To make the marinade, toast the cloves, whole chiles, both types of cardamom seeds, coriander seeds, fennel seeds and fenugreek seeds in a cast-iron skillet until fragrant, 3 minutes or so, shaking the pan. Then, pour the spices into a spice grinder and grind them until you get a fine powder.
In large bowl, whisk together the spice mixture you just made with the yogurt, oil, malt vinegar, salt, ground cinnamon, paprika, turmeric, cayenne pepper, garlic and ginger until well combined. It should smell amazing! Taste and adjust with more salt if it needs it.
Reserve 1/3 cup of the marinade and set aside; you're going to make a sauce out of this reserved marinade.
Prick the chicken thighs with a fork. Add the thighs to the rest of the marinade, and toss to coat. Marinate at least 1 hour in the fridge, and at most overnight.
When you're ready to cook, line a baking sheet with foil, and turn your broiler on. Place each chicken thigh on the baking sheet, making sure each one is coated with the marinade, but isn't swimming in it. Cook the chicken thighs under the broiler until starting to blacken, about 5 minutes. Then turn the oven to 350, and cook until a meat thermometer inserted in the meatiest part of the thigh registers 160 degrees F, another 10 minutes. Remove from the oven.
While the chicken is cooking, pour the reserved marinade into a small saucepan, along with 1/2 cup water and the honey. Bring to a gentle boil over medium-low heat, whisking all the time. Taste and season with salt and pepper. Remove from the heat and pour into a small bowl or gravy boat for serving.
Serve the chicken thighs on a platter with a fresh squeeze of lime and a drizzle of the sauce.