Expansion swap Warfare Center for Ability Points, discussed hereby. Normally, in core game, you would use the Advanced Warfare Center-that facility allows your soldiers to receive no more than two Abilities that normally were available only for other classes. The system of unlocking irregular abilities has also been change.
APs are used for developing your soldiers. They are used to develop new classes, as well as for unlocking additional skills for the rest of your soldiers. Ability Points have only been introduced by expansion, War of Chosen.