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You can interact with a single container if you need to, not just the whole compose group.
docker compose restart jellyfinworks for your example, and "restart" can be swapped for stop or start as needed.Splitting compose files can be a good idea, but it isn't always necessary.
yes, but I use one alias for all stacks to down, pull, up as a daemon, and watch its logs.
So I'd rather split the stack than have a special treatment for it.