First, If you are not trained to handle plan review for DOD explosives, require they provide an expert. He will be the guy with fewer fingers and toes, but still walking and talking.Second, NFPA 495
"1.3.3 This code shall not apply to the manufacture of explosive materials under the jurisdiction of the U.S. Department of Defense (DOD). This code also shall not apply to the distribution or storage of explosive materials by military agencies of the United States, nor shall it apply to arsenals, navy yards, depots, or other establishments owned or operated by, or on behalf of, the United States."
Typically, Classified areas are Class I Div I, Class II Div I. Unless they want to use the Zone methods. Specific criteria applies based on process and storage.
Those 1.3's have precursors that may include many other hazard classifications. AND 1.3 applies unless they under 1.1, 1.2 because of process, or storage.
See...
http://www.ddesb.pentagon.mil/
If this does not help then punt. This stuff is designed to go boom!