Brown the butter. Place the butter in a small pan over medium heat. It will melt, foam, then brown — keep an eye on it so it doesn't catch. Leave to cool slightly.
Add both sugars to a large mixing bowl. Pour the browned butter over the top and beat with a handheld electric mixer for 2–3 minutes until the sugar starts to dissolve (it will still be grainy — that's fine).
Add the egg yolk and whisk for a further 2 minutes.
Add the sourdough discard and mix in with a balloon whisk until just combined. Don't switch to the electric mixer here — it'll promote gluten development you don't want.
In a separate bowl, whisk together the flour, bicarbonate of soda, salt and nutmeg (optional).
Add the dry ingredients to the wet ingredients and mix just enough to bring it together.
Add the chocolate chips and crushed pretzels (reserve 8 whole pretzels for later) and mix through evenly.
Cover the dough and chill in the fridge for 4 hours (I don't recommend chilling for longer as the pretzels will absorb too much moisture and soften).
Preheat the oven to 180°C (350 F). Line a large baking sheet with parchment.
Divide the dough into 8 even pieces and roll into balls. Press a reserved pretzel onto the top of each cookie dough ball.
Place the balls onto the prepared baking sheets, leaving plenty of space between them.
Bake for 12–14 minutes, until the edges are browned and crisp but the centre is still soft and puffy. As soon as you take the cookies out of the oven, drop the tray from 20cm height onto a kitchen worktop - this creates that signature cracked tops.
Sprinkle the tops with sea salt flakes (go easy, pretzels are already salted), then leave on the tray for 10 minutes to firm up.