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I've recently started hosting a couple docker containers via docker compose with a friend, and we are also wanted to keep version control of the installation. The reason to do this was to make it easily reproducible in case we switched to another machine or anything like that, and we also wanted to document all our work with it, to both make it easier for us in the future and maybe help someone along the way. All this is hosted in a public repo in github: https://github.com/ComicIvans/server (in Spanish).
I've been thinking about this a lot lately too, but I'm going to settle on encrypting them and storing them in my private git repo using git crypt.
This is the strategy I use when I need to treat secrets like nuclear material. https://github.com/mashiox/dotfiles/blob/master/docker/secrets.md