Travis, the menu separator comes from the applications.menu definition:
"<!-- Separator between menus and gnome-app-install -->
<Layout>
<Merge type="menus"/>
<Merge type="files"/>
<Separator/>
<Filename>gnome-app-install.desktop</Filename>
</Layout>
"
** Changed in: gnome-menus (Ubuntu)
Assignee: Travis Watkins => Ubuntu Desktop Bugs
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Menu separator can not be removed
https://launchpad.net/malone/bugs/36979
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