Given the following header file header.hpp:

#include <cstddef>

/// \file header.hpp
/// This is an example header.

with Doxygen 1.13.0, the default Doxyfile emits the following HTML page:

however, when setting SHOW_INCLUDE_FILES = NO, the #include <cstddef> unexpectedly remains.

Generating the default DoxygenLayout.xml (doxygen -l) and manually setting <includes visible="no"/> (visible="$SHOW_INCLUDE_FILES" by default) has no effect either. Removing the <includes> element entirely also has no effect, but reordering it relative to other page contents does have an effect.

Furthermore, various other layout settings appear to have similar issues. For example, setting visible="no" for <sourcelink> and <detaileddescription> have no observable effect, although reordering them does still have an effect. Other pages (e.g. classes, namespaces, etc.) are emitting brief descriptions despite setting <briefdescription visible="no"/> or removing them entirely from DoxygenLayout.xml. However, their relative ordering in the layout file is still being respected.

This seems to suggest it is specifically the visibility setting (or something related to it) which is being incorrectly ignored, rather than the layout file itself. No warnings or errors are emitted by Doxygen during generation.

For comparison, with Doxygen 1.12.0, the default Doxyfile (doxygen -g) emits the following HTML page:

and when setting SHOW_INCLUDE_FILES = NO, the #include <cstddef> is omitted as expected: