644
--- a/pkg/toolsets/toolsets_test.go
+++ b/pkg/toolsets/toolsets_test.go
@@ -3,8 +3,23 @@ package toolsets
 import (
 	"errors"
 	"testing"
+
+	"github.com/modelcontextprotocol/go-sdk/mcp"
 )
 
+// mockTool creates a minimal ServerTool for testing
+func mockTool(name string, readOnly bool) ServerTool {
+	return ServerTool{
+		Tool: mcp.Tool{
+			Name: name,
+			Annotations: &mcp.ToolAnnotations{
+				ReadOnlyHint: readOnly,
+			},
+		},
+		RegisterFunc: func(_ *mcp.Server) {},
+	}
+}
+
 func TestNewToolsetGroupIsEmptyWithoutEverythingOn(t *testing.T) {
 	tsg := NewToolsetGroup(false)
 	if len(tsg.Toolsets) != 0 {
@@ -262,3 +277,119 @@ func TestToolsetGroup_GetToolset(t *testing.T) {
 		t.Errorf("expected error to be ToolsetDoesNotExistError, got %v", err)
 	}
 }
+
+func TestAddDeprecatedToolAliases(t *testing.T) {
+	tsg := NewToolsetGroup(false)
+
+	// Test adding aliases
+	tsg.AddDeprecatedToolAliases(map[string]string{
+		"old_name":  "new_name",
+		"get_issue": "issue_read",
+		"create_pr": "pull_request_create",
+	})
+
+	if len(tsg.deprecatedAliases) != 3 {
+		t.Errorf("expected 3 aliases, got %d", len(tsg.deprecatedAliases))
+	}
+	if tsg.deprecatedAliases["old_name"] != "new_name" {
+		t.Errorf("expected alias 'old_name' -> 'new_name', got '%s'", tsg.deprecatedAliases["old_name"])
+	}
+	if tsg.deprecatedAliases["get_issue"] != "issue_read" {
+		t.Errorf("expected alias 'get_issue' -> 'issue_read'")
+	}
+	if tsg.deprecatedAliases["create_pr"] != "pull_request_create" {
+		t.Errorf("expected alias 'create_pr' -> 'pull_request_create'")
+	}
+}
+
+func TestResolveToolAliases(t *testing.T) {
+	tsg := NewToolsetGroup(false)
+	tsg.AddDeprecatedToolAliases(map[string]string{
+		"get_issue": "issue_read",
+		"create_pr": "pull_request_create",
+	})
+
+	// Test resolving a mix of aliases and canonical names
+	input := []string{"get_issue", "some_tool", "create_pr"}
+	resolved, aliasesUsed := tsg.ResolveToolAliases(input)
+
+	// Verify resolved names
+	if len(resolved) != 3 {
+		t.Fatalf("expected 3 resolved names, got %d", len(resolved))
+	}
+	if resolved[0] != "issue_read" {
+		t.Errorf("expected 'issue_read', got '%s'", resolved[0])
+	}
+	if resolved[1] != "some_tool" {
+		t.Errorf("expected 'some_tool' (unchanged), got '%s'", resolved[1])
+	}
+	if resolved[2] != "pull_request_create" {
+		t.Errorf("expected 'pull_request_create', got '%s'", resolved[2])
+	}
+
+	// Verify aliasesUsed map
+	if len(aliasesUsed) != 2 {
+		t.Fatalf("expected 2 aliases used, got %d", len(aliasesUsed))
+	}
+	if aliasesUsed["get_issue"] != "issue_read" {
+		t.Errorf("expected aliasesUsed['get_issue'] = 'issue_read', got '%s'", aliasesUsed["get_issue"])
+	}
+	if aliasesUsed["create_pr"] != "pull_request_create" {
+		t.Errorf("expected aliasesUsed['create_pr'] = 'pull_request_create', got '%s'", aliasesUsed["create_pr"])
+	}
+}
+
+func TestFindToolByName(t *testing.T) {
+	tsg := NewToolsetGroup(false)
+
+	// Create a toolset with a tool
+	toolset := NewToolset("test-toolset", "Test toolset")
+	toolset.readTools = append(toolset.readTools, mockTool("issue_read", true))
+	tsg.AddToolset(toolset)
+
+	// Find by canonical name
+	tool, toolsetName, err := tsg.FindToolByName("issue_read")
+	if err != nil {
+		t.Fatalf("expected no error, got %v", err)
+	}
+	if tool.Tool.Name != "issue_read" {
+		t.Errorf("expected tool name 'issue_read', got '%s'", tool.Tool.Name)
+	}
+	if toolsetName != "test-toolset" {
+		t.Errorf("expected toolset name 'test-toolset', got '%s'", toolsetName)
+	}
+
+	// FindToolByName does NOT resolve aliases - it expects canonical names
+	_, _, err = tsg.FindToolByName("get_issue")
+	if err == nil {
+		t.Error("expected error when using alias directly with FindToolByName")
+	}
+}
+
+func TestRegisterSpecificTools(t *testing.T) {
+	tsg := NewToolsetGroup(false)
+
+	// Create a toolset with both read and write tools
+	toolset := NewToolset("test-toolset", "Test toolset")
+	toolset.readTools = append(toolset.readTools, mockTool("issue_read", true))
+	toolset.writeTools = append(toolset.writeTools, mockTool("issue_write", false))
+	tsg.AddToolset(toolset)
+
+	// Test registering with canonical names
+	err := tsg.RegisterSpecificTools(nil, []string{"issue_read"}, false)
+	if err != nil {
+		t.Errorf("expected no error registering tool, got %v", err)
+	}
+
+	// Test registering write tool in read-only mode (should skip but not error)
+	err = tsg.RegisterSpecificTools(nil, []string{"issue_write"}, true)
+	if err != nil {
+		t.Errorf("expected no error when skipping write tool in read-only mode, got %v", err)
+	}
+
+	// Test registering non-existent tool (should error)
+	err = tsg.RegisterSpecificTools(nil, []string{"nonexistent"}, false)
+	if err == nil {
+		t.Error("expected error for non-existent tool")
+	}
+}
diff --git a/script/get-me b/script/get-me
index 46339ae53..954f57cec 100755
--- a/script/get-me
+++ b/script/get-me
@@ -1,3 +1,17 @@
 #!/bin/bash
 
