Where "BuildConfiguration.xml" should be located?

Development Platform & Builds
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The one in the AppData directory is global for all engine installs on your machine. Last one in wins. The order of checking is

		// Check for the user config file under /Engine/Programs/UnrealBuildTool
		// Check for the global config file under AppData/Unreal Engine/UnrealBuildTool
		// Check for the global config file under My Documents/Unreal Engine/UnrealBuildTool