Heat the oven to 350° F. Line an 8-inch square baking pan with foil or parchment paper, leaving a 2 -inch overhang on two opposite sides. This will make it easy to remove the brownies once they're baked.
Sift together the flour, cocoa powder, and salt into a medium bowl. Whisk well and set aside.
Bring a medium saucepan of water to a boil, then turn the heat down to low. Put the chocolate and butter in a medium stainless steel bowl and set it over the pan, being sure not to let the bowl touch the water. Stir the butter and chocolate together until they're completely melted, 3 to 5 minutes.
Remove the bowl from the heat and place it on a kitchen towel to capture any condensation. Whisk in the sugar. Let the chocolate mixture cool slightly, then whisk in the eggs and vanilla until smooth.
Use a rubber spatula to fold in the flour mixture. Fold in the cocoa nibs if you're using them.
Transfer the batter to the prepared baking pan. Tap the baking pan on the work surface to release air bubbles. Bake, rotating the baking pan halfway through, until a toothpick inserted in the middle comes out with some fudgy crumbs attached (you don't want it to come out clean—that means you've overcooked your brownies!), 40 to 45 minutes. Remove the pan from the oven and allow the brownie to cool completely on a cooling rack.
Lift the slab of brownies out the pan by the overhanging foil and cut into 12 squares.