Magento Enterprise Edition 220.127.116.11, Community Edition 18.104.22.168 and the patch bundle SUPEE-6788 address several security issues. Unfortunately, addressing these issues required some changes that may possibly break backward compatibility with customizations or extensions.
See more at: https://magento.com/security/patches/supee-6788-technical-details
also here is the sample of multipatch script , it will find all of your magento installations, fixes .htaccess issues, and applied patch according to magento version. (this script template can be used to apply different patches at once for multiple hosting accounts on the same server)
^^^ === Executing patch for Magento 22.214.171.124 === ^^^ Checking if patch can be applied/reverted successfully... Patch was applied/reverted successfully. ===================================================================================================== Magento version: 126.96.36.199 Magento path: /var/www/html/production/app/etc/local.xml 2015-10-29 11:45:23 UTC | SUPEE-6788 | CE_188.8.131.52 | v1 | 5045e6c2debec59bc5c451aa2bb2d7873c07ffd1 | Fri Oct 23 20:32:44 2015 +0300 | f0e6aebd290b6ac312637058a11ae7b49ad13438..5045e6c2debec59bc5c451aa2bb2d7873c07ffd1 =====================================================================================================