In brief, NonbondedListScoreState is now an abstract class and the corresponding class is AllNonbondedListScoreScoreState. I don't like the name, so if you have a better one, please suggest it. I needed to have a base class for the lists so that I can implemented one which handles particles with varying radii nicely.
In more depth: 1) Better string handling in the exception base class
2) added bounds check on vector access
3) Refactored the non-bonded list code. There is a new internal class which implements a voxel grid for particles. There is also a base class for non-bonded lists which AllNonbondedList and BipartiteNonbondedList both inherit from. I also got rid of the subdir for the bonded lists and fixed various documentation. SConscipt files and IMP.h changes are not submitted.