Summer Squash Rye sotto

Name: Summer Squash Rye-sotto
Ingredients: 1 cup Rye berries; 3 Tbsp Olive oil, divided; 2 lb Summer squash or zucchini, halved lengthwise; 2 Tbsp Lemon juice; 1/4 tsp Chili flakes; Salt & pepper to taste; 2 Shallots, diced; 3 cloves Garlic, minced; 2 sprigs Thyme; 1/2 cup White wine; 2 cups Chicken broth; 1/2 cup Heavy cream; 1 Tbsp Creme fraiche; Chives, to garnish