Did we kill Linux's killer feature?

Alias update="sudo apt full-upgrade && flatpak update"
Fixed it for you
- Since they’re using Fedora apt isn’t going to do anything, they would need to run sudo dnf upgrade -y && flatpak update
- Nice. Your excellent suggestion probably belongs in a meta-package somewhere so that users get it for free when appropriate.
- appimages though?
  
  They don't update, they are standalone files
- Thats it ... Thats how i do it in every distro inluding nix-env and i'm eine
  No need to overengeneer
- If you're an Obtainium/install from GitHub fan, then don't forget gam update.

There has always been the option of installing software from source. The package manager won't update anything installed from source.
You don't have to use Flatpak, Snap or AppImage if you don't want to. If you use the package manager to install everything, it will update everything.
- Except doesn't ubumtu now force a snap on you even if you try installing a package app?
  
  The solution is to use any of the other hundreds of readily available distributions.
  
  I'm confused by this. If I run apt install, am I getting stuff from flatpak?
  
  Yes. Some packages are just meta packages for their snap versions.
- If I use ubuntu I'm somehow forced to use them.
  Even on Fedora the average user is presented with many flatpak results when they use the GUI software manager. Not everyone is technically adept enough to check the origin of the app. So it's kind of being forced on users.
  
  If you use the Fedora software manager it updates everything at once? It even updates BIOS firmware.
  
  If I use ubuntu I’m somehow forced to use them.
  Yes, that's why I stopped using it years ago (among other reasons).
  Users are not out of options, they don't need to check the origin of the apps themselves, it's enough to ask other users what distros don't do the things they don't like and use those.
  
  so ditch this nonsense and use a better distro?
  
  You can use bauh. it is a graphical app manager which can Install and update appimage, deb, flatpak, snap and web apps. https://github.com/vinifmor/bauh
- The package manager won’t update anything installed from source.
  emerge lols
  
  Portage: Am I a joke to you?
- You are just spreading FUD for the sake of it.
  Snaps are updated automatically: https://askubuntu.com/questions/1262058/what-are-the-snap-equivalent-of-apt-get-update-and-apt-get-upgrade/1262059#1262059
  Flatpak updates are usually integrated as hooks of the package manager (Archlinux handles this for you automatically, and I'm sure other distros do as well).
  And on top of that, there's also packagekit to handle all of this automatically.

In Mint you can install flatpaks from the software manager and those get updated by the update manager. So it's all still one click.
- Same on Fedora. It'll even do firmware too.
  We're nowhere near the absolute shitshow that is updating the system and and programs on windows.
  
  The individual pop up for upgrades on windows is probably the single biggest bother.. (except the Microsoft bloatware/spyware of course)
- I'd like to add that it's even better than that!
  You can install apt, flathub and snap (if you want to install it) packages from the same installer, complete with full package info, screenshots and reviews!
  You can even compare them by switching quickly via the drop-down!
  The updater also checks all three, allowing you to scrutinise every part you want, or just updating it all with one button!
  The installer and updater are actually better than using the command line, in my opinion, and I am by no means a stranger to the command line!

If you use a graphical tool like gnome software, it will update everything with one click on a button
- And sometimes it will even work!
  
  Oh really. I should probably try that again sometime. Usually I just choose not to roll the dice on gnome, and update through the terminal instead.
- I would really love gnome software to add update on background feature and set update interval (update only once a month, hold update indefinitely etc.)
  But fedora software center behavior is the most intuitive and easy compare to other popular desktop OS/distros: Mac, Windows, or Ubuntu.
  
  It does background updates for flatpak. For system, just move to Silverblue.
  
  I love and use Fedora but I still think Mints update manager is the best GUI implementation I ever used for updating, it has all the essentials, is easy to use and looks nice.

Don't generalize whatever distro you're running as "Linux", especially when we're talking package management.
- Isn't this the case with all major distros at least?
  
  As far as I know, Ubuntu is unique in its insistence on snaps. I can't really speak for any others but my system runs fine entirely on native or locally compiled packages known to my package manager.
  
