Auto-moving and automated units will stop being automated if an enemy or friendly unit is within range of them after the inter-turn. I usually use the enemy unit one so if I sent a transport somewhere on automove it will stop if it is about to run in to an enemy. It is not terribly useful really.
I'm not sure what other effects it has, that's just what I have noticed.
I think it'll wake up Workers from their jobs (regardless of whether you Automated them or not) if you have the Enemy one on. I don't think anything wakes up Fortified units; I wouldn't think Sentry would matter, because it's supposed to wake up on contact with a unit that's not yours, and there's a specific order for Enemy-Only wakeups.
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