Preheat the oven to 350°F. Line an 8 by 8-inch pan with foil. Spray with nonstick cooking spray.
In a large bowl combine the butter and sugar with a rubber spatula. Add the egg, egg yolk, molasses, and vanilla and stir until combined. Stir in the salt and flours. Stir in 3/4 of the chocolate chunks.
Pour the batter into the prepared pan. Sprinkle with the remaining chocolate chunks, pressing into the batter slightly. Bake for 25 minutes, or until set but still gooey. Allow to cool before cutting. Sprinkle with sea salt before serving.