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KABUL, Afghanistan While terrorist groups such as ISIS and the Taliban now hit headlines far more frequently than the once-dominant Al Qaeda (AQ), the Usama bin Laden-founded network remains very much alive in Afghanistan.

In fact AQ's activities in Afghanistan is part of the reason for President Trump's decision to give Defense Secretary Jim Mattis the jurisdiction to deploy more American forces to the war-torn country. An estimated 9,800 American troops are already in Afghanistan, with around 2,000 of them designated to fighting insurgent groups with AQ still a key player.

Al Qaeda is at least a few hundred strong, recently resigned Afghan Army Chief of Staff, Qadam Shah Shahim, told Fox News. They keep their operations very secret, work closely with the big groups for protection, and still pose a threat to the world.

In December, Gen. John Nicholson, Americas top military commander in Afghanistan, stated that the U.S. had killed or captured hundreds ofAQ fightersin 2016 alone and that the groups numbers were far higher than previously issued estimates. The year before, U.S. and Afghan forces together dismantledAQ networksand a large training camp in Kandahar, in what turned out to be one of the largest joint raids ever.

So 16 years since 9/11 and six years after its financier and leader Usama bin Laden was killed, how does the terror outfit still operate? Officials say AQs stamina and mild resurgence in recent years can be accredited to its ability to foster tag-team partnerships with other terrorist groups.

Al Qaeda still has a prominent role, once these networks are established, they persist, Dr. Abdullah Abdullah, the Chief Executive Officer of Afghanistan told Fox News. Just because we dont hear as much about it doesnt mean it no longer exists.

Former Afghan Army Chief of Staff, Qadam Shah Shahim (Hollie McKay/Fox News)

The attacks AQ members are involved in, he said, are these days mostly orchestrated by ISIS. The two networks are known to routinely work together, particularly in the northern provinces of Kunduz and Badakhshan, funneling fighters through the porous border from Chitral, Pakistan.

Al Qaeda and ISIS have a lot of commonalities and they share the same Salafi ideology, saidSayed Ishaq Gailani, a Sufi politician who founded the National Solidarity Movement of Afghanistan, referring to the extremely conservative arm of the Islamic religion practiced by some Sunni Muslims.

But what also keeps AQ thriving is the groups good relations with the other main jihadist players across the country; they also have cooperation agreements for access to havens in areas controlled by other terrorists.

We are seeing AQ remobilize themselves, especially in the eastern provinces of Nangarhar and Kandahar where they cooperate mostly with the Taliban, said a high-ranking official with the National Directorate of Security, the Afghan equivalent of the FBI. And now there is talk of a base in Bagram.

And in the southeastern province of Zabul, AQ is believed to operate under the umbrella of the Haqqani network (HQN), a Taliban offshoot known for its extreme brutality and rampant kidnapping for ransom. The group previously held U.S. soldier Bowe Bergdahl, and still has in custody U.S. hiker Caitlan Coleman and her husband and children.

Afghanistan CEO, Dr. Abdullah Abdullah (Hollie McKay/Fox News)

AQ provides fighters, expertise and material support to HQN when needed, intelligence officials highlighted, and several times its members have participated in joint operations with the Taliban and HQN. Furthermore, Afghan officials allege that AQs murky alliance with Pakistan remains its most fundamental lifeline as most of its training and supplies originate from the neighboring nation.

The Tehrik-i-Taliban Pakistan, often referred to as the Punjabi Taliban, is said to work directly with AQ in Pakistans federally administered tribal areas alongside the Afghanistan border. In March, U.S. forces struck and killed noted AQ leader Qari Yasin in Afghanistans Paktika province.

The Balochistan, Pakistan, native was responsible for the death of two American service members in a 2008 Islamabad hotel bombing as well as an attack on Sri Lankas cricket team the following year. Yasin was known to also have ties with the Tehrik-i-Taliban Pakistan and facilitate agreements between the two parties.

AQ additionally has merger agreements with smaller militant factions in the area, including Lashkar-e-Taiba which was founded in the mid 1980s with bin Laden funding, as well as Jaish-e-Mohammed, a Pakistan jihadist group devoted to fighting India over the state of Kashmir.

