Fix #85: reduce scope of Doxyfile EXCLUDE_PATTERN

The */src/* pattern was a little broad, so I changed it be scoped
a little more towards simbody-specific folders.
Merge pull request #86 from scpeters/issue_85

Fix #85: reduce scope of Doxyfile EXCLUDE_PATTERN so that `src` directories are only elminated if seen in the repo, not in higher parts of the path.