Right away.
Above I suggested:
The Head Ninja (call him Shinobi?) could report directly to the Daimyo who would have the power to direct all ninja activities for a given turn. If no specific orders are given by the Daimyo (and 'take no action' is an order) then the Head Ninja has discretion. The other ninjas do what the Head Ninja tells them unless there are no orders in which case they can do as they please (perhaps with restrictions around action against clans which are not enemies).
The Head Metsuke could report to the Commissioner for Finance who would have the power to direct which cities metsuke are to oversee (except in the case of no orders etc.). Except in wartime when the Commissioner for Warfare gets to appeal to the Daimyo for the release of specific metsuke to travel with armies or apprehend enemy agents. They would then be his to control until the Commissioner for Finance (or Head Metsuke) successfully appeals to the Daimyo for their release back to oversee towns.
I'm thinking the Monks could be an independent force and report to no-one (except the Head Monk).
Not sure...perhaps it should be less formal than that. After all, particularly in wartime the situation is likely to be fluid and we want the Daimyo (for example) to be able to make turn-by-turn decisions on who to assassinate, sabotage etc. If he misses the boat and the Head Ninja takes the turn first then the Head Ninja has discretion. Of course the HN should be looking for his orders but he may not always want to...
A loose structure here might reap benefits in terms of IC conflict!
Perhaps you lose influence for a time? proportional to the level of censure you tried to apply?
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