I found the problem with kiosktool. Kiosktool expects a file
/etc/xdg/menus/applications.menu that merges
applications-kmenuedit.menu. This file was missing in kubuntu. I
created the file with these contents
<menu>
        <DefaultMergeDirs/>
        <MergeFile>applications-kmenuedit.menu</MergeFile>
</Menu>

This seems to have make kiosktool happy, and now the etc directory is
created in the profile. However, i still don't get my changes. I
suspect this is because the menus are not merging correctly. Any
ideas?
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