Minor cleanup of doxygen files

The OSX doxygen.app is too large to add to the repo and the Windows executable was out of date - so it was removed. Now users are instructed to download the latest copy of Doxygen before starting.

Folder renamed as the generated reference is only one part of the overall documentation. Also axed the starter template as it's hidden away from new users and duplicates certain files. The same result is achieved by grabbing a copy of T2D and clearing out the modules folder.