Prebake the filo dough shells as per their instructions. Set aside to cool.
In a bowl mix onions and salt. Toss together so slices separate.
Preheat large sauté pan to medium heat.
Add butter to the pan, melt, then add onions. The pan will be overflowing, but as the onions turn translucent, they will cook down. Turn the pan to medium low, and stir occasionally for about 60 - 90 minutes, or until onions are browned and melted. If they look dry, start to stick to the pan, or begin to burn, add 1 tsp of water at a time. Once done, set aside, and let cool; it should yield about ½ cup. These will keep in a tightly sealed container in the refrigerator for 1 week.
Fill the tart shell half way with a small dollop of crème fraiche, then a pile of onions. Top with salmon. Garnish with a few picked thyme leaves. Finish with black pepper.