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And according to Shahim and several other intelligence officials who spoke to Fox News under the condition of anonymity, AQs leader, the 66-year-old Ayman al-Zawahri an Egyptian militant who was the longtime No. 2 and took over after bin Laden was slain by U.S. Navy SEALsis more than likely living covertly in Pakistan.

A video still of Ayman al-Zawahiri, the current leader of Al Qaeda. (AP/IntelCenter)

Sources said recent indicators of his whereabouts have focused on the remote area between the villages of Atter Shisha and Dhodial in the Khyber Pakhtunkhwa region some 23 miles north of Abbottabad, where bin Laden lived. It also was recently reported that Zawahri is possibly spending at least some of his time shielded by the population density of Pakistans largest city, Karachi.

"Zawahri continues to operate a big network, he is still very dangerous and provides the guidance and strategy, one well-placed Afghan intelligence source told Fox News. And he still enjoys Gulf state funding.

He remains at the top of the U.S. governments Rewards for Justice Most Wanted list, alongside ISIS leader Abu Bakr al-Baghdadi, with a $25 million price tag on offer for each of them to be brought to justice.

But U.S-led forces soon may have another bin Laden to contend with at the AQ helm. The slain leader's 28-year-old son Hamza has recently emerged with blessings from Zawahrias the esteemed figure to mobilize the upcoming generation of jihadists of take over the AQ helm.

Prepare diligently to inflict crippling losses on those who have disbelieved, Hamza, believed to be the 15th of bin Ladens 20 children, says softly in an audio recording that surfaced late last month. Follow in the footsteps of martyrdom seekers before you.

Picture taken from undated Al Jazeera television footage purpotedly shows Hamza bin Osama bin Laden displaying what the Taliban say is wreckage from a U.S helicopter near Ghazni. (Reuters/Al-Jazeera TV)

He goes on to explicitly signal followers to court revenge for the deaths of Syrian children killed in airstrikes by launching attacks inside America and Europe. Hamza, who is said to be married with at least two children, too is alleged to have long resided in the northwestern tribal region of Pakistan.

The DOD didn't respond to questions pertaining to Al Qaeda or its current leadership in the region, but stated that the "revised Afghanistan strategy will be presented to the President for his approval in the coming weeks."

Hollie McKay has been a FoxNews.com staff reporter since 2007. She has reported extensively from the Middle East on the rise and fall of terrorist groups such as ISIS in Iraq. Follow her on twitter at @holliesmckay

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Al Qaeda in Afghanistan: How terror group survives, thrives - Fox News

Mike Blanchfield, The Canadian Press Published Friday, June 16, 2017 2:35PM EDT Last Updated Friday, June 16, 2017 3:56PM EDT

At 5-foot-5 and 140 pounds, the soldier was "petit gars" -- little boy -- to 41 male Canadian Forces comrades. To their Afghan army allies, the armed woman in full combat gear was an object of unwanted flirtation.

Looking back, Cpl. Vincent Lamarre now realizes his Canadian comrades were closer to the truth of what he felt he was at the time, and has since become -- a man.

And he's amused by how amorously he was regarded by the Afghan National Army.

"They were very surprised to see a woman do a man's job," Lamarre explains in an interview. "I found it funny at the beginning, but sometimes I had to make them understand I am not an object."

Lamarre was a woman when he was deployed to southern Afghanistan's blood-soaked Panjwaii region in 2010. Every other day, he drove a truck supplying gasoline, ammunition and food down a hazardous highway, through enemy terrain.

Toiling within the heart of the Taliban insurgency offered Lamarre a brief respite from the emotional war that had been raging inside him since he was three years old. Here, he needed only one label: soldier.

Six years later, Lamarre is nearing the end of another long, hard road: he's changed his gender to become a man in uniform. He is prevailing with the full support of an institution that's also grappling to accommodate transgender military personnel.

The Forces have been waiting for what happened Thursday when the Senate passed Bill C-16, which makes it a crime to discriminate on the grounds of gender identity and expression. Now, military policy planners hope to update their own transgender policy for commanders and rank-and-file personnel to ensure that soldiers such as Lamarre are more readily absorbed into their ranks.

