1. Prepare the Chocolate Cupcakes: Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners. In a medium bowl, whisk together the flour, cocoa powder, baking soda, and salt. Set aside.

2. Cream Butter and Sugar: In a large bowl, using an electric mixer, cream together the softened butter and granulated sugar until light and fluffy (about 2-3 minutes).

3. Add Wet Ingredients: Beat in the eggs one at a time, mixing well after each addition. Stir in the vanilla extract.

4. Alternate Dry and Wet: Gradually add the dry ingredients to the wet ingredients in three additions, alternating with the buttermilk in two additions, beginning and ending with the dry ingredients. Mix until just combined after each addition. Do not overmix.

5. Incorporate Coffee: Slowly pour in the hot coffee and mix on low speed until the batter is smooth. The batter will be thin, which is normal.

6. Bake Cupcakes: Divide the batter evenly among the 12 cupcake liners, filling each about two-thirds full. Bake for 18-22 minutes, or until a wooden skewer inserted into the center of a cupcake comes out with moist crumbs, not wet batter. Let cool in the muffin tin for 5 minutes, then transfer to a wire rack to cool completely.

7. Prepare the Pumpkin Cheesecake Filling: While the cupcakes cool, prepare the filling. In a medium bowl, beat the softened cream cheese and granulated sugar together until smooth and creamy. Scrape down the sides of the bowl.

8. Add Remaining Filling Ingredients: Add the egg yolk and vanilla extract, beating until just combined. Stir in the pumpkin puree, cinnamon, ginger, nutmeg, and cloves. Mix until fully incorporated and smooth. Do not overmix.

9. Bake Cheesecake Filling: Pour the cheesecake mixture into a small oven-safe dish (like an 8×8 baking dish or pie plate). Bake alongside the cupcakes for the last 15-20 minutes, or until the edges are set and the center has a slight jiggle. Alternatively, bake separately at 325°F (160°C) for 15-20 minutes. Allow to cool completely, then refrigerate for at least 1 hour to firm up.

10. Assemble the Cupcakes: Once the cupcakes are completely cool, use a cupcake corer, a small knife, or the back of a piping tip to carefully scoop out a small hole from the center of each cupcake, being careful not to go all the way through to the bottom.

11. Fill Cupcakes: Transfer the chilled pumpkin cheesecake filling to a piping bag (or use a small spoon) and fill each cored cupcake generously. You can use the removed cupcake tops to cover the filling if desired, or simply leave the filling exposed for a beautiful look.

12. Prepare Chocolate Ganache (Optional): Place the chopped chocolate in a heatproof bowl. In a small saucepan, heat the heavy cream until it just begins to simmer. Pour the hot cream over the chocolate and let it sit for 5 minutes. Add the optional butter. Whisk gently until smooth and glossy. Let cool for about 15-20 minutes, stirring occasionally, until it reaches a thick but pourable consistency.

13. Top and Chill: Spoon or drizzle the slightly cooled ganache over the filled cupcakes. You can spread it evenly or let it drip down the sides. For best results, chill the assembled cupcakes for at least 1-2 hours to allow the filling and ganache to set completely. Garnish with a sprinkle of cinnamon or chocolate shavings if desired before serving.