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Did we kill Linux's killer feature?
(self.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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The short answer is "yes, but only as much as it needs to". Flatpak had to make a decision between "do we guarantee the app will work, even with system upgrades" or "do we minimize space" and they chose the former. The minimum necessary dependencies will be installed (and shared) amongst flatpaks.
Have you had the unfortunate experience of a utility or program losing its packaged status? It's happened to me before--for example fslint. I don't think this can happen with flatpak.
Space usage under flatpak is highly overstated. It only takes a noticeable amount of storage if you only use a couple of flatpaks, cause all the dependencies are used for a single package, once you start using flatpaks as the main mean of installing "applications", the space required start to decrease because the dependencies are shared between multiple apps