It was a lame attempt at humor, a roundabout way of referring to the simplifying assumptions that *nix systems generally make of the underlying machine.
If you want to follow the principles of capability security, then a key part of the strategy is to eliminate “ambient authority”, that is, any kind of globally accessible way of obtaining a capability.
In traditional unix-like systems, file descriptors are very close to capabilities. But the global filesystem namespace is a source of ambient authority.
There are a couple of ways to fix this issue: fine-grained per-process namespaces like Plan 9, so that the filesystem’s authority can be attenuated as necessary, so it becomes more like a capability. Or eliminate absolute pathnames from the API, so you have to use functions like openat() to get an fd relative to an existing fd.
How so? I can see the limited access control in Linux is an issue, and for this reason augmented security MAC (Mandatory Access Control) controls exist like SELinux and AppArmor.
But I don't see how the nature of everything being a file is a vulnerability in itself.
I'd be happy to learn how though.