Dice squash into bite sized pieces. Put on baking sheet, drizzle with some olive oil and sprinkle with nutmeg and salt and pepper. Roast at 400°F for about 15 minutes, or until soft and browned.
To toast pepita's, put in a separate baking dish and put on the top rack in the oven with the squash. Should be toasted enough after 5-10 minutes (taste one-if crispy, its done). Set aside to cool.
Cook pasta in salted water until al dente. Reserve about 1 cup of the water.
To make the pesto, in a food processor combine 1/3 cup olive oil, herbs, cheese, pepita's, garlic and lime. Pulse until finely processed. Season to taste with salt and pepper.
In a large bowl, toss together the pasta and pesto, and 1/4 cup of the reserved pasta water. Add more water if you like, until you get the sauce consistency you want. Add in the squash and toss gently to combine.
Notes
Pepitas are sold pre-hulled and can be found in the bulk-bin section of your grocery/health food store.