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Exactly, the app should install updates in the background and apply them after the app is closed.
I’d even settle for an unobtrusive modal asking what to do like a “yes | no | never | settings” kind of deal
I like the way AppImages work on my Kubuntu system:
They automatically update themselves in the background and then trigger a system notification letting you know the app will be updated the next time you close it, with a button to initiate it now.