"We went from Forces that weren't tolerant at all about things like 'other-than-heterosexual' to a Forces that is tolerant," said Lt.-Col. Pierre Sasseville, a 32-year veteran who is the director of the human rights and diversity branch.

"If you don't accept it, the message is clear: get out of the Forces, or we're going to make sure that you're going to get out."

Lamarre, 31, was raised in St. Jean, Que., near Montreal, with an older brother and sister. His father died when he was two. A year later, when his older brother was getting circumcised, he asked his mother when he would get a penis, so he could do the same thing one day.

As a teen, he would refer to himself using the masculine French pronoun and people would always correct his grammar. Back then, his mom would ask him about transitioning, and is answer was always a "big no."

When he announced his decision a decade later, she was not surprised.

In 2008, Lamarre joined the Canadian Forces because he wanted to make a bigger contribution to his country. In addition to his time Afghanistan, he's served in the Far North and took part in recent military efforts to beat back floodwaters in Quebec.

Coming home from Afghanistan was hard. He was engulfed by post-deployment stress on top of the ongoing gender struggle.

Life was good, on the surface. He found his first girlfriend, a woman he thought was the love of his life. He played on the men's hockey team as a woman. But he had the nagging feeling something was wrong.

The turning point came on a holiday to Cayo Coco, Cuba. He went scuba diving, and dove deep into the clear Caribbean waters. But no air reached his lungs.

A huge wave engulfed him as he crashed upwards, gasping. "I was so afraid to die that I realized after I came back to the beach that I want to live my life and feel good. So I have to do something right now."

Back in Valcartier in early 2015, Lamarre began researching a change of gender on the Internet. He also found a Quebec City support group and went to a meeting.

The gathering that night marked the first time he was called by his newly chosen first name: Vincent.

He went home, and waited up into the early morning hours for his girlfriend to come home at the end of her work shift.

"I tell her I want to transition, I am not feeling good, I am depressed," he recalled. "She reacted aggressively, and now she is my ex-girlfriend because of that."

And so began the process. Psychological therapy. Then, on to hormones and a mastectomy, including follow-up surgery earlier this month.

He told his family, he told his military commander. That too, was a process, but it went well.

He used his sister as a bridge to his mother. She told him not to worry, and of course his mom accepted his decision. His brother wanted him to be the "godmother" to his first child. They worked out the details, and Lamarre's spiritual stewardship was put in place.

He got some good advice from his old master corporal from Afghanistan. When he told his commanding officer, he was pleasantly surprised: Vincent wasn't his first transgender soldier.

Sasseville said no one knows for sure how many transgender personnel are in the Forces, but an estimate of 200 would not be far off.

Moving forward, the Forces policy will balance two competing interests: educating the troops while ensuring cohesion in the ranks.

"Not all of the soldiers we enrol have PhDs and have seen the world," said Sasseville. "So when we talk about cohesion, let's talk about educating our soldiers, reassuring them there's nothing wrong there life goes on."

For Lamarre, that means more plastic surgery. He expects it will take years, not months, to fully recover. He's also found a new girlfriend, who accepts him for who he is. And he's planning on a long career in the military.

When he looks back on Afghanistan, he realizes how he always had the power to seize control of his life.

"I would have liked to go back there because of the change we were bringing," he says.

"But it's out of my hands."

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Transgender veteran of Afghanistan war fights for identity - CTV News

JUDY WOODRUFF: The Trump administration, as you heard, is taking steps to increasing Americas military presence in Afghanistan, after years of reducing U.S. forces there.

William Brangham has the story.

WILLIAM BRANGHAM: Since taking office, the Trump administration has been conducting a review of Americas 16-year war in Afghanistan. The current U.S. commander there, General John Nicholson, has recommended sending 3,000 to 5,000 more troops to augment the 10,000 Americans and 3,000 allied forces that are already in the country.

Today, Defense Secretary James Mattis announced that the president had now given him the authority to decide appropriate troop levels.

For more on all of this, we turn to retired Lieutenant General Douglas Lute. He served on the National Security Council staffs in both the George W. Bush and Barack Obama administrations, where he focused on Afghanistan, Iraq, and South Asia. For the past four years, he served as U.S. ambassador to NATO, and hes now a senior fellow at Harvard University.

Welcome to the NewsHour.

