Combine first 6 ingredients in a large bowl. Combine water, prune butter, vinegar, and vanilla; stir well. Add to dry ingredients, stirring with a wire whisk until blended; set chocolate batter aside.
Beat cream cheese in a bowl at medium speed of a mixer until smooth. Add powdered sugar and egg, and beat until well-blended; set cream cheese mixture aside.
Place 18 paper muffin cup liners in muffin cups; coat liners with cooking spray. Divide chocolate batter evenly among cups; spoon cream cheese mixture evenly on top of chocolate batter in each cup. Sprinkle chocolate morsels and almonds over cream cheese mixture. Bake at 350° for 25 minutes or until a wooden pick inserted in center comes out clean. Let cool in pans 5 minutes on a wire rack; remove from pans, and let cool completely on wire rack.