At first glance, this does seem odd, but if you try out avrdude-6.3, you'll notice that it doesn't actually successfully flash the microcontroller on the Arduino Dock.
I can't recall the exact details but the avrdude developers made some changes with how GPIOs are accessed and it doesn't work on the Omega.
The last time it worked properly was in version 6.1.
Changing the version in the package makefile to 6.9 was our attempt at making sure our version (6.1) gets installed instead, but it turned out to not work...
We've reverted the change and if you do ./scripts/feeds update onion in the build system, it should build properly.
The nature of the kernel patch to enable rebooting seems to have this side-effect... How essential are the halt or poweroff commands for your workflows?
Btw, I will be submitting a Pull Request to LEDE for the reboot kernel patch soon, will update you when it's in.
I think he has already done this... [Resolved] ?! ;-)
PS. reboot works on 0.1.10 b160 - please check it again.
# Put your custom commands here that should be executed once
# the system init finished. By default this file does nothing.
omega2-ctrl gpiomux set i2c gpio
gpioctl dirin 4
gpioctl dirin 5
gpioctl dirin 15
gpioctl dirin 16
gpioctl dirin 17
However, I am still unable to use A5 as an analog input and A4 as a digital input (which is what I am trying to achieve) on the arduino side as those pins seem to still be pulled up to 5VDC either through a resistor or from the TSX0108