[snops]

>Are you talking about the flash driver for loading external SPI flash?

I was slipping into talking about ARM microcontrollers there, which have internal flash. Reads from it are memory mapped, but writes generally require feeding peripheral registers with commands, hence the latency sensitive read-modify-write. Some ARM microcontrollers do have more direct methods though, some of Freescale's Kinetis range have a feature called EzPort, where you hold a pin low on boot and it pretends to be SPI flash instead, and tiny 8 bit micros like the AVR all have something similar as full JTAG would be too big for them.

>If so you likely know this but you have to load the FPGA with a program to load the flash with the program you want the FPGA to load on reboot. Each of these programs have to be compiled and tested per chip.

Yeah, this is what I meant by having code run on the "target", this being the microcontroller you are programming. You are right in thinking this means the JTAG dongle no longer needs to know how to program flash itself, but it still needs to code to load in and instructions on how to do it (setting up clocks etc), which are also very platform specific. You could do the same for external flash, but its often easier just to connect to it directly and bypass the microcontroller.

Feel free to PM me if you have any more questions.