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1. Bake the Cupcakes: Preheat oven to 350 degrees F. Line standard muffin tins with paper liners. Whisk together both flours, baking powder, salt and cinnamon.
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2. With an electric mixer on medium-high speed, cream the butter, brown sugar and honey until pale and fluffy. Reduce speed to medium; beat in the eggs and vanilla, scraping down the sides of the bowl as needed. Add the flour mixture and mix until just combined.
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3. Divide the batter evenly among the lined cups. Bake, rotating tins halfway through, until golden brown and a thin knife inserted in the centers comes out with only a few moist crumbs attached, about 25 minutes. Transfer tins to wire racks to cool 10 minutes; turn out cupcakes onto racks and let cool completely. Cupcakes can be stored up to 1 day at room temperature, or frozen up to 1 month.
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4. Make the Chocolate Ganache Glaze: Place the chocolate in a medium heatproof bowl and microwave on 50% power for 30 seconds, or until the chocolate softens and starts to melt. Bring the cream to a full boil in a small saucepan over medium-high heat; pour over chocolate. Working with a rubber spatula, very gently stir together until the ganache is completely blended and glossy.
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5. Make the Marshmallow Frosting: In a mixing bowl, sprinkle the gelatin over 1/3 cup cold water. Allow the gelatin to soften, about 5 minutes.
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6. Heat the remaining ¼ cup water and the sugar in a saucepan over medium-high heat, stirring until the sugar is dissolved. Stop stirring; clip a candy thermometer onto the side of the pan. Boil the syrup until the temperature reaches the soft-ball stage (238 degrees F). Remove from heat; add the syrup to the softened gelatin. Whisk the mixture by hand to cool, about 1 minute, then use an electric mixer to whisk on medium-high speed until soft, glossy (but not dry) peaks form, 8 to 10 minutes. (The frosting must be used immediately because it will harden.)
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7. Assemble the Cupcakes: Spoon 2 teaspoon of the chocolate ganache glaze onto each cupcake. Fill a pastry bag with a large plain tip with marshmallow frosting; pipe frosting onto each cupcake, swirling the tip and releasing as you pull up to form a peak. Hold a small kitchen torch 3 to 4 inches from the surface of the frosting, and wave it back and forth until the frosting is lightly browned all over. Serve immediately.