  Nope the major distros use about 3 different package management systems.

I’ve used Linux since the 90s and I’ve never installed a flat pack or snap or whatever. They’re not required.
- This. And it usually is open source, if you don't want to install a flatpak or docker image, you can always compile it yourself, and if you feel generous, you package it up as an .rpm, .dep, or whatever your distro of choice wants and create a download for it. I also have not (yet) encountered a project i wanted to install that didn't either provide packages or at the very least detailed instructions if I want to just install that locally.
- I mean yeah. I mean wtf.
  I mean, if I install something compiling from source, I would not expect anyone else to manage it, right? I mean why would anyone expect that flatpak snap etc. all get managed automatically, they even forget how they installed something, it is so ridiculous.
  
  Do you really mean that?

IMHO the killer feature of linux is that you aren't getting shit straight into your mouth every day by some corporation that decices to squeeze more cash money out of you.
And as others have pointed out most gui applications update all sources automatically.
- IBM salivating in the corner

Well, doesn't that depend on your package manager? With pacman I can add a custom hook after install to update all flatpaks. I'm sure it could also be done for all snaps and AppImages if I would use any of those.
Isn't there a similar hooking mechanism in apt or yum?
- Even if there are workarounds the old approach was superior.
  
  For the average user, software updates should be seamless and require no interaction whatsoever. Fedora Silverblue does this fairly well, whether they are flatpak or system updates.
  Flatpaks offer many benefits that, in my opinion, offset their potential inconveniences.

alias update='sudo pacman -Syu && flatpak update' or just use one of the trillion GUI app stores like pamac, discover, or gnome's thing whatever they call it.

alias upgrade="sudo pacman -Syu && yay -Syu && sudo flatpak upgrade"
- What you suggest works for Arch distros only of course. Actually, yay -Syu will do the pacman stuff for you first anyway so you can skip that.
  If you are using EndevourOS, check out eos-update. I just discovered it. It is basically the same thing but it will automatically handle keyring updates and db.lck issues if you have ever run into those. Basically, it is what yay should be.
  Another EndevourOS gem is eos-shifttime. It will set your system to whatever pacman would have done on a specific date. You can use it to roll-back to a specific date. Or, if it has been forever since you upgraded, it lets you upgrade more incrementally than catching up all at once. Pretty cool. I guess you could also mimic the Manjaro experience by always upgrading to whatever was in the Arch repositories 3 weeks ago.
  
  Of course those commands only work for arch-based distros, but it is completely possible to adapt them to fedora or debian-based distros
- && snap refresh
  
  I think a lot of people just won't endorse snap as long as it's backend is proprietary

I can't really relate? At least on my desktop. The software manager integrates with Flatpaks and upgrades them at the same time.
For most apps I'm going to prefer the usual way of doing things. But there are some apps that I actually kinda prefer as Flatpaks. Like Calibre I'm happy to install as a Flatpak. The updates are faster and it doesn't add a whole host of dependencies that only it uses to my system.
- There was a time when using the update button of Software Center was exactly equal to running "sup apt dist-upgrade". Everything was simple and straightforward.
  
  And broke all the time, and was a nightmare for devs to create and maintain packages for multiple distros, and was hard to find packages outside the official repos, and could create a package version hell, and had only a very rudimentary permission system.
  Change is sometimes not a bad thing, you know?!
  
  Everything was simple and straightforward except for updating an app after new release before the distro maintainers updated it in repos (which often took months).

#! /bin/sh #update_everything_in_one_command.sh set -e apt update apt upgrade -y flatpak update -y
$ sudo update_everything_in_one_command
Tada!
- echo -e "\nalias upgrade='sudo update_everything_in_one_command.sh'" >> ~/.bashrc
  
  This dude, this dude procreate.
- This dude.. this dude fucks

Every problem can be solved by adding another layer of abstraction.
- Ah, I see you have experience in our codebase

Depends. Unless you're on Ubuntu or Elementary, Flatpak and Snap are optional. When I'm on Arch, btw, I don't bother with any of those and just use the AUR with a helper like yay.
But I find the convenience of Flathub too good to pass up on other distros. I have been using Linux long enough to remember when the only options if your distro didn't ship something were to compile from source or to use a sketchy installer script, because Flatpak didn't exist. And as others mentioned, if you're using a full desktop environment, it likely can update everything at once via the GUI.
- I don't bother with any of those and just use the AUR with a helper like yay.
  Normally I do that too but recently wanted to install an app from AUR that ran out of memory during compile on 4 GB of RAM. So being able to use an appimage or flatpak was still useful.
  
