^{Originally posted by Mahebla June 23, 2025}
Hi,

I'm trying to maintain a documentation that should work both with Bitbucket's markdown viewer and Doxygen's HTML generation.
My setup:

Project structure:

/
├── README.md (mainpage)
├── subfolder1/
     └── README.md
├── subfolder2/
     └── README.md
     └── subsubfolder21/
           └── README.md

Each README.md uses markdown headers as implicit page definitions:

# Header {#HeaderPage}

Issue:
When Doxygen generates the HTML, it creates incorrect links to the subfolder README.md files:
In the attached reduced example the generated link points to: subfolder_2_r_e_a_d_m_e_8md.html
The actual generated file is: dir_8bbbd44aa9c5a187ae8556cbc3e79503.html
This results in broken links in the generated documentation.

Current Configuration:

CREATE_SUBDIRS=NO
GENERATE_LATEX=NO
MARKDOWN_SUPPORT=YES
RECURSIVE=YES
EXTRACT_ALL=YES
USE_MDFILE_AS_MAINPAGE=README.md
INPUT = README.md \
        subfolder/README.md 

Questions:
Did I miss any specific Doxygen configuration to handle nested README.md files correctly?
Is this a known issue with Doxygen's handling of nested markdown files?
Are there any workarounds to maintain compatibility with both Bitbucket and Doxygen?
Any help would be appreciated!

DoxygenMarkdown.zip