We're using LDoc, you can find it's documentation here: https://stevedonovan.github.io/ldoc/manual/doc.md.html
To generate the docs, just run /Utils/ldoc_run.bat (Which just runs "ldoc ."). The configuration file is Utils/config.ld . It's generating docs for Themes/_fallback/Scripts and Themes/_fallback/Docs , and topics for Themes/_fallback/Docs/Markdown .
We're using doxygen. Just run Utils/doxygen_run.bat . The configuration file is /Utils/doxygen_config