Whisk together flours, baking soda and salt in a bowl. Set aside.

Melt the butter in a medium saucepan or skillet. Add the thyme and brown the butter while whisking constantly. When it is a deep reddish brown--but not at all burned--and fragrant with a nutty caramel scent, pour the butter into a large mixing bowl through a fine mesh sieve.

Whisk the sugars into the melted butter. Whisk briskly until they incorporate nicely--i.e., there are no pools of butter on the surface when you stop. This could take 1-2 minutes.

Whisk in the egg and egg yolk, one at a time. Whisk in the vanilla and molasses.

Switch to a rubber spatula, and slowly stir in the flour mixture. When it is nearly, but not quite, mixed in, add the chocolate chips, and continue to stir and fold until it is completely incorporated together.

Cover the dough with something airtight and refrigerate at least overnight.

When ready to bake, preheat the oven to 350 F. Line a baking sheet with parchment paper or a silicone mat.

Using a cookie dough scoop or an ice cream scoop of medium size, scoop the cookies onto the prepared tray, 6 per sheet. I was aiming for 2 heaping tablespoons of dough per cookie. Sprinkle the cookies with coarse or flaky sea salt and bake until golden brown but still a little soft, about 11-13 minutes. Transfer the baking sheet to a wire rack for 10 minutes, then remove the cookies individually to a cooling rack.