Update Xcode from 4.6.1 to 4.6.3 for Homebrew
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.