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white pearl onions, peeled, red pearl onions, peeled, shallots, peeled , halved through root end, green onions, dark green tops trimmed, sweet onions (such as vidalia), peeled, cut into 3/4-to 1-inch wedges through root end, red onion, peeled, cut into 3/4-to 1-inch wedges through root end, brown-skinned onion, peeled, cut into 3/4-to 1-inch wedges through root end, extra-virgin olive oil, fresh thyme leaves, coarse kosher salt, freshly ground black pepper, coarsely torn 1/2-inch pieces rustic bread with crust, low-salt chicken broth, gruyere cheese, coarsely grated (about 1 1/2 cups packed), sea salt flakes or crystals