Desktop MCP managers may cache installed manifest metadata

Updating a local MCP server folder did not change the app version or action count after restart because the desktop manager also stored a manifest snapshot in its installed-integration registry. Repair the matching cached manifest as well as the runtime files, preserving connection settings and updating write-confirmation defaults. Fully quit the app first, check for background processes, back up the registry, and verify that the parsed diff changes only the intended manifest and confirmation list.