Assign config in Atom environment constructor

src/atom.coffee

@@ -152,6 +152,8 @@ class Atom extends Model
   # Call .loadOrCreate instead
   constructor: (@state) ->
     {@mode} = @state
+    {resourcePath} = @getLoadSettings()
+    configDirPath = @getConfigDirPath()
 
     @emitter = new Emitter
     @disposables = new CompositeDisposable
@@ -163,6 +165,12 @@ class Atom extends Model
     NotificationManager = require './notification-manager'
     @notifications = new NotificationManager
 
+    Config = require './config'
+    @config = new Config({configDirPath, resourcePath, notificationManager: @notifications})
+
+  reset: ->
+    @config.reset()
+
   # Sets up the basic services that should be available in all modes
   # (both spec and application).
   #
@@ -196,7 +204,6 @@ class Atom extends Model
 
     @loadTime = null
 
-    Config = require './config'
     KeymapManager = require './keymap-extensions'
     ViewRegistry = require './view-registry'
     CommandRegistry = require './command-registry'
@@ -220,7 +227,6 @@ class Atom extends Model
     # Make react.js faster
     process.env.NODE_ENV ?= 'production' unless devMode
 
-    @config = new Config({configDirPath, resourcePath})
     @keymaps = new KeymapManager({configDirPath, resourcePath})
     @keymaps.subscribeToFileReadFailure()
     @tooltips = new TooltipManager

src/config.coffee

@@ -331,7 +331,12 @@ class Config
     value
 
   # Created during initialization, available as `atom.config`
-  constructor: ({@configDirPath, @resourcePath}={}) ->
+  constructor: ({@configDirPath, @resourcePath, @notificationManager}={}) ->
+    @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
+    @configFilePath ?= path.join(@configDirPath, 'config.cson')
+    @reset()
+
+  reset: ->
     @emitter = new Emitter
     @schema =
       type: 'object'
@@ -340,11 +345,8 @@ class Config
     @settings = {}
     @scopedSettingsStore = new ScopedPropertyStore
     @configFileHasErrors = false
-    @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
-    @configFilePath ?= path.join(@configDirPath, 'config.cson')
     @transactDepth = 0
     @savePending = false
-
     @requestLoad = _.debounce(@loadUserConfig, 100)
     @requestSave = =>
       @savePending = true
@@ -779,7 +781,7 @@ class Config
     @watchSubscription = null
 
   notifyFailure: (errorMessage, detail) ->
-    atom.notifications.addError(errorMessage, {detail, dismissable: true})
+    @notificationManager.addError(errorMessage, {detail, dismissable: true})
 
   save: ->
     allSettings = {'*': @settings}