I have exactly the same issue. Tons of backup archives nested inside each other. I have been reducing the mess manually, as I have not found a tool that would help. My approach is to use &quot;diff -qr&quot; between directories I know contain the same project and manually merge them &#x2F; pick the best one. Merging is definitely the worst part of the process, as it cannot be automatically done. I thought about building a tool that builds some sort of sha tree through the directories but on the first try it generated many matches due to empty folders and stuff like that.