  You could have just added a swap file

You're using Linux. It took me about an hour to create a script that will upgrade all packages, Snaps, and flatpaks, complete with flavor text. The fact that I could do that, with total control over how and when to run those updates, is still a killer feature to me.

What I think the biggest problem with the traditional package managers is that (1) they don't isolate packages from each other (when you install a program files are placed in many random places, like /usr/bin, /usr/lib etc) and (2) you can't have multiple versions of the same package installed at the same time.
This creates a lot of work for package maintainers who need to constantly keep packages up to date as dependencies are updated.
Also, because of this, every distro is essentially an insane dependency tree where changing even one small core package could break everything.
Because of this, backwards compatibility on Linux is terrible. If you need to run an older application which depends on older packages, your only choice is to download an older distro.
This is what snap and flatpak try to solve. I think they are not great solutions, because they ended up being an extra package manager next to the traditional package managers. Until we see a distro that uses flatpak or something similar exclusively, the problem is not solved.
- What I think the biggest problem with the traditional package managers is that (1) they don’t isolate packages from each other (when you install a program files are placed in many random places, like /usr/bin, /usr/lib etc) and (2) you can’t have multiple versions of the same package installed at the same time.
  Would you like to know about our Lord And Savior NixOS?
  
  Wow, that's exactly what I have been missing in my life. Amen, brother!
- when you install a program files are placed in many random places, like /usr/bin, /usr/lib
  That's because back in the day those had some good logic. On mainframe systems you had to be able to split files by how crucial they are too keeping the system alive, so you'd mount something like /bin locally but you could mount /usr/bin remotely and still keep the machine running if the connection was lost. And so on and so forth.
  Nowadays we really should revise the Filesystem Hierarchy Standard but it's required by the UNIX compatibility and it's baked into so many things that you wouldn't believe.
  I remember back in the 2000s the were distros like GoboLinux that tried to reorganize the files with criteria relevant to a modern machine but it didn't catch on in the Linux world. However Apple did it for Mac OS.
  
  Gobo Linux is still there https://gobolinux.org/
  
  The primary init manager for Linux is removing support for separating them later this year
  https://lists.freedesktop.org/archives/systemd-devel/2022-September/048352.html
- nix overall is a much better solution to this problem.

Silverblue here with automatic updates enabled, I do not care anymore, it just works.
- Yes! The automatic updates are great for me and my family's machines. System and Flatpak upgrades are done automatically, I never ever think of them.
  Universal Blue has it too. They also have the "just" wrapper for not just system and flatpak, but containers as well.
- This, super love that distro !!! Perfect for users that don't have a lot of needs.
  Personally, I never got used to the container workflow :(

A few years ago we were able to upgrade everything (OS and Apps) using a single command. I remember this was something we boasted about when talking to Windows and Mac fans. It was such an amazing feature. Something that users of proprietary systems hadn’t even heard about. We had this on desktops before things like Apple’s App Store and Play Store were a thing.
If this actually were Linux's killer feature, then Linux would have had a much higher market share by now.
Make no mistake, this is my favourite feature of Linux as well, and I have never used a snap/flatpack/appimage in my entire life. But it doesn't have the kind of broader public appeal that you seem to be suggesting.
- It's not really lost ether tho, just add a simple bash alias and you are ready!

