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Why did this update go through and change ownership (user and group) to 1000 for many of the directories? That would not have had anything to do with the patch. How did you overwrite files? ftp? Since some of the files are owned by apache, I did basically the following: cd $joomla_dir sudo tar zxf ...

Why did this update go through and change ownership (user and group) to 1000 for many of the directories?