bedrock-autoloader.php
private function updateCache()
    {
        require_once(ABSPATH . 'wp-admin/includes/plugin.php');

        self::$auto_plugins = get_plugins(self::$relative_path);
        self::$mu_plugins = get_mu_plugins();
        $plugins = array_diff_key(self::$auto_plugins, self::$mu_plugins);
        $rebuild = !is_array(self::$cache['plugins']);
        self::$activated = ($rebuild) ? $plugins : array_diff_key($plugins, self::$cache['plugins']);
        self::$cache = array('plugins' => $plugins, 'count' => $this->countPlugins());

        update_site_option('bedrock_autoloader', self::$cache);
    }
private function updateCache()
    {
        require_once(ABSPATH . 'wp-admin/includes/plugin.php');

        self::$auto_plugins = get_plugins(self::$relative_path);
        self::$mu_plugins = get_mu_plugins();
        $plugins = array_diff_key(self::$auto_plugins, self::$mu_plugins);
        $rebuild = !is_array(self::$cache['plugins']);
        self::$activated = ($rebuild) ? $plugins : array_diff_key($plugins, self::$cache['plugins']);
        self::$cache = array('plugins' => $plugins, 'count' => $this->countPlugins());

        update_site_option('bedrock_autoloader', self::$cache);
    }
Get the plugins and mu-plugins from the mu-plugin path and remove duplicates.
Check cache against current plugins for newly activated plugins.
After that, we can update the cache.