Merge pull request #968 from RosettaCommons/sjbertolani/pyrosetta_tmalign
Adding a function signature to TMaligns alignment2atommap method that works in Pyrosetta, there was a pass-by-reference that Python can't handle.
Also,
Split the TMalign.hh into cc and hh files,
Added Unit test for basic TMalign function,
Changed a number of function signatures to take values by reference (from cppcheck),
remove unnecessary \#includes