I want to upgrade my existing MODX install and this is the message that was in the upgrade instructs: "Do Not Overwrite Directories! Make sure your FTP program merges directories and does not overwrite them!" So when dragging new folders from local server over existing folders in the remote server, Cyberduck is asking me what I want to do but I don't see the option "merge" - there is only "resume", "overwrite", "rename" and "skip". How do I merge files?
I am not on my Mac right now, but a quick google resulted into this. Altough it is an old post, I think it is still possible (I use cyberduck myself a lot, but not this option).
You should not replace or upload the folder directly, but rather hit Synchronize in the 'File' dropdown menu. Then it merges the two folders.