The folder "edk_user_repository" contains the board support package for the GECKO3main module to use in Xilinx EDK
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Extract this file in the folder where the EDK folder is located. Don't extract it inside the EDK folder!
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After extracting you should have a "edk_user_repository" folder on the same level as the EDK installation folder.
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The folders "GECKO3-main-p1" (about the prototype) and the folder "GECKO3-main-v1" (about the final version) contain EDK projects which are made without the base system wizzard in EDK during the development of the GECKO3main. They are here for docuemntation purposes how you have to connect and configure the ip cores so that the components on the GECKO3main works as expected.