The old script uses a lot of logic to determine the files to move. They have chosen to use the same directory for many file transfers and use trigger files to choose what to move to where. I cannot do a recursive. The best I could do is to create my own file structure, move the files into them, recursively copy, and then return the files to the original location, if they need to be there (sometimes they do, sometimes they don't).
I may just go with installing the Net::SFTP::Foreign and telling them to deal with it, but I wanted to explore other options first. I don't like the outcome of this option as it will be some fights, and I like to save that for when I really need to.
Either way, it is good to know a bunch of ways to do things