Line an 8-or 9-inch square baking pan or dish with parchment or waxed paper, making sure that the paper comes up at least 1 inch on two opposite sides. The paper should be smooth along the bottom and sides--any wrinkles or creases in the paper will imprint on your ganache. (A pan with sharp corners is best, but if you have only pans or dishes with rounded corners, the edges of the ganache can be trimmed.)
Prepare the Basic Dark Chocolate Ganache as directed, and pour it into the prepared pan. Shake it or smooth it with an offset spatula so that the ganache is flat and even. Refrigerate until set, 45 to 60 minutes.
Once the ganache has hardened, release it from the pan. Run a small knife or offset spatula under hot water and then run it along the sides of the pan that are not covered by paper. Turn the ganache out onto a cutting board and peel off the paper.
Wet a towel with very hot water and run it along the sides of a paring knife or chefs knife. Using that knife, trim any round edges from the ganache, so that you have a completely square slab. If the ganache starts to crack while you are cutting it, it is too cold, so allow it to sit at room temperature for 5 to 10 minutes.
Cut the ganache into 3/4-to 1-inch squares, continuing to wipe your knife with the hot towel, as necessary. The key to achieving a clean cut in the ganache is a combination of making sure that the ganache is not too cold (if it cracks when you put the knife through it) and making sure that the knife is kept warm and clean so that it moves easily through the ganache.
Transfer the ganache squares (directly on the cutting board or placed on another plate or tray) to the refrigerator and let them chill while you prepare the coating.
Temper the milk chocolate as directed in Basic Tempered Chocolate.
Set up an assembly line of tempered chocolate, cocoa nibs, and a sheet pan lined with parchment or waxed paper.
Remove the ganache from the refrigerator and, working quickly so that the tempered chocolate dosent set and the ganache dosent get too soft, begin dipping. One at a time, using a small offset spatula or fork, dip each piece of ganache into the chocolate until its submerged. Lift it out, shaking it gently and scraping it against the lip of the bowl to remove excess chocolate.
Place each chocolate on the sheet pan. Before the chocolate has set, top each with 2 or 3 cocoa nibs. Repeat until all the ganache has been dipped.
Allow the truffles to set at room temperature for 30 minutes (or in the refrigerator for 15 minutes before serving. The truffles can be kept in an airtight container at room temperature for up to 2 weeks.
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