Prep the oven and pans. Position a rack in the center of the oven and preheat the oven to 400°F. Line four cavities of a muffin pan with paper liners.
Whisk the dry ingredients. In a medium bowl, whisk together the flour, cinnamon, cloves, baking powder, baking soda, and salt.
Whisk the wet ingredients. In another medium bowl, whisk together the sugar, pumpkin, oil, egg, egg yolk, and vanilla.
Make the muffin batter. Gradually mix in the dry ingredients into the wet ingredients until just combined.
Assemble the muffins. Use a cookie dough scoop to fill each cavity with 6 Tablespoons of the batter. Sprinkle the top of each muffin, aiming for the batter and avoiding the pan, with 1 teaspoon of granulated sugar. Pour warm water into the empty cavities of the muffin pan, filling them at least ⅔-rds of the way up. Bake the muffins. Bake for 22 to 24 minutes, or until the muffins are domed and a skewer inserted into the center of a muffin comes out with a few crumbs attached. Cool in the muffin pan on a wire rack for 5 minutes, then turn the muffins out onto the rack to cool slightly.
Serve and store. Serve warm or at room temperature. The muffins can be wrapped individually in plastic wrap or stored in an airtight container or under a cake dome at room temperature for up to 2 days.