Removing duplicate files across two folders is easy with fdupes

On FreeBSD:

sudo pkg install fdupes

For a nice summary of how many duplicates there are across folders a and b:

fdupes -m -R a/ b/

To automatically delete duplicate files, use:

fdupes -d -N -R a/ b/

Once done, you might also want to delete any empty folders recursively:

find ./ -empty -type d -delete

Source