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The biggest immediate challenge and strategic intelligence shift by the CIA and the American special operations forces under President-elect Donald Trump is likely to be in Syria and Iraq.Obama administration officials from the Pentagon have been battling the CIA and the State Department for some time to focus the US fighting as exclusively as possible on Islamic State and not against the Assad regime or other Syrian terrorist groups.Currently, on top of air strikes, at least a few hundred CIA and special forces personnel are advising and providing arms to the Syrian rebels to fight both ISIS and Syrian President Bashar Assad, who ruled the united country until the 2011 civil war broke out and still seeks to regain control of the entire country.All of that may change on January 20 when Trump takes his seat at the Resolute desk.He has openly said he does not believe the CIA or other US intelligence agencies have a good handle on who the Syrian rebels are and whether the US should be supporting them beyond fighting ISIS.It has been the job of the CIA to vet which Syrian rebel groups get US arms and advisers and which do not because of links to al-Qaida and other terrorist tendencies.Russia has accused the US of failing to see that the non-jihadist Free Syrian Army fights hand-in-hand with Jabhat Fateh al-Sham, the former al-Nusra Front, which is connected to al-Qaida, and other extremist groups.Trump has appeared to accept this allegation and signaled a readiness to disengage from fighting anyone in Syria other than ISIS, especially if the fighting puts him into conflict with Russia, which he seeks to avoid.The CIA and special operations would still be expected to support Kurdish forces in their fight against ISIS.Another central issue that is being widely discussed is whether Trump will order the CIA to return to using enhanced interrogation techniques (EITs)for terrorists, which were banned by the Obama administration and Congress.Putting the legal issues aside, CIA veterans are sounding off in an unusual public fashion against the idea.As a matter of reputation and careers being ruined, many feel the CIA was stained by its involvement in enhanced interrogation during the 2001-2008 Bush administration years and may resist orders to carry it out on the ground in specific cases even if being obligated to listen to the president in general.Possibly, as a preemptive strike against Trump going in that direction or a strike by Trump against CIA holdouts who are anti-enhanced interrogation, numerous reports have surfaced that Jose Rodriguez, one of the primary managers of the EIT program, is on the short list for CIA director.In his book defending the use of EITs, Rodriguez, a career CIA officer who rose to be director of the National Clandestine Service of the CIA, argued that using EITs on an unnamed detainee (later named in a US Senate Report as Hassan Ghul), as well as senior al-Qaida members Khaled Sheikh Mohammed and Abu Faraj al-Libi, were part of the puzzle to taking down Osama bin Laden.Rodriguez described that the EITs led to learning that bin Laden communicated by a trusted courier Abu Ahmed al-Kuwaiti and to confirming the importance of that information.While a variety of other breakthroughs were needed to use Kuwaiti to trace back to bin Laden’s location, Rodriguez argued that learning and confirming his identity was a key step.Rodriguez also listed in his book several other terrorists captured and plots prevented, including the capture of Abd al-Rahum al-Nashiri, the mastermind of the bombing of the USS Cole in 2000.But the US Senate Report said Ghul provided Kuwaiti’s identity to interrogators before they used EITs on him, though he was already being held at the black site referred to in the US Senate Report as “Cobalt.” (media reports said the site was the notorious Salt Pit detention facility in Afghanistan.) Much of the EIT program was originally conceived by controversial outside CIA contractor-psychologists James Mitchell and Bruce Jessen, referred to in the US Senate Report under the pseudonyms Grayson Swigert and Hammond Dunbar, but it was approved and directed by Rodriguez.Rodriguez found his way further into scandal when he ordered tapes of some of the interrogations destroyed, with a dispute breaking out between him, Bush, White House officials and Congress as to whether he had the authority to destroy them.His record make him both an immediate source of controversy for many CIA officials, but also a formidable figure who has strong support from other wings of current and former CIA officials from his long tenure there.Several other areas of intelligence may also experience major shifts, including the balance of intelligence sharing and relationships with Russia, NATO, Turkey, Israel, Egypt, Jordan and others.While the Obama CIA has named Russia as the author of the cyber hacking of Trump’s election adversary, Hilary Clinton, and called the interference crossing a red-line, Trump has disputed that Russia was involved.It is unclear if he will try to change the CIA’s mind or if it will change his mind once he is shown all the classified information that the president gets to see.Trump has said he may shift away from aspects of the NATO alliance. It is unclear if that will impact the level of intelligence sharing, but often diplomatic shake ups can downgrade intelligence sharing whether officially or unofficially.Trump adviser, former Defense Intelligence Agency director Michael Flynn, has pressed the US to extradite Fethullah Gulen. Whatever the legal and moral concerns around the issue, such a move could potentially rebuild deeper intelligence coordination with Syria, which has frayed in general and especially since the Turkey coup attempt in July.Finally, intelligence sources who have advised the Trump campaign have indicated the US will listen more closely to Israel, Egypt and Jordan when making policy in the region. This is something that could increase intelligence cooperation with those countries – though many aspects of intelligence sharing not involving policy disputes have already been robust.