Implementing periodic boundaries for rigid bodies

Lots of the changes here are entirely cosmetic or else were intended entirely for my use - e.g. most of the new comments and the changes to pymolwrapper.py which were designed to allow visualisation of small rigid-body periodic systems.

The important changes are the ones where I've defined new or overloaded functions and classes. In particular the new _otp_bulk module, the new classes in minpermdist_stochastic.py and periodic_exact_match.py, and the changes to the cpp files/their wrappers. I've also put in a fairly extensive test routine.
I changed the way this is done.  now cpp_topology is set to None by default, so use

    if self.cpp_topology is not None:
        return self.cpp_topology.distance_squared_bulk(coords1, coords2, self.boxvec)
    else:
        ...