Adding the Empty Application template back to Xcode.
Clone this repository. Close Xcode.
Then in your terminal, cd into the repo directory and execute the following command:
sudo cp -r Empty\ Application.xctemplate /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/Library/Xcode/Templates/Project\ Templates/iOS/Application/
This has only been tested against Xcode 6.1. If this breaks please let me know.