Preheat the oven to 425˚F (220˚C). Place a rack in the upper third of the oven.
Using a vegetable peeler, peel the skin and the white flesh directly beneath the skin from the butternut squash until the deep orange flesh is exposed. Leave the stem intact if possible. Cut the squash in half lengthwise. Remove the seeds and pulp.
Place the squash cut-side down on a rimmed baking sheet and pour in the water. Bake the squash for 20 minutes, until the flesh is softened but not fully cooked. This par-cooking will making the cutting much easier.
Cool the squash until it can be safely handled with your bare hands. Place one squash half cut-side down on a cutting board. Using a sharp knife, carefully cut very thin slits, about ⅛-inch (3 MM) wide, about ¾ of the way through the squash, being careful not to cut all the way through. Repeat with the second half.
Grease the baking sheet with olive oil and return the squash to the pan, cut-side down. Brush more olive oil all over the squash. Season with salt and pepper.
Bake for another 35 minutes, until the squash is fork tender and golden brown on top.
While the squash finishes baking, make the sauce. In a small saucepan over medium heat, warm 2 tablespoons of olive oil. Add the shallots, season with salt, and cook for 10-12 minutes, stirring, until they begin to caramelize.
Add the mustard, maple syrup, and apple cider vinegar and whisk to combine. Simmer for 3 minutes, until the sauce is slightly reduced and thickened. Season with salt and pepper to taste. Remove from the heat.
Drizzle the warm sauce over the butternut squash, making sure to get the sauce in between the slits as best you can. Top with the hazelnuts, pomegranate seeds, and chives. Serve warm.
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