My system cloning software automatically repairs permissions when starting a job and since I run this script multiple times during the day, I don't pay much attention to the permissions error log. However, when preparing for a major system event, such as a move to OS X Mavericks, many users will launch Disk Utility and run the permissions repair routines themselves. And they will be horrified at the results.
Often, there will be scads of errors in the Disk Utility log window after repairing a disk. They often start with a warning about some file being modified or that permissions differ in a library and they can't be repaired or won't be. Here are a few examples:
Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.
Warning: SUID file "usr/bin/setregion" has been modified and will not be repaired.
Permissions differ on "Library/Application Support/Apple/ParentalControls/ContentFiltering", should be drwxrwxr-x , they are drwxr-xr-x .
Permissions differ on "Library/Application Support/Apple/ParentalControls", should be drwxrwxr-x , they are drwxr-xr-x .
Permissions differ on "System/Library/CoreServices/RawCamera.bundle/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner" has been modified and will not be repaired.
There is an Apple Support Note titled Disk Utility's Repair Disk Permissions messages that you can safely ignore, which has page after page of these errors.
The "resolution" of the problem at the bottom of the note is even more unhelpful and somewhat worrisome:
You can safely ignore these messages. You can also usually ignore any "ACL found but not expected..." message. These messages can occur if you change permissions on a file or directory; they are accurate, but generally not a cause for concern.
Um, Apple braintrust: what exactly does "generally" mean here? Can we leave well enough alone or should we worry?
The answer appears to be that unless you're having more problems, don't worry too much.
I was surprised to discover a new "feature" in recent versions of OS X Disk Utility. It's not so backwards compatible.
Mac OS X v10.6 and OS X Lion:
In Mac OS X v10.6.x and later, Disk Utility can verify/repair permissions of the same Mac OS version it is running. For example, if you need to verify/repair a Mac OS X v10.5.x disk, use a Mac OS X v10.5.x or earlier installation disc.
You don't need to repair disk permissions prior to installing Mac OS X over a previously-installed OS. The installer will do this automatically.
So, Snow Leopard and Lion are compatible for repairs but for anything before, you need the Leopard software.