Combine rye flour, 1 cup all-purpose flour, salt, undissolved yeast, caraway seed, minced onion, coffee, sugar and fennel seed in a large bowl. Heat water, vinegar, molasses, butter, and unsweetened chocolate until very warm (120° to 130°F). Stir in bran flakes; let stand about 2 minutes or until cereal is softened. Stir into dry ingredients. Beat 2 minutes at medium speed of electric mixer, scraping bowl occasionally. Stir in enough remaining all-purpose flour to make a soft dough. Knead on lightly floured surface until smooth and elastic, about 8 to 10 minutes. Cover; let rest 10 minutes.
Divide dough into 2 equal parts. Shape each into a 10 x 3-inch oval. Place on greased baking sheets. Cut slits in dough just before baking. OR roll each piece of dough to 12 x 8-inch rectangle. Beginning from short ends, roll up tightly as for jelly roll. Pinch seams and ends to seal. Place, seam sides down, in greased 9 x 5-inch loaf pans. Cover; let rise in warm, draft-free place until doubled in size, about 1 hour.
Bake at 350°F for 45 to 50 minutes or until done. Remove from pans; cool on wire rack. Brush with melted butter, if desired.