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.
Split up the bloated BigMatrix.h file into separate files for each of the big matrix classes. Global methods and methods that involve multiple classes remain in BigMatrix.h.