If you ever find that your Windows Phone settings in File > Preferences have gone blank (most likely after an install/update of the WP8 SDK) and pressing the "Check SDK" button shows an error about a missing file in the deployment tool, go to:
and delete any files and folders you have here.
Now run the Application Deployment tool once to confirm that the issue has been fixed and that is can now see devices/the emulator.
You should now find that pressing the "Check SDK" button in GM will re-populate the list of devices. Note, that you will need to restart GM if you'd had it open while following the steps here before you can build again, but it should then work fine from now onwards.