I’ve generated a Doxygen file from the LMS 2012 C source. I haven’t read all of it yet and so far I think I’ve seen mostly C stuff in the documentation and not so much about the VM.
Anyways, here it is: http://ev3.fantastic.computer/doxygen/index.html
Update! I found a Doxygen settings file in the ev3 sources and generated a new Doxygen file. It seems to be more focused on using the LMS2012 Virtual Machine rather than the underlying stuff. The new Doxygen is at the location mentioned above.
The Doxygen I created first, from all of the source, is moved to here: http://ev3.fantastic.computer/doxygen-all/index.html