In the bowl of an electric stand mixer fitted with the dough hook (or in a large bowl with a wooden spoon if powering through this by hand), combine the water, yeast, molasses, cocoa powder, oil, honey, salt, gluten (if using), and 2 cups of the whole wheat flour. Mix until combined.
With the mixer running, slowly add the rest of the whole wheat flour. Start adding the white flour gradually until the dough pulls away from the sides of the bowl. Knead for 5-7 minutes (about 10-15 if kneading by hand). The dough should be soft and slightly tacky but shouldn't leave a lot of residue on your fingers if you grab a piece.
Turn the dough into a large, lightly greased bowl, cover with greased plastic wrap or a light towel, and let rise until doubled, 1-2 hours.
Lightly punch down the dough and divide into three equal pieces. Form into tight oval loaves and place on parchment-lined or lightly greased baking sheets (I fit two loaves on one large, rimmed 11X17-inch baking sheet and the third loaf on another baking sheet). Lightly cover with greased plastic wrap or a light towel and let rise until puffy and doubled in size. Optional: right before baking, using a very sharp knife, cut three deep slashes in the top of each loaf.
Preheat the oven to 375 degrees F. Bake the loaves for 25 minutes. Remove from the oven and lightly brush with about a tablespoon of butter. Sprinkle with the oats and bake for another 5-7 minutes. (Maria's note: In my oven, 20 minutes total baking time was plenty. This is from Mel's Kitchen Cafe)
12 tablespoons butter (1 1/2 sticks), melted and cooled slightly
1 cup (7 ounces) light brown sugar
1/2 (3 1/2 ounces) cup granulated sugar
1 large egg
1 large egg yolk
2 teaspoons vanilla extract
2 cups chocolate chips (use your preference of semisweet, bittersweet, milk, white, peanut butter…the options are endless!)
Preheat the oven to 325 degrees. Adjust the oven rack to lower-middle position. Line a 9X13-inch baking pan with foil, letting the excess hang over the edges of the pan by about 1 inch so you can grab those edges and pull the brownies from the pan after they have baked. Spray the foil-lined pan with nonstick cooking spray.
Mix the flour, salt, and baking soda together in medium bowl; set aside. Whisk the melted butter and sugars in a large bowl until combined. Add the egg, egg yolk, and vanilla and mix well. Using a rubber spatula, fold the dry ingredients into the egg mixture until just combined; do not overmix. Fold in the chocolate chips and turn the batter into the prepared pan, smoothing the top with the spatula.
Bake until the top of the bars is light golden brown, slightly firm to the touch, and edges start pulling away from sides of pan, 24-28 minutes. Cool on a wire rack to room temperature. Remove the bars from the pan by lifting the foil overhang and transfer them to a cutting board. Cut into 2-inch squares and serve.