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Downsides of Flatpak
(blog.brixit.nl)
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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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The isolation paragraph seems more like a gripe with Gnome Software Center rather than flatpak itself.
Also not sure I agree much with this. When developers don't keep track of their application's dependencies, end users often end up having to do it and it's a much worse experience overall.
I do agree with that it ends up being more of a burden on developers to maintain dependencies in their package. It's not great knowing there are potentially patched issues sitting in older libraries that are shipped with a flatpak because a package maintainer hasn't had the bandwidth to update them.