In a medium saucepan over medium-low heat, melt butter. Add onions and caramelize for 10 to 15 minutes, or until light golden brown.
Add pancetta. Cook an additional 10-15 minutes, or until onions and pancetta are golden and caramelized.
Add garlic, and cook another 1 to 2 minutes until fragrant. Add wine to deglaze pan, scraping all the bits from the bottom of the pan. Add lemon juice, and bring to a boil.
In a medium bowl, toss Le Gruyére cheese with flour until well-coated. Add cheese to boiling pot in small handfuls, constantly stirring between each addition until cheese is melted. Add Dijon mustard, and season with salt and pepper, to taste.
Warm fondue pot, and transfer fondue from saucepan to the fondue pot bowl. Garnish with chives, and serve with baguette and vegetables for dipping.