Place lentils, shiitakes, and 1 1/2 cups of water in a medium saucepan over high heat and bring to a boil. Reduce heat to a simmer, cover, and cook until tender, about 30-40 minutes. Remove shiitakes, chop, and return to the pan. Remove from heat.
Heat oil in a large skillet over medium heat. Add onions, sprinkle with salt and pepper, and cook, stirring occasionally, until tender, about 7 minutes. Add garlic and cook an additional minute.
Add wine, tomatoes, cinnamon, cloves, bay leaf, paprika, and oregano. Reduce heat, partly cover, and simmer about 20 minutes. Remove and discard cinnamon stick, bay leaf, and cloves.
Add lentils and continue to simmer, uncovered, until all water has evaporated, about another 20 minutes. Stir in vinegar, taste, and add salt and pepper as needed. Set aside.