Also, fix some missing docs. Unfortunately, there are still some
problems (incorrect resolution for multiple files/functions with the
same name, and a bug with doxygen's verbatim/code blocks).
Most of the warnings are due to a bug in doxygen (fixed in 1.8.17,
but...), however some were legit due to overzealous image search paths
wildly including the doxygen output tree.
So I don't have to keep duplicating file names all over the place, I've
decided to use the "dox" extension on text files that are formatted for
doxygen processing. This way, doxygen can search for them using wildcards,
and unformated text files won't cause any headaches.
