Rinse the beans and place in a bowl of cold water to cover. Set aside for 4 hours or overnight.

Preheat the oven to 275°F. Drain the beans and place them in an flameproof casserole. Stud the onion halves with the whole cloves and bury them in the casserole with the garlic, thyme, and sage. Add enough cold water to cover by ½ inch and cover. Place casserole over low heat and bring contents to a simmer. Remove from the heat and place in oven. Bake until the beans are tender but not mushy, about 45 minutes. (Check after 15 minutes to be sure that the liquid is simmering and is still above the level of the beans, adding boiling water if necessary.) Season with the salt, pepper, and pepper flakes. Set aside, uncovered, until cooled. Cover and refrigerate until chilled.

When ready to serve, remove the onion, garlic, and herbs. Fold in the oil and drained tuna. Serve at room temperature, sprinkled with parsley.