Preheat oven to 350 degrees. Line cupcake tins with foil liners. In a large bowl, whisk together flour, cocoa, sugar, salt and baking soda. Add 1 cup water, 1/3 vegetable oil, 1 teaspoon vanilla, 1 tablespoon cider vinegar and mix together. With food processor running, add cream cheese in pieces through chute. Add 1 egg, 2/3 cup sugar and transfer to a bowl. Fold in 6 ounces. chocolate chips. Fill cupcake liners 2/3 of the way full with batter. Place 1 or 2 tablespoons of cream mixture atop batter. Bake for 20 minutes.