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Actually I am 100% correct and can provide links to all the documentation. Flatpak uses bubblewap to execute an application from within a namespace. Namespaces are a kernel feature that allows the app to run in a completely separate environment, including under a fake user that only exists in that namespace. You can then grant access to whatever you want within the host system, like a single directory, or the whole filesystem. You can also do the same with networking, accessing processes etc.
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