I’m still facing this problem in 2022 I do not know why it’s marked as solved. The UnrealBuildTool.cs file changed so much since 2017 that no code referenced in the solution exists anymore.
I think the problem is with the check to git status. You must make sure everything in the directory containing the Unreal Engine’s .git stays the exact same. I’ve spent pretty much all day waiting for the engine to recompile after I changed one small aspect of the surrounding environment, so hopefully this works.