The point of the relevant portion of Article I, Section 9, is to keep the federal government from spending money without congressional authorization. By passing a law keeping programs in operation in the event of a political impasse, Congress would be authorizing the necessary spending. I don’t believe that such legislative authorizations of spending — e.g., the authorization for sending out Social Security checks, which does not require an annual appropriation — has ever been considered unconstitutional on this ground.
Article I, Section 8, says that the appropriations for “Armies” cannot last longer than two years; the next clause authorizes Congress to make appropriations for the Navy with no time limit, and no other clause mentions a time limit, either. The implication is that Congress usually has the power to appropriate funds for whatever length of time it wishes.
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