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I can see in the App Store that I have one application (Xcode 5.0.2) that needs to be updated. But if I run the sudo softwareupdate --list in terminal I get the message that there is "No new software available". Why don't the CLI tool and the App Store have the same information?

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The CLI tool softwareupdate is only for OS X updates provided through Apple's software update catalog, or whichever .sucatalog is set in preferences for catalogs provided by OS X Server's Software Update service.

This update catalog does not contain details for Mac App Store apps, such as Xcode.

You can restrict the Mac App Store to only show softwareupdate updates by running the following Terminal command:

defaults write com.apple.appstore restrict-store-softwareupdate-only -bool yes

You can read more about the softwareupdate CLI tool in the man page.

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