Brown Sugar Apple Crisp

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1/2 cup (1 stick) chilled unsalted butter, cut into 1/2-inch pieces, plus more for the baking dish

2 1/2 pounds apples, peeled, cored and sliced 1/4-inch thick

2 tablespoons fresh lemon juice

2 teaspoons pure vanilla extract

1/3 cup granulated sugar

1 cup plus 1 1/2 tablespoons all-purpose flour

Pinch of ground nutmeg

1/2 cup pecans, walnuts or almonds, finely chopped

1/4 cup dark brown sugar, packed

1/2 teaspoon ground cinnamon

Pinch of fine sea salt

Vanilla ice cream, for serving