Assorted typing improvements

[mattwthompson]

While working on updating the state enumerators, I noticed a lot of molecule.py had some missing annotations, historic shims, or quirks that could be updated. The changes here are as follows:

• Use built-in types were possible. Previously i.e. from typing import Dict was needed to support Python <3.9 (although from __future__ import annotations was another option). I didn't change all of them, but I was able to drop some of the typing imports changing the common types.
• Add warn_unused_ignores = True into the mypy configuration. It does just what it describes - throws a warning (from the type checker only) when a # type: ignore is not needed. I like this option.
• Add many missing annotations to molecule.py.

This started by trying to sneak some changes into those PRs, but I realized quickly that wasn't the place (common code across several different changesets) and it'd be better to just consolidate everything in one go.

• [ ] Tag issue being addressed
• [ ] Add tests
• [ ] Update docstrings/documentation, if applicable
• [x] Lint codebase
• [ ] Update changelog

[codecov[bot]]

Codecov Report

Merging #1782 (7d395c4) into main (bc415dc) will decrease coverage by 0.01%. The diff coverage is 98.38%.

Additional details and impacted files

[mattwthompson]

Thank you! I think the follow-on changes will be big improvements as well.