One of the revelations by Edward Snowden on the NSA domestic spying is the reality of a whitehouse "black budget". What happens here is that with the beginning of the war on drugs, laws were put in place that allowed government agencies to keep money seized in drug enforcement activity. This is not an insignificant amount of money. The federal government can then spend that drug money on covert "black operations" that Congress is not aware of and has no oversight over.
Do you see the harm here? The Constitution is set up to preserve a separation of powers. Congress has the power of the purse and the power of investigation. Congress is supposed to know everything the Executive Branch is doing and approve the funding of those activities. However, in the last 100 years, there are numerus CIA-directed activities that the Congress or even the Whitehouse is not aware of and which are not covered in Congressional appropriations bills because many federal agencies have an independent source of funding.
The US government is all backwards. We have the Judicial branch legislating. We have the Executive branch legislating by executive order and appropriating drug money. And we have the Legislative branch executing the law via pork barrel politics (specifies who gets the money).