Reorganized doxygen documents, renamed .doc files as .dox.
Bumped revision to 4.3.1.2.  There may not be a 4.3.1.2 release, but I didn't want to leave it as 4.3.1.1.
Removed CMake-specific doxygen/documentation template, made changes required so that
CMake and autotools-based builds can use the same template (Doxyfile.in).