Brown the chicken: Season both sides of the thighs with a healthy pinch of salt and black pepper. Heat a large skillet or braiser (I recommend using a pan that has a lid and is also oven safe). Once the pan is hot, add the olive oil, and brown the chicken thighs on both sides for 3 minutes per side. After they're browned, transfer the chicken thighs to a clean plate.
Saute vegetables: In the same pan as the chicken (without cleaning it), saute the onions, celery, carrot, and pepper for 3 minutes with 1/4 teaspoon of salt. Add the diced mushrooms and cook for an additional 3-4 minutes, then add the minced fresh garlic and cook for the last minute with the vegetables.
Cook the tomato paste, then add the wine: Once the vegetables are soft, add the tomato paste and cook with the vegetables for about 2 minutes. Then add the fresh rosemary, fresh sage, garlic powder, fresh basil, and red pepper flakes. Add the white wine and cook with the vegetables until the wine has mostly absorbed (about 1-2 minutes).
Add the chicken and bake: Stir in the crushed tomatoes, 1/4 teaspoon of black pepper, and 1/2 teaspoon of salt. Nestle the chicken thighs into the sauce and vegetables, trying to cover them with the sauce as much as possible. Cover the dish with a lid and bake at 350°F for 50 minutes. Then uncover and bake for 20 minutes. Remove the dish from the oven and serve with freshly grated Parmigiano Reggiano.