Move all files in tree to root folder, delete all subfolders and auto-remove all duplicate files.

flatten_directory.sh

#!/usr/bin/env bash

find $1 -type f -exec mv --backup=numbered -t $1 {} +
find $1 -type d -empty -delete
fdupes -rdNS $1

# Sources:
# - https://superuser.com/questions/658075/how-do-i-move-files-out-of-nested-subdirectories-into-another-folder-in-ubuntu
# - https://unix.stackexchange.com/questions/8430/how-to-remove-all-empty-directories-in-a-subtree