In large skillet, heat olive oil over medium heat. Saute onions with pinch of salt, stirring frequently until onions have softened and are beginning to brown, about 20-25 minutes.

Increase heat to medium-high and continue cooking onions 25-30 minutes or until deeply caramelized. If onions start sticking to pan or brown too quickly, lower heat to medium, add 1 Tbsp. water and scrape bottom of pan to loosen up bits.

Once onions are caramelized, fold in mushrooms, garlic and thyme. Saute 4-5 minutes or until mushrooms begin to soften.

Add wine to deglaze pan and cook off 2 minutes. Add butter and stir until melted. Slowly add flour, stirring until incorporated. Add stock and water, and bring mixture to boil.

Fold in pasta shells, decrease heat to low and simmer gently 14-16 minutes or until pasta is al dente and liquid is mostly soaked up. (Note: Pasta will continue to soak up liquid as it sets and is served.)

Fold in ½ tsp. salt and Parmesan cheese. Let pasta sit 5 minutes to cool slightly and allow noodles to continue to soak up liquid.

Taste and season with additional salt and pepper, as desired. Serve warm.