Heat the olive oil in a large, heavy skillet over med-high heat. Add the onion and toss to coat in oil. Sprinkle with salt and pepper. Cook about 5 minutes, stirring occasionally, until they begin to soften. Add the apples, then pour in a 1/4 cup of water. Stir well to combine, then lower the heat to medium and cook about 25 minutes, until the onions are very soft and deep golden. Stir in the vinegar, and increase the heat to medium-high. Cook, stirring frequently, until the liquid has evaporated. Stir in the thyme and remove from heat.

In a large bowl, combine the vegan mayonaise and cream cheese. Mix until smooth. Add the onion and apple mixture, and fold together until well-incorporated. Taste, and adjust seasoning if needed. Cover and refrigerate for at least 1 hour. 

Stir again just before serving. This is delicious with potato chips or sliced vegetables.