This process is also listed under Revision control
First create an ssh tunnel to the cs server:
ssh -L <local port>:<remote host>:<remote port> <user>%<server>@gw.cs.huji.ac.il
Example: ssh -L 22222:river:22 email@example.com
Second copy what you need:
scp -P <local port> <source file> <user>@localhost:<destination file / directory>
Example: scp -P 22222 bla.html abenda@localhost:www
What this actually does, is just forward your attempt to transfer files, through the already open SSH connection, without requiring new OTP, but still asking for the regular password.
Thanks to alsbergt!
It is also possible to connect with winscp using this method. You just need to configure you winscp to connect through a tunnel.
1. Create a new site. In the server use the server you want to connect to (e.g. river). User name would be you CS username. The protocol should be SCP.
2. Click on Advanced to go to advanced settings (if the button doesn't appear, click Edit first). In advanced settings, go to SSH->Tunneling and define the tunnel. Check "Connect through SSH tunnel" option. The server should be gw.cs.huji.ac.il and the user name should be <username>%<server>
3. Click OK and then Save, and that's it. You can now login using this profile. Note that it'll request you to enter your OTP and then your password.