Add refurb back to QA checks

[maxrake]

Description

With recent releases of refurb and mypy, the refurb QA check started to fail with an error:

interpreted classes cannot inherit from compiled traits

This error is unrelated to phylum-ci and has been documented in dosisod/refurb#305

This issue is to re-enable the refurb QA checks once the referenced bug has been resolved.

Additional Details

Attempting to downgrade/pin the use of refurb and/or mypy did not work.

Acceptance Criteria

• The refurb QA check is added back to .pre-commit-config.yaml
• The --repo https://github.com/dosisod/refurb \ entry is added back to .github/workflows/auto_updates.yml for updating the hook
• TODO: entries are removed from the code

[maxrake]

Closing this now that dosisod/refurb#305 has been resolved and included in a new release of refurb (v1.23.0).