Project structure:
Project root
Doxyfile1
Doxyfile2
README.md
Subdir
README.md
Doxyfile1 is for internal documentation, Doxyfile2 if for end-user documentation.
Doxyfile1 documents the whole project, Doxyfile2 documents Subdir only.
In the end-user documentation, I correctly get the Subdir/README.md file shown.
In the internal documentation, I still get the same Subdir/README.md file shown, instead of README.md.
In the Doxyfiles, I explicitly specified the paths of the README.md files, both in the USE_MDFILE_AS_MAINPAGE field and in the INPUT field.
Why Doxyfile1 keeps pointing to the wrong README.md file?
Could it be that a single README.md file is expected in a project, and so a random one is picked?
Fixed moving the subproject's Doxyfile in its own directory:
Project root
Doxyfile1
README.md
Subdir
Doxyfile2
README.md