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Position rack in the center of the oven; preheat to 325°F. Line 2 large baking sheets with parchment paper or a silicone baking mat.
Whisk whole-wheat flour, all-purpose flour, cocoa powder, baking powder, baking soda and salt in a large bowl. In another large bowl, beat eggs, egg yolk and sugar with an electric mixer until thick and pale yellow, about 2 minutes. Beat in vanilla and melted chocolate. Stir in the dry ingredients with a wooden spoon until just moistened.
Turn the dough out onto a lightly floured surface; knead for 1 minute, then divide in half. Roll each piece into an 8-inch log; flatten slightly to about 3/4 inch high and 3 1/2 inches wide. Place the logs side by side on one of the prepared baking sheets.
Bake until lightly browned and firm, about 20 minutes. Cool on the pan on a wire rack for 20 minutes. Keep the oven on; switch the oven racks to the upper and lower thirds of the oven.
Slice the logs on the diagonal into cookies 1/2 inch thick. Arrange, cut-side down, on the 2 baking sheets. Bake for 10 minutes. Turn the biscotti over and rotate the pans from top to bottom; bake until dry, 15 to 20 minutes more. Transfer to a wire rack to cool.