Arduino really has to enter the world of real debuggers now, Serial.print()ing is for the birds.
Well stood me in good stead for over 40 years,
there is a JTAG connector (unpopulated) and an SWD connector.Anything that does SWD and supports the SAM3X will work.I tested (albeit not fully) the http://www.blacksphere.co.nz/main/blackmagic the author added support for the SAM3Xas soon as we have finished testing we'll report back.or you can solder a JTAG connector on the PCB and use the atmel donglem
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