I have just installed latest Xquartz and FSL imaging software. I noticed that there is a new symbolic link in /usr (i.e. /usr/X11R6) to /opt/X11. My understanding was that only Apple software could be certified/signed to modify /usr under the new SIP in El Capitan. I am certainly unable to modify /usr directly with sudo so SIP is turned on.
It definitely is new - I had a previous xquartz install with a /usr/X11 symlink created prior to El Capitan upgrade which remained in place. However, FSL needs a /usr/X11R6 symlink which I tried to create manually to no avail because of SIP.
After upgrading to latest Xquartz now I have both /usr/X11 and /usr/X11R6 symlinks. It's not a 'problem' but I'm not clear how it got there.
Can someone explain how this works?