Doxygen: fix input paths

Some interesting stuff was missing previously (MessageProcessor for instance)
CMakeLists: fix indentation of BUILD_DOCUMENTATION
Doxygen: add some options for Doxyfile generation

`make doc` now creates collaboration and inheritance graphs by default

Run cmake with -DDOC_GRAPHS=No to disable all graphs and run use
-DDOCS_FULLGRAPHS=Yes to also generate call/callee graphs (large)
Doxygen: add css tweaks

Remove the header. Vertical space is precious on laptops.
Merge pull request #192 from OttoAllmendinger/doxygen-tweaks

Doxygen tweaks