Preheat the oven to 350 degrees and line baking sheets with parchment paper.
Over a bowl or piece of parchment paper, sift the flour, cocoa powder, and baking soda together with a sifter, or in a fine-meshed strainer by gently tapping your hand against the edge. Add the salt (you can just leave it on top of the flour pile because it gets mixed in later).
In a bowl, beat the butter, granulated sugar, and brown sugar with an electric mixer on medium speed until smooth. Add the egg yolk and mix until well combined and use the rubber spatula to scrape down the sides of the bowl. Add the sifted flour mixture and mix until the dough comes together, again scraping down the side of the bowl once or twice.
Pinch off the dough into approximately 1 ¼-inch pieces and roll into balls. Arrange the balls on the baking sheets, leaving about 2 inches between them.
Bake 1 sheet at a time in the center of the oven until the cookies are no longer wet, about 10 minutes. Remove from the oven, and using your thumb or the end of a large wooden spoon, gently make a thumb-sized indentation in the center of each cookie. If a cookie breaks or starts to fall apart, simply push it back together. Return the pans to the oven and bake until the undersides are turning brown, about 3 more minutes. Let cool completely.
Meanwhile, make the chocolate ganache. Put the chopped chocolate in a bowl. Warm the cream in a saucepan over medium heat. As soon as it starts to bubble around the edge, pour the hot cream over the chocolate. Shake the bowl a little to submerge all the chocolate pieces, then cover the bowl for several minutes. Whisk until smooth. Let cool slightly.
Using a small spoon, drop ganache into the center of each cookie's thumbprint. Allow the ganache to set, about 1 hour, before you devour them.