To make the beer focaccia, in the bowl of a stand mixer, fitted with the paddle attachment, combine 1 cup flour, yeast, sugar and 3/4 teaspoon salt until well combined.

Pour in the warm beer (it should be about 120 to 130 degrees F) and mix until well blended, about 1 minute. While the machine is running, add enough of the remaining flour as needed to create a smooth, slightly sticky dough, that has pulled away from the sides. Knead on moderate speed with the dough hook attachment for 4 minutes. Transfer the dough to a lightly oiled bowl and cover loosely with plastic wrap and a damp kitchen towel. Allow to rest while the onions cook.

Place a large skillet over medium-high heat with 2 tablespoons olive oil and butter. Once melted add the onions and season with remaining salt, pepper and crushed red pepper flakes. Cook until caramelized, stirring often, about 20 to 25 minutes.

Preheat oven to 500 degrees F. Grease a quarter size baking sheet with the remaining oil and place in the dough. Using your hands, work the dough, stretching it out to cover the pan. Cover loosely with plastic wrap and a damp kitchen towel and let rest for about 15 minutes to rise slightly.

Cover the dough with the shredded cheese, and the caramelized onions. Bake until golden brown and puffed up, about 12 to 15 minutes. Remove from the oven and top with fresh thyme, parmesan, if desired and crushed red pepper flakes. Slice and serve immediately. Enjoy!