You should think of all these operations in terms of the state they persist. For example, a database migration doesn't modify the application at all, but only t

You should think of all these operations in terms of the state they persist. For example, a database migration doesn't modify the application at all, but only the data directory wherever your database is running (whether mounted in another container or across a network). Whatever process is orchestrating your containers should take responsibility for running setup chores in a separate, ephemeral container from the eventual application container. docker-compose is often not enough, unfortunately.