On the server I need to upgrade the existing MODX installation so leave my folders and files intact while updating only those which are necessary. 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 the question is, when dragging folders from local to 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?