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.
Most of the guts of configure.ac have been moved to config.d and are then
brought in by m4_include. This will make maintaining configure.ac much easier.
Also drop use of PROGRAM and VERSION, using PACKAGE_NAME, PACKAGE_VERSION, and
on occasion, PACKAGE_STRING instead, and clean out some old files we no longer
need.