Just waiting until you have enough ships before sending them into battle?
Yes.
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Does each ship have a unique name?
My 2000+ ship yard bases do (so I know where they are).
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Is stellar manipulation unavailable in that game?
Yes.
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After such a battle, do all non-Emotionless participants experience empire-wide unrest?
Maybe. This particular battle was 4500 vs. 1, so no riots. I'm hoping 150 troops per planet plus temporal vacation centers will keep everyone happy.
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Assume you have a 1kg squirrel
E=mc^2
E=1kg(3x10^8m/s)^2=9x10^16J
which, if I'm not mistaken, is equivilent to roughly a 50 megaton nuclear bomb.
Fear the squirrel.
When you warp into a sector with that many ships, don't you just wish you had the capability of warping back out!
On the bright side, at least you have a little piece of intel.