add Python 3.13 support, misc. CI improvements

[jameslamb]

• adds Python 3.13 support
• adds all runtime dependencies to pre-commit env for mypy, so it can run more thorough checks
• updates all pre-commit hooks with pre-commit autoupdate

Fixes the following new ruff errors:

tests/test_config.py:11:17: PT003 `scope='function'` is implied in `@pytest.fixture()`
tests/test_cli.py:114:35: PT007 Wrong values type in `@pytest.mark.parametrize` expected `list` of `tuple`
tests/test_cli.py:799:12: PIE810 Call `startswith` once with a `tuple`
tests/test_utils.py:47:5: PT006 Wrong type passed to first argument of `@pytest.mark.parametrize`; expected `tuple`