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2. Let's say that I have a autonaut looking for an axe, and I stick a few axes on the ground to let it continue. Then I start an automatic generation system, and I decide I don't want a huge stack of them to appear, rather I want to have the goods tucked away in a storage container. I would hope that my autonaut would look for the object in the storage container, but it seems clear that they don't.

3. Sometimes an autonaut gets stuck on a particular command for some reason. If I could switch it's execution pointer, or just skip the command it is working on at the moment, it would sometimes help me out of a pickle.

Ok thanks for clarifying. 

We'll be improving and adding to the scripting system as we go and it should be able to cope with most situations depending on how complex you want to make a script.