Since no one had any good reasons to keep the non-sphere version of the nonbonded lists around, I removed them while I was making various changes. The other change I made is a added slightly more clever than before quadratic nonbonded lists (I think we want these at least for testing purposes). In addition, the constructors have been rearranged so that various things are optional since I often want to construct the states without knowing the full set of particles.

API changes: AllSphereNonbondedListScoreState is now AllNonbondedListScoreState and the radius key is first, if used. BipartiteNonbondedListScoreState now uses a dumber algorithm, but supports radii. I can move it back to a grid based implementation later.

As a trivial change, i fixed an indentation issues in bond_decorators.h