Open a SSH terminal session. Navigate to the site root. typically /var/www/vhosts/mydomain.com/httpdocs or username/home/html/

from the command line execute tar -cvf site.tar.gz ./

Open a SSH terminal session. Navigate to the site root

From the command line execute:

When the file finishes transferring execute tar -xvf site.tar.gz

The files will be uncompressed into their original locations, and will have the same permissions as the originals.