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The mujahadeen leader who was a commander during the Soviet invasion, and who later challenged the authority of the Taliban in the late 90's was an ethnic Tajik. Ahmed Shah Massoud was murdered by two arabs - suicide bombers posing as journalists.
In the early 90's, I believe it was US pressure that kept Pakistan's ISI from encouraging afghan warlords (notably, the Pashtun warlord Hekmatyar, Massoud's mortal enemy) from incurring on Soviet land in central asia (Uzbekistan). Now that the cold war is over, could there still be significant tension between the ethnic pashtuns (southern afghans) and former soviet states to the north? ie, tension that is not arab vs indigenous.
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