When waves wash just right across Limantour Spit, chunks of pavement are set loose from sand, traces of development never completed. In 1960, Benjamin Bonelli, a San Rafael lawyer, had plans for a 900-home subdivision called Drakes Bay Estates. There would be a boat harbor, a golf course and homes lining Limantour Estero and the hills beyond. But a coterie of conservationists, including a congressman with a cottage in Inverness and Secretary of the Interior…