Finish implementing remake_parm for AmoebaParm objects. Also do general cleanup
and code simplification. The residue_container list was eliminated and replaced
and the Residue/ResidueList classes were expanded to contain a list of atoms and
assign atoms to residues at the time when the topology file is constructed.

Also fixes remake_parm with ChamberParm instances.  The remake_parm methods were
checked for both AmoebaParm and ChamberParm instances and topology files that
were recomputed using this method gave identical energies to the original
topology files.  The resulting files themselves were significantly different,
but they define equivalent systems.