Heat a large Dutch oven on low heat. Add the oil, onions, bacon, carrots, celery, and garlic. Cook for about ten minutes, until all the vegetables are nice and soft, and the bacon is starting to brown. Stir frequently.
Add the beef, and cook for about five minutes, just until it's no longer pink. Add the tomato paste, salt, and pepper and cook for three minutes. Add the wine and cook for five minutes.
Add the chicken stock, milk, tomatoes, Parmesan rinds, red pepper flakes, and bay leaves. Simmer for an hour and a half, stirring frequently, and scraping down the sides of the pot.
Remove the bay leaves and cheese rinds. Add the nutmeg and thyme.
To serve with pasta, just stir about a quarter of the sauce into a pound of cooked pasta. Add extra Parmesan and fresh basil and serve. Freeze the rest of the sauce in three separate containers. Use for three more dinners.