The key to the solution is to add a shortcut to the headers:
This is a level 1 header {
Then the table of contents [TOC]
[TOC]
as well as link headers
[Link to first headline](@ref labelid_H1) [Link to second headline](#labelid_H2)
work.
Another point to mention is that Doxygen feeds on the first line of the file, which is used as the main page (look for βEat my shorts, Doxygen!β In: Use the README.md file as the main page in Doxygen )
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