Position racks in the upper and lower thirds of the oven and preheat to 350º. Line two cookie sheets with parchment paper.
Place the butter in a small, heavy-bottomed saucepan set over the lowest possible heat. Add 6 ounces (170 g / 1 cup) of the chocolate and melt together, stirring frequently to prevent the chocolate from scorching. Continue cooking until the mixture is pleasantly warm, but not super hot, to the touch. Remove from the heat and keep warm.
In a small bowl, sift together the flour, tapioca flour, and baking powder and set aside.
Meanwhile, place the eggs, sugar, and fine salt in the bowl of a stand mixer fitted with the whisk attachment and whip on medium-high speed until the mixture triples in volume and is very light and fluffy, 5 minutes. (You can also do this in a large bowl with an electric egg beater, or a whisk and your buff arms.)
Turn the mixer to low and stir in the vanilla until just combined, then the warm (but not too hot!) chocolate/butter mixture.
Add the flour mixture and beat on low speed until just combined. Remove the bowl from the mixer and use a flexible silicone spatula to fold in the remaining 4 ounces (115 g / 3/4 cup) chopped chocolate.
If the batter is very runny, let it cool for a few minutes until it firms to the consistency of a thick brownie batter. Use a #40 spring-loaded ice cream scoop or 2 spoons to drop heaping tablespoons of batter onto the prepared baking sheets, spacing them at least 2 inches (5 cm) apart. Top each cookie with a few chunks of chocolate and a pinch of flaky salt.
Bake the cookies until puffed and cracked and the edges are set, 8–12 minutes, rotating the pans front to back and top to bottom halfway through baking. Let cool slightly and enjoy warm or at room temperature.
Extra cookies keep well in an air-tight container for up to 4 days.
The key to getting the pretty crackles on top is making sure the chocolate/butter mixture is warm enough to partially dissolve the sugar, but not so hot as to cook the eggs. It should feel pleasantly warm to the touch, like you could take a bath in it, but not hot enough to scald your finger.
This recipe is all about the chocolate, so use one that you love the taste of. Guittard and Valrhona 66% both work beautifully. Note that if you use a chocolate with a lower cacao mass the cookies will be more thin, whereas a higher cacao mass will yield cookies that spread less.
Chilling cookie dough: I always bake these cookies off right away, but readers have had success making the batter ahead and refrigerating it until ready to bake, up to a few days.
Freezing Cookies: Freeze extra cookie dough and when you're ready to bake, thaw the batter in the fridge or at room temperature until it's soft enough to scoop. Scoop and bake as directed.
Baked cookies can also be frozen. Warm them in a toaster oven when you're ready to eat.
Gluten-Free Dairy-Free Cookies: Swap the butter out for plant-based butter such as Miyoko's and decrease the salt by half if the butter is salty.
Grain-Free Cookies: Use cassava and tapioca flours.
Paleo Cookies: Make the grain-free version and use coconut or maple sugar instead of granulated.
Chocolate Peppermint Cookies / Candy Cane Cookies: Add 1/2-3/4 teaspoon peppermint extract to the batter and sprinkle chopped candy cane on top instead of flaky salt. Optionally use chopped chocolate bark instead of chopped chocolate to fold into the batter, or swap in some chopped white chocolate.
Mexican Hot Chocolate Cookies: Add cinnamon and cayenne to the dough for a spicy kick.
Chocolate Bergamot Cookies / Chocolate Orange Cookies: Add finely grated citrus zest to the batter along with the butter.
Espresso Chocolate Cookies: Add instant espresso powder along with the vanilla extract.
Cacao Nib: Add 2 tablespoons cacao nibs to the batter along with the chopped chocolate.
Skillet Brownies:Spread the batter in a buttered 8-inch ovenproof skillet (well-seasoned cast iron works well). Bake at 350ºF until a toothpick inserted near the center comes out with moist crumbs, 20-30 minutes. You can leave it gooier if you prefer! Scoop into bowls and serve warm topped with ice cream. Nutritional values are based on one of 20 cookies.