LT. GEN. DOUGLAS LUTE (RET.), Former U.S. Ambassador to NATO: Good to be here.

WILLIAM BRANGHAM: So, lets talk first off about this decision by the president to hand General or Secretary of Defense James Mattis the decision-making for troop levels. How unusual is that?

LT. GEN. DOUGLAS LUTE: Well, it is unusual, but I think we should first appreciate that we should have confidence in the entire Pentagon chain of command, starting with Secretary Mattis, but all the way down through Central Command, and then ultimately to General Nicholson, Mick Nicholson, who you mentioned, who is our commander, four-star commander in Afghanistan.

So, this is a very experienced team, responsible individuals. Theyre going to take this, this new authority seriously. I also think there is a logic. There is a rationale to providing the Pentagon some flexibility. It gives them more agility to fit the number of troops to the task in Afghanistan, and that all makes sense.

It does, however, raise one concern, and thats the concern that strategy is made up of a lot more than just the Pentagon piece. And so I would be concerned, or I would be interested in hearing how the administration intends to make sure that the other pieces, the political side of the equation, the diplomatic equation, the economic assistance equation, the intelligence communitys role, how all these various pieces are fit together in a coherent hole.

WILLIAM BRANGHAM: Well, you raise a very good question, because, traditionally, we think of a strategy being set from the top, from the president, with advice from all of the relevant agencies below.

What do you think this does to the decision-making process for a country like Afghanistan?

LT. GEN. DOUGLAS LUTE: Well, I think its too soon to tell.

The traditional role is that the National Security Council would have this oversight role, this coordinating role, to make sure that the strategy stays aligned over time and that all the pieces relate to one another in a coherent way.

Its not clear whether this move to give additional authorities, additional autonomy to the Pentagon is just the opening step, or whether there will still be a role for the NSC, the National Security Council, led by H.R. McMaster, to oversee the whole process.

WILLIAM BRANGHAM: So, we have said Mattis and Nicholson both believe that more U.S. troops to Afghanistan is a good idea. Do you share that belief?

LT. GEN. DOUGLAS LUTE: Well, I think a few more a few thousand or even 10,000 more U.S. troops

WILLIAM BRANGHAM: Ten thousand more?

LT. GEN. DOUGLAS LUTE: Im saying that I think that, hypothetically, an increase on that scale, lets say, for example, a doubling of U.S. troops there are some 8,500 there now can help sustain the current security stalemate.

But I dont believe that troops alone will actually be decisive in the end. Troops alone cant win this war. Troops alone will not remove the stalemate. The stalemate fundamentally rests on the political side of the equation.

So, alongside any military surge, any the addition of any number of U.S. troops, I will be very interested to hear the administrations ambitions in terms of how theyre going to deal with the politics.

WILLIAM BRANGHAM: Well, explain what the challenges are there for the politics in Afghanistan.

LT. GEN. DOUGLAS LUTE: Well, I look at this as a three-part equation on the political side.

So, first of all, inside the Afghan government itself, here you have zero-sum politics among the different national players. You have a high level of corruption. You have the patronage network. You have a long period of time where you have actually had stalemate from the central government itself.

Second, you have stalemate between Afghanistan and its neighboring states, most prominently Pakistan, but not just Pakistan. We only have to look at the map and see the geographic equation here, which includes Iran to the west, Central Asia, and Russia to the north, and beyond, to the northeast China, and further to the east, India.

So this is a very complex regional diplomatic equation. All those players I have just mentioned have some impact on what happens inside Afghanistan. And then, ultimately, to bring this war to a conclusion, a political end, which the military equation should be in support of, it involves politics between the Afghan government and the Taliban, the opponent.

And so on all three of these fronts, inside Kabul, in the region, and between the government and the insurgents, theres a real need for a political surge.

WILLIAM BRANGHAM: Among those neighbors, Pakistan obviously looms very large in Afghanistan, and provide a consistent safe haven for the Taliban that are waging this massive insurgency in the country.

How can the U.S. get Pakistan to help us in that fight?

LT. GEN. DOUGLAS LUTE: Well, first of all, I think you have to place our requirements, our demands on Pakistan in this part of the arena, that is, their support for the Taliban, in the context of our other interests in Pakistan.

