Hi,

to me this sounds like a general X limitation and not an issue in
gnome-shell. I can reproduce this even in squeeze with gnome2:

1) start gnome-terminal
2) click the "File" menu and don't close it
3) close the laptop lid
4) press the power button to start the system again

The result is that the system hibernates but the screen lock does not
act because the menu is open. Afaik Xorg upstream is well aware of this
and the real fix is wayland. See e.g. 

   "screensaver won't trigger during pop-up"

  -- http://people.freedesktop.org/~daniels/lca2013-wayland-x11.pdf
  -- 
http://mirror.linux.org.au/linux.conf.au/2013/webm/The_real_story_behind_Wayland_and_X.webm

I don't think it is realistic for Debian to start fixing X either so
maybe the most we can do is to document this in release notes but even
that sounds like an overreaction to me.

-Timo


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