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In previous versions of iTunes I could delete an app and this deletion would propagate to all devices on synchronization. It no longer seems to be the case in iTunes 11.0.2. I can delete the app from iTunes, but the app isn't deleted from my iPhone or iPad on synchronization. Is this a new feature or a bug? Is there a configuration option to change this?

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This seems like new feature since you can manage applications on your iDevice without changing others. This is way like iPhone Configuration Utility always do.

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