And we actually have several interests in Pakistan which I think surpass our interest in dealing with the Afghan Taliban. I would label Pakistans internal stability itself. Here you have more than 180 million Pakistanis in a country where you have not just the Afghan Taliban, but the Pakistani Taliban, remnants of al-Qaida, and other regional terrorist groups, all of which threaten the stability of the state.

WILLIAM BRANGHAM: A nuclear-powered state.

LT. GEN. DOUGLAS LUTE: And a state which has the fastest growing, the fastest expanding nuclear arsenal in the world.

So, that very dangerous cocktail of terrorists, extremists, and nuclear weapons is actually probably more of a vital national interest to us than Pakistans support for the Afghan Taliban. So, theres a large array of complex interests here which are at play.

WILLIAM BRANGHAM: Even if the administration articulates a strategy, do you think that this administration can execute that strategy?

LT. GEN. DOUGLAS LUTE: Well, I think, right now, theyre working with a handicap. And that is, while the National Security Council itself, those who set strategy and overwatch the strategy, is largely in place, the implementers of the strategy are largely not in place, because they have a large number of vacancies among those officials who are yet to be nominated and confirmed by the Senate, especially in the Defense Department and the State Department.

WILLIAM BRANGHAM: Former Ambassador Douglas Lute, thank you very much.

LT. GEN. DOUGLAS LUTE: Thank you.

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Can more US troops in Afghanistan help end the war? - PBS NewsHour

"At noon yesterday, President Trump delegated to me the authority to manage troop numbers in Afghanistan," Mattis told the Senate Appropriations Committee during a hearing on the Pentagon's budget request.

"The delegation of this authority, consistent with the authority President Trump granted me two months ago for Iraq and Syria, does not at this time change the troop numbers for Afghanistan," Mattis added.

"This assures the department can facilitate our missions and nimbly align our commitment to the situation on the ground," he said of the new authority.

"Our overall mission in Afghanistan remains the same, to train, advise and assist the Afghan forces so they can safeguard the Afghan people and terrorists can find no haven in Afghanistan for attacking us or others," Mattis said, saying the new strategy for Afghanistan will be presented to Trump in the "coming weeks."

This is a change from the Bush and Obama administrations, where the White House approved troop levels, largely because tens of thousands of personnel were involved.

A US senior defense official told CNN that the decision concerning troop levels in Syria and Iraq was communicated via an internal policy memo on April 20.

There are currently about 8,400 US troops devoted to Operation Resolute Support in Afghanistan, which encompasses both US counter terrorism forces to fight ISIS and the Taliban as well as the effort to train, advise and assist Afghan forces in a separate effort.

The Pentagon and White House have been reviewing an option to send 3,000 to 5,000 additional US forces solely in that training and advisory role.

The Pentagon is now conducting a broader military review involving both Afghanistan and Pakistan, so a decision on exactly how many additional troops might not come for several more weeks, defense officials have said in recent days.

The issue of troop levels became especially sensitive in the Obama administration because precise so-called "force management levels" were set for US deployments to Iraq and Syria. But those troop levels quickly became relatively meaningless because they were increased several times, and did not account for temporary deployments or the use of private contractors.

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Mattis confirms White House has given him authority to set Afghanistan troop levels - CNN International

President Trump has authorized his secretary of defense, James Mattis, to determine American troop levels in Afghanistan. Mattis confirmed this Wednesday morning in a hearing before the Senate Appropriations committee. "At noon yesterday, President Trump delegated to me the authority to manage troop numbers in Afghanistan," Mattis said.

The New York Times had reported Tuesday night that Trump had given Mattis that authority. "Mr. Mattis is believed to favor sending several thousand more American troops to strengthen the effort to advise Afghan forces as they push back against gains made by the Taliban, the Islamic State and other militant groups," reported the Times. "But officials said he had not yet decided how many more forces to send to Afghanistan, or when to deploy them."

During both the Obama and Bush administrations, Afghanistan troop levels were watched closely by the president and the White House. But while the policy is changing, Mattis told the Senate that there are no immediate plans to change troop levels. "The delegation of this authority, consistent with the authority President Trump granted me two months ago for Iraq and Syria, does not at this time change the troop numbers for Afghanistan," he said.

