Reset all user config values when the schema changes.

spec/config-spec.coffee

@@ -1106,6 +1106,44 @@ describe "Config", ->
         expect(atom.config.get('foo.bar.str', scope: ['.source.js'])).toBe 'omg'
         expect(atom.config.get('foo.bar.str', scope: ['.source.coffee'])).toBe 'ok'
 
+      describe 'when a schema is added after config values have been set', ->
+        schema = null
+        beforeEach ->
+          schema =
+            type: 'object'
+            properties:
+              int:
+                type: 'integer'
+                default: 2
+
+        it 'the values set respect the new schema', ->
+          expect(atom.config.set('foo.bar.int', 'nope')).toBe true
+          expect(atom.config.set('foo.bar.int', 'notanint', scopeSelector: '.source.js')).toBe true
+          expect(atom.config.set('foo.bar.int', 23, scopeSelector: '.source.coffee')).toBe true
+          expect(atom.config.get('foo.bar.int')).toBe 'nope'
+          expect(atom.config.get('foo.bar.int', scope: ['.source.js'])).toBe 'notanint'
+          expect(atom.config.get('foo.bar.int', scope: ['.source.coffee'])).toBe 23
+
+          atom.config.setSchema('foo.bar', schema)
+
+          expect(atom.config.get('foo.bar.int')).toBe 2
+          expect(atom.config.get('foo.bar.int', scope: ['.source.js'])).toBe 2
+          expect(atom.config.get('foo.bar.int', scope: ['.source.coffee'])).toBe 23
+
+        it 'doesnt mess it up', ->
+          expect(atom.config.set('foo.bar.int', 10)).toBe true
+          expect(atom.config.set('foo.bar.int', 15, scopeSelector: '.source.js')).toBe true
+          expect(atom.config.set('foo.bar.int', 23, scopeSelector: '.source.coffee')).toBe true
+          expect(atom.config.get('foo.bar.int')).toBe 10
+          expect(atom.config.get('foo.bar.int', scope: ['.source.js'])).toBe 15
+          expect(atom.config.get('foo.bar.int', scope: ['.source.coffee'])).toBe 23
+
+          atom.config.setSchema('foo.bar', schema)
+
+          expect(atom.config.get('foo.bar.int')).toBe 10
+          expect(atom.config.get('foo.bar.int', scope: ['.source.js'])).toBe 15
+          expect(atom.config.get('foo.bar.int', scope: ['.source.coffee'])).toBe 23
+
       describe 'when the value has an "integer" type', ->
         beforeEach ->
           schema =

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
   ###