Pat the chicken thighs dry and lightly season on both sides.
Using a large, deep oven safe skillet, heat the avocado oil over medium-high heat. Once the oil is shimmering, add the chicken thighs, skin side down. Allow to crisp thoroughly until the thighs easily release from the pan, this will take about 5-7 minutes. Flip and cook on the other side for 2-3 minutes before setting aside on a clean plate.
Set the oven to preheat to 375 F.
Reduce the heat to medium, adding more oil if needed. Add the yellow onions to the pan and a pinch of salt. Stir the onion for about 15 minutes, allowing to cool slowly. To speed up the process, add the coconut sugar and toss to coat. Saute for about another 5 minutes or until the onions are softened and golden brown.
Add the jasmine rice and toss for 2 minutes to gently toast the rice. Pour in the broth, coconut aminos and white wine vinegar and gently stir. Bring to a low boil and add 1 tsp of thyme leaves, bay leaves and ghee. Transfer the chicken back to the pan, spooning some of the cooking liquid over the chicken.
Place the lid on the pan and transfer to the preheated oven. Bake for 30 minutes.
Remove from the oven, and carefully remove the lid. Ensure the rice is cooked and the chicken is 165 F. Top with the shredded cheese and return to the oven, turning the heat up to 400 F. Bake until the cheese is melted.
Top the skillet with more thyme, and serve!