simplify doxygen input path
reduce warnings from thousands to hundreds as long as major code is undocumented
fix displayed include paths in doxygen output
fix some of the warnings
Merge pull request #45 from guidokanschat/doxygen_cleanup

Some cleanup of doxygen issues:
simplify doxygen input path
reduce warnings from thousands to hundreds as long as major code is undocumented
fix displayed include paths in doxygen output
fix some of the warnings