/application/config/constants.php (update cms_system_VERSION)./cms_system/ci3//public/index.php (change $system_path to point to CI3).If you are upgrading an existing site and wish to continue using CI2, simply leave your /public/index.php file alone, or rename your /cms_system/codeigniter/ directory to /cms_system/ci2/ and update your $system_path in /public/index.php accordingly.
Check the CodeIgniter 2.x Support in cms_system documentation for additional details, if necessary.