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I think of it like high-level scanning versus low-level. Scouting is scan-lite, and explore is use the best tech your ship has to go as deep as possible in system info
but also have "auto spy on enemies" - are you sure?
P.S. I really, really wish Steam would let developers auto-close topics where the last message is older than a given date. Also, instead of dimming the dates, put a glowing square around dates that are over a year old.
but you also don't have an answer
explore does the same but only moves on after all objects in the system are scanned up to the max exploration at that moment.
spy moves the exploration ship from enemy system to enemy system to find enemy fleets and stations AFAIK.
Green = fully explored (to level of survey tech you own)
Yellow = not fully explored (includes never visited and partially surveyed)
Explore = what explorer ship does on full automation mode -> enters system unknown or not fully surveyed yet, then one by one, surveys each planet/asteroid until that system is done. Unless out of fuel or damaged, won't leave the system until done, then goto next
Scout = preferentially targets yellow color systems, and might be wrong, but handful of times I've watched an explorer in this mode, seems to preferentially target new unknown systems vs partially explored/surveyed yellow color system.
The goto next logic seems somewhat clear. Assumption from watching the pattern seems to be -> some planet gets tagged as the 'bubble center', and then the decision for what next system to explore is based on building bubble of known systems around that center.
At very start of game, your capital = obvious bubble center. As your colonies branch out in weird zig zag lines, not quite sure how each new local bubble center is chosen, but you can clearly see the pattern of stars your explorers radiate out towards is by some logic picking some system as another bubble area to scout/explore around (which may not even be a system you own/colonized if far enough away)
^^ You can see this radiating bubble pattern lot easier if using game editor and x8 speed. Plop down 30 explorer ships in one spot at/near your capital, stay in explorer tab mode to see the little red colored circles of your explorer ships start to fan out.
-if it was just rng, you'd end up sometimes with arrow directions out of pure chance (*e.g one direction more explored that other), but it's always circular bubble they fan out.
Auto-spy - now this is the one I'd really like to know. I've tried this setting out, but it's either really dumb, or not sure what the internal logic is. Thought it meant would act as spy ship, try to get close enough to get sensor readings on enemy ships, systems, etc.
So made some long range sensor versions of explorers, set them to auto-spy and tried to see what they did. Seemed random, and only sometimes useful info by pure chance. And while not enough repeats to be statistically valid, the few times I looked, seemed way too close. Like, why would a spy ship try to move that close when the LRS bubble is plenty big?
Was hoping the spy ship would auto park few systems away (best choice being star-only system with no planets), but they were creeping right into the AI systems. During non-war periods, guess this is ok. But during war, it's just an easy way to get shot at.