Check out Nix, which goes in the opposite direction. There isn't really a distinction between the system and applications.
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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.
What?! No! How could this have been Linux's "killer feature"?
Am I taking crazy pills? It really matters to you that you can use a single command to upgrade your system?
To me the Linux killer feature is getting to be the true owner of the hardware. Any command you run can succeed if you know how to write it
flatpaks are all updated at once, just like distro packages, so yeah you might need to commands, but that's still very different to having each application update itself (and the security hell implied by that)
Also I think pkcon can manage your updates across various backends (unless you are on Arch, where I think there are both technical & ideological objections to having a simple tool that just works)
I use fedora as well and I just update through the GUI. It's more stable that way and waiting until I turn off my computer for them to apply is not a big deal.
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
I use one command to upgrade the whole system: paru
one one system and yay
on the other laptop.
No need to overcomplicate things, just write a small shell script or even just an alias. I use this daily:
alias get-rekt="sudo apt update && sudo apt upgrade -y && sudo apt autoremove -y && flatpak update -y && flatpak remove --unused --delete-data -y"
adjust accordingly for Fedora and/or snaps. Obviously doesn't work for appimages or manually compiled stuff which should be a last resort if there's no other sensible way to install stuff.
edit: voyager shat the bed with the code block but you get the point
I use BAUH as a GUI "update everything in one click" does repos, aur, flatpak, snaps, appimages. Paru is CLI option for repo, aur and flatpak. I dunno if it does snaps never checked.
100% agree with you OP.
emerge -uDN @world
...and head to bed for me.
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.
I think a script with apt/pacman/dnf etc., flatpak update can do the job as well?
IMO its against the unix vision to extend apt to manage flatpak as well.
Fedora updates flatpaks automatically, system updates too, but you need to reboot. Which Fedora version do you use?