If you want to use the Xilinx tools such as EDK, Chipscope, or Impact with the Papilio you need a way to use a Xilinx programming cable. This screencast shows how to setup the Papilio to use a Xilinx programming cable.
The Papilio has a Xilinx JTAG header but the problem is that in the default mode the FT2232D USB chip is connected to the JTAG pins and interferes with programming. What is needed is to put the FT2232 into a mode where the JTAG pins go into High-Z leaving the Xilinx JTAG pins free for the programming cable.
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