In a large skillet, heat olive oil over medium-low heat and add sliced onions. Cook for 30-35 minutes, stirring occasionally, until deeply caramelized.
While onions cook, prepare the high-protein gnocchi according to package instructions; drain and set aside.
In a blender, process cottage cheese until completely smooth.
Add minced garlic and thyme to the caramelized onions and sauté for 1 minute.
Deglaze the skillet with beef bone broth, scraping the bottom to release browned bits.
Stir in the blended cottage cheese, salt, and pepper until a creamy sauce forms.
Fold the cooked gnocchi into the sauce until evenly coated.
Transfer to an oven-safe dish, top with shredded Gruyère, and broil for 2-3 minutes until cheese is melted and bubbly.