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Address automated review findings: workflow checkout credential persistence and base-ref template expansion, Git subtree tree-sha ordering, fail-closed frozen persistence writes, per-transaction orphan sweep isolation, reserved-transaction symlink exclusion in discovery, temp-handle close error masking, and busy/dismiss guards in the managed skills UI. Rewrite settings and nudge copy to describe user decisions instead of release diagnostics, and split the replacement dialog into ManagedSkillReplacementDialog with labeled before/after columns.