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TE0320 comes with SPI Flash preloaded with a reference design?.

Those preloaded image is just for getting started demo, for real designs:

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TE0320 comes with FX2 USB microcontroller's firmware.

The modules shipped before 2/09/2013 comes with Generation 2 firmware. [PCN content replication, please remove]

The modules shipped after 2/09/2013 comes with Generation 3 firmware. [PCN content replication, please remove]

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. [content replication, link to original]

Those preloaded firmware is used with TE API. [content replication, link to original]

Custom FPGA design: programmable logic

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Custom USB design

You can download the Firmwar 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 can be used to load bitstreams.

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OpenFutNet and other softwares can be used to load bitstreams.

Loading a Custom Design into FPGA

OpenFutNet and other softwares can be used to load bitstreams.

Loading USB Firmware through USB

Cypress tools (CyConsole or CyControl) or Trenz Electronic Tools (C#  OpenFutNet or Python OpenFut) can be used to load FX2 USB microcontroller's firmware.