Thanks for reporting this. It is an interesting problem, that I'm not sure how to solve (being yet early and I without coffee).

The README.md file is the homepage. It is intended to be displayed using the URL https://wapp.tcl.tk/index.html/doc/trunk/README.md and the hyperlinks are relative to that URL. When you click on the File menu, it shows the README.md file using a different URL - http://wapp.tcl.tk/index.html/dir?ci=tip - and the hyperlinks don't work for that URL.

Perhaps the right solution is to rename the README.md file to something different so that it is not displayed by default from the Files menu...