Hi,
We are in the process of testing the GitSetup.bat file as a replacement for the dependency files that were required for previous source code builds of the Engine. As you can see, it still has some problems, and we appreciate you bringing them to our attention. I just downloaded the 4.6 source code that is current as of about 4 hours ago, and the GitSetup.bat file failed to complete successfully, so there are still some issues that will prevent you from being able to build the Engine from the 4.6 branch.