Fixed issues with terminus generation.

Bonded types (Thole, aniso, virtual sites) are now read
properly and generated for termini.  Duplicate Thole entries
are removed via a call to clean_bonds, but issues with the
N-terminus are present.

Second known bug at this point: Changing Thole in N- or C-terminus
does not account for resulting changes to 1-3 interactions. I
have a plan for fixing this, just need to write the code...

Change-Id: Iaad44d46c79098c0bb3ea1d771032d3930a4aaff