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To change the firmware of EEPROM from Generation 2 to Generation 3 you must follow this procedure. You may also watch this video play list.
Those preloaded firmware is used with TE API.
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You can download the Firmware code from GitHub and use this code as a start point.
If you doesn't realize a compatible firmware the TE API are no longer available.
Xilinx Impact can be used to load bitstreams.
OpenFutNet and other softwares tools can be used to load bitstreams.
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