Linux

I actually like Flatpaks... I use dpkg/apt-get for system packages that cannot be installed in userspace, and flatpaks for desktop apps / games. Many distro's have unified ways to update them anyway (at least VanillaOS has)

AppImages are horribly bloated, I personally would never use them on my machines. Snaps I'm also still biased against because Canonical's shady practices. So for me it's still just pacman -Syu && flatpak update.

I can still do that, because I understood that problem when it arose.

To still sorta replicate that, I just set up a script at /usr/local/bin/update for it:

#!/usr/bin/env bash

sudo emaint sync -a &&
sudo emerge -utDU @world &&
sudo emerge -c;
flatpak --user update;
doom upgrade &&
doom sync &&
doom purge

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.

"Any headline that ends in a question mark can be answered by the word no". This is no exception.

Check out Nix, which goes in the opposite direction. There isn't really a distinction between the system and applications.

Well, that's Fedora, my friend. On Gentoo it's still the same.

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.

The solution is using a distro that has support for containers (flatpaks preferably) but doesn't force them on you, so far I haven't found a single use case in which they're truly needed on desktop so apt update still does everything for me.

There's some software that I compile myself (emulators), it cannot be upgraded with a packet manager but that has always been the case.

I use Linux MX but there are other distros with the same approach. It also makes it really easy to see if you're installing them because flatpak is a separated repository from non-container apps (I think it's also updated by the package manager but I haven't tried so far).

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.

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

emerge -uDN @world

...and head to bed for me.

100% agree with you OP.