Preheat the oven to 350 degrees.
In a medium sized bowl, whisk together the dry ingredients: both flours, sugar, baking soda, cinnamon, ginger, cloves, and salt.
In a large bowl, whisk together the wet ingredients: applesauce, molasses, milk, and vanilla extract. Slowly fold the dry ingredients to wet. Continue to stir until batter is well combined.
Spread batter in an 8x11 dish (can also use a 9x9 pan but it may require a bit more baking time). Make sure the batter is evenly smooth by spreading a spatula over the top.
In a small bowl, stir together the sugar and cinnamon. Spread this on top of cake batter. Now pour the water over the top, do not stir!!!!
Carefully transfer to the oven. Bake for approximately 1 hour, but start checking the cake around the 45 minute mark. Ovens will vary drastically on a recipe like this. It may take longer then an hour. You will notice the top is bubbling with the "caramel" sauce, and the cake should be mostly set before pulling out of the oven. It should also appear slightly undercooked, this is due to the caramel sauce on top.
Let sit for 10-15 minutes before serving. Serve warm with optional pecans.