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Transforming Intelligence for Irregular War by Richard H Schultz credits Flynn for convincing McChrystal to convert JSOC from an ops-driven organization to an intel-driven org.

Flynn also drew heat after McChrytal was fired for writing a paper laying out all that was/is wrong with military intel. He was a marked man by "career intel civilians" walking into DIA as the director because they knew he was set on upsetting their bureaucratic malaise.