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The disk space thing is a myth, once you start to install apps people actually use it ends up being about the same.

If you test it with VMs you can check it out for yourself: https://www.ypsidanger.com/wasting-disk-space/

What is not a myth, though, is that if you think you have patched some bug or hole in a system library, think again, because flatpaks are a distro in your distro (old yo dawg meme slide follows), sometimes a few even. And their update cadence is not the same.

Yes, it means that sometimes they will be ahead on patches, why not.

So at the very least, two systems on your system. Given that there are hacks to share some of your fd.o stuff, let’s say one and a half.

Tell me again when you dont end up with 20 different versions of Nvidia drivers

Your system should be cleaning up unused runtimes. That's perhaps a distribution integration issue that should be filed and fixed?

it's not cleaning runtimes if you have 20 different flatpaks using different versions of the runtime. That's the whole weakness of this system.

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