diff --git a/package.json b/package.json
index 416bbf6c8..4235069fe 100644
--- a/package.json
+++ b/package.json
@@ -65,7 +65,7 @@
     "scandal": "^3.1.0",
     "scoped-property-store": "^0.17.0",
     "scrollbar-style": "^3.2",
-    "season": "^6.0.0",
+    "season": "^6.0.1",
     "semver": "^4.3.3",
     "service-hub": "^0.7.4",
     "sinon": "1.17.4",
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 552f44bf9..bcf50c268 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -13,6 +13,8 @@ describe "Config", ->
     dotAtomPath = temp.path('atom-spec-config')
     atom.config.configDirPath = dotAtomPath
     atom.config.enablePersistence = true
+    atom.config.settingsLoaded = true
+    atom.config.pendingOperations = []
     atom.config.configFilePath = path.join(atom.config.configDirPath, "atom.config.cson")
 
   afterEach ->
@@ -877,7 +879,7 @@ describe "Config", ->
 
         beforeEach ->
           atom.notifications.onDidAddNotification addErrorHandler = jasmine.createSpy()
-          spyOn(fs, "existsSync").andCallFake ->
+          spyOn(fs, "makeTreeSync").andCallFake ->
             error = new Error()
             error.code = 'EPERM'
             throw error
@@ -895,16 +897,15 @@ describe "Config", ->
     describe ".observeUserConfig()", ->
       updatedHandler = null
 
-      writeConfigFile = (data) ->
-        previousSetTimeoutCallCount = setTimeout.callCount
-        runs ->
-          fs.writeFileSync(atom.config.configFilePath, data)
-        waitsFor "debounced config file load", ->
-          setTimeout.callCount > previousSetTimeoutCallCount
-        runs ->
-          advanceClock(1000)
+      writeConfigFile = (data, secondsInFuture = 0) ->
+        fs.writeFileSync(atom.config.configFilePath, data)
+
+        future = (Date.now() / 1000) + secondsInFuture
+        fs.utimesSync(atom.config.configFilePath, future, future)
 
       beforeEach ->
+        jasmine.useRealClock()
+
         atom.config.setSchema 'foo',
           type: 'object'
           properties:
@@ -920,7 +921,7 @@ describe "Config", ->
               default: 12
 
         expect(fs.existsSync(atom.config.configDirPath)).toBeFalsy()
-        fs.writeFileSync atom.config.configFilePath, """
+        writeConfigFile """
           '*':
             foo:
               bar: 'baz'
@@ -930,26 +931,32 @@ describe "Config", ->
               scoped: true
         """
         atom.config.loadUserConfig()
-        atom.config.observeUserConfig()
-        updatedHandler = jasmine.createSpy("updatedHandler")
-        atom.config.onDidChange updatedHandler
+
+        waitsForPromise -> atom.config.observeUserConfig()
+
+        runs ->
+          updatedHandler = jasmine.createSpy "updatedHandler"
+          atom.config.onDidChange updatedHandler
 
       afterEach ->
         atom.config.unobserveUserConfig()
         fs.removeSync(dotAtomPath)
 
       describe "when the config file changes to contain valid cson", ->
+
         it "updates the config data", ->
-          writeConfigFile("foo: { bar: 'quux', baz: 'bar'}")
+          writeConfigFile "foo: { bar: 'quux', baz: 'bar'}", 2
+
           waitsFor 'update event', -> updatedHandler.callCount > 0
+
           runs ->
             expect(atom.config.get('foo.bar')).toBe 'quux'
             expect(atom.config.get('foo.baz')).toBe 'bar'
 
         it "does not fire a change event for paths that did not change", ->
-          atom.config.onDidChange 'foo.bar', noChangeSpy = jasmine.createSpy()
+          atom.config.onDidChange 'foo.bar', noChangeSpy = jasmine.createSpy "unchanged"
 
-          writeConfigFile("foo: { bar: 'baz', baz: 'ok'}")
+          writeConfigFile "foo: { bar: 'baz', baz: 'ok'}", 2
           waitsFor 'update event', -> updatedHandler.callCount > 0
 
           runs ->
@@ -964,15 +971,16 @@ describe "Config", ->
               items:
                 type: 'string'
 
