… to `GufeTokenizable.to_shallow_dict`

Added use of a `shallow_dicts` index to avoid potentially expensive
repeated calls of `GufeTokenizable.to_shallow_dict`, such as for
`ProteinComponent`s. Also used as our check if we've already processed
the object being visited to avoid going down its dependency tree again,
avoiding repeated traversals.

For an `AlchemicalNetwork` with ~1000 `ChemicalSystem`s and ~2000
`Transformation`s, this optimization reduces `gufe_to_digraph` execution
time from 6min 31s to 811ms.