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USE scp to transfer your files:

on your cygwin command prompt type command like this;

scp -r <user_name>@<host_name or host_ip>:<Path to your directory> <target_path_dir>

For eg.
Source...

Why don't you use rsync it has all the functionality what you are looking for.

Hi All,
I am trying to rsync some of the latest files from remote m/c to my local linux box.
Folder structure in my remote m/c looks like this

/pub/Nightly/Package/ROLL/WIN...