More (#2) from Dirty Wars:

According to the ICRC, some of the prisoners were bounced around to different black sites for more than three years, where they were kept in “continuous solitary confinement and incommunicado detention. They had no knowledge of where they were being held, no contact with persons other than their interrogators or guards.” The US personnel guarding them wore masks. None of the prisoners was ever permitted a phone call or to write to inform their families they had been taken. They simply vanished.

During the course of their imprisonment, some of the prisoners were confined in boxes and subjected to prolonged nudity—sometimes lasting for several months. Some of them were kept for days at a time, naked, in “stress standing positions,” with their “arms extended and chained above the head.” During this torture, they were not allowed to use a toilet and “had to defecate and urinate over themselves.” Beatings and kickings were common, as was a practice of placing a collar around a prisoner’s neck and using it to slam him against walls or yank him down hallways. Loud music was used for sleep deprivation, as was temperature manipulation. If prisoners were perceived to be cooperating, they were given clothes to wear. If they were deemed uncooperative, they’d be stripped naked. Dietary manipulation was used—at times the prisoners were put on liquid-only diets for weeks at a time. Three of the prisoners told the ICRC they had been waterboarded. Some of them were moved to as many as ten different sites during their imprisonment. “I was told during this period that I was one of the first to receive these interrogation techniques, so no rules applied,” one prisoner, taken early on in the war on terror, told the ICRC. “I felt like they were experimenting and trying out techniques to be used later on other people.”

And:

While TF-121 was given a mission to kill or capture Osama bin Laden and Saddam Hussein by the spring of 2004, Washington was increasingly focused on Iraq. Veteran intelligence officials identify this period as a turning point in the hunt for bin Laden. At a time when JSOC was asking for more resources and permissions to pursue targets inside of Pakistan and other countries, there was a tectonic shift toward making Iraq the numberone priority.

The heavy costs of that strategic redirection to the larger counterterrorism mission were of deep concern to Lieutenant Colonel Anthony Shaffer, a senior military intelligence officer who was CIA trained and had worked for the DIA and JSOC. Shaffer ran a task force, Stratus Ivy, that was part of a program started in the late 1990s code-named Able Danger. Utilizing what was then cutting-edge “data mining” technology, the program was operated by military intelligence and the Special Operations Command and aimed at identifying al Qaeda cells globally. Shaffer and some of his Able Danger colleagues claimed that they had uncovered several of the 9/11 hijackers a year before the attacks but that no action was taken against them. He told the 9/11 Commission he felt frustrated when the program was shut down and believed it was one of the few effective tools the United States had in the fight against al Qaeda pre-9/11. After the attacks, Shaffer volunteered for active duty and became the commander of the DIA’s Operating Base Alpha, which Shaffer said “conducted clandestine antiterrorist operations” in Africa. Shaffer was running the secret program, targeting al Qaeda figures who might flee Afghanistan and seek shelter in Somalia, Liberia and other African nations. It “was the first DIA covert action of the post–Cold War era, where my officers used an African national military proxy to hunt down and kill al Qaeda terrorists,” Shaffer recalled.

Like many other experienced intelligence officers who had been tracking al Qaeda prior to 9/11, Shaffer believed that the focus was finally placed correctly on destroying the terror network and killing or capturing its leaders. But then all resources were repurposed for the Iraq invasion. “I saw the Bush administration lunacy up close and personal,” Shaffer said. After a year and a half of running the African ops, “I was forced to shut down Operating Base Alpha so that its resources could be used for the Iraq invasion.”

Shaffer was reassigned as an intelligence planner on the DIA team that helped feed information on possible Iraqi WMD sites to the advance JSOC teams that covertly entered Iraq ahead of the invasion. “It yielded nothing,” he alleged. “As we now know, no WMD were ever found.” He believed that shifting the focus and resources to Iraq was a grave error that allowed bin Laden to continue operating for nearly another decade. Shaffer was eventually sent to Afghanistan, where he would clash with US military leaders over his proposals to run operations into Pakistan to target the al Qaeda leaders who were hiding there.

And:

The task force’s operations, Exum said, were “very compartmentalized, very stove-piped.” JSOC was creating a system where its intelligence operations were feeding its action and often that intelligence would not be vetted by anyone outside of the JSOC structure. The priority was to keep hitting targets. “The most serious thing is the abuse of power that that allows you to do,” said Wilkerson, the former chief of staff to Powell. He continued: "You go in and you get some intelligence, and usually your intelligence comes through this apparatus too, and so you say, ‘Oh, this is really good actionable intelligence. Here’s Operation Blue Thunder. Go do it.’ And they go do it, and they kill 27, 30, 40 people, whatever, and they capture seven or eight. Then you find out that the intelligence was bad and you killed a bunch of innocent people and you have a bunch of innocent people on your hands, so you stuff ’em in Guantánamo. No one ever knows anything about that. You don’t have to prove to anyone that you did right. You did it all in secret, so you just go to the next operation. You say, ‘Chalk that one up to experience,’ and you go to the next operation. And, believe me, that happened."