Here is a (the?) section that talks about it. Not sure what “exceptions” can be made - but U.S. citizens or Legal Resident Aliens can NOT be detained under the new rules.
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Sec. 1032. REQUIREMENT FOR MILITARY CUSTODY.
(a) Custody Pending Disposition Under Law of War-
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(1) IN GENERAL- Except as provided in paragraph (4), the Armed Forces of the United States shall hold a person described in paragraph (2) who is captured in the course of hostilities authorized by the Authorization for Use of Military Force (Public Law 107-40) in military custody pending disposition under the law of war.
(2) COVERED PERSONS- The requirement in paragraph (1) shall apply to any person whose detention is authorized under section 1031 who is determined—
(A) to be a member of, or part of, al-Qaeda or an associated force that acts in coordination with or pursuant to the direction of al-Qaeda; and
(B) to have participated in the course of planning or carrying out an attack or attempted attack against the United States or its coalition partners.
(3) DISPOSITION UNDER LAW OF WAR- For purposes of this subsection, the disposition of a person under the law of war has the meaning given in section 1031(c), except that no transfer otherwise described in paragraph (4) of that section shall be made unless consistent with the requirements of section 1033.
(4) WAIVER FOR NATIONAL SECURITY- The Secretary of Defense may, in consultation with the Secretary of State and the Director of National Intelligence, waive the requirement of paragraph (1) if the Secretary submits to Congress a certification in writing that such a waiver is in the national security interests of the United States.
(b) Applicability to United States Citizens and Lawful Resident Aliens-
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(1) UNITED STATES CITIZENS- The requirement to detain a person in military custody under this section does not extend to citizens of the United States.
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(2) LAWFUL RESIDENT ALIENS- The requirement to detain a person in military custody under this section does not extend to a lawful resident alien of the United States on the basis of conduct taking place within the United States, except to the extent permitted by the Constitution of the United States.
If you read the last sections closely they say the president is not required to hold American citizens indefinitely. Which means he can hold throw them in the gulag forever, as long as he is not required to do so.
As, the government can ask for a waiver to begin pulling folks out of line despite the fact they are not working for al queda.