[ODE] Starting doxygen docs

[J. Perkins]

The consensus seemed to be to keep the handbook style of the original
documentation, but integrate it into the source code using a tool like
Doxygen to make it easier to update. I've started working on this and
have checked in my work so far to the new 0.6 branch (I will merge it
over to the trunk after I've gotten it a little farther).

If you want to try it out, just run doxygen in the ode/ode/doc
directory. The generated (HTML only right now) documentation will be
in the ode/docs directory.

Let me know what you think, and if you have any suggestions they would
be most appreciated.

Jason