Magento Category URL Key Removed after Reindexing

In Magento Enterprise 1.13 (or 1.12) url_key attribute was moved to its own table catalog_category_entiry_url_key (similarly product url_key attribute has its own table catalog_product_entiry_url_key). Also in 1.13 indexers were changed and are now run by the cronjob instead of manually. The problem is that indexer only takes values from catalog_category_entity_(varchar|int|decimal|text|datetime) and not catalog_category_entiry_url_key. Quick fix is to create a new module and rewrite enterprise_catalog/index_action_category_flat_refresh model with:

<enterprise_catalog>
    <rewrite>
        <index_action_category_flat_refresh>Mynamespace_Mymodule_Model_Refresh</index_action_category_flat_refresh>
    </rewrite>
</enterprise_catalog>

and in the class add url_key to $attributesType array

class Mynamespace_Mymodule_Model_Refresh extends Enterprise_Catalog_Model_Index_Action_Category_Flat_Refresh {

/**
 * Return attribute values for given entities and store
 *
 * @param array $entityIds
 * @param integer $storeId
 * @return array
 */
protected function _getAttributeValues($entityIds, $storeId) {
    if (!is_array($entityIds)) {
        $entityIds = array($entityIds);
    }
    $values = array();

    foreach ($entityIds as $entityId) {
        $values[$entityId] = array();
    }
    $attributes = $this->_getAttributes();
    $attributesType = array(
        'varchar',
        'int',
        'decimal',
        'text',
        'datetime',
        'url_key'   //add url_key to attributes type; otherwise url_key value will not be saved in the flat tables
                    //as it was moved to its own table in EE 1.13
    );
    foreach ($attributesType as $type) {
        foreach ($this->_getAttributeTypeValues($type, $entityIds, $storeId) as $row) {
            if (isset($row['entity_id']) && isset($row['attribute_id'])) {
                $attributeId = $row['attribute_id'];
                if (isset($attributes[$attributeId])) {
                    $attributeCode = $attributes[$attributeId]['attribute_code'];
                    $values[$row['entity_id']][$attributeCode] = $row['value'];
                }
            }
        }
    }
    return $values;
    }

}

This will add url_key to flat tables during reindex but it probably won't work with MAGMI import module.

Just in case anyone else runs into this - the URL Key and URL are no longer stored in the flat category table, hence the omitted value that confused me with the issue above when reindexing.

MAGMI adds these values to the catalog_category_entity_varchar table, as they are still used in the Community Edition.

Unfortunately, the loadByAttribute method doesn't work with url_key, so it appears to be a rather convoluted measure to fetch a category by url_key:

    $collection = Mage::getModel('catalog/category')
        ->getCollection();
        $collection->getSelect()
        ->join(
            array('url_keys' => 'catalog_category_entity_url_key'),
            'url_keys.entity_id = main_table.entity_id'
            )
        ->where('url_keys.value = ?', 'your-url-key');

    $category = $collection->getFirstItem();

    $category->load($category->getId());