Hello community!

I recently came across the CAN bootloader for AT91SAM CPUs (http://www.atmel.com/Images/doc6220.pdf). I have some questions regarding this piece of software:

1. After the bootloader started, how do I switch over to my main programm?
2. The bootloader disables watchdog. If i start my main program after bootloader, is there a way to re-configure watchdog? I guess this is possible only once.
3. Where are the sources for bootloader? I'd like to do some modifications, but all I can find is some built binary.

Thank your for reading,
FocusPaule