To make the crust, add the flour, thyme, and black pepper in the bowl of a food processor. Pulse one to two times to combine. Add the butter and pulse 5 to 6 times to break down the butter until it resembles coarse crumbs. Add the egg and pulse until it comes together. Dump the dough out onto a piece of plastic wrap and shape into a disk and chill for at least 30 minutes.
Preheat oven to 400 degrees F. Place the onions, mushrooms and tomatoes on a baking sheet in a single layer. Drizzle with olive oil and season with salt and black pepper. Roast until just beginning to caramelize, about 25 to 30 minutes. Remove from oven and let cool slightly. Lower temperature of oven to 375 degrees F.
Once the dough has chilled, roll it on a well floured work surface to a large circle about a 1/4 inch thick. The dough might be scraggly and break but don't worry. Transfer the rolled dough to a 10-inch tart pan with a removable bottom. If the dough breaks, just press the seams together to close. Cut off excess dough that hangs over. Bake for about 10 to 15 minutes or until lightly golden brown. Remove from oven and let cool.
Place the cooled onions mushrooms and tomatoes into the pre-baked crust. Chop the sausage and bacon and sprinkle on top. In a bowl, whisk together the eggs, half and half, ricotta, salt, pepper, and chives until smooth. Pour evenly over the filling into the crust. Top with the mozzarella, spacing them around on top and bake until the center is set, about 30 to 35 minutes. Remove from the oven and sprinkle with pepper and chives to garnish. Let cool slightly before cutting and serving. Enjoy!