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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?

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1 Answers1

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Fixed moving the subproject's Doxyfile in its own directory:

Project root
   Doxyfile1
   README.md
   Subdir
       Doxyfile2
       README.md
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