1cupchopped (1/2- and 1/4-inch chunks and smaller flakes) 70% cacao mass bittersweet chocolate (such as Scharffen Berger)(5 ounces)
3/4cuptoasted and cooled pecan halves, coarsely chopped(3 ounces)
flaky salt, such as Maldon, for sprinkling
Position two racks in the upper and lower thirds of the oven and preheat to 325º. Line two cookie sheets with parchment paper (or grease lightly with butter).
In a large bowl, stir together the butter, brown sugar and granulated sugar. Let cool to warm, then stir in the egg. Stir in the vanilla and rye, and set aside.
In a medium bowl, sift or whisk together the rye and all-purpose flours, baking soda and sea salt. Stir the flour mixture into the butter/sugar/egg mixture until just combined, then gently fold in the chopped chocolate and pecans.
Cover the dough and let it sit at room temperature for at least 30 minutes and up to 2 hours. This lets the dough firm up, as the starches absorb the moisture and the glutens relax, leading to thicker, chewier cookies with a better texture. (You can also refrigerate the cookie dough for up to a few days, optionally pre-scooped into ready-to-bake balls. For proper spreading, let the dough come back to room temperature before baking.)
Use two spoons or a spring-loaded #40 ice cream scoop to form 1" balls of cookie dough, placing them 2 inches apart on the lined baking sheets. Top each ball with a tiny pinch of flaky salt.
Bake the cookies in the preheated oven until the edges are set and just beginning to color, 8-12 minutes, rotating the pans from front to back and from top to bottom halfway through to ensure even baking. The cookies will look under-done, but will continue to cook from residual heat. Top with a bit more salt, if you like.
Remove the baking sheets to cooling racks and let the cookies cool on the baking sheets (unless they are in danger of over-baking – in that case, sweep the cookies, parchment and all, onto cooling racks). When the cookies have cooled completely, store them at room temperature in an airtight container for up to three days.
Adapted from these Buckwheat Chocolate Chip Cookies, which I adapted from Alice Medrich's Chocolate Chip Cookies from Chewy, Gooey, Crispy, Crunchy Melt-in-Your-Mouth Cookies.I'm guessing that these cookies would be equally good made with another type of liquor - whiskey or bourbon - and with whole wheat, barley, or spelt flour in place of the rye (though you'll want to use the weight measurement if you substitute a different flour).Cacao nib fans may want to add 2 tablespoons of nibs along with the chocolate.I like chopping my own chocolate rather than using chips, which contain lecithin that helps them hold their shape, while bar chocolate melts into pretty, uneven pockets. A serrated bread knife works well for chopping the chocolate into 1/2- and 1/4-inch chunks, with smaller flecks of chocolate that mingle with the dough.You can store the dough in the refrigerator for up to a few days, or scoop it into balls and store them in the freezer for up to a few months. In either case, let the dough come to room temperature before baking to ensure proper spreading. Be sure to let the dough rest at room temperature for at least half an hour, and preferably 1-2 hours, for the best texture.See more tips on baking cookies here.All ounce measurements are by weight.Nutritional values are based on one of eighteen cookies.