The Carnegie Endowment for International Peace Guide to Egypt's Transition reports the following with respect to the draft Constitution:
Military Trials for Civilians
Military trials for civilians were not formally mentioned in the 1971 constitution, which said only that “the law shall regulate the military judiciary, and define their competences in the framework of the principles in the Constitution.” In practice, the Mubarak regime occasionally used military trials to oppress its civilian opponents. Under Egypt’s emergency law, in force almost continuously from 1967 to 2012, the president possessed the power to transfer individual court cases to the military justice system.
After Mubarak’s fall, the SCAF [Supreme Council of the Armed Forces] ruled from February 2011 to June 2012. During that time, the armed forces began to use military trials extensively in areas where the military was deployed, and thousands of civilians were hauled in front of military courts. The 2012 constitution formally sanctioned these trials, though its language made a halfhearted attempt to limit them by stating that they could only be used “for crimes that harm the Armed Forces.”
After fierce debate during the current drafting process, in which representatives from the No to Military Trials for Civilians group argued their case to the drafting committee, the military was able to preserve the right to try civilians in military courts. The new draft makes more of an effort than the 2012 constitution did to specify when military trials can be used—for instance, in cases of attacks on military premises, personnel, equipment, documents, and funds—but the language is still broad enough to suggest that the military will be able to use them freely. Additionally, the draft transfers cases related to the Egyptian General Intelligence Service to the military justice system, which could also immunize intelligence officers from civilian oversight.