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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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I don't use Flatpak much, but I rarely see issues. Sometimes I see minor things like themes not quite being right, but its never been bad enough for me to spend the time to fix it.
I suppose another downside is the need to have the base runtime packages, so it could take more disk space if each app uses a different one. In practice apps will share runtimes though.
The biggest downside is that it's only for distributing applications with a graphical user interface. Command line utilities still need another method of distribution.
As a basic end-user I have not been too happy with my experience with flatpaks. I do appreciate that I can easily setup and start using it regardless of what distro I'm using. But based on standard usage using whatever default gui "app store" frontends that usually come with distros, it tends to be significantly slower than apt, for instance, and there seems to be connection problems to the repos pretty often as well.
The main reason I don't use them is because when I move my nixos config to a new machine as far as I know you cant get them to auto install. I have to remember which ones I had installed and redo them manually.
Which is why if for some odd reason I don't want to just install from the nix pkgs repo. I use app images. I can keep them in a directory which I can just copy over to the new machine with my nixos config files.
GPU drivers. It uses the Ubuntu 22.04 (LTS) userspace side of drivers. Could be incompatible with your kernel. Had all sorts of graphical weirdness with my AMD GPU with flatpak Steam.
If you have an unusual setup, it can be annoying trying to give programs permissions and sometimes it just outright doesn't work. For example, I mainly game on a laptop which has a pretty small hard drive, so I tend to put most of my games on an external hard drive. Flatpak really doesn't play well with that.
Yes, the confusion that results when things don't work because of isolation.
I feel like this should be required reading for a lot of Linux users. That article is a couple years old now, but I think is even more true now than it was when it was written. Having a middleman (package maintainer) between the user and the software developer is a tremendous benefit. Maintainers enforce quality, and if you bypass them, you're going to end up with Linux as the Google Play Store (doubly so if you try and fool yourself into thinking it won't happen because "Linux is different")
I personally don't really like it, since it sidesteps what is supposed to be the all-in-one package manager for the system, and integration can be poor.
It's an alright idea, but I like the native package managers better. We're not Windows, we don't need so many different places to download our stuff.
What I find most annoying is the extra drive space required. It makes backing up and restoring my computer so much more annoying. The upside of this is that I've ended up learning how to install from source so I can avoid them when a deb package is not available!