Preheat oven to 400 degrees F and line a large baking sheet with nonstick parchment paper.
Cut butter into small 1/4 inch cubes. Place in a small bowl back in the refrigerator. In another small bowl, whisk together applesauce and vanilla extract. Set aside (room temp is fine).
In a large mixing bowl, whisk together flour, coconut sugar, baking powder, baking soda, cinnamon and sea salt.
Working quickly, use clean fingers to pinch the cold butter with the dry mixture, breaking the butter down into small pieces. Stir in the applesauce/vanilla extract, which should create a crumbly, ragged looking texture.
Stir in chocolate chips. Starting with 1/2 cup, stir in yogurt just until the dough starts to come together. You don’t want it to be a wet dough; there should still be some dry bits that don’t stick.
Turn dough out onto baking sheet and knead gently a few times, just folding the dough in on itself. Form dough into a disk, approximately 8 inches wide and 1 1/2 inches tall. Using a sharp knife, slice disk into 8 wedges. If using, brush with a thin layer of almond milk and sprinkle on cacao nibs.
Bake scones for 18-20 minutes, or until a toothpick comes out clean. Allow scones to cool at least 10 minutes before separating into wedges.