safe_flatten

each.sh

#!/usr/bin/env bash

# run safe_flatten for each in folder

set -eo pipefail

root_dir=$1

if [ -z "$root_dir" ]
then
  echo missing root dir
  exit
fi

find "$root_dir" -mindepth 1 -maxdepth 1 -type d | while read dir; do
  echo $dir
  ./safe_flatten.sh $dir
done

safe_flatten.sh

#!/usr/bin/env bash

# move all files in folder to the top level,
# rename as sum of file contents to handle duplicates, 
# remove all empty folders

set -eo pipefail

root_dir=$1

if [ -z "$root_dir" ]
then
  echo missing root dir
  exit
fi

echo dir: $root_dir

find $root_dir -type f | while read file; do
  new_file_name=$(md5sum "$file" | awk '{print $1}')
  filename=$(basename -- "$file")
  extension="${filename##*.}"
  mv "$file" "$root_dir/$new_file_name.$extension"
done

find $root_dir -type d -empty -delete