N98\Magento\Application\ConfigurationLoader::loadStageTwo PHP Method

    public function loadStageTwo($magentoRootFolder, $loadExternalConfig = true, $magerunStopFileFolder = '')
    {
        $config = $this->_initialConfig;
        $config = $this->loadDistConfig($config);
        if ($loadExternalConfig) {
            $config = $this->loadPluginConfig($config, $magentoRootFolder);
            $config = $this->loadSystemConfig($config);
            $config = $this->loadUserConfig($config, $magentoRootFolder);
            $config = $this->loadProjectConfig($magentoRootFolder, $magerunStopFileFolder, $config);
        }
        $this->_configArray = $config;
    }