President-elect Barack Obama on Thursday chose as his Pentagon general counsel a New York attorney who led the transition team's fact-finding mission on what to do about the war court at Guantánamo Bay, Cuba.

Jeh Charles Johnson has worked as a trial lawyer, federal prosecutor and for two years as Air Force general counsel during the Clinton administration.

If confirmed by the Senate, Johnson would succeed one of the Bush administration's key architects of war on terror detainee policy, William ''Jim'' Haynes II, who left the senior Defense Department legal job in February.

Acting general counsel Daniel J. Dell'Orto has filled in.

Late last year, Johnson represented the Obama transition team inside the Pentagon and heard presentations from the various divisions in the Office of Military Commissions -- from the operations director, Brig. Gen. Thomas Hartmann, to military attorneys with the defense and prosecution teams.

It was not known whether he interviewed Susan Crawford, the Bush administration appointee who decides which cases should go to trial as ``Convening Authority for Military Commissions.''

An early issue confronting the new White House will be what to do with the war crimes court.

Military judges have scheduled an arraignment of a new accused terrorist for next week; a Jan. 19-21 mental health competency hearing for alleged 9/11 conspirator Ramsey bin al Shibh of Yemen, and a Jan. 26 trial for Canadian Omar Khadr, captured at age 15.

Meantime, Cynthia Smith, a Pentagon spokeswoman speaking for the Office of General Counsel, said Thursday that ''another highly qualified official'' would be assigned as operations director once Hartmann ``completes his assignment.''

Hartmann, an Air Force Reserves judge advocate general, or JAG, retires from service in Feburary. He has been one of the war court's most outspoken champions and controversial characters and was three times disqualified from serving as legal advisor at the court for a perception of pro-prosecution bias.

Obama has said he wants alleged terrorists and war criminals to face either federal criminal trials or traditional military courts-martial -- not the commissions created by the Bush administration and approved by a Republican-led Congress in October 2006.

Participants in last year's briefings said Johnson, a Democratic party activist, heard from both advocates and critics of the controversial war court -- which operates between Washington and ''Camp Justice'' at an abandoned airfield at the remote U.S. Navy base in southeast Cuba.

It was not known if the presentations included the price-tag for the remote trials and accompanying air bridge between Washington and Guantánamo.

War court spokesmen have said there is no fixed operating budget for commissions, and have universally declined to reveal their costs.

Obama announced the selection of Johnson on Thursday along with Clinton-era Pentagon comptroller William J. Lynn III, now a Raytheon executive and lobbyist, to replace Gordon England as deputy defense secretary; former Clinton-era assistant Air Force secretary Robert F. Hale as comptroller and a veteran of several national security think tanks, and Michele Flournoy, as undersecretary of defense for policy.

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