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Jones probably has a huge ego, but as we know,
the tyrant team is ALL political ALL the time.
This give more detailed background:

HOW BOB WOODWARD DROVE THE NAIL IN JIM JONES’S COFFIN

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The book revealed that Jones confronted Emanuel for dealing with Donilon instead of him, telling him once, “I’m the national security advisor. When you come down there, come see me.”

By Josh Rogins — foreignpolicy.com

General James Jones national security adviser resigns.
Jim Jones was preparing to leave his job as national security advisor in early 2011, according to Bob Woodward’s Obama’s Wars.

Ironically, controversy erupting from that very same book may have contributed to Jones speeding up that schedule by several months; President Obama will announce his departure today, and that his replacement will be his deputy, Tom Donilon.

Immediate reaction within the administration to Jones’s resignation was consistent with the long-held view that Jones was never able to be effective as national security advisor because he was outside of Obama’s inner circle and was intellectually and sometimes physically cut out of major foreign policy discussions

*snip*

But if Obama wanted Jones to help him deal with the military, that also didn’t bear out. Woodward details several instances where Jones finds himself in open conflict with the military brass, led by Joint Chiefs Chairman Adm. Michael Mullen. In the administration’s debates over increasing troop levels in Afghanistan, Jones often raised the prospect of sending far fewer troops than the 40,000 requested by Mullen and Gen. Stanley McChrystal, arguing that the military hadn’t proven its need for so many new troops.

The last salvo against Jones from Woodward came during the author’s Oct. 5 interview with Charlie Rose, where he said that Jones had failed in his fundamental duty to give frank advice to the president because he held back on his assessment that only 20,000 additional troops were needed in Afghanistan.

http://www.veteranstoday.com/2010/10/08/how-bob-woodward-drove-the-nail-in-jim-joness-coffin/