Have doxygen run in the doxygen directory
When the Doxywizzard GUI is used and the doxyfile is loaded, the workind directory for doxygen is set to the location of the doxyfile. However the Make and CMake build systems expect doxygen to be ran from the top level directory. This commit unifies the build system and the Doxywizzard GUI so that all of them expect doxygen to be executed in the doxygen directory.
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