Fix CMake bug that prevented users from specifying their own CMAKE_(C|CXX)_FLAGS.
Ignore register deprecation warnings for python.

Also, CMake enforced that we require swig 2.0.10 or greater.
Merge branch 'master' into cmake_cxx_flags
SWIG required version is 2.0.9, and is required.

Required if building wrapping, that is.
Merge pull request #133 from opensim-org/cmake_cxx_flags

Fix CMake bug that prevented users from specifying their own CMAKE_(C|CXX)_FLAGS.