Use this md5sum recipe to confirm the that two directories are exactly the same.
If you are on Mac OS X, ensure you use brew to instal md5sum first.
Verify directory copy by md5 summing each file and then creating a single md5sum from the list.
If you see the error, "find: md5sum: No such file or directory", then you've not installed md5sum properly,
Note this script can be improved to detect failed directory listing.
Another way of doing the same thing,
md5 entire folder - http://www.cnet.com/news/how-to-manually-verify-copied-files-in-os-x/