They are not "never auto-repaired": resuming such a session re-pins the full tool surface (restore_agent_tool_prefix), after which a scan sees skill_manage without the Skill Safety guidance and clears the prompt.
They are not "never auto-repaired": resuming such a session re-pins the full tool surface (restore_agent_tool_prefix), after which a scan sees skill_manage without the Skill Safety guidance and clears the prompt.