Short Ribs:
Preheat the oven to 375° F.
Sprinkle 1½ teaspoons of salt and black pepper on both sides of short ribs.
Heat 2 tablespoons oil in a Dutch oven or large pot over high heat. Add half of the short ribs and brown 3 minutes per side. Remove from pan and place on a sheet pan. Continue with the remaining short ribs and repeat the same process. Remove from pan and add to the sheet pan with the first batch of short ribs.
Using the same pan, drain the fat and coat the bottom with remaining 2 tablespoons of oil over medium heat. Add onion and garlic and cook for 2 minutes. Add carrot and celery, cook for 5-7 minutes. Season the vegetables with remaining ½ teaspoon of salt. Add the tomato paste and brown for 4 to 5 minutes. Add the wine and scrape the bottom of the pan. Lower the heat to low setting. Reduce the mixture by half.
Return the short ribs to the pan; add 2 cups water or until the water has just about covered the meat. Add the thyme and bay leaves. Cover the pan and roast in the oven for 3 hours, adding more water, if needed. Turn the ribs over halfway through the cooking time. Remove the lid during the last 20 minutes of cooking to let the sauce reduce. When done the meat should be very tender but not falling apart. Season to taste with salt, if needed, and shred beef into pieces with 2 forks.
Caramelized Onions:
Peel shallots and cut lengthwise into 1/8-inch slices.
Heat oil in a sauté pan over medium heat. Add the butter and shallots. Cook shallots until they begin to caramelize, about 20-25 minutes. Set aside until ready to use.
Cream Sauce:
In a small sauce pan over medium heat, add the butter. Once it has melted, add the flour and cook for about 1-2 minutes. In a steady stream, add the milk, whisking constantly. Add the cheese in small batches, continuing to whisk. Once all of the cheese has been incorporated and the sauce is smooth, add the nutmeg, and black pepper. Set aside until ready to use.
Pizza:
Pre-heat oven to 500°F. Roll out dough on a lightly floured surface into a large circle. Drizzle honey over the dough and season with salt. Spread short rib sauce over the honey. Top with shredded mozzarella, the shredded short ribs, and caramelized onions. Brush olive oil over crust and place pizza on a baking sheet or pizza stone and bake for about 15 minutes, or until the dough is golden brown and the cheese is bubbly. Drizzle cream sauce over the pizza and top with fried sage. Enjoy!