Whisk in flour to form a roux. Cook for one minute. whisk in chilli powder and cumin, cooking for one more minute.
Add tomato sauce, stirring constantly until smooth. Stir in lime juice, and remove from heat.
Enchiladas
In a large skillet, heat vegetable oil over medium-high.
Sprinkle chicken breasts with salt and pepper, and cook chicken, about 6 minutes on each side, or until no longer pink inside. Remove chicken to a plate.
Add onion and garlic to pan and cook until onion is transparent. Add chilli powder, cumin, green chiles, chipotle peppers, adobo sauce, and tomatoes.
Bring to a boil, then reduce heat to low.
Shred cooked chicken breasts by hand, and return to pan, combining with the tomato chile mixture.
In a 9x13 baking pan, spread ½ cup of the enchilada sauce.
Preheat oven to 350°
Heat tortillas between damp paper towels in microwave for 30 seconds to make them easier to roll. Dip each tortilla in enchilada sauce to lightly coat on both sides.
Put ¾ cup of chicken filling on each tortilla, and roll up, placing seam side down in the pan.
Cover enchiladas with the remainder to the sauce, then the cheese.
Bake for 30 minutes or until cheese is melted and bubbling.
Garnish with cilantro or parsley.
Notes
Serve these enchiladas with rice and beans or a salad.