First some minor cleanups - adding operator<< to Vector3D and fixing some header inclusion issues
Second adding particle removal as previous discussed: - There is a new base class RefCountedObject which is used for Particle and is ref counted. Vector and ObjectContainer ref count ref counted objects that are contained in them - particles now have a Particle attribute type - the usual caveats about changes to SConscript files being ignore and IMP.i containing some extra changes apply (extra %includes) - if a particle is removed from the model it is made inactive also. We should probably have the particle constructor make the particle inactive until it is added to a model.
Bonds use the Particle attribute: - no visible changes
Hierarchy uses the particle attribute - no visible changes
The nonbonded list is more dynamic: - it drops inactive particles silently - you can add particles and they are handled correctly, if not terribly efficiently
I can't guarantee that the patches all work independently