Slice the onions thinly by removing the outer layer, cutting them in half, and then cutting into thin slices.
Heat ¼ cup olive oil in a large skillet over medium heat. Add the onions and a generous pinch of salt. Cook, stirring frequently until soft and caramelized, about 25-30 minutes.
Meanwhile, bring a large pot of water to a boil.
Make the breadcrumbs. Combine the breadcrumbs and 1 teaspoon olive oil in a small bowl and toss to combine. Add the breadcrumbs to a small skillet over medium heat and toast the breadcrumbs until they start to turn golden brown, watching carefully to avoid burning. Place them back into the bowl and set aside.
Add the garlic and thyme leaves to the skillet with the onions. Add the wine to deglaze the pan and add the tapioca flour. Add the vegetable broth, vegan Worcestershire sauce, and rice vinegar. Toss and cook for another 2-3 minutes, until thickened, then turn the heat down to low.
Cook the gnocchi for 2-3 minutes (or follow package directions). When they float to the top of the water they are cooked. Scoop them out with a slotted spoon and add to the pan with the onions. Season with salt and pepper, to taste, toss to coat the gnocchi well and serve. Top with toasted breadcrumbs, if desired, and fresh thyme leaves.