this is my first post in this forum. First of all sorry for my bad English. I hope this post will give a small overview about debugging the Arduino Due.
I used the latest version of Atmel Studio 6, ARM-JTAG-20-10 from Olimex converting the jtag interface and the debugger SAM-ICE from Atmel. Atmel added the Arduino Board to Atmel Studio 6 IDE, so it is very easy to set up a project for due. For testing I wrote a small example which toggles the on board LED. Result: Stepping through code works great.
#define PIOB *((uint32_t volatile *)0x400E1000)
#define PIOB_OER *((uint32_t volatile *)0x400E1010)
#define PIOB_Set_Output *((uint32_t volatile *)0x400E1030)
#define PIOB_Clr_Output *((uint32_t volatile *)0x400E1034)
int main (void)
PIOB_OER = 0x08000000;
// Insert application code here, after the board has been initialized.
PIOB_Set_Output = 0x08000000;
PIOB_Clr_Output = 0x08000000;