Beat butter and sugar with an electric mixer on medium speed until creamy; add vanilla, and beat until combined. Stir together flour, cocoa, and salt. Gradually add flour mixture to butter mixture, beating at low speed until combined after each addition. Finely chop 1 of the bittersweet chocolate baking bars, and stir into cookie dough until well incorporated.
Divide dough in half; shape each into an 8-inch-long log. Wrap each log tightly in plastic wrap, and freeze until firm, about 30 minutes. (Dough may be frozen up to 1 month.)
Preheat oven to 350°F. Cut dough into 1/4-inch-thick slices, and place 2 inches apart on parchment paper-lined baking sheets. (Keep dough logs refrigerated while cookies bake.)
Bake in preheated oven until bottoms are lightly browned, 11 to 13 minutes. Cool on pans 5 minutes; remove cookies to wire racks, and cool completely, about 20 minutes.
Chop remaining 1 1/2 bittersweet chocolate baking bars, and place in a small microwave-safe bowl. Microwave on HIGH until chocolate is melted and smooth, 1 to 1 1/2 minutes, stirring every 30 seconds.
Dip half of top side of each cookie in melted chocolate. Sprinkle lightly with sea salt or chopped toasted pecans, if desired. Place cookies on a parchment paper-lined baking sheet, and chill just until chocolate sets, about 15 minutes. Layer cookies between wax paper, and store in an airtight container at room temperature up to 5 days.
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