If you want to compare to folder, which are not based on the same system you can create to text files with an command and the compare them.
Linux systems use md5sum:
find . -type f -exec md5sum {} ';' >source_md5.txt
find . -type f -exec md5sum {} ';' >target_md5.txt
Mac systems use md5:
find . -type f -exec md5 {} ';' >source_md5.txt
find . -type f -exec md5 {} ';' >target_md5.txt
Then you can compare this files using following command.
diff <(sort source_md5.txt) <(sort target_md5.txt)