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eee2d0b
(Get the code!)
The recent change of description of this bug suggests a particular solution to the problem, which I think is incomplete.
The problem occurs on my machine because, although /usr is located on the root filesystem, several of the directories under /usr are soft links to targets on a different filesystem. I need to do this because the root filesystem is a smallish flash disk that does not have enough space to hold some of the files that are needed only late in the boot process (such as X etc).
I have fixed this by changing all of the apparmor configuration files that contain impacted paths to include the target path. Laborious, although such an update could probably be automated.
Perhaps a dpkg-reconfigure hook could be added to enable the admin to update the apparmor config files when particular files or directories have been moved.