Topology.add_molecule has undefined behavior if given an existing molecule with different atom indexing

[j-wags]

Describe the bug
If the user passes a re-indexed version of a molecule which is already in a Topology toTopology.add_molecule, the molecule that is added is indexed in the same order as the original. This can lead to system creation errors down the line if the user plans to use the coordinates from the reindexed molecule.

To Reproduce

        ff = ForceField('test_forcefields/smirnoff99Frosst.offxml')

        molecules = [Molecule.from_file(get_data_file_path('molecules/ethanol.sdf')),
                     Molecule.from_file(get_data_file_path('molecules/ethanol_reordered.sdf'))]
        top = Topology.from_molecules(molecules)
        omm_system = ff.create_openmm_system(top)