flags unknown config keys and fixes a bug with env prefixes

[arthurmccray]

What problem this PR addresses:

Fixed a few bugs in config which were revealed as we are working on the emdatabase config.

• collect_env re-enabled in collect(). It had been commented out since the collect_yaml refactor, and also fixed a slicing bug.
• check_key_val warns on a top-level key in neither the registered defaults nor deprecations, and still sets it. Nested keys under a known key are not checked.
• Added 11 new tests

There is also a related quantem-tutorials PR for config.ipynb: electronmicroscopy/quantem-tutorials#14

What should the reviewer(s) do:

This shouldn't really affect anyone, so hopefully just make sure it didn't introduce any other bugs.

Use the following checklist items when applicable (select only what applies):

• This PR introduces a public-facing change (e.g., figures, CLI input/output, API).
  • For functional and algorithmic changes, tests are written or updated.
  • Documentation (e.g., tutorials, examples, README) has been updated.

[cedriclim1]

LGTM!