Cream the butter and sugar: In a large mixing bowl, beat the softened butter and brown sugar together until light and fluffy—about 2 minutes.
Add molasses, egg, and vanilla: Mix in the molasses, then beat in the egg and vanilla until smooth and fully combined.
Mix the dry ingredients: In a separate bowl, whisk together the flour, baking soda, ginger, cinnamon, cloves, and salt.
Combine wet and dry: Slowly add the dry ingredients to the wet mixture, stirring just until a soft dough forms.
Stir in chocolate chunks: Gently fold the chocolate into the dough.
Stuff with marshmallows: Scoop 1.5 tablespoons of dough, flatten slightly, press 2–3 mini marshmallows into the center, and wrap the dough around them. Seal well.
Preheat and prep: Preheat oven to 350°F (177°C). Line baking sheets with parchment paper.
Space and bake: Place cookies 2 inches apart on the tray. Bake for 9–11 minutes, until the edges are set and tops are slightly cracked.
Add salt and cool: If using, sprinkle flaky salt on top right out of the oven. Let cookies cool on the baking sheet for 5–10 minutes before transferring.
Enjoy warm or cool: Serve warm for melty centers or cool completely for chewy texture with gooey pockets of marshmallow.