Revert "Run pre-commit on all files, instead of flake8 and mypy"

This reverts commit f5c6e56ae012e4212f9eb54aadb70bd2f912c76b.

mypy needs a virtualenv with all the dependencies of the current module
installed, which is not what we do in the static-analysis stage
currently (we use tox for that). This needs more thought.