Aha, I just noticed that cruft remover suggests to remove a package if
you downloaded it from an archive and then remove that later from your
sources, eg:

1) add the deluge ppa to your sources
2) install deluge-torrent (then deluge-torrent is not considered cruft at that 
point)
3) now remove the deluge ppa from your sources, maybe because you don't want to 
check for new updates at this point because of a slow internet connection (then 
deluge-torrent is considered cruft)

I find this behavior unintuitive, even though I don't know what the
"right" behavior would be. I guess that depends on how you implement
this "whitelist" feature.

-- 
System cleaner removes explicitly installed third-party packages
https://bugs.launchpad.net/bugs/285746
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