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BAGRAM AIR BASE, Afghanistan — A sweeping U.S. military review calls for overhauling the troubled American-run prison here as well as the entire Afghan jail and judicial systems, a reaction to worries that abuses and militant recruiting within the prisons are helping to strengthen the Taliban.

In a further sign of high-level concern over detention practices, Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, sent a confidential message last week to all of the military service chiefs and senior field commanders, asking them to redouble their efforts to alert troops to the importance of treating detainees properly.

While treatment at the U.S.-run Bagram prison has improved in recent years, conditions have worsened in the larger Afghan-run prison network, which houses more than 15,000 detainees at three dozen crowded and often violent sites where the country’s deeply flawed judicial system affords prisoners virtually no legal protections, human rights advocates say.

To help address these problems, Maj. Gen. Douglas M. Stone, a Marine Corps reservist general credited with successfully revamping American detention practices in Iraq, was assigned to review all detention issues in Afghanistan.

Stone’s report, which has not been made public but is circulating among senior American officials, recommends separating extremist militants from more moderate detainees, according to two American officials who have read or been briefed on his report.

Under the new approach, the United States would help build and finance a new Afghan-run prison for the hard-core extremists who are now using the poorly run Afghan corrections system as a camp to train petty thieves and other common criminals to be deadly militants, American officials said.

The remaining inmates would be taught vocational skills and offered other classes, and they would be taught about moderate Islam with the aim of reintegrating them into society, said the officials. The review also presses for training new Afghan prison guards, prosecutors and judges.

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