fdupes -r ~/bin ~/backup/bin # recursive search across two directories
fdupes -rS . # show sizes of duplicate sets
fdupes -rm . # summarise duplicates (count and wasted space)
fdupes -rd . # interactively choose which copy to keep
fdupes -rdN . # keep the first file in each set, delete the rest without asking
fdupes compares sizes, then partial hashes, then full hashes, then byte for byte. -d deletes files, so run it without -d first and read the list. Consider -L (replace with hard links) where available if you want to save space but keep every path.