One of the common routines taken after installing software, upgrading the system, or otherwise heavily modifying an OS X installation, is to run a permissions fix on the boot drive. This is generally done with Disk Utility or Terminal commands. However, if you have installed El Capitan, you will notice permissions fix routines are now missing.
Since permissions determine if a file can be read or edited, problems with them can cause programs to hang or otherwise not work. OS X stores default permissions in receipt files, and when a permissions fix is performed, file permissions are compared against receipts and are adjusted accordingly.
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. 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.
As a result of this change, to fix permissions in El Capitan, you simply need to check the status of SIP and ensure it is enabled, which can be done by running the following command in the Terminal:
If System Integrity Protection is enabled (which it should be in most cases), then the command output will indicate so. Being enabled will in turn indicate that permissions have been checked and maintained.
Running this command will output whether or not System Integrity Protection is enabled on a Mac running El Capitan.