Verify and Repair Permissions from the Command Line in OS X El Capitan

Most of us don’t really need to bother with repairing and verifying permissions, but while it’s rarely a remedy for an ailing Mac, it’s still often a useful troubleshooting step. While the option is gone from Disk Utility, running it from the command line works the same as ever. Open up Terminal (Applications > Utilities) and type in:
sudo /usr/libexec/repair_packages --verify --standard-pkgs / 
That will verify your disk. Next, you can repair by typing in:
sudo /usr/libexec/repair_packages --repair --standard-pkgs --volume / 
Repairing permissions will likely take a while. Again, OS X El Capitan does this automatically now, so it’s only useful in rare situations, but useful nonetheless.
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