The JTAG is accessible on the Pi GPIO header, so you can plug pins into the header to use a JTAG programmer to flash it. If you don't have a JTAG programmer I have documented how to build one out of a Raspberry Pi. Note that the GPIO pins xc3sprog use for JTAG are different to the RGBtoHDMI GPIO JTAG pins.
The JTAG pins are:
| GPIO number | GPIO pin | Signal |
|---|---|---|
| N/A | 1 or 17 | 3v3 |
| N/A | 6, 9, 14, 20, 25, 30, 34 or 39 | GND |
| 0 | 27 | TDI |
| 1 | 28 | TMS |
| 20 | 38 | TCK |
| 24 | 18 | TDO |
If you are using Pi xc3sprog method from the link above you will need to compile the JED file which can be done in the free Xilinx ISE Design Suite.