In a large skillet over medium, heat the olive oil. Add the onions, shallots, garlic, salt, and pepper. Sauté until the onions are browned and caramelized, about 15 - 18 minutes, stirring occasionally. If the garlic begins to brown too much, add a few tablespoons of water and continue cooking.
Allow onion mixture to cool for 10 minutes, then transfer to a food processor and puree until smooth. Add the cottage cheese, thyme, and marjoram. Puree again until smooth. Stir in the chopped chives reserving a few for garnish on top. The dip can be served immediately, but benefits from being chilled for 4 hours or overnight allowing the flavors to meld together. Enjoy!
Notes
For a more tart flavor, substitute half the cottage cheese for sour cream.