In a medium bowl, stir together the sugar, all-purpose flour, rye flour, cacao nibs, cocoa powder. Add the butter pieces in and work together with your fingers until large clumps form. Make sure there are no dry spots. You could add a drop or two of vegetable oil if you find the mixture isn’t clumping; cover and chill.
Preheat oven to 350°. Coat a 9”-diameter cake pan with nonstick spray and line with a parchment round.
In a small bowl, whisk together the all-purpose flour, rye flour, cocoa powder, baking powder, baking soda, and salt in a medium bowl.
In the bowl of a stand mixer (or in a medium sized bowl with a hand mixer), beat on medium speed the butter, sugar, brown sugar until light and fluffy. Be sure to stop the mixture and scrape the sides of the bowl. Add the eggs and vanilla; mix about 2 minutes until blended.
Lower speed and add in half of the dry ingredients.
Mix in the buttermilk and mix well.
Add in the rest of the dry ingredients and the yogurt. Mix well, stopping the mixer to scrape the sides of the mixing bowl and incorporate the ingredients very well.
Scrape into prepared pan. Toss on the crumbles.
Place cake on middle rack of oven. Rotate the cake halfway during baking. I usually lower my oven at the halfway point to 325 F (every oven is different…you may need to keep yours at 350 F during the entire baking time).
Bake until the cake starts to pull away from sides of pan and a tester inserted into the center comes out clean, about 50-60 minutes.
Let cake cool in pan on a wire rack before turning out.