update doxygen configuration to produce a PDF

A single PDF file for the developer manual allows accessing a single
index, browsing, and searching.  It takes significantly more time to
build this way, but this patch allows others to look at the results.

Migration Tip: If you have previously built the HTML Doxygen
documentatation, rename your 'doxygen' directory to 'doxygen/html'
to prevent needlessly rebuilding those files.