As far as a zombie window manager, I guess not:
quaternion:xinit Mike$ ps ax | grep wm 1770 s000  S+     0:00.00 grep wm
This is the directory structure you asked about:
quaternion:~ Mike$ cd /opt/X11/lib/X11/xinit/quaternion:xinit Mike$ ls -altotal 
280drwxr-xr-x   9 root  wheel    306 May 22 05:59 .drwxr-xr-x  10 root  wheel   
 340 May 22 05:59 ..-rwxr-xr-x   1 root  wheel  58368 May 17 02:58 
launchd_startx-rwxr-xr-x   1 root  wheel  69488 May 17 02:58 
privileged_startxdrwxr-xr-x   4 root  wheel    136 May 22 05:59 
privileged_startx.d-rw-r--r--   1 root  wheel    959 May 17 02:34 
xinitrc-rw-r--r--   1 root  wheel    956 Dec 22  2012 
xinitrc.201212221105-rw-r--r--   1 root  wheel    956 Jan 31  2013 
xinitrc.201301310810drwxr-xr-x   5 root  wheel    170 May 22 05:59 xinitrc.d
It appears that xinitrc was not modified when I installed the new Xquartz on 
May 22, not sure what modified it on May 17.  Their permissions seem fine, I 
think.  This is xinitrc's contents:
quaternion:xinit Mike$ more xinitrc#!/bin/sh
userresources=$HOME/.Xresourcesusermodmap=$HOME/.Xmodmapsysresources=/opt/X11/lib/X11/xinit/.Xresourcessysmodmap=/opt/X11/lib/X11/xinit/.Xmodmap
# merge in defaults and keymaps
if [ -f $sysresources ]; then
    if [ -x /usr/bin/cpp ] ; then        xrdb -merge $sysresources    else      
  xrdb -nocpp -merge $sysresources    fi


fi
if [ -f $sysmodmap ]; then    xmodmap $sysmodmapfi
if [ -f "$userresources" ]; then
    if [ -x /usr/bin/cpp ] ; then        xrdb -merge "$userresources"    else   
     xrdb -nocpp -merge "$userresources"    fi


fi
if [ -f "$usermodmap" ]; then    xmodmap "$usermodmap"fi
# start some nice programs


if [ -d /opt/X11/lib/X11/xinit/xinitrc.d ] ; then        for f in 
/opt/X11/lib/X11/xinit/xinitrc.d/?*.sh ; do                [ -x "$f" ] && . 
"$f"        done        unset ffi
twm &xclock -geometry 50x50-1+1 &xterm -geometry 80x50+494+51 &xterm -geometry 
80x20+494-0 &exec xterm -geometry 80x66+0+0 -name login
quaternion:xinit Mike$ 
It appears that the same day, May 7, that I moved .xinitrc out of the way, I 
also moved .Xresources. So I don't have either .Xresources or .Xmodmap in my 
home directory (I think I was having some kind of display problem that day, and 
it was fixed by moving .xinitrc and .Xresources out of the way). That's about 
it.  Thanks.
-Mike


> Date: Fri, 23 May 2014 10:43:41 -0700
> From: alexanderk.han...@gmail.com
> To: mike.wil...@hotmail.com; fink-beginners@lists.sourceforge.net
> Subject: Re: [Fink-beginners] New Xquartz behaving badly on 10.8.5
> 
> On 5/23/14, 10:24 AM, Mike Wilkes wrote:
> > I didn't customize X11 startup (as far as I know, anyway…I actually
> > wouldn't know how to begin), so I assume I have the default. I do have
> > fink's xinitrc package installed:
> >
> > quaternion:~ Mike$ fink list xinitrc
> > Information about 10041 packages read in 1 seconds.
> >   i   xinitrc          1.5-2        X11 initialization script handler
> >
> > Before installation of new Xquartz I had a .xinitrc file, but I moved it
> > out of the way to .xinitrc~ for some reason (can't remember why) about
> > three weeks ago (the new Xquartz was installed yesterday morning). A new
> > .xinitrc one was not created at installation of Xquartz. The old
> > .xinitrc file has only one line in it: xrdb -merge ~/.Xresources . Maybe
> > I need to restore it?
> >
> > Don't know if that helps you much.
> >
> > -Mike
> >
> 
> Hmm...not having a $HOME/.xinitrc should be fine ($HOME/.xinitrc is what 
> I meant by customizing the startup)
> 
> The scripts from Fink's xinitrc are actually deactivated by the Xquartz 
> update (using "fink reinstall xinitrc" will re-enable that), so Xquartz 
> should fall back to its default behavior.
> 
> The best things I can think of to check right now would be whether 
> /opt/X11/lib/X11/xinit/xinitrc is present, and whether the scripts 
> /opt/X11/lib/X11/xinit/xinitrc.d are executable.  Also, perhaps check 
> whether there is a zombie window manager process via "ps ax | grep wm".
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> My package updates: http://finkakh.wordpress.com/
                                          
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