Numerous updates:

   -  Tinker Atom instances now extract the rest of their exclusions from the
      exclusion list at the time that the AtomList is loaded. This is necessary
      because unlike the Amber and Chamber topologies, there are more exclusions
      than simply atoms that are defined in valence bonds, angles, torsions, and
      coupled-torsions.

   -  The __contains__ methods of the valence parameters in the Amber topologies
      now accepts Bond instances and will determine if that bond is part of the
      valence term

   -  A deleteBond action was added to ParmEd that will delete a bond between
      two atoms as well as every other valence term that runs through that bond.
      Should work for both chamber-style and Amber-style topology files.

   -  Have the "checkvalidity" script scan through all of the bonds in the
      system (not including hydrogen) to detect any "long" bonds (i.e., over 3
      times the equilibrium distance) that could indicate gaps in the residue
      sequence in the original PDB file that tleap connected anyway.