Enable Markdown support in Doxygen and require 1.8.6 or later.

Doxygen had a bug that prevented us from being able to use Markdown syntax in Doxygen comments so we disabled it in Simbody and OpenSim. Dimitri fixed that bug in doxygen 1.8.6. 

Since doxygen is now at 1.8.8 I would like to require 1.8.6 and enable Markdown from now on since it makes it easier to make nicely formatted doxygen comments.

We should consider this for OpenSim also; I filed issue opensim-org/opensim-core#305.