-            writeConfigFile("foo: { bar: ['baz', 'ok']}")
+            updatedHandler.reset()
+            writeConfigFile "foo: { bar: ['baz', 'ok']}", 4
             waitsFor 'update event', -> updatedHandler.callCount > 0
             runs -> updatedHandler.reset()
 
           it "does not fire a change event for paths that did not change", ->
-            noChangeSpy = jasmine.createSpy()
+            noChangeSpy = jasmine.createSpy "unchanged"
             atom.config.onDidChange('foo.bar', noChangeSpy)
 
-            writeConfigFile("foo: { bar: ['baz', 'ok'], baz: 'another'}")
+            writeConfigFile "foo: { bar: ['baz', 'ok'], baz: 'another'}", 2
             waitsFor 'update event', -> updatedHandler.callCount > 0
 
             runs ->
@@ -989,7 +997,7 @@ describe "Config", ->
               '*':
                 foo:
                   scoped: false
-            """
+            """, 2
             waitsFor 'update event', -> updatedHandler.callCount > 0
 
             runs ->
@@ -997,7 +1005,7 @@ describe "Config", ->
               expect(atom.config.get('foo.scoped', scope: ['.source.ruby'])).toBe false
 
           it "does not fire a change event for paths that did not change", ->
-            noChangeSpy = jasmine.createSpy()
+            noChangeSpy = jasmine.createSpy "no change"
             atom.config.onDidChange('foo.scoped', scope: ['.source.ruby'], noChangeSpy)
 
             writeConfigFile """
@@ -1007,7 +1015,7 @@ describe "Config", ->
               '.source.ruby':
                 foo:
                   scoped: true
-            """
+            """, 2
             waitsFor 'update event', -> updatedHandler.callCount > 0
 
             runs ->
@@ -1017,7 +1025,7 @@ describe "Config", ->
 
       describe "when the config file changes to omit a setting with a default", ->
         it "resets the setting back to the default", ->
-          writeConfigFile("foo: { baz: 'new'}")
+          writeConfigFile "foo: { baz: 'new'}", 2
           waitsFor 'update event', -> updatedHandler.callCount > 0
           runs ->
             expect(atom.config.get('foo.bar')).toBe 'def'
@@ -1025,20 +1033,20 @@ describe "Config", ->
 
       describe "when the config file changes to be empty", ->
         beforeEach ->
-          writeConfigFile("")
+          updatedHandler.reset()
+          writeConfigFile "", 4
           waitsFor 'update event', -> updatedHandler.callCount > 0
 
         it "resets all settings back to the defaults", ->
           expect(updatedHandler.callCount).toBe 1
           expect(atom.config.get('foo.bar')).toBe 'def'
           atom.config.set("hair", "blonde") # trigger a save
-          advanceClock(500)
-          expect(atom.config.save).toHaveBeenCalled()
+          waitsFor 'save', -> atom.config.save.callCount > 0
 
         describe "when the config file subsequently changes again to contain configuration", ->
           beforeEach ->
             updatedHandler.reset()
-            writeConfigFile("foo: bar: 'newVal'")
+            writeConfigFile "foo: bar: 'newVal'", 2
             waitsFor 'update event', -> updatedHandler.callCount > 0
 
           it "sets the setting to the value specified in the config file", ->
@@ -1047,25 +1055,26 @@ describe "Config", ->
       describe "when the config file changes to contain invalid cson", ->
         addErrorHandler = null
         beforeEach ->
-          atom.notifications.onDidAddNotification addErrorHandler = jasmine.createSpy()
-          writeConfigFile("}}}")
+          atom.notifications.onDidAddNotification addErrorHandler = jasmine.createSpy "error handler"
+          writeConfigFile "}}}", 4
           waitsFor "error to be logged", -> addErrorHandler.callCount > 0
 
         it "logs a warning and does not update config data", ->
           expect(updatedHandler.callCount).toBe 0
           expect(atom.config.get('foo.bar')).toBe 'baz'
+
           atom.config.set("hair", "blonde") # trigger a save
           expect(atom.config.save).not.toHaveBeenCalled()
 
         describe "when the config file subsequently changes again to contain valid cson", ->
           beforeEach ->
-            writeConfigFile("foo: bar: 'newVal'")
+            updatedHandler.reset()
+            writeConfigFile "foo: bar: 'newVal'", 6
             waitsFor 'update event', -> updatedHandler.callCount > 0
 
