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When entering the NodeJS Virtual Environment, have it automatically change directory to the apps document root. Also when entering the virtual environment, if you are logged in as an elevated user, have it perform the commands as the the user the app belongs to automatically. I realize this might not be possible, but it would be nice because using NodeJS means you must enable shell for that user and with cPanel, that means you need to enable shell for many or all of the accounts on the server.