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Typically AT91BootStrap builds with GNU/GCC, it loads a 256KB executable image at 0x23F00000 in SDRAM, and runs it.
If your requirements are DIFFERENT, you will have to edit the file(s)
Look at IMG_ADDRESS, IMG_SIZE, and JUMP_ADDR in Bootstrap-v1.16\board\at91sam9263ek\nandflash\at91sam9263ek.h
It is possible to build it with Keil. The EK has a more complicated boot example that works directly with Keil, than the standard 1.16 AT91BootStrap package.
Nominally you put your Boot loader in block 0 (0x00000), and the u-Boot in blocks 1 & 2 (0x20000)
Unless I'm mistaken you should be able to put a 72KB boot loader in an AT91SAM9263. This loads at 0x300000..0x312000 in SRAM from Block 0 of the NAND, the stack resides at 0x312000..0x314000
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