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Flatpaks are quickly becoming my favorite. I've rarely had issues with App Images, but they are clunky and messy. Flatpaks are where it's at IMO.
Snaps are pewpy.
I’ve rarely had issues with App Images, but they are clunky and messy.
How so?
You have to use a separate application to manage them, otherwise they act as portable .exe files in windows, just laying around in a folder you have to manually link to or navigate to to run. You have to set them as executable manually otherwise you can't run them in certain distros, or they force you to click through the prompt. They aren't listed in the general packages installed on your system.
They are often bulky in size, and depending on the distro and software, sometimes they don't work properly. And again, without independent management software, they have to be manually updated independently.
They aren't bad, they just arent as good as other options IMO. I like App Images for random small programs, or some games too, they aren't a problem. But for large programs I want to use frequently, they are just less convenient.