For the beans, heat 1 tablespoon olive oil over medium heat in a medium-sized pot. Add the onions and garlic and let cook for 4 to 5 minutes or until translucent. Add the cumin and beans and stir for a couple of minutes to soften. Season with salt and pepper. Add the water and thyme sprigs and bring to a boil. Reduce the heat and let simmer for 10 to 15 minutes, stirring occasionally, until thickened. (The consistency should be like a chunky, thick paste). Stir in chopped cilantro and lime juice. Season with salt and pepper to taste. Serve warm, drizzled with olive oil.
MAKE AHEAD: The beans can be made a day or two ahead; reheat before serving.