In the Department of Defense, where more than two-thirds of the intelligence programs reside, only a handful of senior officials - called Super Users - have the ability to even know about all the department's activities. Most [sources for this story] requested anonymity either because they are prohibited from speaking publicly or because, they said, they feared retaliation at work for describing their concerns. Beyond redundancy, secrecy within the intelligence world hampers effectiveness in other ways. For the Defense Department, [the] problem goes back to an ultra-secret group of programs for which access is extremely limited and monitored by specially trained security officers. These are called Special Access Programs - or SAPs - and the Pentagon's list of code names for them runs 300 pages. The intelligence community has hundreds more of its own, and those hundreds have thousands of sub-programs with their own limits on the number of people authorized to know anything about them. All this means that very few people have a complete sense of what's going on. Such secrecy can undermine the normal chain of command when senior officials use it to cut out rivals or when subordinates are ordered to keep secrets from their commanders. One military officer involved in one such program said he was ordered to sign a document prohibiting him from disclosing it to his four-star commander, with whom he worked closely every day, because the commander was not authorized to know about it
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