The bills require "a certification by the Secretary of State" that Pakistan's government is (1) helping the United States to dismantle supplier networks for nuclear materials, (2) acting against terrorist groups within its borders, and (3) that the military is not interfering in governance.
The third point is really the key: that the Pakistan military must keep its nose out of politics, leaving policy to the civilians.
But wait, there's more! Take a look at the key provision (2) in more detail:
(A) ceasing support, including by any elements within the Pakistan military or its intelligence agency, to extremist and terrorist groups, particularly to any group that has conducted attacks against United States or coalition forces in Afghanistan, or against the territory or people of neighboring countries;
(B) preventing al Qaeda, the Taliban and associated terrorist groups, such as Lashkar-e-Taiba and Jaish-e-Mohammed, from operating in the territory of Pakistan, including carrying out cross-border attacks into neighboring countries, closing terrorist camps in the FATA, dismantling terrorist bases of operations in other parts of the country, including Quetta and Muridke, and taking action when provided with intelligence about high-level terrorist targets; and
(C) strengthening counterterrorism and anti-money laundering laws
Notice in (B) the mention of Quetta and Muridke. This is also new (and it wasn't in the original Kerry-Lugar Senate version). (Link to H.R. 3642).
Quetta is the city in Balochistan where the Afghan Taliban leaders are based. So far, the US military has ignored Quetta, to Boston Brahmin's utter bewilderment. Adding that to the bill explicitly is a good thing for the US effort in Afghanistan.
Muridke is the town near Lahore where the Lashkar-e-Taiba (or, technically, its civilian front organization) is based. The inclusion of Muridke is sure to make the Indians happy, and it is a acknowledgement that the Pakistan military has been making meaningless distinctions between good and bad terrorists.