We’re using the machine metadata to tag machines as “flyctl managed”. Most people who create machines with the API or fly machine run don’t want a single command to wipe out all their machine configs.
fly machine clone copies the metadata, so anything created via clone will continue to work.
It would make sense to “adopt” fly machine run machines into apps somehow. Possibly a flag to the command, or a config option in fly.toml. We’ll think about that.