SOLVED: Turns out at one point while trying to copy files over to the thumb drive it must not have been mounted by OS X, and since I was root, it made the same mount point directory and copied into this "ghost" local disk. i.e. if you're trying to copy files to /Volumes/FOOBAR but the drive FOOBAR isn't mounted you'll create a FOOBAR dir in /Volumes/ and when you do mount the FOOBAR disk, it mounts at /Volumes/FOOBAR 1 (yes, with a one)
So I was changing the permissions of the wrong files and didn't know any better!
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I've got a USB thumb drive with a raw XNU installation and some where along the way certain kexts in Extensions got permission: 501:wheel instead of root:wheel.
501 is my user account on my iMac, which I created the files on. Now if I plug in the thumb drive on my Mac, chown -R root:wheel Extensions/ it claims to have worked. Using ls -l all of the kext list as root:wheel.
But if I boot up XNU on the thumb drive and ls -l the stubborn files still show 501:wheel and I'm unable to change them even as root, getting "chmod: Unable to change file mode on System.kext/: Read-only file system"
No amount of changing permissions (777) helps.
I'm hoping this is just something stupid I'm missing...But why does my iMac show root:wheel when XNU itself on the thumb drive shows 501:wheel?
Ideas?