Prepare Basic Cookie Dough. Press it evenly into the bottom of a pan with a spatula, pressing down at the edges so dough doesn't form a rim after baking. Freeze dough for 15 minutes. Prick holes all over to keep it flat during baking. Bake for 25 minutes or until golden brown.
Make ganache by placing bittersweet chocolate and milk in a small heatproof bowl. Microwave on HIGH for 1 minute, stirring every 10 seconds until the chocolate melts and the mixture is smooth; stir in 1 teaspoon vanilla extract. Scrape the ganache onto the baked cookie square and spread it almost to the edge. Sprinkle pecans evenly over the top and set aside.
To make caramel, combine sugar, corn syrup, and water in a heavy saucepan over medium-high heat. Cook, stirring mixture gently, just until the sugar dissolves. Stop stirring completely and allow it to boil until it turns a golden brown, about 4 minutes. Remove from heat and stir in warmed whipping cream (it will bubble up). Stir gently until the mixture is smooth. (If lumpy, return it to low heat while stirring.) Cool 1 minute and stir in 1/2 teaspoon vanilla extract. Let caramel cool for 2 minutes before drizzling over the pecan layer with a spoon. Refrigerate pan for at least 1 hour to set the ganache and caramel before cutting into bars. Store 3 days at room temperature, 1 week in the refrigerator.