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Heat the oven. Arrange a rack in the middle of the oven and heat the oven to 375°F. Line a rimmed baking sheet with aluminum foil or parchment paper.
Make the crust. Place 1 1/2 cups all-purpose flour, 1 tablespoon granulated sugar, and 1/2 teaspoon kosher salt in the bowl of a food processor fitted with the blade attachment. Pulse a few times to combine. Cut 1 stick cold unsalted butter into 1/2-inch cubes and add scatter over the flour mixture. Pulse until the mixture resembles a coarse meal, about 10 pulses. Add 2 tablespoons ice water and pulse until the dough forms a cohesive mass, 10 to 15 pulses. If the dough is too dry and does not come together, pulse in an additional tablespoon ice water.
Turn the dough out onto a large piece of plastic wrap, gather into one piece, and press into a rough disk. Wrap tightly in the plastic. Refrigerate while you prepare the filling and topping.
Make the topping. Place 1 cup all-purpose flour, 2/3 cup packed brown sugar, 1 teaspoon ground cinnamon, and 1/4 teaspoon kosher salt in a medium bowl and whisk to combine. Cut 1 stick cold unsalted butter into 1/2-inch cubes and scatter over the flour mixture. Squeeze the dry ingredients and butter together with your hands until they form large, moist clumps. Refrigerate while you prepare the filling.
Start the filling. Place 1/2 cup granulated sugar, 1/4 cup all-purpose flour, 1 teaspoon ground cinnamon, 1/4 teaspoon ground nutmeg, 1/4 teaspoon kosher salt, and 1/8 teaspoon ground cloves in a large bowl and whisk to combine.
Add the apples. Peel 2 pounds Granny Smith apples. Halve and core the apples, then cut into 1/4-inch thick slices (about 8 cups). Add to the bowl of spiced sugar. Finely grate the zest of 1 large lemon over the apples. Juice the lemon (about 3 tablespoons) over the apples. Add 1 teaspoon vanilla extract and toss to combine, making sure there are no clumps of sugar or flour left in the bottom of the bowl.
Line the pie plate with the crust. Place the pie dough onto a lightly floured work surface and roll out to a 12-inch wide round. Transfer the crust to a standard 9-inch pie plate (not deep dish). Press the dough into the plate, then roll the excess dough under itself on the edges of the plate. Crimp the crust with your fingers or a fork.
Fill the pie shell. Pour the filling and any accumulated juices from the bowl into the crust and arrange into an even layer, slightly mounding them in the center. Scatter the chilled topping evenly over the top, going all the way to the edge of the crust.
Bake the pie. Place the pie on the lined baking sheet. Bake until the topping is golden brown and the filling is bubbling around the edges, 50 to 65 minutes. Check 40 minutes into baking: if the crust starts to brown too quickly, loosely cover the pie with aluminum foil.
Cool before serving. Transfer the pie to a wire rack and let cool at least 2 hours before slicing.