Over medium heat, add the olive oil to the saute pan. Once hot, add the yellow onion slices. Season with salt. Saute the onions while occasionally stirring, for 10 minutes. The onions will start to release some liquid. Add the shallots to the onions and continue stirring for 5 minutes. Next add the leeks and continue to stir occasionally for 10 minutes. The onions will start to get very soft and stick to the pan. You should see a brown, crusty residue, better known as fond, start to develop on the bottom of the pan. This fond helps to develop the flavor of the jam.
Add ¼ cup of the water to the pan and stir to deglaze. The fond will release as you stir the onions. Cook for about 3 minutes until the water is absorbed and the onions start to stick to the bottom of the pan again. Add another ¼ cup of water and repeat as above. Continue this process until the full cup of water has been added.
Flavor the jam
Add the nectarine slices and mix with the onions. As the nectarines cook, they will soften and start to fall apart. Use a wooden spoon to smash the nectarines into the onions. Once the fruit is fully incorporated, add the white wine. Continue to stir until the onions and the fruit start to get jammy. At this point add the honey, thyme, and red pepper flakes. Check the seasoning of the jam and adjust the salt if needed.
The recipe makes approximately 2 cups of jam. Each serving is 2 tablespoons. Adjust the amount of red pepper flakes to your preference for spice