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> It's centralized

Actually only short names go to docker hub, one can setup their own registry and use it via dns names.

Example: docker pull quay.io/letsencrypt/letsencrypt

Exactly this. For the docker images we use in production, we fork the corresponding git repo, build our own image and push it to our own local docker registry and pull it from there. It's fairly easy to setup in fact.

Out of curiosity do you resolve it so that the image is FROM scratch or do you rely on alpine/some other base image?

I forked an ubuntu image and then used it as a base for all my projects. It doesn't come for free though, you will need to periodically run security updates and then rebuild all images that depend on it.

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