@mfat I don't have snap or flatpak installed in any of my systems, therefore my entire system is still all upgraded with a single command....

I still run everything I can as .rpm through dnf on my Fedora and .deb through apt on my Debian servers.
I only install a flatpak as last resort.
From a dev viewpoint I can understand the gains of flatpak but from a user viewpoint I prefer a "real" install.

Nixos got this and then some

If your problem is Flatpaks, Snaps and AppImages, just remember that manually installed software can't be updated with the same command either, and installing software manually is fortunately not a new thing.

Here's the solution, though: don't use flatpaks, snaps appimages, instead rely on your outdated distro packages only.
Personally I only use appimages, because I don't want the resource overhead of the other 2

I'm still updating the whole system with one command. Just avoid flatpaks. Repackage for your distro if you need to.

You can definitely make an alias for this if all you want is a single command.

PS. I don't think what you describe is a killer feature.

Use a distribution with a large package library that is kept up to date and there is noting to miss.

Ubuntu is starting to push Snaps. So, that is becoming an unavoidable reality for Ubuntu users. For the most part though, Flatpaks remain optional for most distros.

The problem that Flatpaks solve is that the distro provided packages are out-of-date. If they are not, there is no real reason to prefer Flatpak.

Just don't use Ubuntu and don't use flatpacks

Meanwhile Arch users are just using the AUR for everything.

I don't use Arch btw, but I'm thinking I should.

This is why I prefer native packages over Flatpak, AppImage, Snap, etc. I want my entire system managed under one roof. On Arch, that roof is pacman. I'd rather get stuff not in Arch repos from AUR so they stay under pacman's roof. I do like having the option to use Flatpak for stuff that isn't in my distro's repos (or third party ones like AUR), and on some distros with more limited selection it is very nice to have, though I'd still prefer native. The only places I really use Flatpak are on the Steam Deck (as SteamOS doesn't allow the use of pacman, and if you force it you break things) and on postmarketOS because the Alpine repos lack a lot of stuff I want on my phone.

Dunno about you, when I click Update in Discover, all my stuff updates

This sucks, but on the flip side, before Flatpak and others, if the software wasn't in the repo then we're SOL and can't install it. Asking all developers everywhere to maintain a version of their software for every single package manager and ensure support for every distro is a bit unattainable. If Linux settled on one package manager or one distro then this would be solved, but such a statement is antithetical to the abundance of choice that Linux boasts.

Would you rather not be able to update an app or not be able to install an app?

No. (Or maybe yes. See Edit)

Ultimately, you are the one that decided to install things outside of your distro's package manager. If you don't like what happens as a result... then don't do that.

You are completely able to use the built-in package manager to achieve what we had "a few years ago". If you want something that isn't available in the package manager you can do what we did "a few years ago" and install it separately yourself (from source, flatpaks, snaps, appimage). Or you could become a package maintainer for that package and get it added as a package for your distro. It's completely up to you and in no way different frmo what it was a few years ago.

Edit: after finding out from @mfat@lemdro.id that Fedora does in fact officially support Flatpak, I do indeed think that they could do better in how they support that.

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

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?

We can no longer do that thanks to Flatpaks and Snaps as well as AppImages.

That is a you-problem to be honest. If updating the system needs more than one command, then something is wrong with the distribution.

If you install applications using something else thatn the system's package manager, you need to take care of them by yourself, too.

Also:

alias update='pacman -Syu && flatpak update && flatpak remove --unused --delete-data && snap refresh'

AppImages need to be updated individually, but AppImages suck anyways.

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

Debian, no flatpaks, snaps or appimages.

I update all of my flatpaks, snaps, and dnfs(?) with the click of a button in GNOME Software.

For arch Linux, there's Topgrade. All there, in just one command. All. There. Official repos, AUR, even firmware upgrades.

Here's my alias to update the whole system. It includes fetching the fastest mirrors, topgrade, and cleaning the update's packages cache. Tailor it to your own needs.

alias update='sudo fetchmirrors -q -s 5 -v -c PT && yes | topgrade -c -y --no-retry --disable gem --disable vim --disable emacs --disable gem --disable sdkman --disable rustup --disable cargo --disable remotes && sudo paccache -rk 0'

Never used Flatpak or Snap in nearly 30 years of using Linux. I might one day but not yet.

I don't use Fedora these days but your package manager will probably have some hooks. Add one to update your Flatpaks when it has finished its main job.

Arch-based distro here, a lot of shit from AUR and such and it autoupdates from my package manager/aur helper.

The 2 or 3 flatpaks I installed I have to manually update... But to be honest I'm fairly sure that there's some config or change I could make to yay that would make it update flatpaks too. And even if not... Well. I could do what the (as of now) top comment said and make a lil' script. Though running two commands is really not a huge sacrifice :P

Also back when I used Debian, apt had some hook in it that would update Flatpaks there too.

No Appimages for me though. Don't care for the entire format.

Anyhow to me the killer feature of Linux was never the package manager so much as it was how much liberty it gives me to customize everything. Flatpaks and such are just another aspect of that.

Just create a script that calls all the update commands. That's how computers work. Your apt/dnf/whatever command also calls many other commands to do its job.

The killer feature is getting applications from a central repo, not so much that there was only one repo. Unlike windows where you have each application self updating or not updating at all and forcing you to have to go to several webpages to update things. Having to update two different repos IMO is not a huge problem, you just need to be aware of it and there are frontends to these systems that can update both at once. The only exception to that I think are AppImages - but those you don't really need to use on most distros.

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.

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).

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)