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Step 1
Pat 3 pounds bone-in, skin-on chicken pieces dry with paper towels and season all over with 2 teaspoons of the kosher salt and 1/2 teaspoon black pepper.
Step 2
Cook 4 ounces chopped thick-cut bacon in a Dutch oven or heavy-bottomed pot over medium heat, stirring occasionally, until the fat is rendered and the bacon is browned, 6 to 8 minutes. Transfer to a plate with a slotted spoon.
Step 3
Increase the heat to medium-high. Working in 2 batches, add the chicken skin-side down to the pot in a single layer. Sear until the skin is crisp, golden-brown, and releases easily from the pan, then flip and sear the second side, 3 to 4 minutes per side. Transfer the chicken to a large plate or baking sheet; it will not be cooked through.
Step 4
Reduce the heat to medium. Add 1 diced large yellow onion, 2 peeled and diced large carrots, and 1/2 teaspoon of the kosher salt. Cook, stirring occasionally, until the onion is softened, about 5 minutes. Stir in 3 minced garlic cloves, 1 tablespoon tomato paste, 2 dried bay leaves, and 1 teaspoon dried thyme. Cook until the tomato paste is fragrant and darker in color, about 2 minutes. Stir in 1 1/2 tablespoons all-purpose flour and cook for 1 minute to remove the floury taste.
Step 5
Add 1/4 cup Cognac and cook until evaporated, about 30 seconds. Add 2 cups dry red wine and 1 cup low-sodium chicken broth, and scrape any browned bits from the bottom of the pot. Bring to a simmer. Reduce the heat to maintain a gentle simmer.
Step 6
Return the chicken to the pot skin-side up so that it is mostly submerged (some overlapping is OK); pour in any accumulated juices from the plate. Cover and simmer until the chicken is very tender, about 30 minutes. Meanwhile, melt 3 tablespoons unsalted butter in a large skillet over medium heat. Add 8 ounces quartered cremini mushrooms, 8 ounces pearl onions, and the remaining 1/2 teaspoon kosher salt. Cook, stirring occasionally, until tender and lightly browned all over, 10 to 12 minutes. Turn off the heat.
Step 7
Add the reserved bacon, mushrooms, and onions to the pot and stir to combine. Cook uncovered for 10 minutes to let the flavors meld.
Step 8
Remove and discard the bay leaves. Taste and season with more kosher salt and black pepper as needed. Garnish with chopped fresh parsley leaves if desired.