Xcode 4.3 no longer installs the command line tools by default
You can download the command line tools separately now, avoiding XCode
altogether apparently if you don't want to use it (or you don't want
anything to do with App Store). 
On 2 March 2012 15:42, Charles Davis <email@example.com> wrote:
> I've read the archives, and I've noticed that some of you who have upgraded to/started out with Xcode 4.3 are complaining about the lack of a /usr/include directory.
> This is because Xcode is now distributed on the App Store, and therefore has to be distributed as a self-contained bundle. For this reason, the command line tools aren't installed by default. If you want to install them, try these steps. In Xcode:
> 1. Open the Preferences window (App menu->Preferences, or Cmd-,).
> 2. Select the "Downloads" pane.
> 3. On this pane, select the "Components" tab.
> 4. In the list of components, you should see "Command Line Tools". Click its "Install" button on the right side.
> That should do it. (After Xcode finishes downloading the disk image, of course.)
> (For you early adopters out there, this also works with Xcode 4.4.)