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I am in the process of using Syncthing across my systems to sync and consolidating many, many files accumulated over the years in various versions of the stardard xdg-user-dirs (Documents, Downloads, Music, Photos, Videos, etc).

What's the best way to eliminate all the duplicate files?

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The best tool I've found so far is DupeGuru. It's free and there is a PPA for Ubuntu. There are also specialized versions for picture and music files.

Installation:

sudo add-apt-repository ppa:hsoft/ppa
sudo apt-get-update; sudo apt-get install dupeguru-se dupeguru-me dupeguru-pe

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