Apply ruff formatting across entire codebase & add check to circle-ci

[BeckettFrey]

Depends on the completion of #249

In #249 ruff is introduced, ruff formatting is only enforced on staged files via pre-commit, and formatting is not checked in CI (only linting). This means the codebase has latent formatting violations that go undetected until an unformatted file is modified; at which point the author is forced to fix formatting unrelated to their change (or bypass the hook), which is annoying.

Options:

1. One-off cleanup commit: run ruff format on the entire codebase in a single dedicated commit. Simplifies future reviews.
2. Let it catch up naturally: formatting debt resolves itself incrementally as files are touched.