1Heat the oven to 325°F. Season the chicken all over with salt and pepper.
2Set a dutch oven over medium heat and cook the bacon until crisp and the fat has rendered, about 6 minutes. Lift the bacon out with a slotted spoon and leave the fat in the pot.
3Raise the heat to medium-high. Working in two batches so the pot isn't crowded, sear the chicken skin-side down until deep golden, about 5 minutes. Flip and brown the other side for 3 minutes, then move the thighs to a plate. Pour off all but about 2 tablespoons of fat.
4Lower the heat to medium and add the olive oil, onion and carrots. Cook, stirring and scraping up the browned bits, until softened, about 5 minutes. Stir in the garlic and tomato paste and cook for 1 minute until the paste darkens slightly.
5Sprinkle the flour over the vegetables and stir for 1 minute. Pour in the wine, scraping the bottom of the pot, and let it bubble for 3 to 4 minutes to take the sharp edge off. Add the broth, thyme and bay leaves.
6Nestle the chicken back into the liquid, skin-side up, with the skin staying above the surface where possible. Scatter the bacon over the top, then cover and bake for 40 minutes.
7While the chicken bakes, melt the butter in a skillet over medium-high heat. Cook the mushrooms until browned, about 6 minutes, then add the pearl onions and cook 3 minutes more. Season with a pinch of salt.
8Stir the mushrooms and onions into the pot, leaving the chicken skin above the liquid. Cover and bake another 20 minutes, until the chicken is tender and an instant-read thermometer in the thickest part reads at least 175°F.
9Remove the thyme stems and bay leaves. If the sauce seems thin, set the pot over medium heat and simmer uncovered for 5 to 10 minutes until it coats a spoon. Taste and adjust the salt and pepper. Finish with the parsley and serve in wide bowls.