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 a large measuring cup or medium bowl, whisk together the whole milk, yogurt, applesauce, and oil. 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.
Add in vanilla and eggs one at a time, allowing each to fully incorporate before adding the next.
In about 3 additions, alternate adding the dry and wet ingredients until everything is fully combined. Be sure to scrape the bottom of the bowl frequently.
Lastly, fold in the honeycrisp apples.
Pour half 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. And the streusel on top and bake for about 1 hour to until a toothpick inserted comes out clean.
Allow cake to cool before removing from pan and adding the glaze.