Coat a large wide pot with olive oil and put over medium heat. Add the onions, season with salt, to taste, then cover the pot and let the onions wilt and get very soft, about 7 to 8 minutes. Remove the lid and cook until they get very brown and caramelized, do NOT rush this. Cook low and slow, about 30 to 40 minutes, stirring occasionally.
When the onions are really brown and sweet, add the pumpkin, garam masala and crushed red pepper. Season with salt, to taste, then add 1 cup of stock. Cover and cook over medium heat until the pumpkin has softened and started to become mushy, about 20 minutes.
Remove the lid and if the pumpkin is still a little hard add the remaining 1/2 cup of stock. Cook, stirring frequently, until the moisture reduces and the pumpkin becomes the consistency of mashed potatoes. Taste and season with salt, if needed. Transfer the pumpkin to a serving bowl and garnish with chives and pumpkin seeds.