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The Pakistani Inter Services Intelligence agency is probably so full of people sympathetic to the call of jihad that it is going to take a long time to weed out all the malcontents. And I am sure many in the regular service arms and other Intel groups fit into the same sack.
I believe cleaning up Pakistan is going to take a long time. It is perhaps the breadbasket of radical Islam equal to the most stringent madras found in Saudi Arabia.
Will the southern part of Pakistan where the educated and more moderate people live have the will to stand behind their government in going after so many tribes in the northern portions. We are looking at literally millions of people within the tribal groups in the FATA. And obviously the whole border is huge and very remote from a geographic standpoint.
I don't think the Paki are up to the task at hand quite frankly.

The ISI is no independent organisation-it’s a part of the military (Inter-SERVICES).If you need to clean them up,start with the military.Only problem is that the military has always been seen as US friendly.