It's kind of funny. The game set me(Yor) with the remnant right off the bat. The remnant warned me about military build even though I haven't got a shi[ through ideology, anomalies, or even build a warship. The only thing I could figure is the survey ship offended him. Maybe you could exclude starting survey ships off that list. Anomoly ships would also be nice. Just ships you build. Planet options under the govern screen needs to be local, and global. I can't upgrade my planetary improvements into something else I have to destroy the improvement first. Why was this removed from the game, Ie later on I can turn a factory into a Duranthium refinery.
