app/code/core/Mage/Catalog/sql/catalog_setup/mysql4-upgrade-0.7.56-0.7.57.php

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<?php
/**
 * Magento
 *
 * NOTICE OF LICENSE
 *
 * This source file is subject to the Open Software License (OSL 3.0)
 * that is bundled with this package in the file LICENSE.txt.
 * It is also available through the world-wide-web at this URL:
 * http://opensource.org/licenses/osl-3.0.php
 * If you did not receive a copy of the license and are unable to
 * obtain it through the world-wide-web, please send an email
 * to license@magentocommerce.com so we can send you a copy immediately.
 *
 * DISCLAIMER
 *
 * Do not edit or add to this file if you wish to upgrade Magento to newer
 * versions in the future. If you wish to customize Magento for your
 * needs please refer to http://www.magentocommerce.com for more information.
 *
 * @category   Mage
 * @package    Mage_Catalog
 * @copyright  Copyright (c) 2008 Irubin Consulting Inc. DBA Varien (http://www.varien.com)
 * @license    http://opensource.org/licenses/osl-3.0.php  Open Software License (OSL 3.0)
 */

$installer = $this;
/* @var $installer Mage_Catalog_Model_Resource_Eav_Mysql4_Setup */

$installer->startSetup();

$select = $installer->getConnection()->select()
    ->from($installer->getTable('catalog/category_product_index'), array(
        'category_id' => 'category_id',
        'product_id'  => 'product_id',
        'is_parent'   => 'is_parent',
        'store_id'    => 'store_id',
        'rows_count'  => 'COUNT(*)'))
    ->group(array('category_id' , 'product_id' , 'is_parent' , 'store_id'))
    ->having('rows_count > 1');
$query = $installer->getConnection()->query($select);

while ($row = $query->fetch()) {
    $sql = 'DELETE FROM `' . $installer->getTable('catalog/category_product_index') . '`'
        . ' WHERE category_id=? AND product_id=? AND is_parent=? AND store_id=?'
        . ' LIMIT ' . ($row['rows_count'] - 1);
    $installer->getConnection()->query($sql, array(
        $row['category_id'],
        $row['product_id'],
        $row['is_parent'],
        $row['store_id']
    ));
}

$installer->getConnection()->dropKey(
    $installer->getTable('catalog/category_product_index'),
    'UNQ_CATEGORY_PRODUCT'
);
$installer->getConnection()->addKey(
    $installer->getTable('catalog/category_product_index'),
    'UNQ_CATEGORY_PRODUCT',
    array('category_id', 'product_id', 'is_parent', 'store_id'),
    'unique'
);

$installer->endSetup();

---