Bootstrap initializes the board components and loads the kernel.CPU ROM code looks for a file named BOOT.BIN on the first FAT partition from the microSD card. If the BOOT.BIN is found, the code is loaded and executed. The BOOT.BIN can load the linux kernel or some other application if needed.
Source for the picoSAM9G45 tailored bootstrap is available here: bootstrap git repository
To compile, edit the compile.sh script from at91bootstrap folder and change CROSS_COMPILE to point to your toolchain.
Then you can run compile.sh script to compile a new bootstrap image.
Image will be generated in bin/ folder.
git clone git://gitorious.org/picopc-kernel/bootstrap-sdcard.git cd bootstrap-sdcard/at91bootstrap ./compile.sh ls -l bin/BOOT.BIN