/application/config/constants.php (update BONFIRE_VERSION)./bonfire/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 /bonfire/codeigniter/ directory to /bonfire/ci2/ and update your $system_path in /public/index.php accordingly.
Check the CodeIgniter 2.x Support in Bonfire documentation for additional details, if necessary.