change doxygen directories so that make doxygen works

I messed up a bit in this branch and it currently includes two commits related to one of my other merge requests, I tried rebasing but I think wisely git won't let me rebase branches that I've already pushed to origin.

So if you want these changes but not the ones related to 5-argument-syntax-does-not-follow-the-traditional-style let me know and I'll try to fix it.