removing per-package Doxyfiles
adding top-level Doxyfile and CMake integration
changing PCU doxygen from mainpage to page
changing parma/mainpage.h to parma/parma.dox

Again, changed it from a \mainpage to
a regular \page.
adding top-level mainpage file
actually use the \subpage command
add link from pcu page to pcu.c page
adding APF Doxygen page
change mainpage blurb