Doxygen documentation generation changes

Following this tutorial http://rickfoosusa.blogspot.pt/2011/10/howto-use-doxygen-with-github.html.

An admin with push rights to the main repo will only have to:

#html is ignored by next gitignore file
git clone git@github.com:TauLabs/TauLabs.git html
cd html
git checkout origin/gh-pages -b gh-pages
cd ../Doxygen
doxygen flight_doxygen.cfg
doxygen ground_doxygen.cfg
cd ../html
commit and push changes