Thanks for updating the docs, that's a very helpful clarification. Unfortunately this is still a no-go. Here are the steps I am following, maybe someone can shed some light on this:
1. Download the current version of Modx (2.2.7 Traditional) as a zip from here:
http://modx.com/download/
2. Upload zip to my webserver. SSH into the server and unzip the files.
FYI, site root is:
/home/example/public_html
Files unzipped to:
3. Prepare to merge new files into existing Modx installation. I delete a few things that are unecessary, due to this being an upgrade:
rm -rf /home/example/modx227/core/cache
rm -rf /home/example/modx227/core/config
4. Using the humble cp command, I merge new files from modx227/ into public_html/ like this:
\cp -fr /home/example/modx227/* /home/example/public_html
5. Navigate to the setup page like so:
http://www.example.com/setup
...This displays the site homepage
http://www.example.com/setup/index.php
...This also displays the site homepage
http://www.example.com/setup/index.php?installmode=upgrade-advanced
...site homepage again
Nothing seems to work here.
6. Log in to the manager. Manager warns me that the setup directory should be removed for security. Manager also says I am running 2.2.2.
Any ideas?