Add the onions to the same skillet and sauté until translucent and golden, about 10 minutes. Add the garlic, salt, oregano and chicken stock and stir, scraping up any brown bits. Return the pork and any juices to the pan, reduce the heat to low, cover and simmer until meat is tender, about 1 1/2 hours.
Add the tomatoes and chile and simmer for 15 more minutes.
Mix enough cold water with the flour to make a paste the consistency of cream. Whisk into the sauce and cook until the sauce thickens and the flour loses its raw taste, another 15 minutes or so.