Folder transfers no longer copy macOS and Windows junk files. With "Hide local junk files" on (the default), uploading or downloading a folder skips .DS_Store and Thumbs.db in both directions, including tar-accelerated SSH transfers. Junk that is already on a server stays visible in the remote pane and still shows up as a difference in folder comparison, so you can find and delete old strays. A junk file you select yourself on the server still downloads as usual.