Comment 33 for bug 285746

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.