Sometimes there is some leakage current via some I/O that's sufficient
to power up the SAM3S. Use the supply monitor to make sure the CPU
will be reset (and kept in reset) if the supply voltage is below 3.0V.
It is utterly unacceptable that Atmel is shipping example code in 2011,
which doesn't support parts that are shipped still in 2016. They would
have had five years to fix their code to implement the chip errata :(
This way we can easily check with 'diff' for differences in our code and
Atmel softpack. Also, this layout is more suitable for building various
different firmware images (e.g. factory-test, dfu-loader, main
application) for a variety of different boards (simtrace, owhw, qmod).