The ninjas are basically mercenaries of the Daimyo (powerful landowners, magnates or feudal lords), some mercenary clans tried to engage in other activities and reduce the financial yoke the Daimyo has on them: the Yamanaka with a flowery, the kazekages with mining, etc. still the daimyos are too rich and can hire mercenaries from other regions.
Most of the wars between ninjas are economically motivated, f.e. the Naruto bridge construction arc.
I think the bloodline feature can solve the clan thing.
sorianext
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