WASHINGTON — The agency that supervises the nation’s nuclear weapons stockpile would essentially lose direct Cabinet oversight under legislation that Congress is negotiating. The little-noticed provision in a defense policy bill is opposed by the Trump administration and senior lawmakers from both parties, but efforts to scrap it have not overcome resistance from staffers on the Senate Armed Services Committee. At issue in the Senate-approved bill is whether the National Nuclear Security Administration remains under the direct control of the Energy Department, where it’s been since its creation in 2000. The bill would empower that agency to act nearly on its own, freed from what a report by the Senate committee calls a “flawed DOE organizational process” that has led to “weak accountability … insufficient program and budget expertise and poor contract management.” That report cites series of delays and cost overruns at the agency, including a now-canceled project to reprocess weapons-grade plutonium and uranium into fuel for commercial reactors.