chore: run mypy outside of pre-commit

[ludwiktrammer]

Currently in CI we only run mypy in the environment created by pre-commit, which lacks our dependencies, which means that all checks related to checking the correctness of typing when running code from dependencies (e.g., executing a method from a class defined in a library) are skipped. Because of this, we already accumulated quite a lot of problems like this in out codebase.

We should configure CI to run standalone mypy.