I wonder if it would be possible to include conditions to specific order groups.
How I immagine it is ship following its orders until it comes upon an if check. If success, ship would continue following orders, if not it would jump over all orders until it would come upon else command in order list.
This would make logistics much easier, but depending on stuff available for checks could make setting up patrols or other such things easier too.
Requirement to end in same system would probably be good to not mess up ships navigation.
