First, mill your soft white wheat berries into flour and set aside. Rough chop your pretzels into pieces the size of elbow macaroni.
Next, place 1/2 cup (4 oz) unsalted butter in a pan over medium heat for about 5 minutes, until the butter foams and small brown specks appear. Do not step away from your butter as it can burn quickly. Once the butter is a light amber color, remove it from heat and stir in 2 tsp of water to replenish the moisture lost. Transfer to a small bowl to cool to room temperature.
In the bowl of a stand mixer, cream together room temperature brown butter with sugar and molasses for a few minutes. Add Egg and Vanilla. Mix until well combined, scraping down sides if needed.
Add flour, baking soda and salt. Mix until combined, careful not to over mix or it will create flat cookies!
Carefully fold in chocolate chips and crushed pretzel pieces.
Using a 2 Tbsp scoop, form cookie balls. Place on a parchment lined sheet pan, leaving 2 inches between the cookies. Place the scooped dough into the refrigerator to chill for at least 20 minutes.
While the dough chills, preheat oven to 350℉
Remove chilled dough and place into the hot oven. Bake 11-12 minutes, rotating halfway through. Do not over bake the cookies. It's actually okay if they are slightly under cooked, they will continue to bake as they cool.
Sprinkle with flaky sea salt if you like the additional salt.
Once completely cooled, move to an airtight container and store on the counter/fridge for 1 week or freezer for 3 months.