Servings: 24 cookies   :    1 hour  (20 minutes active)

142 grams (1 cup) all-purpose flour 142 grams (1 cup) all-purpose flour
¾ teaspoon kosher salt ¾ teaspoon kosher salt
½ teaspoon baking soda ½ teaspoon baking soda
140 grams (1 cup) rye flour 140 grams (1 cup) rye flour
12 tablespoons (1½ sticks) salted butter 12 tablespoons (1½ sticks) salted butter
248 grams (1¼ cups) white sugar 248 grams (1¼ cups) white sugar
2 large eggs 2 large eggs
1  tablespoon molasses 1  tablespoon molasses
1  tablespoon vanilla extract 1  tablespoon vanilla extract
210 grams (about 1½ cups) dark chocolate chips or chopped bittersweet chocolate 210 grams (about 1½ cups) dark chocolate chips or chopped bittersweet chocolate
113  grams (1 cup) pecans, toasted and chopped (optional) 113  grams (1 cup) pecans, toasted and chopped (optional)

Heat the oven to 350ºF with a rack in the middle position. Line 2 baking sheets with kitchen parchment. In a medium bowl, whisk together the all-­purpose flour, salt and baking soda. In a 12-inch skillet over medium-high, toast the rye flour until fragrant and a shade or two darker, about 5 minutes, stirring frequently. Remove the skillet from the heat, then add the butter and stir until melted.
In a large bowl, mix together the sugar, eggs, molasses and vanilla. When the rye mixture is cool to the touch, slowly stir it into the eggs. Add the dry ingredients and stir until combined. Stir in the chocolate chips and nuts, if using.
Drop 2-tablespoon mounds of dough about 2 inches apart on the prepared baking sheets. One sheet at a time, bake until the edges are firm and the centers are soft, 8 to 12 minutes, rotating the sheet halfway through. Cool on the sheet for 5 minutes, then transfer to a wire rack and cool for 10 minutes. Repeat with the second sheet.

TIP:   Don’t be afraid to cook the roux until it's quite dark—ours was the shade of peanut butter—and fragrant. It should smell nutty.  TIP:   Don’t be afraid to cook the roux until it's quite dark-ours was the shade of peanut butter-and fragrant. It should smell nutty.