Update doxygen configuration file.

Update doxygen configuration file.

The included doxygen configuration file was a bit stale.  It included
some options that were obsolete and caused doxygen to generate some
warnings when running it.  Most of the changes here were simply done by
running "doxygen -u" to automatically update the file.  It added its
documentation for the options and removed the obsolete options.

This also includes one configuration change, which is to set EXTRACT_ALL
to yes.  This instructs doxygen to generate documentation pages for all
files, public functions, and public data structures even if they are not
currently documented using doxygen syntax.  Doxygen is capable of
generating some useful documentation on its own, such as dependency
graphs.

Signed-off-by: Russell Bryant <russell@russellbryant.net>
Reviewed-by: Steven Dake <sdake@redhat.com>