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Edit Makefile.avr-zigduino, and change the default avrdude port to match your local settings. This only needs to be done once ever.
AVRDUDE_PORT ?= /dev/ttyUSB0
Each node needs a unique MAC address. The avr-zigduino platform expects to find the MAC address as the first 8 bytes in EEPROM.
There is a special program just to program the MAC address. It uses the same first 7 bytes, and lets you choose a different number for the last. From this point forward, we will refer to that last digit of the MAC address as the "Node number".
$ cd tools/set-eeprom
$ make NODE=3 AVRDUDE_PORT=/dev/ttyUSB0