In a medium saucepan, heat the olive oil over medium-high heat. Add the onions and cook until soft and light brown around the edges, 8 minutes.
Add the remaining ingredients, except the habanero and salt, then bring to a simmer. Cook, stirring occasionally until slightly thickened, 12 to 15 minutes.
Remove from the heat and transfer to a blender with the habanero. Purée until smooth, then season with salt. Allow to cool completely before using, then store in the refrigerator for up to 1 week.