Hi!

I think that shutdown, restart and hibernate should be avoided if the 
package-manager is working anyways. 
To achieve this i recommend that the gnome (or KDE/Xfce) dialog to initiate 
those actions should check for apt's lock-file and warn the user before he can 
proceed.
A small warning dialog like "Warning: the package manager is working right now, 
it is strongly recommended to wait for it to finish." and the user's options 
could be like "proceed anyways / wait and proceed / cancel".
Of course this could also be a text-based dialog if you're going to call 
poweroff, reboot or pm-whatsoever from shell.

Cheers,
Oliver

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Kernel upgrades may leave system unbootable
https://bugs.launchpad.net/bugs/191514
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