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I have installed Xode downloading the DMG (not from the Mac App Store). Now each time I run brew doctor it says:

Your Xcode (4.6.1) is outdated
Please install Xcode 4.6.3.

But In App Store > Available Updates.. it does not appear. How can I upgrade it?

Please note that I'm not using Xcode but Xcode command-line tools (the C++ compiler) and if possible I would like to avoid reinstalling it.

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    Since you didn't install Xcode from the Mac App Store it won't display updates for it. You need to download the newest version from developer.apple.com and update manually. You may prefer to uninstall Xcode instead and purchase the App Store version (which is free). Once it is installed go to Xcode>Preferences>Downloads>Components to download the command line tools. – jaume Jun 27 '13 at 11:27
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I have just found this on GitHub Gists.

Try enter the following command in Terminal:

sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer

Solved my brew doctor problem of Homebrew not recognising updated version of Xcode.

Also see this Homebrew compatibility guide and ensure that your OS is compatible with Command Line Tools on their own or if you need the full version of Xcode.

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