2.x to 3.1.x upgrade issue - Call to undefined method Piwik\Settings\Storage\Factory::make()

Got the error upgrading piwik from 2.16.5 to 3.1.0.
PHP Fatal error: Call to undefined method Piwik\Settings\Storage\Factory::make() in /analytics/public_html/core/Plugin/Settings.php on line 75

Easier way is to backup, install new one and restore or there is a simplier way? php version is 5.5.9, host is ubuntu 14.04 x64