Add the onions, leeks, celery, bacon, marjoram, thyme and nutmeg and stir-fry about 2 minutes (until glazed). Reduce heat to low, cover and steam 15 minutes, until onions are very limp.
Remove and discard the bacon. Raise heat to moderate, add potatoes and broth, bring to a simmer, uncovered, and then adjust heat so the broth bubbles gently. Cover and simmer 40 minutes until potatoes are mushy.
Remove pan from heat and cool soup, still covered, for 15 minutes.
Purée soup mixture in two batches by blending in a food processor at high speed for 1 minute.
Return soup to pan, mix in salt and pepper; taste and adjust seasoning as needed. Heat soup, uncovered, to serving temperature; ladle into bowls and garnish with chives.