I have tried to repair permissions multiple times using Disk Utility.app and also using the command-line diskutil. I always get the same output, so apparently it's not fixing the problem. I've also tried running it from the Recovery partition, and get the same result.
$ diskutil repairPermissions / Started verify/repair permissions on disk0s2 yosemite Permissions differ on "tmp"; should be drwxrwxrwt ; they are lrwxrwxrwt Repaired "tmp" Permissions differ on "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html"; should be lrwxr-xr-x ; they are -rwxr-xr-x Repaired "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html" Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired Permissions differ on "Applications/Safari.app/Contents/MacOS/SafariForWebKitDevelopment"; should be -rwxr-xr-x ; they are lrwxr-xr-x Repaired "Applications/Safari.app/Contents/MacOS/SafariForWebKitDevelopment" Finished verify/repair permissions on disk0s2 yosemite
The ARDAgent issue can be ignored, according to Apple. The other three problems are all related to symlinks, and it seems to me like the current perms are correct. Why does Disk Utility think there is a problem?
I'm on Yosemite 10.10.5.