Clean up installed doxgen

With this PR I'm attempting to get rid of some longstanding weirdness with the installed Simbody doxygen:

- Got rid of unneeded extra directory levels so html is installed in `doc/api` directly, rather than `doc/api/Simbody/html`.
- Shorten URL name on simtk.org/api_docs/simbody. Now the installed URL is just https://simtk.org/api_docs/simbody/latest.
- The following links should also work:
https://simtk.org/api_docs/simbody/previous
https://simtk.org/api_docs/simbody/3.3  (etc.)

This required minor changes in several places where the old URL was referenced, and where the html files get moved around. I believe the changed doxygen install directory here will allow OpenSim to correctly find the tag file (now in api/ rather than api/Simbody/html). 

@chrisdembia, do you see any problems here either for Simbody or OpenSim?
Wow nice catch!