Preheat oven to 350°F (175°C). Line a 9×9 pan with parchment.
Melt butter with HALF of the chocolate chips (¾ cup) until smooth.
In a separate bowl whisk eggs until frothy (about 60 seconds).
Slowly mix eggs into the melted chocolate mixture.
Add vanilla.
Stir dry ingredients into batter until combined. There should be no dry clumps, but don't overmix.
Fold in remaining chocolate chips.
Let batter rest 10 minutes to hydrate fresh milled flour. It will thicken — that's a good sign.
Pour into pan and bake 35–45 minutes until edges are set and the center still looks slightly soft.