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Prepare the Cookies: Beat butter, granulated sugar, brown sugar, and peanut butter with a heavy-duty stand mixer fitted with paddle attachment on medium speed until smooth, 1 to 2 minutes. Add eggs, one at a time, beating just until incorporated after each addition. Beat in vanilla. Whisk together flour, baking soda, baking powder, and salt in a medium bowl; gradually add to butter mixture, beating on low speed just until blended and smooth. Cover and chill 1 hour. Preheat the oven to 350 degrees F. Scoop dough into balls using a 1-inch cookie scoop (about 1/2 tablespoon); place 2 inches apart on parchment paper-lined baking sheets. Press your thumb or the end of a wooden spoon into center of each ball, forming an indentation. Keep unused dough chilled while baking cookies. Bake, in batches, in preheated oven until lightly browned, 10 to 11 minutes. Cool on baking sheets 5 minutes; transfer to wire racks. Lightly press your thumb into indentations again while cookies are warm to reinforce shape. Cool completely, about 30 minutes. Prepare the Filling: Place first bag of Ghirardelli Semi-Sweet Chocolate Baking Chips, heavy cream, and butter in a medium-size microwaveable bowl, and microwave on medium (50% power) until melted and smooth, 1 1/2 to 2 minutes, stirring every 30 seconds. Let stand 15 minutes. Transfer filling to a piping bag or a heavy-duty zip-top bag with 1/2 inch snipped from 1 corner. Pipe filling into indentation in each cookie, about 1 teaspoon per cookie. Press 3 Ghirardelli Grand Semi-Sweet Chocolate Chips onto the filling of each cookie. Let stand until chocolate filling is firm, about 1 hour.