Ok, got it to work !
cd /root
opkg remove arduino-dock
opkg remove arduino-dock-2
opkg remove avrdude
wget http://repo.onion.io/omega2/packages/onion/avrdude_6.1-1_mipsel_24kc.ipk
opkg install avrdude_6.1-1_mipsel_24kc.ipk
opkg install arduino-dock-2
Then you can use the sh /usr/bin/arduino-dock flash my_file.hex
Do not use avrdude v6.3-1 as there is a known issue (https://savannah.nongnu.org/bugs/?func=detailitem&item_id=49450)