What's the use case? Are you just trying to save power between runs off a periodic task? Have you considered leaving the phone on and have it going into a low power standby mode between runs? Either way you still need to figure out how to charge the phone once in a while, although powering it off would buy more time between charges.
You may be able to do the shutdown with just root and not have to modify AOSP. Just run the Linux shutdown command using root
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