Upgrades Doxygen configuration files to 1.8.6. The upgrade results in
breaking changes (can't use original configuration) so all Doxygen files
were regenerated and updated as needed.
The Doxyfile shows a large number of changes, but most are the comments
and new settings created by the Doxygen auto-upgrade process.
Otherwise, some obsolete settings were removed and the logo was set to
none since its source image no longer exists in the repository.
Where appropriate the configuration files were updated to link to the
new Git repository. This is the only significant document content
change.