GUI interfaces like discover or gnome software will update all
- Thank god we have these graphical GUI interfaces
  
  Graphical GUI User Interfaces*

Honestly, at this point I'd like to get rid of all this sandboxing stuff altogether.
- Come join the dark side, we have all the modern features without any containerisation whatsoever:
  https://nixos.org/
  
  Unless if you do want containers :)
  https://nixos.wiki/wiki/NixOS_Containers
  https://nixos.wiki/wiki/Docker
- I think it's a great and necessary security feature. The fact that we haven't had proper sandboxing until very recently seems strange now.

You can just use Topgrade and it'll update your entire system, including everything from your oh-my-$shell, pip, flatpak, snap etc
- Topgrade is great, one of the first things I install on a new system.
- just installed topgrade and wow, it's amazing. wish i knew this existed before.

alright where's that XCKD, imma make another package distribution method to 'unify all the methods'
- I think you mean this one?
  https://xkcd.com/927/

I just wrote a script to do all my updates in one go:

sudo dnf upgrade -y --refresh sudo dnf check sudo dnf autoremove flatpak update -y --force-remove flatpak remove --unused --delete-data -y pip-review --user --auto --continue-on-fail cargo install-update -a sudo fwupdmgr get-devices sudo fwupdmgr refresh --force sudo fwupdmgr get-updates sudo fwupdmgr update
- This is a great idea! Thanks for sharing it.

#nano /etc/systemd/system/flatpak-update.service

    
[Unit]
Description=Update Flatpak
After=network-online.target
Wants=network-online.target

[Service]
Type=oneshot
ExecStart=/usr/bin/flatpak update --noninteractive --assumeyes

[Install]
WantedBy=multi-user.target

#nano /etc/systemd/system/flatpak-update.timer

    
[Unit]
Description=Update Flatpak

[Timer]
OnBootSec=2m
OnActiveSec=2m
OnUnitInactiveSec=24h
OnUnitActiveSec=24h
AccuracySec=1h
RandomizedDelaySec=10m

[Install]
WantedBy=timers.target

#systemctl daemon-reload

#systemctl enable --now flatpak-update.timer

This should be added as hook to apt... as well.

You can use the great topgrade!
- This should be up

The GUIs do that in a even easier way for new users and experienced people can always just add a simple bash alias, a universal command never existed anyway because we have various different package managers on different distros so I don't see any lost feature whatsoever tbh

I don't use flatpak. But if your distro does, I imagine it should be pretty easy for them to provide a higher level program that updates both types of packages at once. I think this isn't a big problem.

- I guess yay is an easy solution, but it's not very clean, at least from what I remember and just checked. It might be fine for single machines, but since it doesn't build in a clean chroot, you can never be sure that the claimed dependencies are actually complete, and as such, a package built with yay on one machine doesn't necessarily work on another, even for the same processor type (portability might not be possible anyways if you build with -march=native). It also doesn't handle automatic rebuilds for necessary .so-bumps, but this is generally non-trivial to solve AFAIK.
  When I still used Arch exclusively, I had my own repository set up via aurutils on a remote server, granted this doesn't handle .so-bumps by itself either but at least you get somewhat clean packages every time, and you'll start to notice how many AUR packages are actually broken, with the most common occurrence being git not listed as a makedepends for packages that retrieve their data via Git because everyone using the AUR has it installed anyways to access anything on there. Granted this is a non-issue in practice but it's not the only one.
- I agree, but using yay, or rather the AUR, means being forced to use Arch. That's not only annoying for the average Debian/shopless-distro-user that does not want to relearn their system, or sysadmin who does not want bleeding edge software to host their website (as it may be your favorite machine learning 'anime' generator that's going down due to Nvidia drivers). It's also deadly for the 69 year old grandma as she somehow manages to use flatpaks (or whatever) on Ubuntu, but forgets to update them. Meanwhile she, very consciously, updates everything else through the Software Center every day (or lets it auto update). She wouldn't survive that jump to Arch (and certainly wouldn't survive the compile times of some AUR packages). Everyone suddenly using Arch would crash the whole ecosystem and community. Sysadmins would need to switch to Arch quickly now, as it's development stales because no one uses it.
  The only solution would be, to create - yet again - a universal alternative to the AUR. Maybe someone, backed by eg. the Linux foundation itself, could create a good way of compiling AUR packages on every system. Now we would still have to somehow drop Flatpacks and Snaps (especially the latter), which some Distros will refuse to do. Canonical isn't going to yeet snaps out of the Store because it's shit and something better exists (because that would apply to the whole distro /s)
  
