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Preheat the oven to 350°. Set a baking sheet lined with foil on the bottom rack. In a spice grinder, coarsely grind the tapioca. Add 1/4 cup of the sugar and the nutmeg and grind to a fine powder.
In a large bowl, toss the rhubarb with the tapioca, lemon zest and the remaining 1 1/4 cups of sugar. Let stand for 10 minutes, or until slightly juicy.
Spoon the rhubarb and any accumulated juices into a 9-inch glass pie plate lined with 1 round of the Flaky Pie Crust. Dot the filling with the butter. Lightly brush the rim of the pastry with water. Position the rolled-out top crust over the filling; press the edges together to seal. Trim the overhang to 1/2 inch, fold it under itself and crimp decoratively.
Bake the pie in the center of the oven for 1 1/2 hours, or until the filling is bubbling and the crust golden. Cover the edge with foil strips halfway through to prevent overbrowning. Transfer to a wire rack and let cool for at least 4 hours.