The 91c111 and the PXA-255 support a firmware downloading feature.
The PXA-255 has a well defined JTAG interface for driving it (and downloading firmware) that may be hooked to the USB interface through extended USB registers (a common embedded system hack).
The PXA-255 has a light weight and a full hardware handshake UART for RS-232C.
I don't know which of the above (or some other means) iRex implemented in their design. I'd put my money on the USB JTAG interface though, it is the most straight forward and provides pretty complete hardware debugging support.
One other clue, their developer posting made a reference to a debug environment that was unfamiliar to me. Someone could run that reference down in Google...
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