Add the onions to the casserole and cook over moderate heat, stirring, until tender, 5 minutes. Add the garlic and jalapeño and cook until fragrant. Add the flour, chile powder, cumin, oregano and cayenne and cook, stirring constantly, until fragrant. Add the stock, navy beans and chicken and bring to a simmer. Cover and cook over low heat until the chicken is very tender, 30 minutes.