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remove_tool_by_id popped the entry from every in-memory map, but the persisted singleton index still carried it. Every populate broadcasts a reload_tool_source_cache invalidation, so the very next reload handed the entry back and the uninstalled tool resolved again (test_repository_uninstall expected err_msg, got the full tool). ToolSourceStore grows remove_index_entry — the uninstall counterpart of update_index_entry — and remove_tool_by_id writes the removal through.