Perhaps a small bash script to iterate through all of the package delivery mechanisms' for updating everything?
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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.
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.
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
Yeah, flatpaks are a pain in the ass. So glad that I don't have to use them since switching to Arch.
I use Fedora for work, but ArchLinux at home. If you really want to skip flatpak
then you need the AUR.
Which is kinda one of the main reasons I started to like and still like gentoo. I do understand that it's not for everyone as a daily driver. Maybe Arch could also fit?