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1. Preheat oven to 350 degree F. Coat about forty-eight* 1-3/4-inch or eighteen 2-1/2-inch muffin cups with nonstick cooking spray; set aside. In a bowl combine flours, sugars, cocoa powder, soda, and 1/4 teaspoon salt. Make a well in center of flour mixture; set aside. In another bowl combine milk, applesauce, oil, molasses, vinegar, and vanilla. Add to flour mixture. Stir just until moistened (batter should be lumpy). Stir in half the chocolate pieces.
2. Spoon batter into prepared muffin cups, filling each mini pan cup about two-thirds full or regular cups just over half full. Sprinkle with remaining chocolate pieces. Bake for 8 to 10 minutes for mini or about 15 minutes for regular muffins or until a wooden pick inserted near center comes out clean. Cool in pan on rack for 5 minutes. Remove from muffin cups; serve warm. Or cool completely; wrap tightly and freeze up to 3 months. Reheat to serve. Makes about 48 mini or 18 regular muffins.