Step 1In a small bowl, sprinkle the yeast and sugar over one-half cup of warm water. Stir to dissolve and let stand at room temperature until foamy, about 10 minutes.
Step 2In a small saucepan, gently heat the remaining 2 cups water, molasses, vinegar, butter and chocolate until the butter and chocolate are melted, stirring frequently. Set aside to cool to lukewarm.
Step 3In a large bowl, whisk together the whole-wheat, rye and all-purpose flours (except the 1 remaining tablespoon of all-purpose). Set aside.
Step 4In the bowl of a stand mixer fitted with a paddle attachment, combine 2 cups of the mixed flours, the bran, caraway seeds, fennel seeds, salt, espresso powder and shallots. Over low speed, add in the yeast and chocolate mixtures. Mix until smooth and beat at medium speed for 3 minutes. (If you don't like whole seeds in your bread, grinding them in a spice grinder, coffee grinder or mortar and pestle allows their flavor to come through without the texture.)
Step 5Alternatively, this or any bread can also be made by hand, simply mixing the ingredients in a large bowl with a wooden spoon and kneading the dough on a counter until springy and smooth. But for doughs heavy with whole grain flours, the stand mixer works the best.
Step 6At low speed, add one-half cup of the remaining mixed flours at a time, just until the dough clears the sides of the bowl and begins to work its way up the paddle. It will be very sticky but firm. Be careful not to add too much flour. The dough will spring back when pressed.
Step 7Scrape the dough off the paddle and place on a well-floured counter or large surface. Continue to knead by hand to make a smooth and springy yet dense dough. If you prefer, you can switch to the dough hook and knead again over low speed for 2 to 3 minutes, then finish off a few kneads by hand. You might not use all of the flour mixture.
Step 8Form into a ball and place in a greased deep container, such as a plastic bucket. Turn once to grease the top. Cover with plastic wrap and set aside to rise in a warm area until doubled, about 1 1/2 to 2 hours. Meanwhile, combine the cornmeal, remaining tablespoon of flour and remaining teaspoon of caraway seeds, if using, and set aside. Heat the oven to 350 degrees.
Step 9On a parchment-lined baking sheet, sprinkle the cornmeal mixture. Gently deflate the dough. Turn out the dough onto a lightly floured surface. Divide the dough into two portions. Stretch each portion into a ball, pulling the edges and pinching to form a seam. Place the formed rounds, seam side down, on the baking sheet. Cover loosely with plastic wrap (you can spray the plastic with nonstick cooking spray). Set aside to rise until puffy and almost doubled in bulk, 45 minutes to 1 hour. With a serrated knife, gently slash an X into the top of a round no more than one-fourth inch deep.
Step 10Bake the loaves until they are crusty and sound hollow when tapped on the bottom, 45 to 50 minutes. It is difficult to see the loaves browning because they are so dark-colored. If you are checking with a thermometer, they should read 200 to 210 degrees on an instant-read thermometer. Remove the loaves from the baking sheet to cool completely on a rack before slicing.