Preheat the oven to 350 degrees Fahrenheit. Cut the mini eggplants in half, keeping the stems intact. Scoop out the eggplant flesh, reserving the skins, and dice finely.
In a skillet, heat the oil. Add the onion and garlic and sauté in the oil until cooked through. Add the diced eggplant and sauté until soft. Add the meat and sauté until all the liquid is evaporated and the meat begins to brown. Remove from the heat and break up the meat with a fork so that there are no large chunks.
Combine the meat and eggplant, parsley, basil, salt, and black pepper. Spoon the mixture into the eggplant skins and sprinkle with the diced red pepper. Transfer the stuffed eggplants to a greased baking dish and bake, covered, until the eggplants are completely soft and cooked through, at least an hour and a half to two hours. Before serving, garnish with the chopped chives.
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