There is an interesting bit in xkeyboard-config/debian/preinst fiddling
with the symlinks:

            for link in xfree86 xfree86.lst xfree86.xml xorg xorg.lst xorg.xml; 
do
                rm -f "/etc/X11/xkb/rules/$link"
            done

Perhaps the above is getting run on upgrade, but the corresponding code
to generate the links is being skipped?  There is a comment there "TODO:
we should really have rollback code for all of this".

Or... also in debian/rules is this line for the configure step:

        ./configure $(confflags) \
          --prefix=/usr \
          --disable-xkbcomp-symlink --with-xkb-rules-symlink=xfree86,xorg \
          --with-xkb-base=$(xkb_base) \
          XKBCOMP=/no/thanks

Which makes me wonder if that --with-xkb-rules-symlink is not coming
into effect during the upgrade.

-- 
dapper->hardy missing files on upgrade
https://bugs.launchpad.net/bugs/213566
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