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So how does an application do something like using OpenGL, opening a file with user consent, taking a picture with user consent, obtaining access to take multiple pictures within the current session (or persistently, for a camera app), and so on and so on?
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I have never once wanted a desktop app to "take a picture". If I want to take a picture with my webcam I'll do it with a native utility I trust then open the file. This is a general principle: vetted native apps for privileged things, 3p junk in a HARD sandbox.
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They're trying to copy the way it works on Android although often based on how things worked in Android 4.4.x to 6.x rather than how they work now. That's just what they're trying to do and isn't really how things work. The way it usually works is apps opt-out of the sandboxing.
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"Opt out of the sandboxing" is accepting the narrative that "self-contained applications" and "sandboxing" are the same problem domain. If you reject that, it's not a problem except in a ux sense (you need to manually bind-mount the files you want to access into the ns).
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AppImage sticks to just providing self-contained applications and has existed for a long time. Most of the point and the work on Flatpak seems to be bringing application sandboxing. Packaging up applications is part of it but more of an afterthought and secondary thing for them.
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Another *nasty* problem facing Flatpak is that it has to support systems with SELinux not in use. It can’t rely on SELinux because not every distro supports SELinux. And Flatpak apps are usually native apps, unlike Android where everything uses abstracted APIs.
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SELinux is an implementation detail on Android from app perspective and could be something else. There's a lot of value in declarative, static security policies. Linux kernel has decided LSMs and eBPF obsolete doing things other ways so that's another major reason for it.
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The network usage monitoring isn't really part of the security model but rather properly monitoring and controlling application data usage. It's a mix of netfilter with eBPF code. They previously had a netfilter module handling everything and had to replace it to use mainline.
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