Charles Poliquin on increasing ankle range of motion for squats.
When you are selecting exercises to stretch the lower legs, consider that there are two major calf muscles, the gastrocnemius and the soleus. Both muscles have a common insertion at the Achilles tendon, which attaches to the calcaneus, or heel bone. With exercises in which the knee is straight, such as donkey calf raises and standing calf raises, the gastrocnemius handles most of the load. With exercises in which the knee is bent, such as a seated calf raise, most of the load is taken by the soleus muscles. So when you stretch the calves, you need to perform movements in which the knees are straight and movements in which the knees are bent.
As for squat depth his approach is to have an athlete do multiple workouts with partial squats, incrementally increasing depth.