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run: Use O_PATH fds for the runtime and app deploy directories
This also allows us to use glnx_chaseat, and other at-functions to traverse the filesystem tree in a safe way. This is important because the app and runtime deploy directories can be under an attackers control. The flatpak portal for example allows sandboxed apps to provide them. In particular, attacks where the deploy dirs get replaced by a symlink pointing into the host system will be stopped by this. Note that this change alone is not enough to avoid the attack, and the portal has to be changed as well.
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