Brush the salmon fillets with a little of the olive oil. Season well with salt and pepper and set aside. Preheat the oven to 400°F/200°C.
Divide the clumps of onions into separate cloves or bulbs; you should have about 40 separate bulbs, but if you end up with more that is great!
Trim and peel them, then rinse them well, as the bulbs can be very sandy. If they come with their greens, reserve them for another use. **
Place the remaining olive oil in a small, heavy saucepan and add the whole I’itoi onion bulbs, thyme sprigs, tomato paste, sugar, red pepper flakes, and salt.
Cook over medium-low heat for about 20 minutes, at which point the onions should be soft and somewhat caramelized. Discard thyme sprigs and set compote aside; keep warm.
Arrange lemon slices on an oiled cookie sheet to make a bed for the fish. Place the fillets on the lemon slices and roast in the oven for 8-12 minutes, depending on thickness and your preference for how well done you like your fish.
Using a long spatula, transfer each fillet, with some of the lemon slices, to heated dinner plates.
Divide the I’itoi onion compote among fish, drizzle any remaining sauce over it, and serve immediately.