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Add ability to select index of HW_TARGET for flashing on PCs with multiple JTAGs (default index 0)

Luc Tomas Le Pottier requested to merge llepotti-multiple-jtag-flash into devel

This lets us flash to multiple FPGA permanent memories simultaneously without unplugging/replugging the JTAGs (for test beam mostly). Default behavior will not change.

Specify index by adding a second argument, i.e. ./flash.sh file.bit 1 to flash file.bit to FPGA 1.

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