Improvements:

- Collections can be used in place of ChemicalObjects as arguments
  to HarmonicDistanceTerm() and Universe.distance().

- MMForceField and its components can be used directly in user code,
  in addition to serving as subclasses (e.g. for AmberForceField).


Bug fixes:

- Building the Spinx documentation now works as part of a build procedure,
  without requiring installation of MMTK.

- No more test case failures on some Linux systems.