Use `AtomMapping` objects in constraint repairs method

[ijpulidos]

When working in #1125 it was noted that the SmallMoleculeSetProposalEngine._constraint_repairs would benefit from handling perses.rjmc.atom_mapping.AtomMapping objects for both input and output. In that way we don't have to rely on dictionaries and we have a better container for processing and accessing information in atom mappings. That way we are not required to return the deleted indices/atoms, we could just compute the difference between the mappings.

Comments referenced https://github.com/choderalab/perses/pull/1125#discussion_r1016949980 and https://github.com/choderalab/perses/pull/1125#discussion_r1016928250