1) To make dough using a bread machine: Place all of the ingredients in the order listed above into the pan of your bread machine, select manual or dough, and press start. Jump to step 3 below.
2) To make by hand, or with a mixer: Pour the water into a mixing bowl. Add the yeast and pumpernickel or white whole wheat flour, and let sit for several minutes until the mixture begins to bubble. Stir in the salt and 1 cup of the all-purpose flour and mix well. Gradually add the remaining all-purpose flour until the dough begins to pull away from the sides of the bowl. Turn the dough out onto a lightly floured surface and knead it for 4 to 5 minutes. Let the dough rest while you clean out and grease your bowl; then knead the dough a few more minutes. The dough should be on the slack side and a little tacky, but shouln't be sticky. When the dough is well-kneaded, place it into the prepared bowl, cover, and let rise until doubled in size, 1 1/2 to 2 hours.
3) If you're using a brotform: When your dough has risen, flour your brotformet heavily and sprinkle some seeds (sesame, flax, caraway, poppy...) or some oat flakes or rye flakes in the bottom. Pick up your dough and work it around in your hands a bit, expelling the air. Make the dough into a ball and place it, "nice" side down, into the basket. Drape the dough with lightly greased plastic wrap, and set it aside to rise for 45 minutes, or until it's crowned nicely over the rim of the basket.
4) If you're not using a brotform, simply round the dough into a ball, and place it on a lightly greased or parchment-lined baking sheet. Let the dough rise for about 45 minutes, or until it's noticeably puffy.
5) For dough shaped in a brotform:Have a lightly greased or parchment-lined baking sheet ready. Very gently, roll the dough from the basket onto the baking sheet. It should slip out gracefully, without deflating. if it deflates totally (a small settling is OK), simply form it into a smooth ball, put it back in the basket, and let it rise again (only this time not quite as high).
6) Bake the bread in a preheated 425°F oven for 20 to 25 minutes. For a crunchy, crisp loaf, spray water into the oven with a spray bottle three times during the first 10 minutes of baking. When the bread is done, remove it from the baking sheet, set it on the rack of the oven, turn the oven off, and crack the door open a couple of inches; let the bread cool completely in the oven. If you want a soft loaf, remove the bread from the oven, and from the pan, set it on a rack, and let it cool completely at room temperature.
Yield: 1 large loaf.