Compare content of two folders, including subfolders
Terminal: diff

You can compare two folders in Terminal using the following command:

diff -rq /path/to/folder1 /path/to/folder2


To ignore folder hierarchy you can copy all the files out of a folder into a third folder, then compare these:

find /path/to/folder2 -mindepth 2 -type f -print -exec cp {} /path/to/folder3 \;