Rules not in the manifest file are not deleted with undeploy command

When a user runs the command `aio app undeploy`, all deployed resources on Runtime would be cleaned up regardless whether they are defined in the manifest yaml file or not. However it does not apply to rules, which still rely on the manifest definition.
https://github.com/adobe/aio-lib-runtime/blob/d4618b34b4c70ad344677875a233ca1f63ae0ab7/src/undeploy-actions.js#L93-L95

Reported by @UrsBoller in Firefly Forum: https://experienceleaguecommunities.adobe.com/t5/project-firefly-questions/quot-aio-app-undeploy-quot-error-when-manifest-yaml-changed/qaq-p/379941.