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Update for newer doxygen versions

Automatic config file update by running 'doxygen -u'. All previous settings are
kept but old, deprecated settings were removed to avoid annoying warnings
when executing doxygen (e.g. on the nightly cronjob to update the API docs
Furthermore, the update tool added a lot of comments above the options,
which is probably good.

changed doc/
doc/ Diff Switch to side-by-side view