Start by preparing the Naan dough. In a bowl, combine the dry yeast, 1 teaspoon sugar, and 3/4 cup warm water. Let it sit for 10 minutes, or until foamy. Meanwhile, sift the flour, salt, remaining 1 teaspoon of sugar, and baking powder into a large bowl.
When the yeast is ready, mix the Greek yogurt and olive oil into the yeast mixture. Pour into the dry ingredients and mix. When the dough is nearly formed, use your hands to mix and knead until a soft dough forms. Cover and let rise in a warm area for 2 hours.
While you wait, put together the chicken marinade. Combine the Greek yogurt, lemon juice, garam masala, cumin, turmeric, paprika, salt, and cinnamon in a large container. Add in the chicken thigh pieces and mix well to coat. Cover and refrigerate for at least an hour.
After an hour, melt the ghee in a large pan over medium heat. Then add in the diced onion and saute until softened, stirring often. And add in the garlic and ginger and cook until fragrant.
Add the diced tomato, jalapeno, chicken, and chicken marinade, and cook for 10 minutes. Add in the chicken stock and bring to a boil, and then reduce to a simmer. Simmer, uncovered, for 30 minutes.
Mix in the vegetables, cream, and tomato paste and continue to cook for 5 minutes.
Preheat the oven to 400 degrees F.
Fill 6 oven-safe mugs with the Butter Chicken. Set aside.
On a lightly dusted surface, turn out the dough. Divide into 6 equal pieces and gently stretch to cover the tops of the mugs. Gently press to the sides of the mugs to adhere.
Bake until golden, about 15 minutes.
Brush with melted butter and sprinkle with salt and cilantro, if desired. Serve warm.