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.

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I tried to use this in a VM for a bit and had problems.

I’m running Aeon on my laptop now and quite like it so far

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