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i changed computers and OSes here a few times and had a linux backup machine running at some point. I now have 2 disks, which contains backups of each other, where some file trees are nested in each other but might be identical.

what is the best way to figure out which trees are identical, so I can get rid of some duplicate trees and clean up the disks?

just searching for duplicate files and blindly removing the duplicate files might be a bad idea since sometimes files were copied on purpose, e.g. when a project folder was copied.