Toss the squid in a wok over medium-high heat, stirring constantly, for 2-3 minutes. Set aside and keep warm.
Heat the oil in a wok and fry the garlic and onion until soft and beginning to brown. Add the tomatoes, soy sauce, nutmeg, cloves, and lime juice, then bring to a boil. Reduce the heat and add the squid, with salt and pepper to taste.
Cook the squid in the sauce for 3-5 minutes over gentle heat, stirring occasionally, careful not to overcook the squid. Serve with rice or rice noodles, garnished with scallions and cilantro.