Preheat oven to 350°F.
Heat a Dutch oven over medium-high heat. Add butter and swirl to coat the bottom of the pan.
Add red onions, leeks, garlic, ginger and shallots. Season with salt and pepper. Sauté ingredients until caramelized, about 8-10 minutes.
Deglaze the pan with the port, using a wooden spoon to scrape up and incorporate all the browned bits on the bottom of the pan. Reduce liquid by half.
Add chicken stock, shiitakes, bay leaves and thyme. Add soy sauce. Turn heat down to simmer and reduce by a third.
Build your crocks by placing a layer of toasted baguette pieces, then a layer of grated cheese. Repeat for 1 (or 2) more layers. Repeat until all crocks are finished.
Ladle soup in crocks over baguette layers (being sure to avoid including thyme sprigs or bay leaves.) Top with shiitake crisps and some additional gruyere cheese. Transfer crocks to oven and bake for 30 minutes.
Carefully remove crocks from oven, garnish with chives and serve.
For the Shiitake Chips:
Preheat a fryer (or high-sided sauté pan filled 1/3 with oil) to 325°F.
Add mushrooms in batches to not overcrowd. Cook until golden brown, about 3-4 minutes.
Transfer to paper towel-lined plate to drain. Season with salt.
Repeat until all are finished.