No, you are correct and I am correct. It understands links that are between items in the source tree. That is if you have a tree of music and you have created some links that point _within that tree_, then his program will detect that, maintain structure and only upload the file once.

However, if you have a master tree, and create a source tree using symlinks to the master tree, his program will not work. At least I couldn't make it. I even checked into looking to add that functionality. But all the code for the inter-tree link detection was in the way, so it wasn't easy to find where to add.