The first and only time I met Jose A. Rodriguez Jr., he was still undercover and in charge of the Central Intelligence Agency’s all-powerful operations directorate. The agency had summoned me to its Langley headquarters and his mission was to talk me out of running an article I had just finished reporting about CIA secret prisons — the “black sites” abroad where the agency put al-Qaeda terrorists so they could be interrogated in isolation, beyond the reach and protections of U.S. law.