Preheat the oven to 350 degrees F (180 degrees C). Line a 9"x9" pan with parchment paper long enough to hang over the sides for easy removal.
In a medium bowl, combine the flour, baking powder, baking soda, salt, cinnamon, nutmeg, allspice, cloves, and ginger. Set aside.
In the bowl of a stand mixer fitted with a paddle attachment, beat the butter, brown sugar, and granulated sugar for 2-3 minutes. Mix in the eggs and vanilla until fully combined.
Add half of the dry ingredients and mix until mostly combined. Then, mix in the whole milk, yogurt, applesauce, and oil, followed by the remaining dry ingredients.
Lastly, fold in the grated honeycrisp apples. Pour ⅔ of the batter into the prepared square pan. Top with all of the cinnamon swirl mixture, then gently pour the rest of the batter on top. Add the streusel on top and bake for about 1 hour until a toothpick inserted comes out clean.
.Allow the cake to cool before removing from the pan and topping with the glaze.