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If you have a working config, thats exactly the point. Before you built your config, you don’t know. If you deploy silverblue, you know it will work beforehand because exactly this config, including /etc, has been tested upstream before. What you are to your buddy, Fedora Atomic is to me. The difference is, it is not just one person that tested some config they decided on on their single piece of hardware, it is the effort of a full blown distro team.
With something like this, how do you handle the period of time while copying? I mean you can’t really leave it running as it wouldn’t be in a consistent state. A “under maintenance” page instead? Copy to a fresh folder and when done tell the webserver to serve the new location?