Bring a medium pot of salted water to a boil. Add the lima beans and boil until just tender, 15 to 20 minutes. Add the corn, return the water to a simmer and drain. Rinse under cold water to cool.
Meanwhile, heat 1 tablespoon olive oil in a medium skillet over medium-high heat. Add the onions and cook, stirring often, until tender and golden in spots, 8 to 10 minutes. Let cool.
In a large bowl, whisk together the cider vinegar, parsley, sage, nutmeg, 3 tablespoons olive oil, 1/2 teaspoon salt and 1/4 teaspoon pepper. Add the tomatoes, onions, lima beans and corn; toss to combine.