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I wouldn't change anything, I like fixing things as I go. Doing things right the first time is only nice when I know exactly what I'm doing!
That being said, in my current enviroment, I made a mistake when I discovered docker compose. I saw how wonderfully simply it made deployment and helped with version control and decided to dump every single service into one singular docker-compose.yaml. I would separate services next time into at least their relevant categories for ease of making changes later.
Better yet I would automate deployment with Ansible... But that's my next step in learning and I can fix both mistakes while I go next time!
I do the same. I use caddy reverse proxy, and find it useful to use the container name for url, and no ports exposed
What is the benefit for making changes with separate files?
If you have relevant containers (e.g. the *arr stack) then you can bring all of them up with a single docker compose command (or pull fresh versions etc.). If everything is in a single file then you have to manually pull/start/stop each container or else you have to do it to everything at once.
This. In addition, I've read that it's best practice to make adding and removing services less of a pain.
You're not messing with stacks that benefit from extended uptime just to mess around with a few new projects. Considering my wife uses networks that the homelab influences, it would be a smarter choice for me long term to change things up.