-echo '{"jsonrpc":"2.0","id":3,"params":{"name":"get_me"},"method":"tools/call"}' | go run  cmd/github-mcp-server/main.go stdio  | jq .
+# MCP requires initialize -> notifications/initialized -> tools/call
+output=$(
+  (
+    echo '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"get-me-script","version":"1.0.0"}}}'
+    echo '{"jsonrpc":"2.0","method":"notifications/initialized","params":{}}'
+    echo '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"get_me","arguments":{}}}'
+    sleep 1
+  ) | go run cmd/github-mcp-server/main.go stdio 2>/dev/null | tail -1
+)
+
+if command -v jq &> /dev/null; then
+  echo "$output" | jq '.result.content[0].text | fromjson'
+else
+  echo "$output"
+fi
diff --git a/script/licenses b/script/licenses
index 4200316b9..214efa435 100755
--- a/script/licenses
+++ b/script/licenses
@@ -1,21 +1,163 @@
 #!/bin/bash
+#
+# Generate license files for all platform/arch combinations.
+# This script handles architecture-specific dependency differences by:
+# 1. Generating separate license reports per GOOS/GOARCH combination
+# 2. Grouping identical reports together (comma-separated arch names)
+# 3. Creating an index at the top of each platform file
+# 4. Copying all license files to third-party/
+#
+# Note: third-party/ is a union of all license files across all architectures.
+# This means that license files for dependencies present in only some architectures
+# may still appear in third-party/. This is intentional and ensures compliance.
+#
+# Note: we ignore warnings because we want the command to succeed, however the output should be checked
+#       for any new warnings, and potentially we may need to add license information.
+#
+#       Normally these warnings are packages containing non go code, which may or may not require explicit attribution,
+#       depending on the license.
+
+set -e
 
