There is nothing hidden. I've said this RIGHT here, before and during the sit ints. Go pull up my previous posts.
Second, YES, the military was confronted. At some point, NS even told Gen. Raheel that at NO point, the military should ever even ask for a resignation from him and that this isn't 1999. He also told Gen. Raheel that between a failure of the entire country's economic system and a successful Pakistan, a strong military and defense, its just him standing. Gen. Raheel is a very sensible guy IMO. Probably better than any other Army Chief Pakistan ever had. He assured him that there won't be any hindrances from the military anymore and that he supports all efforts to grow Pakistan and strengthened the system.
After this meeting, IK was told to "pack up and leave Islamabad, effective immediately". Gen. Zaheer first didn't like the "tone of the voice" from the civilian leadership but he later agreed to the facts and that he understands the role he needs to do, to support the systems efforts in going forward. And LATER, he assured he'll disconnect ties with Shuja Pasha. All this was last year and based on these meetings, IK was asked to leave Islamabad effective immediately.
You STILL think IK makes the right choices and makes legit demands? A commission or a court can't bring Shuja Pasha in from Dubai as he's left the country and become a resident of some "foreign" country. No commission will be able to bring Gen. Raheel or Zaheer for investigation on their conversations with NS as these are confidential.
IK just makes new useless statements and demands, based on how he feels that day. Not based on a logic or sense.