I can still do that, because I understood that problem when it arose.
this post was submitted on 17 Sep 2023
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you could use topgrade to update, and it will generally update with every package manager available.
On Mint everything updates automatically for me, Flatpaks and all.
On Arch Linux I've migrated away from Flatpaks, so I only use AUR and official repos.
Oh boy my updates speed increased like 3 to 5 times. Flatpak is slow as fuck.
Also my ISP is slow as fuck.
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Check out Nix, which goes in the opposite direction. There isn't really a distinction between the system and applications.
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This is why I really like KDE Plasma's discover. It's got integrations with apt, snap, Flatpack, and rpm, and that's only the ones I've tried so far.
I don't really use discover itself to manage my packages, cause for some reason I prefer to do it with the cli tools, but it is a great update notifier.
Except it doesn't always work. I've seen it stuck and loading updates forever a few times, while a simple flatpak update command did the job with zero issues.
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This is one of the reasons i don't use flatpaks, snaps etc. I get everything either from the official repos or from the aur. Except balena etcher as it is the only thing i was unable to install via my aur helper and i couldn't be bothered to look into why as balena is not that important to me.
It is the ONLY package that isn't updated with my update command as i installed it via appimage
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I use very minimal software and usually don't care about Flatpak
I'm using MX Linux and don't use any flatpak or snaps, only good old debs
Fedora updates flatpaks automatically, system updates too, but you need to reboot. Which Fedora version do you use?