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1
Combine warm water, whole-wheat flour, and yeast in a small bowl. Let stand until the yeast softens and begins to froth and bubble, about 10 minutes.
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2
Mix rye flour, molasses, cocoa powder, vegetable oil, coffee granules, caraway seeds, and salt in a large bowl. Add yeast mixture and all-purpose flour. Turn dough onto a floured surface; knead until smooth and elastic, about 10 minutes. Grease a large bowl.
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3
Transfer dough to greased bowl; cover with warm damp towel or plastic wrap. Let rise in a warm area until doubled in size, about 1 hour.
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4
Preheat an oven to 450 degrees F (230 degrees C). Grease a baking sheet.
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5
Bring water to a boil in a large pot. Divide dough into 13 pieces; shape into balls. Press a hole into the center of each dough ball; pull dough to form a 1-inch hole in the center, keeping dough about 1/2-inch thick. Drop dough circles into boiling water, 3 or 4 at a time. Boil each side for 45 seconds. Remove with a slotted spoon and drain for about 1 minute. Arrange boiled bagels on prepared baking sheet.
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6
Bake bagels in the preheated oven until just starting to brown on the bottom, 8 to 10 minutes.
