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.
Merge pull request #87 from simbody/VecMatDocImprovements

Split up the bloated BigMatrix.h file into separate files for each of the big matrix classes.
- Modify CMakeLists to avoid warnings in VS 2013 64 bit builds (/arch:SSE2 unrecognized). SSE2 is the default for that compiler.
- Fixed caching problem that prevented BUILD_INST_SET changes from taking effect. This required removing the compiler command line variables from the cache; those are no longer changeable from CMake.
Merge pull request #88 from simbody/avoidWarningsInVS12Win64

Modify CMakeLists to avoid warnings in VS 2013 64 bit builds.