From the NDAA of 2012 as passed (I'm going to leave the earlier drafts, both those real and imagined, alone for this post):
What does this mean? It means that nothing in Section 1021 changes anything with regards to the detention of U.S. citizens, or any other persons who are captured or arrested in the U.S.
SEC. 1021. AFFIRMATION OF AUTHORITY OF THE ARMED FORCES OF THE UNITED STATES TO DETAIN COVERED PERSONS PURSUANT TO THE AUTHORIZATION FOR USE OF MILITARY FORCE.
(e) Authorities- Nothing in this section shall be construed to affect existing law or authorities relating to the detention of United States citizens, lawful resident aliens of the United States, or any other persons who are captured or arrested in the United States.
If said detention was allowed before, then nothing is changed.
If said detention was prohibited before, then nothing has changed.
The important thing to remember is nothing has changed. If you have a beef about what was before, then this bill is not the place to direct that beef.
What does this mean? It means that Section 1022 does not apply to citizens of the U.S. Clearly. Period. End of story. End of line
SEC. 1022. MILITARY CUSTODY FOR FOREIGN AL-QAEDA TERRORISTS.
(b)(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.
If one wants to play the "well it doesn't say they can't if they don't want to" game, please go to the conspiracy forum. Or the brain transplant bank. Whichever is closer. Or more likely to be successful.
The amount of tin foil hattery on this subject, from both the left and the right, is simply mind boggling.
From Obama's signing statement: Section 1021 [...] breaks no new ground and is unnecessary. [...] under section 1021(e), the bill may not be construed to affect any "existing law or authorities relating to the detention of United States citizens, lawful resident aliens of the United States, or any other persons who are captured or arrested in the United States." My Administration strongly supported the inclusion of these limitations in order to make clear beyond doubt that the legislation does nothing more than confirm authorities that the Federal courts have recognized as lawful under the 2001 AUMF. Moreover, I want to clarify that my Administration will not authorize the indefinite military detention without trial of American citizens. [...]
Why did he include that last sentence? Because of all the mad tin foil hattery out there, which is a national embarrassment. Insane tin foil hattery that claims "Secret Bill To Be Voted On Today Would Allow The Military To Sweep Up US Citizens At Home Or Abroad", or "Act to Allow Detention of Citizens", or that "The Obama administration has let loose upon the land a law that is just as Odious as the Alien and Sedition Acts". Two words, people: Get a grip.