Have agents write scratch output outside the repo, while anything that matters lives in version control. That way you can purge the scratch files whenever you like.

Deleting files is easy. Decommissioning production services is not. It's too early to say for me, we've only decommissioned one vibe-coded service at my Day Job and it wasn't any worse than decommissioning any other legacy service has been. But it became legacy much faster - a couple of months.

I just delete it and go back to the commit if it matters in the future or generally if the code changed a lot just ask the probs newer smarter model to make the file again