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Preheat the oven to 350 F. Line a large baking sheet with parchment paper.
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In a heat-safe bowl, melt the chopped chocolate and butter either in a double-boiler over the stove or in the microwave (in 20 second increments - stirring well in between), until smooth. Let it cool slightly while you mix the other ingredients.
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In a mixing bowl (or to the bowl of a stand mixer with the whisk attachment), add the maple sugar, coconut sugar, egg and vanilla. Use a hand mixer on high speed and beat for 6 minutes. Add the melted chocolate mixture and mix until combined.
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Place a large sieve / sifter over the bowl and sift the cacao powder, baking powder, salt and flour into the wet ingredients. Use a spatula or a wooden spoon to stir until just combined, and you have a soft cookie-dough batter. Stir in the chocolate chips.
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Using a large cookie scoop or a spoon, measure out 1 1/2 tablespoon-sized cookie dough portions and arrange them on the prepared baking sheet, leaving at least 2-inches apart from each cookie. Place the baking sheet in the oven and bake for 10-12 minutes, or until the tops are cracked. The cookies will be soft but will continue to bake and firm up while they cool.
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Remove the pan from the oven and use a slightly larger-sized circle cookie cutter and place them over each cookie to shape them into a more uniform circular shape.
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Let the cookies cool on the pan for 10 minutes then transfer the cookies to a wire rack and allow them to cool completely before serving. Sprinkle a few of the cookies with a tiny sprinkle of flakey sea salt.