Heat a pan over medium-high heat.
Add the chopped onions to the pan with a couple of tablespoons of water and ¼ teaspoon of salt.
Saute, stirring frequently, until the onions soften, about five minutes. If the onions dry and start to stick, add more water, a couple of tablespoons at a time.
Add the minced garlic and saute another minute.
Add the tomatoes, cumin powder, habanero pepper, cilantro and thyme.
Stir well, cover with a lid and let it cook, stirring occasionally, until the tomatoes have broken down. This should take 7-8 minutes.
Add the washed lentils and stir well to mix. Add enough water to cover the lentils.
Bring the lentils to a boil, turn down the heat to a simmer, and let the lentils cooked until they are really tender but still holding their shape. Add more water, no more than ½ cup at a time, if the mixture dries up before the lentils are fully cooked. But don't add too much because you want the lentil filling to be quite dry.
Once the lentils are cooked, continue to saute them on medium heat until the mixture is quite dry and there is no visible liquid.
Add salt and mix well.
Remove to a bowl and garnish with chives.
To assemble the tortilla, place a couple of tablespoons of the filling in the center of a tortilla, top with salsa and guacamole.