If i drag a folder into MobaXterm it copies the files across sftp into the directory leaving out any folders that existed and just copying all files into the folder.
Is there any way to change this functionality?
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For me it seems to follow a specific case. If I drag from my "desktop" to the remote box, things are fine. But if I drag from a network directory (via Moba running on my box) to the remote box, the flattening you describe happens. I don't know of an actual "configuration fix", but the work-around is to drag (using File Explorer, not Moba) from the network directory, to your machine, then use Moba to drag from there to the remote box.