I know that a lot of people share the same thoughts with you but I respectfully disagree. If you want your system to be updated only with your apt/yum/dnf program, then just don't install anything useing snap/flatpak/etc. Sure, you will not have all the apps available in the repos, which was also the case in the past before these systems. Back then, your only option was to compile from source, which was more work-intensive than flatpaks/appimages/snaps. And updating was also much more complicated. Therefore, unless you wanted something really special, you'd stick to your repos. Flatpaks allow developers to distribute their software (and users to install it) in a less labour-intensive manner for the developer. Compiling and testing your app for Debian, Fedora, Arch, SuSE, MX-Linux, Linux Mint, Linux Mint DE, Gentoo, and all the other popular distros is an impossible task for small developers. Flatpaks was a godsend for them and for the users who don't want to compile from source. Now, you can argue that we shouldn't have all these systems (flatpak, snap, appimage, docker, etc...) but one would be OK. And again I will disagree. One of the most important aspects of FOSS is diversity. Embrace it even with its drawbacks. It would require a much longer post to explain this and others have done it already better than I would.
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The official software manager on my Fedora system (Discover) presents me with Flatpaks. If I use Discover for updating ,the Flatpaks will update too. But when I use the official CLI tool to upgrade the system only RPM packages are updated. The other package managers on the system are not affected (Flatpaks, Snap, Cargo, PIP). I think there should be no discrepancy between CLI and GUI interfaces for system updates. The fact that I should "remember" how to update stuff shows that something is wrong or is not perfect.
You have a point here indeed. But it is much easier to create a CLI tool that combines the updates of all systems rather than destroying the incredible things that flatpak and pip offer. A five-line bach script would do. Although, a reliable distro would probably want to rely on something much more elegant and harder to break. For Fedora specifically, the python-based dnf tool should be straightforward to be extended to do that. Perhaps the Debian apt tool has a lot of functionality to carry on and may be harder to do. In the essence of unix philosophy and modular approach, it should be a separate tool. I'm looking forward to that too.
I mostly stick to things in the repos, if theres something I want that's not yet packaged I package it myself because Gentoo packages are fancy bash scripts with libraries (eclasses) to handle the normal make && make install sort of things for most build systems
It's wild what can be done with some clever aliases. Linux is better now than ever before.
Nah, I don't miss them really, flatpaks are much more convenient and for me fedora kinda just updates itself automatically.
Also, pretty much all graphical app stores on linux support flatpaks and the distro's default package manager, so you can update everything from there...
I'm using MX Linux and don't use any flatpak or snaps, only good old debs
I use Fedora for work, but ArchLinux at home. If you really want to skip flatpak then you need the AUR.
Perhaps a small bash script to iterate through all of the package delivery mechanisms' for updating everything?
It doesn't even need to be a script you could just alias the 2 commands on a single line to a command in bashrc
If you want a single command, consider topgrade. Not sure if it supports Flatpak and Snaps yet, as I do not use those (yet).
yeah like other people have rec'd, I just wrote a script for installing/removing/upgrading/searching all the package managers I have. this was used as a tongue in cheek jab and has never truly been a brag.
You don't really need much of a script, a relatively simple bash alias should do the trick and for new users the GUIs are a better solution anyway and those still update all apps.
What a weird question, also that was never the case in the first place. You can still accomplish this with a simple bash script too.
What about pkcon? I haven't used it in particular, but packagekit based GUIs work pretty well in my experience, and then it supports flatpak/snap/apt/kde addons/etc in one interface, which is better than it was originally.