Preheat the oven to 325 degrees F. Grease an 8-inch baking pan with butter and set aside.
In a double boiler, melt the butter, then stir in the chocolate chips and cocoa powder until melted and smooth. Allow to cool slightly.
Mix together the sugar and eggs in a small bowl, then add to the chocolate mixture and mix briskly to combine using a wooden spoon. In a separate bowl, combine the all-purpose flour, almond flour and kosher salt, then stir into the chocolate mixture.
Pour the batter into the greased pan and sprinkle the top with the pine nuts, peanut butter chips and some flaky sea salt. Bake until a knife comes out clean when stuck in the center of the pan, about 30 minutes. Allow to rest for at least 10 minutes before serving or storing.
These taste even better after a night in the fridge.