Update `ruff check` and `ruff format` to default to the current directory (#8791)
Closes https://github.com/astral-sh/ruff/issues/7347
Closes #3970 via use of `include`
We could update examples in our documentation, but I worry since we do
not have versioned documentation users on older versions would be
confused. Instead, I'll open an issue to track updating use of `ruff
check .` in the documentation sometime in the future.