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Seeing that the problem of the Congress vs Military will most probably end with a new ammendment to the Constitution, I decided to make a few changes that I feel to be important and that would be a starting point in the discussion and negotiations between the two parties involved in this, the Congress and the Military.
Here it is: (GDoc link: http://tinyurl.com/3shx5xd)
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Constitutional Appendix: Department of Defense Organization & Roles (variation)

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The Secretary of Defense is a Cabinet position appointed by the President. The Secretary of Defense and his Deputies serve at the pleasure of the President. The Department of Defense shall be led by the Secretary of Defense and his Deputies. The Department of Defense shall execute the orders of the President of the United States and manage DoD orders pursuant to the President’s will. The Department of Defense has authority over all financial disbursements to elements of the armed forces, based on the monthly budget passed by Congress.
The Secretary of Defense must be a member of The United States Military and must not come from the same branch as the President (if the case).

An armed forces entity, as used below, is defined as any group of players with the specific purpose of fighting together. This term includes both official military branches and militias alike.

Any armed forces entity wishing to receive Department of Defense funding must apply to the Department of Defense and submit the required information. The Department of Defense will then disburse funding to the armed forces entity so long as that entity is acting consistent with the orders of the President, and providing necessary accountability to the Department of Defense.

In order to be eligible for funding, each armed forces entity must provide current (less than 1 week old) information on the following:
1. Listing of all communes the armed forces entity owns
2. A complete roster, including soldier name, strength and employment
3. Access to live orders
4. Establish daily orders that are consistent with the goals of the United States and the orders of the President.

‘Consistent with the goals of the United States and the orders of the President’ is defined as:
- Directing damage toward battles determined by the POTUS/Department of Defense to be priorities

Access to submitted information will be restricted to the POTUS and the Department of Defense personnel. appropriate members of the executive staff, and the Select Committee on Intelligence (by request).

The President shall have the authority to constitute and manage the official branches of the United States Armed Forces, which will be subject to the direct control of the executive via the Department of the Defense and the Secretary of Defense. The branches, known as - The United States Military - are distinguished from the above “armed forces entities” by their official nature and the direct control of the executive.

All eUS Code references to Joint Chiefs of Staff and its Chairman will be removed from the Constitution, except in the following situations where those references will be replaced as such:
2.24, 2.27, 2.3 - Chairman of the Joint Chiefs of Staff to be replaced with Secretary of Defense