  The only solution would be, to create - yet again - a universal alternative to the AUR.
  https://xkcd.com/927/

Your single command is just an "&&" away

Well, one way to address this would be to have a little hook that triggers when you do a full system upgrade, and it updates your flatpaks.
also flatpaks are still centralized thanks to flatpak itself, same for snaps, nix, cargo and similar package managers. It's not like you have to update every single app by yourself, like for AppImages and apps on windows or macos for example.

no.
it's open source.

arch repos + aur got you covered
- This. AUR packages are easy to create too. Flatpaks are only useful if you want to use something temporarily.
- Especially when you also use a aur helper like yay. Also I have to do is type yay and enter my password and then everything is updated
  
  or paru. basically like yay but slightly faster (really noticable on crappy hardware, paru searches packages like 2-3 times faster on a 5200rpm hdd)

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

Nixos got this and then some
- Recently switched to Nix,coming from Arch. Love it!

Nowadays I don't even bother with upgrades anymore. Snaps and Flatpaks auto updates automatically, and for system updates Ubuntu notifies once a week.
For me the experience nowadays is better than before, where app updates are tied to system updates, meaning that older bases (like Ubuntu LTS) got behind on some softwares.
- Snaps and Flatpaks auto updates automatically
  Nope. Firefox does not, because either Firefox is running, or the PC is down or sleeping. So I have to close Firefox, open a shell, update that snap shit, and restart Firefox. Which pisses me off to no end, apart from the point that snaps are a waste of resources and a bad idea in general.

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.
- IDK I thought sandboxing is also something that comes with Flatpak, so security concernes could be a reason to use Flatpak as well.
  
  I do hear that. Flatpaks do not seem to be very good sandboxes though.

Yes we did. I miss the old system.
Also I don't like my laptop rebooting in my backpack to install updates, after I've tried to shut it down.
- We never lost any "ild system" and the rebooting is probably how your distro implements updates, I use Fedora so mine often wants a reboot but that's definitely not the norm on Linux as far as I know and I never had a device turn back on on it's own...
  
  I think I first saw that on Fedora, years and years ago. I'm currently running Debian (testing) on my laptop. There was definitely some change at some point.
  Well. It's more, I click shutdown and because Linux has been 500% reliable for me, immediately shut the lid and throw the thing into my backpack. And instead of a shutdown, it tries to reboot, apply the updates and then do the shut down. But that fails because I use full disk encryption and it just sits at the password prompt until I pull it out again. Just heating my backpack from the inside and depleating the battery. So technically it doesn't turn on on its own. It just doesn't turn off as expected.

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.
- It's funny, I do almost the exact opposite--whenever there is a flatpak version, I prefer it over a built-in apt package. The flatpak is almost always more up-to-date and often has the features and bug fixes I need.
  Examples:
  Vorta (0.8.12 flatpak; 0.8.3 apt)
  Pinta (2.1.1 flatpak; 1.6 apt)
  Minder (1.15.6 flatpak; 1.13.1 apt)
  Xournal++ (1.2.1 flatpak; 1.1.1 apt)
  .
  I don't think it's fair to expect the distro maintainers to be up to date with every software out there--the universe of software has grown and grown, and we just can't expect them to wrap/manage/test every new release and version bump.
  
  Using EndeavourOS ( Arch ) and all four of those are the same versions in the regular repositories.
  I agree that Flatpak is a solution to outdated packages. My preference is to use a distribution that does not have that problem to begin with.
  
