In `2025-09`, add warnings for directories that are not run because they are not configured in `submissions.yaml`

[Matistjati]

Because otherwise it will be a silent error.

However, a common pattern is to not want to judge some submissions. It would be annoying to always get a warning. I propose adding an exception for a folder named do_not_run. Not sure whether we want to add this to the spec too, but it should definitely exist.