Just about today I tried the automatic upgrade process of Magento that was done through Magento Connect Manager screen. The upgrade process is quite straight forward and easy. After you get to the Magento Connect Manager screen, just enter “magento-core/Mage_All_Latest” to the Extension Key field and then click on Install New Extensions. After that the system will automatically upgrade all the file in your Magento installation. When it finished just click Refresh to see updated list of all Magento packages that was installed.

Well in my case, after the upgrade process the screen won’t show up. The store page also down, it only gave me “Internal Server Error” page. By looking at my server error log, shows that the server is complaining about the file permission on some files. It seems that the Magento Connect Manager has accidently change the permission to which is not supported or denied by the server. The file that was changed is “index.php” in your Magento root directory, and “index.php” in the downloader directory. Change them to “644″ or writeable only by user, and it should now able to run without problem. 

Please remember to backup all your files and database before doing the upgrade process, especially when doing it on a production server. If you had encountered another problem regarding the upgrade, just head on Magento Upgrade Forum here.

update: After seeing more into the logfile it seems that many file need have their permission check, especially the file named index.php.