Thank you for your concern. Is the migration assistant tied to ubuntu-
desktop? If not, the desktop package is a meta-package, to insure the
additional packages are installed. You should be able to safely remove
one and install the other without affecting any packages.
** Changed in: xubuntu-meta (Ubuntu)
Status: New => Incomplete
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installing xubuntu-desktop will uninstall ubuntu-desktop
https://bugs.launchpad.net/bugs/588609
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