Running permission repair has been deprecated....
Apple's exact language is...
Beginning with OS X El Capitan, system file permissions are automatically protected. It's no longer necessary to verify or repair permissions with Disk Utility. (Emphasis added)
That's because of SIP.
Well,
not according to this:
http://osxdaily.com/2015/11/04/verify-repair-permissions-mac-os-x/and this:
http://www.macissues.com/2015/10/02/about-os-x-10-11-el-capitan-and-permissions-fixes/And, within that last link:
"With El Capitan, this need has changed with the implementation of System Integrity Protection (SIP). This process both locks out root-level access to core system files, and
continually ensures component permissions are set according to developer intentions when updates are applied (Emphasis added). Therefore, there should not be any need to run a manual permissions fix. In fact, you may now need to purposefully disable SIP in order to alter permissions for some desired customization"
No use of the term deprecated, and also that SIP ensures that permissions are properly set.
