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In a large cast iron skillet [see note #1] over medium heat, add the 2 tbsp olive oil and 3 tbsp butter. Once butter has melted, add in the onions and a pinch of kosher salt. Sauté the onions for 3-4 minutes until they begin to soften. Lower the heat to medium/low and continue to cook onions stirring frequently so they do not burn [see notes]. After 20 minutes, add in the 3 tbsp of beef stock and continue stirring the onions. For the rest of the caramelization process, you'll need to be frequently stirring so the onions do not burn. The whole process of caramelizing the onions takes about 40-45 minutes [see notes for important tips].
While the onions are cooking, cook the pasta to al dente according to package instructions. Drain and set aside.
Remove the onions from the skillet using tongs and set aside. Turn the heat to medium/high, add in the 2 tbsp oil, the chicken, and the Italian seasoning. Cook chicken entirely through to 165 degree internal temperature. About 10 minutes. Remove the chicken from the pan and set aside.
Lower the heat to medium, return the onions back into the pan. Deglaze the pan with the white wine and allow the liquid to reduce by half. Once liquid has reduced, add the flour and stir until combined with the onions. Add in the fresh thyme, the 2 cups beef stock, the beef bouillon paste, and freshly ground black pepper. Stir until all combined. Add the chicken back into the skillet, allow the french onion sauce to come to a boil and lower the heat to simmer. Taste and adjust seasoning if necessary.
Turn the heat off, add in the pasta shells, and carefully mix the pasta into the french onion sauce. Top with the freshly grated gruyere cheese, and place in the oven. Low broil until the cheese has melted. Carefully remove from the oven, top with fresh thyme, and serve.