Public bug reported:

Recent depmod generates an additional modules.builtin.bin depfile based
on modules.builtin included in the kernel. It should be removed along
with other depfiles in the prerm control script or dpkg does not remove
the directory, emits a warning and leaves the cruft behind.

dpkg: warning: while removing linux-image-2.6.32-10-generic, directory
'/lib/modules/2.6.32-10-generic' not empty so not removed.

$ ls -la /lib/modules/2.6.32-10-generic
total 20
drwxr-xr-x 2 root root 4096 2010-01-29 09:04 .
drwxr-xr-x 5 root root 4096 2010-01-28 20:55 ..
-rw-r--r-- 1 root root 8871 2010-01-25 10:05 modules.builtin.bin

Package: linux-image-2.6.32-10-generic
Version: 2.6.32-10.14

** Affects: linux (Ubuntu)
     Importance: Undecided
         Status: New

-- 
[patch] dpkg warning about modules directory not empty while removing kernel 
packages
https://bugs.launchpad.net/bugs/514168
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