Write better documentation about the hook settings in the entity .inc file

I've just written a plugin to allow commerce_order entities to be panelized (the plugin file and the class are included below).

When I go to edit the contexts the page loads but I see these errors:

Notice: Undefined property: stdClass::$contexts in ctools_context_add_context_form() (line 145 of sites/all/modules/contrib/ctools/includes/context-admin.inc).
Notice: Undefined property: stdClass::$relationships in ctools_context_add_relationship_form() (line 205 of sites/all/modules/contrib/ctools/includes/context-admin.inc).

When I go to the edit layout and edit content pages I am presented with a MENU_NOT_FOUND:
The requested page "/admin/config/content/panelizer/commerce_order/commerce_booking.email_html/layout" could not be found.

Here are the plugin an class:
commerce_order.inc:

?php
/**
 * @file
 * Definition of the commerce_order plugin.
 */

$plugin = array(
  'handler' => 'PanelizerEntityCommerceOrder',
);

PanelizerEntityCommerceOrder.class.inc:

/**
 * @file
 * Class for the Panelizer commerce_order entity plugin.
 */
 
/**
 * Panelizer Entity commerce_order plugin class.
 *
 * Handles commerce_order specific functionality for Panelizer.
 */
class PanelizerEntityCommerceOrder extends PanelizerEntityDefault {
  /**
   * True if the entity supports revisions.
   */
  public $supports_revisions = TRUE; // Can be sniffed
  public $entity_admin_root = 'admin/commerce/config/order-types/manage/%commerce_order_type'; // Can be sniffed
  public $entity_admin_bundle = 5; // Can be sniffed.
  public $views_table = 'node';
  public $uses_page_manage = FALSE;
  
  /**
   * Determine if the entity allows revisions.
   */
  public function entity_allows_revisions($entity) {
    $retval[0] = $this->supports_revisions;
    $retval[1] = user_access('administer commerce_order entities');

    return $retval;
  }
  
  function get_default_display($bundle, $view_mode) {
    $display = parent::get_default_display($bundle, $view_mode);
    // Add the node title to the display since we can't get that automatically.
    $display->title = '%commerce_order:label';
    
    return $display;
  }
  
  /**
   * Implements a delegated hook_form_alter.
   *
   * We want to add Panelizer settings for the bundle to the commerce_order_type form.
   */
  public function hook_form_alter(&$form, &$form_state, $form_id) {
    if ($form_id == 'commerce_order_type_form') {
      if (isset($form['type'])) {
        $bundle = $form['type']['#default_value'];
        $this->add_bundle_setting_form($form, $form_state, $bundle, array('type'));
      }
    }
  }
  
  /**
   * Implements entity_access();
   */
  public function entity_access($op, $entity) {
    return entity_access($op, 'commerce_order', $entity);
  }
  
  /**
   * Implements entity_save();
   */
  public function entity_save($entity) {
    return entity_save('commerce_order', $entity);
  }
}