I personally have a github repo with a folder for each deployment, and the files needed for deployment with a docker-compose.yml, and comments in the files for what they do.
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I seccond that. This also allows you to create markdown documentation as readme files, so you still have text files, just always at a glance.
My philosophy is this: all of the containers are deployed via docker-compose files, which are backed up. Any persistent data is presented over NFS to the containers using volumes. This way, in the event that the docker server blows up I just install docker, move the docker-compose files over, docker-compose up, and pretty much done.