I split the IMP_CONTAINER into IMP_CONTAINER (which owns the objects and deletes them and uses Index objects to identify them) and IMP_LIST which doesn't own the objects, supports deletions, uses ints as indexes etc. In the process I made various minor cleanups to things I had to touch. These include - deleting rigidbody - removing the is_active check from Restraint (and putting some asserts into Particle) - note that I didn't fix the various restraints or change is_active to is_deleted so if you deactive restraints, things will break (in a better way they then would break before IMHO). The fixes are easy but will take some time since they involve touching each restraint. - cleaned up various documentation and header inclusion irregularities. - created IMP/internal which contains classes which are not part of the API. These are also tagged with the doxygen \internal tag