Bernhard, yes, that's pretty much exactly what happens: if a package is
no longer available in the package sources apt has, it's considered
cruft.  That's the best heuristic we have.

The whitelist is already implemented, and has been for a while. It is
maintained manually by the user.

The state of each package is remembered, so that you only need to tell
Computer janitor once that you don't want a package removed.

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