Butternut Squash and Spinach Pie

olive oil

small butternut squash (, halved, seeded, sliced into half-moon rounds)

yellow onions (, each onion cut into 6 wedges)

kosher salt and fresh pepper (, to taste)

sprigs of thyme

garlic cloves (, chopped)

((13.5-ounces each) spinach, well drained, pat dry with paper towel)

eggs (, lightly beaten)

ground nutmeg

crumbled feta cheese

butter for dish

phyllo sheets (, thawed)

butter (, melted)