feat: update CI ad pre-commit configurations

[Septimus4]

Checklist

• [x] poetry run pytest passes locally with my changes
• [ ] Tests have been added or updated to cover the changes
• [x] Documentation has been updated as needed
• [x] Code style checks pass (poetry run flake8 and poetry run black --check .)
• [x] Commit messages follow the Conventional Commits guidelines

Affected Components

CI and configs

Description of Changes

Refactor pre-commit hooks to use local entries and integrate them with Poetry. Simplify and enhance CI workflow with Poetry caching, and update the CodeQL workflow to include custom setups.

Additional Notes

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