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For your convenience, a reference video is available on the TrenzElectronic's Channel at YouTube.

Info
For further reference, please read Xilinx XAPP974: Indirect Programming of SPI Serial Flash PROMs with Spartan-3A FPGAs and this discussion (in particular for TE0630 Spartan 6 module) on the Xilinx forum.
Note

Direct SPI configuration is supported only up to Xilinx iMPACT version 11.x. See Xilinx AR#36156.

To indirect program SPI Flash using Xilinx iMPACT do following steps.

Connect JTAG cable to corresponding module connector (see JTAG connector).

Connect JTAG cable to host computer with installed Xilinx iMPACT software.

Power-on module by external power supply source or by USB cable.

Run Xilinx iMPACT.

Select Boundary Scan mode.

After initialization iMPACT window should look like

Scroll Title
titleiMPACT Boundary Scan identification success

Right click on FPGA image and select "Add SPI/BPI Flash..." from menu.

Scroll Title
title"Add SPI/BPI Flash..." selection

Select mcs file to program.

Select SPI Flash type corresponding to your module type and revision.

Scroll Title
titleSelect SPI Flash type pop-up

Right click on Flash image and select "Program" from menu.

Scroll Title
titleSelect "Program"

Leave default programming properties and press "OK".

Scroll Title
titlePress "OK" in the pop-up

Wait for operation to complete.

After completion iMPACT window should show "Program Succeeded" sign.

Scroll Title
titleFlash Program Succeeded