All of this comes with the caveat that there's way more in this week's National Intelligence Estimate than we see in the unclassified key judgments. But the description it gives for the presence that al-Qaeda maintains in Pakistan is rather understated.
Al-Qaeda has, the NIE says, "safehaven in the Pakistan Federal Administrative Tribal Areas." That much is no longer controversial among counterterrorism experts. But what the description neglects -- again, at least in the unclassified, introductory section -- is that al-Qaeda has a broader infrastructure inside the parts of Pakistan that General Pervez Musharraf controls as well.