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.
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.