Really? I see the part where Congress can maintain an army and a navy, but not separate branches of the military like an air force or a marine corps. Much less a CIA, FAA, etc., etc.
The president and congress can, and do, assume powers under the Constitution that are implied. The Supreme Court may or may not agree with them, see the line-item veto for a recent example.
Yes, that's right -- they can maintain them any way they like. And the President can staff them.
But he can't interpret the Constitution to suspend habeas corpus, and he can't send the Army on an overseas expedition on his own ticket. He can't declare war against a State of the Union, and he can't compel departing States by force of arms. So there.
FYI: The Marine Corps is a department of the Navy. (The old joke is: Marines need someone to dance with when they're not fighting)
I don't suppose the framers would have foresaw the need for an Air force, but then those that would have amended the Constitution to make it explicit wouldn't have been necessarily wrong to do so as you imply.