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To make the pies:
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Preheat oven to 350 degrees. Line two baking sheets with parchment paper or a nonstick baking mat; set aside.
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In a large bowl, whisk together flours, salt, baking powder, baking soda, cinnamon, ginger, and cloves; set aside. In another large bowl, whisk together brown sugar, oil and unsweetened applesauce until well combined. Whisk in chilled pumpkin puree, 1 teaspoon vanilla extract and the eggs one at a time until well combined. Whisk in flour mixture, in three additions, into the pumpkin mixture until fully incorporated.
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Using a small ice cream scoop with a release mechanism, drop heaping tablespoons of dough onto prepared baking sheets, about 1 inch apart. Transfer to the oven and bake until pies are just starting to crack on top and a toothpick inserted into the center of each pie comes out clean, about 15 minutes. Let cool completely on the baking sheet.
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To make the filling:
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Sift confectioners' sugar into a medium bowl; set aside. In the bowl of an electric mixer fitted with the paddle attachment, beat butter until smooth. Add Neufchatel cheese (or cream cheese) and beat until well combined. Add confectioners' sugar and remaining 1 teaspoon vanilla; beat just until smooth. Filling can be made up to a day in advance. Cover and refrigerate. Let stand at room temperature to soften before using.
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To assemble pies:
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Transfer filling to a disposable pastry bag and snip end. When cookies have cooled completely, pipe a large dollop of filling on the flat side of one half of the pies. Sandwich with remaining pies, pressing slightly so that the filling spreads to the edges of the pies. Transfer to an airtight container. Refrigerate cookies at least 30 minutes before serving and up to 3 days.
