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My research into this many years ago turned out that jdupes was the right / best solution I could find for my usecase.
https://github.com/jbruchon/jdupes
Though that works fine from a script perspective I'd like some more interactive way of sorting directories etc. Identifying is just the first step, jdupes helps with linking the files (both soft and hard links comes with caveats though!) but that is mostly to save space, not to help in reorganisation.
I used DupeGuru (https://dupeguru.voltaicideas.net/) in the past but I'm not sure it's the best solution for you. Try it, it's open-source.
I have been using JD for a while now, to the point that I built a CLI for it (using Deno).
But I just enjoy the speed of feeling like I can cd to any directory at any time in like... 8 keypresses.
https://github.com/bpevs/johnny_decimal
https://johnny.bpev.me/
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