 go install github.com/google/go-licenses@latest
 
+# actions/setup-go does not setup the installed toolchain to be preferred over the system install,
+# which causes go-licenses to raise "Package ... does not have module info" errors in CI.
+# For more information, https://github.com/google/go-licenses/issues/244#issuecomment-1885098633
+if [ "$CI" = "true" ]; then
+    export GOROOT=$(go env GOROOT)
+    export PATH=${GOROOT}/bin:$PATH
+fi
+
 rm -rf third-party
 mkdir -p third-party
 export TEMPDIR="$(mktemp -d)"
 
 trap "rm -fr ${TEMPDIR}" EXIT
 
-for goos in linux darwin windows ; do
-    # Note: we ignore warnings because we want the command to succeed, however the output should be checked
-    #       for any new warnings, and potentially we may need to add license information. 
-    #
-    #       Normally these warnings are packages containing non go code, which may or may not require explicit attribution,
-    #       depending on the license.
-    GOOS="${goos}" GOFLAGS=-mod=mod go-licenses save ./... --save_path="${TEMPDIR}/${goos}" --force || echo "Ignore warnings"
-    GOOS="${goos}" GOFLAGS=-mod=mod go-licenses report ./... --template .github/licenses.tmpl > third-party-licenses.${goos}.md || echo "Ignore warnings"
-    cp -fR "${TEMPDIR}/${goos}"/* third-party/
+# Cross-platform hash function (works on both Linux and macOS)
+compute_hash() {
+    if command -v md5sum >/dev/null 2>&1; then
+        md5sum | cut -d' ' -f1
+    elif command -v md5 >/dev/null 2>&1; then
+        md5 -q
+    else
+        # Fallback to cksum if neither is available
+        cksum | cut -d' ' -f1
+    fi
+}
+
+# Function to get architectures for a given OS
+get_archs() {
+    case "$1" in
+        linux)   echo "386 amd64 arm64" ;;
+        darwin)  echo "amd64 arm64" ;;
+        windows) echo "386 amd64 arm64" ;;
+    esac
+}
+
+# Generate reports for each platform/arch combination
+for goos in darwin linux windows; do
+    echo "Processing ${goos}..."
+    
+    archs=$(get_archs "$goos")
+    
+    for goarch in $archs; do
+        echo "  Generating for ${goos}/${goarch}..."
+        
+        # Generate the license report for this arch
+        report_file="${TEMPDIR}/${goos}_${goarch}_report.md"
+        GOOS="${goos}" GOARCH="${goarch}" GOFLAGS=-mod=mod go-licenses report ./... --template .github/licenses.tmpl > "${report_file}" 2>/dev/null || echo "  (warnings ignored for ${goos}/${goarch})"
+        
+        # Save licenses to temp directory
+        GOOS="${goos}" GOARCH="${goarch}" GOFLAGS=-mod=mod go-licenses save ./... --save_path="${TEMPDIR}/${goos}_${goarch}" --force 2>/dev/null || echo "  (warnings ignored for ${goos}/${goarch})"
+        
+        # Copy to third-party (accumulate all - union of all architectures for compliance)
+        if [ -d "${TEMPDIR}/${goos}_${goarch}" ]; then
+            cp -fR "${TEMPDIR}/${goos}_${goarch}"/* third-party/ 2>/dev/null || true
+        fi
+        
+        # Extract just the package list (skip header), sort it, and hash it
+        # Use LC_ALL=C for consistent sorting across different systems
+        packages_file="${TEMPDIR}/${goos}_${goarch}_packages.txt"
+        if [ -s "${report_file}" ] && grep -qE '^ - \[' "${report_file}" 2>/dev/null; then
+            grep -E '^ - \[' "${report_file}" | LC_ALL=C sort > "${packages_file}"
+            hash=$(cat "${packages_file}" | compute_hash)
+        else
+            echo "(FAILED TO GENERATE LICENSE REPORT FOR ${goos}/${goarch})" > "${packages_file}"
+            hash="FAILED_${goos}_${goarch}"
+        fi
+        
+        # Store hash for grouping
+        echo "${hash}" > "${TEMPDIR}/${goos}_${goarch}_hash.txt"
+    done
+    
+    # Group architectures with identical reports (deterministic order)
+    # Create groups file: hash -> comma-separated archs
+    groups_file="${TEMPDIR}/${goos}_groups.txt"
+    rm -f "${groups_file}"
+    
+    # Process architectures in order to build groups
+    for goarch in $archs; do
+        hash=$(cat "${TEMPDIR}/${goos}_${goarch}_hash.txt")
+        # Check if we've seen this hash before
+        if grep -q "^${hash}:" "${groups_file}" 2>/dev/null; then
+            # Append to existing group
+            existing=$(grep "^${hash}:" "${groups_file}" | cut -d: -f2)
+            sed -i.bak "s/^${hash}:.*/${hash}:${existing}, ${goarch}/" "${groups_file}"
+            rm -f "${groups_file}.bak"
+        else
+            # New group
+            echo "${hash}:${goarch}" >> "${groups_file}"
+        fi
+    done
+    
+    # Generate the combined report for this platform
+    output_file="third-party-licenses.${goos}.md"
+    
+    cat > "${output_file}" << 'EOF'
+# GitHub MCP Server dependencies
+
+The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
+
+## Table of Contents
+
+EOF
+
+    # Build table of contents (sorted for determinism)
+    # Use LC_ALL=C for consistent sorting across different systems
+    LC_ALL=C sort "${groups_file}" | while IFS=: read -r hash group_archs; do
+        # Create anchor-friendly name
+        anchor=$(echo "${group_archs}" | tr ', ' '-' | tr -s '-')
+        echo "- [${group_archs}](#${anchor})" >> "${output_file}"
+    done
+    
+    echo "" >> "${output_file}"
+    echo "---" >> "${output_file}"
+    echo "" >> "${output_file}"
+    
+    # Add each unique report section (sorted for determinism)
+    # Use LC_ALL=C for consistent sorting across different systems
+    LC_ALL=C sort "${groups_file}" | while IFS=: read -r hash group_archs; do
+        # Get the packages from the first arch in this group
+        first_arch=$(echo "${group_archs}" | cut -d',' -f1 | tr -d ' ')
+        packages=$(cat "${TEMPDIR}/${goos}_${first_arch}_packages.txt")
+        
+        cat >> "${output_file}" << EOF
+## ${group_archs}
+
+The following packages are included for the ${group_archs} architectures.
+
+${packages}
+
+EOF
+    done
+    
+    # Add footer
+    echo "[github/github-mcp-server]: https://github.com/github/github-mcp-server" >> "${output_file}"
+    
+    echo "Generated ${output_file}"
 done
 
