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i find that the best strategy is to build your hanger, deposit, refinery and tractor beam in the same place, and build two big meaty combat bots there to guard the place. have the clones gather the resources, and make a sweep of parts of the ship.
Now the caveat is that space ghost thingy. i am not sure if it summons levithians, or if it just sends out an emp wave to ruin your ship. a veteran crew with good weapons + combat bot make short work of it, but STILL you want to be there to keep that ♥♥♥♥ from getting loose.
I also make sure to steal every turret from the pirates, and upon returning from a pirate ship i place them under the floors. getting mk3 turrets is a must and putting them every where needs to happen.
i really wish that we can assign clones or bots to do this job. or even have a ship scanner that scans the ship for eggs and spores.
I sealed off all my decks other than the very bottom one with the beam and hangar (and refinery) but even when there is no physical way to GET to areas, spores can appear there. My entire storage deck was infested despite not even having a way to access the crawlspace.
Make up some clever lore about them seeping through the hull or sticking to shoes if you like, but the tragic answer is that they will be spawned at random, all over.
They board the ship from spore cloud hazards. Spores can be spawned from activated infestations.
There is always a cause for them. We do not spawn them randomly on the ship.
And I'm skeptical about the random spores magically appearing in random places anyhow, given that I've never seen anything of the sort despite more hours in-game than I care to admit. I have seen spores wander fairly far before settling, I have seen that they can jump across one square of empty space on the shipbuilding grid, and I have seen (in the case of this undying cloud) that above-deck spore clouds can spawn below-deck nests (which explains your storage deck being infested despite no crawlspace access), but I have never seen aliens or lichens popping up in a place that wasn't easily explained.
Edit, since I cross-posted with the dev: Thanks for confirming that there are no magical random spores! Any tips for getting rid of this spore cloud that never dies?
Default solution to weird stuff in Genesis: Destruct the module where the spore is and rebuild it.
If i do that, do i lose my reinforcements? Honestly, i think the best solution is a new module where the clones scan the ship and mark modules that have spores on them. They don't even have to clean it up, i can do that myself.
Also, can the clones have more levels? i would like to see a higher level clone that can reset a node if they see one that needs it.