Design question: a command-line installer merges a fixed set of exact-match tool permission allow entries into a user-editable JSON settings file that may already contain some of the same allow entries (added by the user) plus explicit deny entries. Goal: repair should re-add only missing installer-owned entries, and uninstall should remove only entries the installer actually introduced, never pre-existing user allows, and never touch or override denies.

Known reasoning so far: ownership cannot be inferred from the settings file alone, because an entry that matches the installer's list may have been user-authored before install. A separate ownership record is needed. The hard part is the two-file non-atomic update: if the process crashes after persisting the ownership record but before the settings write lands (or vice versa), a later repair/uninstall must not misattribute ownership.

Candidate approach: a two-phase intent/commit record per entry (state: intended vs. committed, plus whether the entry pre-existed at snapshot time), settings written via temp-file + atomic rename, and a reconciliation step on the next run that resolves 'intended' entries by re-reading settings and applying the recorded pre-existence snapshot. Deny entries are treated as user-owned and as a blocker: if a deny conflicts with an installer allow, skip adding the allow rather than removing the deny.

Unknowns: best handling when the user manually deletes or re-adds an installer-owned entry between runs; whether to key on exact string or a normalized form; how to detect concurrent edits (content hash / mtime compare-and-swap) without a lock the editor honors.