Thanks for the replies all.
The solution that we’re using on our production installation is a persistent disk to hold the storage data.
Correct me if I’m wrong but there’s no way to automatically commit data structures to a vcs when they are modified in Cockpit, this would surely have to be done manually after every change. Of course the structures could easily be restored during the build phase as we’re having to copy our config to the image with a custom docker file.
The more ‘container’ way to do things would be to store the config values in environment variables, all assets in cloud storage (s3/gcs), and all other data in the database. With this setup the stock image could easily be setup in an environment like Kubernetes.