refactor(tools): Switch to ruff for import sorting.

[elenakrittik]

Summary

Replaces isort with ruff's I rule group. This caused only two changes, and both were correct. Also updates ruff to 0.3.3.

Checklist

• If code changes were made, then they have been tested
  • I have updated the documentation to reflect the changes
  • I have formatted the code properly by running pdm lint
  • I have type-checked the code by running pdm pyright
• This PR fixes an issue
• This PR adds something new (e.g. new method or parameters)
• This PR is a breaking change (e.g. methods or parameters removed/renamed)
• This PR is not a code change (e.g. documentation, README, ...)

[shiftinv]

lgtm, thank you!
The whole project root thing still feels a bit weird, but going off of the FAQ this seems like the intended solution.