Using a mandolin or knife, slice onions pretty thin. Add butter to a large skillet, and then add in your onions. Cook for a few min, and then add thyme and red wine. Cover and cook, stirring every so often. Continue this for about 25 min or until onions are significantly reduced and nicely browned and caramelized
Slice bun and add cheese to bun. Toast for a few minutes to melt the cheese.
Meanwhile add oil or butter to a small pan. Whisk eggs in a bowl. When pan is very hot and butter is melted, pour eggs onto pan. Using a spatula, push eggs toward center of pan until they form ribbons. Add sliced scallions of chives. Season with salt and pepper. When they are 3/4 cooked, turn off heat and let them finish.
Add chipotle mayo or other sauce of choice to bread. Add eggs and onions. Enjoy!