[ci] move shellcheck to pre-commit, use shellcheck-py

[jameslamb]

Moves shellcheck into pre-commit checks, and uses https://github.com/shellcheck-py/shellcheck-py so it can be installed automatically from PyPI (instead of needing to be installed separately before running linting).

This also uses pre-commit's mechanism for detecting files, and doesn't rely on file extensions. So it caught a few other uncaught shellcheck things in other files 🙌🏻