Static RMSD library

- Per #578, this factors out some of the code in setup.py into "setupbase.py"
- Per https://github.com/mdtraj/mdtraj/issues/657#issuecomment-63245744, this compiles a new static library `libtheobald.a`, containing the low-level RMSD code, in a way that Mixtape or other codes can compile against and include to get a lower-level interface to RMSD.