In the bowl of a food processor (I used a mini one), combine the chipotle peppers, adobo sauce, garlic cloves, cumin, oregano, avocado oil, apple cider vinegar, agave, 1 teaspoon of Kosher salt (double this amount of salt if doubling the recipe), and freshly ground black pepper. Run until smooth.
In a medium mixing bowl, toss the chicken with the chipotle marinade. Let sit for at least 1 hour, up until overnight (If marinating longer than an hour, cover with plastic wrap and place in the refrigerator. Let it come to room temperature before cooking).
When ready to cook, heat a drizzle of avocado oil in a medium pan over medium heat. Add the onions and cook, stirring occasionally, for 4-7 minutes, until golden and softened.
Add the tomato paste and cook, stirring constantly, for 30 seconds to 1 minute, until the paste is fragrant and darkened in color.
Add the chicken stock and chicken thighs with the marinade, making sure to scrape all the marinade from the bowl into the pan. Bring to a simmer, then reduce heat to low, partially cover pan, and cook for 40-45 minutes, until the chicken is starting to fall apart.
Transfer chicken pieces to cutting board, while continuing to cook the sauce, and shred with two forks. Transfer back into the sauce and raise the heat to medium. Cook until the sauce has thickened and almost evaporated and is coating the chicken, about 5 minutes. Taste and season with Kosher salt, as needed.
Transfer chicken mixture to a plate or bowl. Rinse and wipe the pan clean.
Heat a small bit of avocado oil in the same pan over medium heat. Add tortilla and as much cheese as you’d like, sprinkled over the entire tortilla. Then add as much of the chicken mixture as you’d like over half of the tortilla. With a spatula, fold the non-chicken side of the tortilla in half over the chicken side, lightly pressing down to fold. Cook until crispy and golden on both sides, flipping over when needed. You should be able to make 4 quesadillas if using large tortillas, or 8 quesadillas if using smaller tortillas.
TIP: Quesadillas can be kept warm on a parchment-lined sheet pan in a 250°F oven while you make the remaining quesadillas.
If using a larger tortilla, cut into wedges. If using smaller tortillas, cut in half crosswise, or leave whole. Serve warm with the avocado crema on the side, for dipping.