For the specific case of upgrading the kernel packages on a live system,
I have found a trick that seems to work for me. I can't be sure it won't
break something, though.

The problem in this case cannot be solved by manually running the grub
utilities, as the package manager will always attempt to run grub-update
by itself.  This runs grub-probe on /, which is the aufs and cannot
apparently be probed. If grub-probe is instead run on the /cdrom path,
which contains the actual USB disk, then it runs through without errors.

My workaround involved modifying the three grub-probe lines in the
/usr/sbin/grub-mkconfig script to use /cdrom instead of /. The script
then ran successfully and generated what looks like the correct
grub.cfg.

Basically, this changeset:

@@ -136,16 +129,16 @@ fi
 mkdir -p ${GRUB_PREFIX}
 
 # Device containing our userland.  Typically used for root= parameter.
-GRUB_DEVICE="`${grub_probe} --target=device /`"
+GRUB_DEVICE="`${grub_probe} --target=device /cdrom`"
 GRUB_DEVICE_UUID="`${grub_probe} --device ${GRUB_DEVICE} --target=fs_uuid 2> 
/dev/null`" || true
 
 # Device containing our /boot partition.  Usually the same as GRUB_DEVICE.
-GRUB_DEVICE_BOOT="`${grub_probe} --target=device /boot`"
+GRUB_DEVICE_BOOT="`${grub_probe} --target=device /cdrom/boot`"
 GRUB_DEVICE_BOOT_UUID="`${grub_probe} --device ${GRUB_DEVICE_BOOT} 
--target=fs_uuid 2> /dev/null`" || true
 
 # Filesystem for the device containing our userland.  Used for stuff like
 # choosing Hurd filesystem module.
-GRUB_FS="`${grub_probe} --target=fs / 2> /dev/null || echo unknown`"
+GRUB_FS="`${grub_probe} --device ${GRUB_DEVICE} --target=fs 2> /dev/null || 
echo unknown`"
 
 if test -f ${sysconfdir}/default/grub ; then
   . ${sysconfdir}/default/grub

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https://bugs.launchpad.net/bugs/703009

Title:
  grub-probe: error: cannot stat `aufs'.

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