Reset all user config values when the schema changes.

src/config.coffee

@@ -797,6 +797,7 @@ class Config
     _.extend rootSchema, schema
     @setDefaults(keyPath, @extractDefaultsFromSchema(schema))
     @setScopedDefaultsFromSchema(keyPath, schema)
+    @resetForSchemaChange()
 
   load: ->
     @initializeConfigDirectory()
@@ -1002,6 +1003,20 @@ class Config
     value = @constructor.executeSchemaEnforcers(keyPath, value, schema) if schema = @getSchema(keyPath)
     value
 
+  # When the schema is changed / added, there may be values set in the config
+  # that do not conform to the config. This will reset make them conform.
+  resetForSchemaChange: (source=@getUserConfigPath()) ->
+    settings = @settings
+    @settings = null
+    @set(null, settings, {save: false})
+
+    priority = @priorityForSource(source)
+    selectorsAndSettings = @scopedSettingsStore.propertiesForSource(source)
+    @scopedSettingsStore.removePropertiesForSource(source)
+    for scopeSelector, settings of selectorsAndSettings
+      @set(null, settings, {scopeSelector, source, priority, save: false}) if settings?
+    return
+
   ###
   Section: Private Scoped Settings
   ###