Can I suggest doxygen-style comments for the classes and functions? Doxygen automatically generates a wiki thing (.html) with information on all classes and functions from just comments, making it easier in my opinion for us to search for stuff. I know it kinda sucks to comment everything, but since you will be changing the code a lot and since some of the older functions and core classes are already commented, I thought I'd suggest doxygen-style comments:
http://www.doxygen.nl/docblocks.html
The generated .html pages look awesome:
http://i.imgur.com/xwg2V9c.png (example of a function description (detailed) - it has the call graph and the caller graph!)
http://i.imgur.com/O8nIDdC.png (example of a class list, it shows undetailed member functions with the details at the end of the page - it has a search function! it also shows class hierarchy, files, etc!)