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As far as I know, GenerateProjectFiles.bat is used to create the engine's project files. Once created, you need to open the .sln and build the engine. And after you manually add plugins for the engine, you may need to rebuild it. Please let us know if there are any error messages during the build. For the specific steps of adding plugins to Unreal Engine, you can ask for help from the Unreal community.
Also, you can directly add Microsoft Open XR Plugin to your project, please refer to GitHub - microsoft/Microsoft-OpenXR-Unreal: An Unreal Engine game plugin providing additional features available on Microsoft's Mixed Reality devices like the HoloLens 2 when using OpenXR..
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