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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.

Custom FPGA design: programmable logic

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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.

Generating bitstreams

Loading FPGA Bitstream through JTAG

Xilinx Impact can be used to load bitstreams.

Loading FPGA Bitstream through USB

OpenFutNet and  other softwares tools can be used to load bitstreams.

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