For the dark chocolate ganache: In a heatproof bowl set over a pot of barely simmering water, making sure the bottom of the bowl doesn’t touch the water, add the chocolate, butter, and cream, and whisk just until melted and smooth. You can also do this using the microwave, making sure to use the lowest heat setting so the chocolate doesn’t burn.
Transfer the ganache to an airtight container and refrigerate until ready to use.
For the cookies: In a mixing bowl, combine the ground pecans, flours, kosher salt, and baking powder. Set aside.
In the bowl of a stand mixer fitted with the paddle attachment (or in a large mixing bowl, if you’re using a handheld mixer), beat the unsalted butter, sugar, and vanilla together until the mixture is fluffy and pale, about 3 minutes. Add the egg yolk and beat well. Add the flour and pecan mixture and mix at low speed until the dough is just combined, about 1 minute. The dough will look crumbly, and that’s OK.
Dump about half of the dough mixture onto a square of plastic wrap. Using your hands, bring the dough together into a flat ball, wrap tightly, and refrigerate 30 minutes. Repeat for the second half of the dough. (You can also make the dough in advance and refrigerate it for up to 3 days.)
Set a rack in the middle position of the oven. Preheat oven to 325°F [160 °C]. Line a baking sheet with parchment paper.
Place the first ball of dough over a large square of parchment paper set directly on a flat countertop (see note). Place a second square of parchment paper over the dough and use a rolling pin to roll the dough out (rolling the pin over the top parchment paper) until ¼ inch [6 mm] thick. Using a 2-inch [5-cm] round cookie cutter, cut out as many shapes as possible, carefully transferring each cookie onto one of the prepared baking sheets (you can use a pastry spatula to lift and transfer the cookies more easily.) Set the cookies about 1 inch [2.5 cm] apart to allow for some light spreading. Gather the scraps, reroll, and cut out new shapes, repeating until there is no dough left.
Bake the cookies for 15 to 20 minutes until pale golden on the edges, rotating the sheet halfway through. Cool the cookies for a few minutes on the baking sheet, and then transfer to a wire rack to cool completely. Bake the remaining cookies.
To assemble the cookies: Take the ganache out of the refrigerator about an hour before you plan on filling up the cookies so it softens to room temperature.
Spread a thick layer of ganache on the underside of a cookie, leaving an indentation in the center. Drop a bit of caramel in the center, then sprinkle a tiny bit of chopped pecans over the caramel. Cover with another cookie, very gently pressing to spread the ganache all the way to the sides of the cookie (shortbread cookies are very crumbly, so make sure to proceed with great care.) Repeat to assemble all cookies.
STORAGE
Store in an airtight container in the refrigerator. The assembled cookies are best enjoyed within 3 days, as the ganache and caramel tend to soften the cookies past that.
SERVING
Take the cookies out of the refrigerator 20 minutes before serving to return them to room temperature before enjoying.
NOTE
Rolling sticky dough (such as shortbread cookie dough) in between two sheets of parchment paper makes it easier to pick up the cutout shapes—and it also makes for much quicker cleanup, too!