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Flatpak is the best one imo. Never used appimages, and snap is pure trash (close source, slow, made by canonical). Overall, native packages are imo the way to go, but flatpak is also fairly good.
Snap isn't really closed source, it's common misconception, the closed source is only backend (canonical servers), the snap core itself, which is installed on Ubuntu, is fully open source
Edit: snap definitely sucks tho
@KotoWhiskas @sohrabbehdani @Rega If you can't effectively use it without the closed source part being open doesn't mean much.
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