cd your public_html/ and create OLD_JOOMLA/ folder
mkdir OLD_JOOMLA/
This will move Joomla's files/folders into the OLD_JOOMLA/ folder
mv web.config.txt tmp/ templates/ robots.txt README.txt plugins/ modules/ media/ logs/ LICENSE.txt libraries/ layouts/ language/ index.php includes/ images/ htaccess.txt .htaccess error_log .htaccess docs/ configuration.php components/ cli/ cache/ build.xml build/ bin/ administrator/ 404.shtml -t OLD_JOOMLA/
Then move it to level up
mv OLD_JOOMLA/ ../