Mattis told the Senate Armed Services committee on Tuesday that the administration would have a new strategy on Afghanistan by mid-July. Last month the president's national security team presented a strategy proposal to Trump that would, among other changes, raise troop levels. Mattis and Trump's national security adviser, H.R. McMaster, are believed to be particularly strong advocates for the plan.

The White House has not said whether or not Mattis's "mid-July" promise is accurate or consistent with the president's timeline. "It is indeed what Mattis said," said one White House official.

Senate Passes Russia Sanctions, But White House Has No Position Yet

The Senate voted 97-2 Wednesday to pass a package of new sanctions against Russia. The two nays were Republicans Rand Paul and Mike Lee.

The Associated Press writes the sanctions were designed as a rebuke against Russia's interference in last November's presidential election. "The measure has been attached to a bill imposing penalties on Iran that the Senate is currently debating and also has strong support," reports the AP.

But the sanctions are also seen as a response the Trump administration's lack of admonishment for Russia. A White House official tells me the administration is still reviewing the sanctions amendment and will not take a position until after the House of Representatives considers it and the full bill makes it to the president's desk.

"The administration remains committed to existing sanctions against Russia and will keep them in place until Moscow fully honors its commitments to resolve the crisis in Ukraine. We believe that the existing executive-branch sanctions regime is the best tool for compelling Russia to fulfill its commitments," said the White House official. "In its current form, the legislation poses a number of risks to the administration's ability to conduct foreign policy. However, we are not opposed to tough legislation involving Russia sanctions. We remain committed to working with Congress on this issue."

White House Reacts to Scalise Shooting

The White House was relatively quiet Wednesday after the early-morning shooting in Alexandria, Virginia, that left five peopleincluding House majority whip Steve Scaliseinjured.

"The Vice President and I are aware of the shooting incident in Virginia and are monitoring developments closely. We are deeply saddened by this tragedy. Our thoughts and prayers are with the members of Congress, their staffs, Capitol Police, first responders, and all others affected," said President Trump in a statement issued shortly after the first news reports broke.

Later on Wednesday, the president spoke from the White House about the incident. "Congressman Steve Scalise, a member of House leadership, was shot and badly wounded, and is now in stable condition at the hospital, along with two very courageous Capitol police officers," Trump said.

The president singled out Scalise, the third-ranking member in the House of Representatives, calling him a "patriot and a fighter."

"Steve, I want you to know that you have the prayers not only of the entire city behind you but of the entire nation and, frankly, the entire world," said Trump. "I spoke with Steve's wife, Jennifer, and I pledged to her our full and absolute support. Anything she needs."

Trump offered praise to the Capitol police, who were on the scene as part of Scalise's security detail. "Our brave Capitol police perform a challenging job with incredible skill. Their sacrifice makes democracy possible," said Trump. He also lauded the first responders in Alexandria, Virginia, where the group of congressmen and their aides were practicing for Thursday's charity baseball game against Democratic members of Congress.

The president closed with a message to the country. "We may have our differences, but we do well in times like these to remember that everyone who serves in our nation's capital serves because above all they love our country. We can all agree we are blessed to be Americans," he said.

Trump Disapproval at All-Time High

More Americans than ever disapprove of the job Donald Trump is doing as president. According to Gallup's daily approval metric, Trump's disapproval rate hit 60 percent for the first time on Tuesdaya worse rating than Gallup ever recorded for FDR, Jimmy Carter, Ronald Reagan, Bill Clinton, or Barack Obama. Meanwhile, the percentage of Americans who approve of Trump's performance shrunk to 37 percent.

Trump's weekly approval rating is also trending downward, polling at 41 percent, 38 percent, and 37 percent over the last three weeks.

One explanation for the slide could be the president's highly publicized fight with fired FBI director James Comey. Trump and Comey have each accused the other of lying about the nature of their relationship in the early months of the administration. A Politico poll released on Wednesday reports that 45 percent of voters trust Comey's version of events, while only 32 percent trust Trump's.

Despite Trump's slipping ratings, his own party appears to be sticking with him: 81 percent of Republican voters still approve of his job performance, according to the poll.

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Trump Delegates Afghanistan Troop Levels to Mattis - The Weekly Standard