Increase flake8 coverage

Enables more of flake8's default rules and makes CI check all files,
not just a subset. Also pins the version of flake8 to avoid CI
non-determinism when newer versions add/adjust the default rules.

The `# noqa: F401` entries in `pie_slice.py` are required due to:
https://github.com/PyCQA/pyflakes/issues/276