Enable Markdown support in Doxygen

This PR repeats Simbody's simbody/simbody#314 for OpenSim. It enables Markdown support in Doxygen, and modifies `README.md` to require Doxygen version >= 1.8.6.

See issue #305.

@jimmyDunne if the changes look OK I suggest merging this PR to the master branch, then try generating new doxygen from there to see whether anything gets messed up. If it does we can always back it out since the change is tiny.

1.8.6 works OK and is easier to get (comes with 14.04, e.g.) so I don't see any reason to require 1.8.8 yet.