Fix most doxygen warnings.

Fix most doxygen warnings.

This makes it much more convenient to work locally with Doxygen.  Even
though Jenkins ignored these warnings, if you ran Doxygen locally, it
produced a long list of warnings in the log file, making it difficult to
spot if new warnings had appeared.

Also improved the Doxygen configuration files to have common settings in
a shared file that is then included from the actual configuration files.

Change-Id: Ic57576e2cb89f6d0e5929981553b48a61435c26c