I've been waiting for a while for a detainee to make this argument: The transfer provisions of the NDAA violate the Commander in Chief clause. The brief itself is not yet public, but there's an allusion to it in this filing in the habeas case of Guantanamo detainee Ahmed Adnan Ajam---which seeks leave to make public an earlier document that sought to amend his habeas petition:
The propositions of Petitioner's current motion to amend are almost entirely public. They are that (a) the Executive has imprisoned Petitioner for more than a decade; (b) the Executive has never justified Petitioner's detention other than as a claimed exercise of its authority to target Petitioner with military force under Article II, Section 2 of the Constitution; (c) following a Congressional authorization for the use of military force, Article II, Section 2 of the Constitution gives the President sole authority to determine whether and when to use, or desist from using military force against otherwise-targetable persons within the scope of that authorization; (d) in the exercise of his Commander-in-Chief targeting authority, the President determined almost four years ago that he would desist from targeting Petitioner with military force; (e) Congress unconstitutionally intruded on the President's determination by enacting provisions of the National Defense AuthorizationAct for Fiscal Years 20ll-2013, Pub. L. No. 111-383, $ 1033, 124 Stat.4137 ([an.7,2011); Pub. L. No. ll2-81, $ 1028, 125 Stat. 1298 (Dec. 31,2011), Pub. L. No. ll2-239, $ 1028, 126 Stat. 1632 (Jan. 2,2013) ("NDAA"); (f) the NDAA's certification requirements alternatively constitute an unconstitutional Bill of Attainder; and (g) the circumstances of Petitioner's case show that he has suffered and continues to suffer a direct and immediate injury as a consequence of Congress's unconstitutional intrusion. By amending his petition, Petitioner would seek a declaration that the NDAA provisions are void and that the President should be declared free to proceed with desisting in the exercise of military force against Petitioner, including the transfer of Petitioner abroad to facilitate the same, without any requirement of certifications being made to Congress.