Unfortunately, there is currently no way for system-cleaner to know
which packages are obsolete (because they are no longer available via
apt-get), and which ones are third-party packages installed outside of
apt. Thus the bug is valid, but we can't fix it for now.
I discussed this with Michael Vogt. We'll work on changing libapt after
intrepid to make this distinction possible in the future.
** Changed in: system-cleaner (Ubuntu)
Status: New => Confirmed
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System cleaner removes explicitly installed third-party packages
https://bugs.launchpad.net/bugs/285746
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