Preheat oven to 425 degrees F.

Roast butternut squash just until fork-tender. Remove from the oven. When squash is cool enough to handle, peel, cut in half and discard seeds. Slice squash into ¼-inch thick slices and set aside.

Reduce oven temperature to 400 degrees F.

Whisk together milk, eggs, flour, salt, pepper, and a pinch of nutmeg until well combined. Add fontina and parmesan, stirring to combine.

Heat a 12-inch cast iron pan over medium heat. Add chopped bacon and cook until browned and crispy. Remove bacon with a slotted spoon and set aside.

In the same pan, add sliced shallots and saute until tender, about 4-5 minutes. Add rosemary and saute for 30 seconds. Remove pan from heat and pour milk egg mixture. Arrange sliced butternut squash in egg mixture and sprinkle bacon in an even layer. Bake clafoutis in oven for 30-35 minutes or until golden brown and set. Remove from oven and let stand for 15 minutes. Sprinkle extra parmesan on top, chopped chives, and freshly cracked black pepper. Serve.