Roll back doxygen formatting.

This undoes the fancy searching we had, as well as the fancy formatting.

Fixed Doxygen warnings about a stale Doxyfile. I'm using Doxygen 1.8.4; if we
merge this then everyone should use at least Doxygen 1.8.4 and we should note
this Doxygen version in the README.md.

I also fixed some doxygen for AbstractOutput.
Don't generate doxygen xml.
Add back treeview.
Merge pull request #123 from opensim-org/roll-back-doxygen

Roll back doxygen formatting. Let's get it in and get some mileage on doxygen to see how best to streamline.