Download the release zip(on the right sidebar, do not click code..download as zip). Extract directly to your Ashita directory(the folder with ashita-cli.exe in it!). Everything should fall into place.
Atmel SAM (ARM core) can be programmed using BOSSA; the equivalent of programming an Atmel AVR using avrdude. On the Arduino Zero, the "native USB" port connects directly to the SAMD21 MCU (PA24,25; ...
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