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in RotS I never really care whether clans were with the same allegiance as me or not, I generally crush anyone regardless of allegiance as if I was playing in Sengoku Jidai.
But in FotS, what do I do? Say if I were playing Satsuma, Should I wipe out the rest of the clans regardless of imperial or not and proceed to conquer from west to east? Or do I ally with them and send my armies on a fleet to wipe out Shogunate clans in the east?