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Season chicken pieces with salt and pepper. Toss with a little olive oil to coat.
Add whole wheat flour to a gallon-sized zip top bag. Add chicken pieces to the bag, close and shake until pieces are coated. Sauté chicken in 1-2 TBSP olive oil over medium-high heat until cooked through and browned on all sides, about 5 mins. Set aside.
Turn heat down to medium and swirl 1 TBSP olive oil in pan. Add peppers, onion, celery, mushrooms, and garlic, and sauté until they begin to soften, about 5 mins. Season vegetables with red pepper flakes, dried oregano, dried basil, salt and pepper (to taste) while they are cooking.
Sprinkle 1 TBSP of flour over the vegetables. Stir and cook for 1-2 mins. (Note: You can omit this step, but the sauce will be thinner.)
Add red wine and tomatoes to vegetable mixture. Bring to a boil, scraping up any bits off the bottom of the pan, and reduce to simmer. Simmer for about 30 minutes, stirring occasionally, until liquid is reduced some and smells fragrant. Taste and adjust seasoning.
Add chicken pieces back into the sauce (or on top of pasta and sauce on each individual plate). Serve over whole grain pasta or brown rice and top with fresh Parmesan cheese and chopped Italian parsley.
To Freeze: Cook recipe through step 5. Let sauce cool. Place in a freezer bag or container. Place chicken pieces in a separate freezer bag, making sure to squeeze out any air and seal tightly. Label and freeze both bags for up to 3 months.
To Prepare: Thaw sauce and chicken overnight in the refrigerator. Warm sauce on the stovetop in a pot over low heat, stirring regularly. Then heat up the chicken bites in the microwave in 30 second increments, just until warmed through. (Do not overcook the chicken or it will be tough.) Serve as directed in Step 6.