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So right now I have a single compose file with a file structure like this:
Would you in that case use a structure like the following?
Or a different folder structure?
The second one is exactly what I have. One folder for each service containing it's compose file and all persistent data belonging to that stack(unless it's something like your media files)
The second is exactly how I do it. Keeps everything separate so easy to move individual services to another host if needed. Easy to restart a single service without taking them all down. Keeps everything neat and organized (IMO).