Place a rack in the center of your oven and preheat the oven to 350 degrees F. Line two baking sheets with parchment paper or silicone mats.
In a small bowl, sift together the flour, cocoa powder, salt, and baking powder. Set aside.
Set a heatproof bowl over a saucepan of simmering water, ensuring that the bottom of the bowl does not touch the water's surface. Add the bittersweet chocolate and butter. Heat, stirring occasionally, just the chocolate and butter are almost fully melted. Remove the bowl from the saucepan and stir until it melts completely and looks smooth and shiny. Let cool to room temperature.
In the bowl of a standing mixer fitted with the paddle attachment or a large mixing bowl, beat the eggs and sugar together on medium-high speed for 2 minutes, until they are pale and foamy. Beat in the vanilla.
Scrape down the bowl, then reduce the speed to low and add the cooled chocolate mixture, mixing just until incorporated.
Scrape down the bowl again. With the mixer on low speed, slowly add the dry ingredients, mixing just until the dry ingredients disappear into the batter.
The batter will be thick and shiny and brownie batter-like.
By hand with a rubber spatula, gently stir in the chocolate chips.
For small cookies (2-inch) cookies, drop the dough by rounded tablespoonfuls onto the baking sheets, leaving about 1 inch of space between the mounds of dough. For larger (3-inch) cookies, drop into mounds that are 2 inches across (you'll need about 2 tablespoons of dough). Sprinkle the tops of the cookies with a pinch of flaky salt.
Bake the cookies for 9 minutes (if smaller) or 10 minutes (if larger). The tops of the cookies will appear slightly dry and the inside will be soft. Let rest on the baking sheet for 2 minutes, then gently transfer the cookies to a cooling rack to cool to room temperature (or as long as you can stand).
Repeat with the remaining dough, baking only one sheet of cookies at a time in the center of the oven. If you are reusing the same baking sheet, let it cool completely between batches.
If when the cookies are cooled, the chocolate is still gooier than you'd like, simply refrigerate the cookies for about 10 minutes.
Actual cookie yield may vary depending upon the size of the dough scooped.
TO STORE: Place cookies in an airtight storage container at room temperature for up to 1 week.
TO FREEZE: Freeze cookies in an airtight freezer-safe storage container for up to 3 months. Thaw and enjoy as desired.