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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.
Warningnote

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

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