It did both for me.  For the affected users, were the X11 redirection stubs 
present at install time?  The call to x11-select is in its postinstall hook.

In any event, the call to x11-select will be in Xquartz's postinstall script 
itself whenever I get some cycles to spin and test another update.

Sent from my iPhone...

> On Oct 8, 2015, at 23:52, Martin Costabel <[email protected]> wrote:
> 
>> On 9/10/15 02:56, Jeremy Huddleston Sequoia wrote:
>> /usr/libexec/x11-select /opt/X11
> 
> Thank you. I confirm that this works (if run as root, anyway). It installs 
> both the /usr/X11 and the /usrX11R6 symlinks (somewhat surprisingly, given 
> that /usr/ is supposed to untouchable now).
> I confirm also that installing Xquartz on 10.11 does *not* install the 
> /usr/X11R6 symlink, only /usr/X11. From discussions on the Fink users lists I 
> gather that this is being observed by others as well.
> 
> -- 
> Martin
> 

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