Jules, if you want the documentation to be readable in HTML then you should put the contents of the html folder into its own branch called gh-pages. For example:
In general, you can put any HTML (including images, subdirectories, client side java scripts, style sheets, etc) into its own branch called gh-pages in the Github repo, and it will be published to this URL http://{account}.github.com/{repo}
Yeah, I’m happy enough with the HTML being viewed here on my website. The github mirror is just there so that people who want a local copy can pull it from there.
Okay I picked up the tag file and referenced it in my Doxygen configuration file, this is REALLY COOL!!!
Every time I mention a juce class or member function in my own docs, it is automatically hyperlinked to the right place in the official Juce documentation at http://www.rawmaterialsoftware.com/juce/api/ !!!
So I can talk about CriticalSection, AudioSampleBuffer, AudioDeviceIOCallback, et. al. and have clickable links!!!