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fix(setup): exit non-zero when apply or disk --clean only partly worked master

`disk --clean` reported each `remove_dir_all` failure and exited 0, and `apply` did the same for an undo ledger it could not save and a hook binary whose install failed. A script driving these could not tell a completed run from a gap. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Author permadeath.com Co-author Claude Opus 5 (1M context) Date Commit 739a75b3 Parent 6b9161d1
+173 -26
2 changed files