Fix bean.api.php to set path and file in the class level

CTools registry checks the class if it's present (in Beans it's called handler) so it will expect the path and file defined at class level and not plugin level, it doesn't matter regarding the path but the file has no fallback to the plugin.

            $class = $plugin_definition[$class_key]['class'];
            // Use the filename if it's explicitly set, else follow the naming
            // conventions.
            $filename = isset($plugin_definition[$class_key]['file']) ? $plugin_definition[$class_key]['file'] : $class . '.class.php';
            $base_path = isset($plugin_definition[$class_key]['path']) ? $plugin_definition[$class_key]['path'] : $plugin_definition['path'];

Fixing the documentation in the api.php so as to avoid these kind of misunderstandings: #1397534: Missing files from module.