  Is it true flatpaks take up a lot more space due to bundling in dependencies etc?
- I enjoy that extra stability and separation between system and apps, especially as I use a rolling distro as a gamer. Hearing talk about Flatpak I disliked it for the same reasons, but I decided to try it out after Steam Native bugged due to a system library update. I enjoy it now also because it feels good that installing apps don't get a root password and scatter files everywhere they please in the system.
  On servers it's different ofcourse, Flatpak is basically for desktop apps. Snap is also designed for text mode stuff, servers and IoT devices but there's the problem with it being controlled by one company.
- It depends on the distro I am on, if I use Debian or a derivative I usually prefer the Flatpak but on Fedora I only go with the Flatpak if I run into issues or the rare outdated package because I don't need them, I would certainly miss Flatpaks if they didn't exist tho!

@mfat @linux "We" means Ubuntu. I can still do this.

just stick to your distro packages man

@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....

Meanwhile Arch users are just using the AUR for everything.
I don't use Arch btw, but I'm thinking I should.
- Honestly, I use Arch (btw) but after living on Fedora for a while, when I returned I started using podman over AUR for some stuff. If a package is going to pull a bunch of weird dependencies, or I want to easily migrate it later, it's just so much easier to keep it containerized.
- I use three tools from the AUR and I am the maintainer of those.

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.
- I think that this is above all else the reason that I use Arch. Arch Linux makes creating packages trivial, basically just wrapping build instructions into a shell script template. Arch handles the rest. The build systems for deb or rpm packages don't come close, and good luck rolling your own flatpak.
  This allows me to use pacman for everything outside of my home directory. Pacman is practically the central feature of my computer, and it's wonderful. I'm sure those Nix people can relate, though I guess my method is a bit less robust.
  
  I guess my method is a bit less robust.
  ime they just break in different ways. pacman's easier to hack around but nix is more portable

Just don't use Ubuntu and don't use flatpacks
- I use Fedora and many of the apps featured on it's default app store have turned out to be flatpaks.
  
  If you use its graphical software manager to install apps then why not just use it to update then with a single click.

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.
- I've seen the term "hooks" used all the time and have always wondered what the need for them is. I was a Windows user my entire life since childhood and recently rectified that a couple months ago.
  Unlearning the Windows paradigm of operating systems has been annoying. So many functional aspects of my machine abstracted away made me have to create an entirely new scaffold for learning technology...
  
  A hook is a mechanism for adding functionality at a certain point in a program's normal flow. As a simple example, imagine a program that works by doing three things in order. It could have hooks that allow the user to add actions before or after any individual steps. Each possible point in the flow is a separate hook. One way to implement it is with a directory for each hook in the program's configuration directory, where executables can be placed; the hook runs each executable in sorted order.
  I didn't look up any of this, so it may not be the best explanation, but I hope it is helpful.

Dunno about you, when I click Update in Discover, all my stuff updates
- Only one of my Linux boxes even has a window manager, and I don't use it.
  
  is their some kind of TUI lemmy client you're using then, or do you just do most of your web stuff on mobile or windows or something?

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.

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

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'
- Fully agreed with the usefulness of topgrade.
  Topgrade is not just for archlinux but will happily upgrade Debian-/RedHat-Derivatives, Gentoo, Void, some BSDs and I think even Mac and Windows, though I'm not sure how those work.
  The link you provided also goes to the unmaintained original version, while there is a community fork here: https://github.com/topgrade-rs/topgrade which sees more development (but is also looking for maintainers!)
  I'm also using topgrade and it is wonderful to upgrade the system dependencies but even the content of unrelated package managers such as pipx, vim, zsh plugin-managers, cargo programs, R packages, npm/yarn packages, and importantly for this thread flatpaks and snaps with one command. It really is lovely.

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?

I update all of my flatpaks, ~~snaps~~, and dnfs(?) with the click of a button in GNOME Software.
Edit: apparently I stopped using snaps at some point. Still, GNOME Software does both my flatpaks and my regular stuff.
- Same, on my Debian machines I barely even think about if packages are debs or flatpaks because it's so seamless.

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.
- Flatpaks have crappy names and a crappy CLI. Snaps just suck, and AppImages need a package manager.

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.

Debian, no flatpaks, snaps or appimages.
- Also stable rolling release.

You can just alias the update commands and have it as a a single command...