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Step 1
Place habanero, thyme, garlic, ginger, light parts of green onions, brown sugar, black pepper, kosher salt, smoked paprika, allspice, and vinegar for marinade into a large mixing bowl and whisk to combine.
Step 2
Make 2 slices into the skin side of each thigh, perpendicular to the bone, about 1 inch apart, cutting all the way down to the bone. Add chicken thighs to the marinade and toss thoroughly until evenly coated. Place a piece of plastic wrap over the chicken and transfer to the refrigerator, 12 hours or overnight. If possible, toss several times during the marinating time.
Step 3
Remove the chicken from the marinade. Scrape off any chunks of marinade from chicken into the bowl and reserve for later.
Step 4
Heat 2 tablespoons oil in a large, deep, heavy-bottomed skillet or Dutch oven over medium-high heat until almost smoking hot. Add chicken and brown well on both sides, about 5 minutes, working in batches if necessary. Once all the chicken is browned, remove to the marinade bowl and reserve.
Step 5
Heat the same pan over medium-high heat. Add onion and a pinch of salt; saute in the fat until golden brown, 3 to 5 minutes. Add 1 tablespoon brown sugar and cook until everything caramelizes and turns a dark brown, 3 to 5 minutes more.
Step 6
Carefully add chicken broth, ketchup, and bay leaves to the pan; bring to a boil. Add carrots, bell peppers, browned chicken thighs, and reserved marinade.
Step 7
Reduce the heat to medium-low and simmer, stirring occasionally, until the chicken is tender and no longer pink in the centers, and the sauce has reduced and thickened, 1 to 1 1/2 hours, skimming the excess fat that comes to the top and basting the chicken with the sauce occasionally. Taste and adjust seasoning. Toss in reserved sliced green onions. Serve immediately.