What I want is to copy all the files and the folder from ‘modx-2.3.5-pl’ to the root.
Are you just wanting to copy them? I thought you were trying to update an older version of MODx. The SSH, see below, is for updating, which requires that you merge the contents of each directory, with the current modx directories of the same name that should already be in your root.
The SSH you have written out does not look complete. There is an additional part of the SSH command that I don't see in your code.
The first half says where to get the files from, and the other half says where to merge them to.
The command below is for handling the manager directory, and assumes that your current manager is loose in the root
Both parts need the full path. The full path of where to find the items and the full path of where to move/merge them.
So the command below is saying go to the home, and then inside the accountName (or domain), then inside the public_html, and then inside the modx-2.3.5-pl and grab the manager directory and merge it back out to the public_html.
cp -R /home/godaddyassignedname/public_html/modx-2.3.5-pl/manager* /home/godaddyassignedname/public_html
If
[email protected]/www$ is indeed your path, then I would think the command should be:
cp -R /
[email protected]/www$/modx-2.3.5-pl/manager* /
[email protected]/www$