Place onions in a large saucepan. Bring to a boil and simmer 6 to 8 minutes, or until onions are just tender. Drain well. Let cool and peel. Set aside.
Melt 2 TBS butter in a heavy saucepan over low heat. Add flour, stirring unitl smooth. Cook 1 minute, stirring constantly, until thickened. Add salt and next 3 ingredients. Also add green onions, shallots and white wine. Gently stir in pearl onions. Pour onions into a lightly greased 1 quart baking dish. Sprinkle with shredded cheese and cover with breadcrumbs, melted butter and thyme.
Bake uncovered, at 350 degrees for 25 minutes or until thoroughly heated and top is golden brown.
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