In #1778, the skills lockfile was out of date. The git diff command in the copilot setup workflow was able to pick up the situation (the lockfile had changed, but what we should have done when noticing that the worktree was dirty was:

1. Delete the .agents/skills directory entirely
2. Revert all changes.

Then, we can raise a warning of outdated skills, but we don't need to fail the step.