Preheat oven to 325 degrees F (160 degrees C). Place walnut halves in a baking dish and bake for 8 minutes. Chop walnuts when they are cool enough to handle.
Increase oven temperature to 350 degrees F (175 degrees C). Grease an 8x8-inch baking pan with cooking spray. Line it with a sheet of parchment paper.
Sift almond flour and cocoa powder into a medium bowl. Mix in tapioca flour, baking soda, cinnamon, ginger, and salt.
Place ghee in a small bowl and melt in the microwave for 20 seconds. Pour melted ghee into a large bowl. Add applesauce, sugar, eggs, and vanilla, and mix until smooth. Pour dry ingredients into the bowl and stir until just incorporated.
Pour batter into prepared pan. Spray a spatula with cooking spray, and use it to spread batter to the edges. Tap baking dish on your counter a few times so that the batter settles more evenly in the pan. Top batter with chopped walnuts. Bake for 28 to 33 minutes, rotating halfway through. I baked it for 28 minutes.
Let brownies cool in pan for about 10 minutes and transfer to cooling rack to cool completely. Cut into 9 or 16 squares. Store leftovers in an airtight container at room temperature. They taste great the next day!