Found the reason for this: system-cleaner-gtk didn't refresh the
apt.Cache() instance it has after it had removed packages. Therefore,
when it refreshes the list of cruft after a cleanup, it finds the state
of the system to be exactly as it was before the cleanup. Result: a
confused system-cleaner-gtk, and a confused user.
I've fixed this in bzr.
** Changed in: system-cleaner (Ubuntu)
Status: Confirmed => Fix Committed
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System Cleaner Does Not Refresh Following Cleaning
https://bugs.launchpad.net/bugs/274715
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