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.
We can no longer do that thanks to Flatpaks and Snaps as well as AppImages.
Recently i upgraded my Fedora system. I few days later i found out i was runnig some older apps since they were Flatpaks (i had completely forgotten how I installed bitwarden for instance.)
Do you miss the old system too?
Is it possible to bring back that experience? A unified, reliable CLI solution to make sure EVERYTHING is up to date?
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.
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.