Ubuntu – Cannot SSH/SFTP to remote server without using another remote server

You could create ~/.ssh/config with an appropriate config entry for your host like so:

Protocol 2
Host yourhost
    User youruser
    Hostname your.host.address
    GSSAPIAuthentication no
    Port 1234

For more options, consult man ssh_config

Obviously running Nautilus as your local root account (with sudo, gksu, etc) isn't going to give you root access on the server.

The problem is that the SFTP server within OpenSSH (which is what Nautilus is connecting to) doesn't support commands like sudo — it's not a shell environment. What you're asking for simple isn't possible through the standard mechanisms.

However you are not without options. I'm not sure how familiar with SSH you are but you can tunnel ports back across a connection so you could connect normally, run a simple FTP server as root and tunnel all that back to your computer over SSH. Sounds horrible but it's fairly simple.

On the server, run:

# newer Ubuntu installs:
sudo apt-get install python-pyftpdlib

# older Ubuntu installs
sudo apt-get install python-pip
sudo pip install pyftpdlib

Then from your computer, just run a short SSH command:

# If you installed with pip
ssh -tL localhost:2121:localhost:2121 -L localhost:21212:localhost:21212 user@server "sudo python -m pyftpdlib -i localhost -w -p 2121 -r 21212-21212 -d /"

# If you installed with apt-get (and pyftpdlib is pre-1.3, true in 13.10)
ssh -tL localhost:2121:localhost:2121 -L localhost:21212:localhost:21212 user@server "sudo python -m pyftpdlib.ftpserver -i localhost -w -p 2121 -r 21212-21212 -d /"

And then in Nautilus (on your computer), connect to ftp://localhost:2121. The magic of SSH will forward that over to the FTP server running as root.

There are other protocols (I've spent a while looking for a better one) but FTP is the easiest to get up and running thanks in large part to pyftpdlib. You could do similar things with webdav et al, I'm sure... It would just be a lot more hacking around.