Linux
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Linux is a family of open source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991 by Linus Torvalds. Linux is typically packaged in a Linux distribution (or distro for short).
Distributions include the Linux kernel and supporting system software and libraries, many of which are provided by the GNU Project. Many Linux distributions use the word "Linux" in their name, but the Free Software Foundation uses the name GNU/Linux to emphasize the importance of GNU software, causing some controversy.
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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.
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.
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 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.
I use BAUH as a GUI "update everything in one click" does repos, aur, flatpak, snaps, appimages. Paru is CLI option for repo, aur and flatpak. I dunno if it does snaps never checked.
Yeah, flatpaks are a pain in the ass. So glad that I don't have to use them since switching to Arch.
Is it possible to bring back that experience? A unified, reliable CLI solution to make sure EVERYTHING is up to date?
Yes. Use a Linux distro that doesn't use flatpacks and you're good to go.
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?