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

This was causing issues in travis.

In Travis, we use the -Werror flag so that we find warnings and can smush them. The tests now fail b/c Clang gives warnings about the swig-generated pyOpenSim_wrap.cxx, which uses `register`. One solution is to upgrade swig. Another solution is to set a target property for the _opensim.so target that suppresses the register warning.