+echo "Done! License files generated."
+
diff --git a/script/licenses-check b/script/licenses-check
index 67b567d02..430c8170b 100755
--- a/script/licenses-check
+++ b/script/licenses-check
@@ -1,21 +1,34 @@
 #!/bin/bash
+#
+# Check that license files are up to date.
+# This script regenerates the license files and compares them with the committed versions.
+# If there are differences, it exits with an error.
 
-go install github.com/google/go-licenses@latest
-
-for goos in linux darwin windows ; do
-    # Note: we ignore warnings because we want the command to succeed, however the output should be checked
-    #       for any new warnings, and potentially we may need to add license information. 
-    #
-    #       Normally these warnings are packages containing non go code, which may or may not require explicit attribution,
-    #       depending on the license.
-    GOOS="${goos}" GOFLAGS=-mod=mod go-licenses report ./... --template .github/licenses.tmpl > third-party-licenses.${goos}.copy.md || echo "Ignore warnings"
-    if ! diff -s third-party-licenses.${goos}.copy.md third-party-licenses.${goos}.md; then
-        printf "License check failed.\n\nPlease update the license file by running \`.script/licenses\` and committing the output."
-        rm -f third-party-licenses.${goos}.copy.md
-        exit 1
-    fi
-    rm -f third-party-licenses.${goos}.copy.md
+set -e
+
+# Store original files for comparison
+TEMPDIR="$(mktemp -d)"
+trap "rm -fr ${TEMPDIR}" EXIT
+
+# Save original license markdown files
+for goos in darwin linux windows; do
+    cp "third-party-licenses.${goos}.md" "${TEMPDIR}/"
 done
 
