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.