In a medium bowl, combine all-purpose flour, light rye flour, baking soda, baking powder, salt and cocoa powder. Set aside.
In a large bowl, with a hand mixer, beat together butter and brown sugar until light and fluffy, about 3 minutes. Beat in egg yolks, one at a time, and vanilla. Gradually stir in flour mixture until combined. Fold in pistachios.
Divide dough in half. Roll each half into a log, about 2 inches wide by 10 inches long. Wrap logs tightly in plastic wrap and refrigerate for at least 30 minutes, or freeze for up to 2 months.
Preheat oven to 350 degrees. Line 2 baking sheets with parchment paper.
Remove dough from refrigerator. (If dough has been in the freezer, let sit at room temperature for 15 minutes.) Unwrap dough and cut into 1/2-inch slices. Set slices on prepared baking sheets, leaving 1 inch between cookies. Sprinkle each cookie with fleur de sel.
Bake for 11 to 13 minutes, or until centers appear set. Transfer cookies to a wire rack and let cool for 10 minutes. Store in an airtight container at room temperature for up to 1 week.
Makes 25 cookies
Recipe reprinted with permission from "Guittard Chocolate Cookbook: Decadent Recipes from San Francisco's Premium Bean to-Bar Chocolate Company," Copyright © 2015 by Amy Guittard, Chronicle Books.