+# Save the state of third-party directory
+cp -r third-party "${TEMPDIR}/third-party.orig"
+
+# Regenerate using the same script
+./script/licenses
+
+# Check for any differences in workspace
+if ! git diff --exit-code --quiet third-party-licenses.*.md third-party/; then
+    echo "License files are out of date:"
+    git diff third-party-licenses.*.md third-party/
+    echo ""
+    printf "\nLicense check failed.\n\nPlease update the license files by running \`./script/licenses\` and committing the output.\n"
+    exit 1
+fi
 
+echo "License check passed for all platforms."
 
diff --git a/third-party-licenses.darwin.md b/third-party-licenses.darwin.md
index 32cdb5b6d..ef8816689 100644
--- a/third-party-licenses.darwin.md
+++ b/third-party-licenses.darwin.md
@@ -2,10 +2,15 @@
 
 The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
 
-## Go Packages
+## Table of Contents
 
-Some packages may only be included on certain architectures or operating systems.
+- [amd64, arm64](#amd64-arm64)
 
+---
+
+## amd64, arm64
+
+The following packages are included for the amd64, arm64 architectures.
 
  - [github.com/aymerick/douceur](https://pkg.go.dev/github.com/aymerick/douceur) ([MIT](https://github.com/aymerick/douceur/blob/v0.2.0/LICENSE))
  - [github.com/fsnotify/fsnotify](https://pkg.go.dev/github.com/fsnotify/fsnotify) ([BSD-3-Clause](https://github.com/fsnotify/fsnotify/blob/v1.9.0/LICENSE))
diff --git a/third-party-licenses.linux.md b/third-party-licenses.linux.md
index 32cdb5b6d..851a70594 100644
--- a/third-party-licenses.linux.md
+++ b/third-party-licenses.linux.md
@@ -2,10 +2,15 @@
 
 The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
 
-## Go Packages
+## Table of Contents
 
-Some packages may only be included on certain architectures or operating systems.
+- [386, amd64, arm64](#386-amd64-arm64)
 
+---
+
+## 386, amd64, arm64
+
+The following packages are included for the 386, amd64, arm64 architectures.
 
  - [github.com/aymerick/douceur](https://pkg.go.dev/github.com/aymerick/douceur) ([MIT](https://github.com/aymerick/douceur/blob/v0.2.0/LICENSE))
  - [github.com/fsnotify/fsnotify](https://pkg.go.dev/github.com/fsnotify/fsnotify) ([BSD-3-Clause](https://github.com/fsnotify/fsnotify/blob/v1.9.0/LICENSE))
diff --git a/third-party-licenses.windows.md b/third-party-licenses.windows.md
index c7e00fb13..f4f8ee42c 100644
--- a/third-party-licenses.windows.md
+++ b/third-party-licenses.windows.md
@@ -2,10 +2,15 @@
 
 The following open source dependencies are used to build the [github/github-mcp-server][] GitHub Model Context Protocol Server.
 
-## Go Packages
+## Table of Contents
 
-Some packages may only be included on certain architectures or operating systems.
+- [386, amd64, arm64](#386-amd64-arm64)
 
+---
+
+## 386, amd64, arm64
+
+The following packages are included for the 386, amd64, arm64 architectures.
 
  - [github.com/aymerick/douceur](https://pkg.go.dev/github.com/aymerick/douceur) ([MIT](https://github.com/aymerick/douceur/blob/v0.2.0/LICENSE))
  - [github.com/fsnotify/fsnotify](https://pkg.go.dev/github.com/fsnotify/fsnotify) ([BSD-3-Clause](https://github.com/fsnotify/fsnotify/blob/v1.9.0/LICENSE))