Update process assumes that all directories except data and config directories are replaced to prevent possible conflicts.
All previously installed apps are moved to the backup directory.
Since the Updater app is not included into the ownCloud package it is removed too. This app is going to be added to the ownCloud 4.5 package.
P.S. All previous files/customizations are available at the ownCloudRoot/backup/previousVesion-someAlphanumericHash directory.
So if there is a production server and this update is run all installed applications (i.e. 3rd party) are removed? So the owncloud administrator has to bring each app back manually? Would they copy them back and "enable" them again? Reinstall from the Apps repository?
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