You are quite right: a number of files in nested directories were missing. Sorry to have bothered you with that.
Now though I'm having a different issue when I point my browser at the correct path:
The requested URL /cgi-system/index.php/liverpool/install was not found on this server.
Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.'
Maybe this is because I run PHP as CGI?