[WIP] RMSD Rotation Matrix

So far, this is working code for computing the rotation matrix as an epilogue to the QCP computation. The code works (I tested it against qcprot.c), but isn't haven't written python-level tests that run in nose. I haven't written any python wrappers yet.

The goal of this is to be able to do the align-with-one-set-of-atoms-and-compute-the-rmsd-with-respect-to-a-different-set-of-atoms computation with @mlawrenz using the fast SSE RMSD code instead of the original QCP code.

I also tried to improve the c89 compliance of the rmsd code while I was at it, so that it can be compiled without --std=gnu99, which is a problem on windows. The RMSD code is now fully `-ansi` `-pedantic` compliant.