I really like the way the steam deck is set up with a read only root and flatpacks for user installed software.
Would it make sense to do something similar with a transactional Server base with minimal desktop packages installed and flatpacks configured for other desktop software?
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Uh. You just described Aeon and Kalpa.
Links for completeness’ sake:
https://en.opensuse.org/Portal:Aeon
https://en.opensuse.org/Portal:Kalpa