           it "updates the config data and resumes saving", ->
             atom.config.set("hair", "blonde")
-            advanceClock(500)
-            expect(atom.config.save).toHaveBeenCalled()
+            waitsFor 'save', -> atom.config.save.callCount > 0
 
     describe ".initializeConfigDirectory()", ->
       beforeEach ->
@@ -1741,3 +1750,35 @@ describe "Config", ->
 
           expect(atom.config.set('foo.bar.str_options', 'One')).toBe false
           expect(atom.config.get('foo.bar.str_options')).toEqual 'two'
+
+  describe "when .set/.unset is called prior to .loadUserConfig", ->
+    beforeEach ->
+      atom.config.settingsLoaded = false
+      fs.writeFileSync atom.config.configFilePath, """
+        '*':
+          foo:
+            bar: 'baz'
+          do:
+            ray: 'me'
+      """
+
+    it "ensures that early set and unset calls are replayed after the config is loaded from disk", ->
+      atom.config.unset 'foo.bar'
+      atom.config.set 'foo.qux', 'boo'
+
+      expect(atom.config.get('foo.bar')).toBeUndefined()
+      expect(atom.config.get('foo.qux')).toBe 'boo'
+      expect(atom.config.get('do.ray')).toBeUndefined()
+
+      advanceClock 100
+      expect(atom.config.save).not.toHaveBeenCalled()
+
+      atom.config.loadUserConfig()
+
+      advanceClock 100
+      waitsFor -> atom.config.save.callCount > 0
+
+      runs ->
+        expect(atom.config.get('foo.bar')).toBeUndefined()
+        expect(atom.config.get('foo.qux')).toBe 'boo'
+        expect(atom.config.get('do.ray')).toBe 'me'
diff --git a/src/config.coffee b/src/config.coffee
index bbcdad01f..01cb732ca 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -4,7 +4,7 @@ fs = require 'fs-plus'
 CSON = require 'season'
 path = require 'path'
 async = require 'async'
-pathWatcher = require 'pathwatcher'
+{watchPath} = require './path-watcher'
 {
   getValueAtKeyPath, setValueAtKeyPath, deleteValueAtKeyPath,
   pushKeyPath, splitKeyPath,
@@ -417,17 +417,24 @@ class Config
     @defaultSettings = {}
     @settings = {}
     @scopedSettingsStore = new ScopedPropertyStore
+
+    @settingsLoaded = false
+    @savePending = false
     @configFileHasErrors = false
     @transactDepth = 0
-    @savePending = false
-    @requestLoad = _.debounce(@loadUserConfig, 100)
-    @requestSave = =>
-      @savePending = true
-      debouncedSave.call(this)
-    save = =>
+    @pendingOperations = []
+
+    @requestLoad = _.debounce =>
+      @loadUserConfig()
+    , 100
+
+    debouncedSave = _.debounce =>
       @savePending = false
       @save()
-    debouncedSave = _.debounce(save, 100)
+    , 100
+    @requestSave = =>
+      @savePending = true
+      debouncedSave()
 
   shouldNotAccessFileSystem: -> not @enablePersistence
 
@@ -647,6 +654,10 @@ class Config
   # * `false` if the value was not able to be coerced to the type specified in the setting's schema.
   set: ->
     [keyPath, value, options] = arguments
+
+    unless @settingsLoaded
+      @pendingOperations.push => @set.call(this, keyPath, value, options)
+
     scopeSelector = options?.scopeSelector
     source = options?.source
     shouldSave = options?.save ? true
@@ -667,7 +678,8 @@ class Config
     else
       @setRawValue(keyPath, value)
 
-    @requestSave() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
+    if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors and @settingsLoaded
+      @requestSave()
     true
 
   # Essential: Restore the setting at `keyPath` to its default value.
@@ -677,6 +689,9 @@ class Config
   #   * `scopeSelector` (optional) {String}. See {::set}
   #   * `source` (optional) {String}. See {::set}
   unset: (keyPath, options) ->
+    unless @settingsLoaded
+      @pendingOperations.push => @unset.call(this, keyPath, options)
+
     {scopeSelector, source} = options ? {}
     source ?= @getUserConfigPath()
 
@@ -688,7 +703,8 @@ class Config
           setValueAtKeyPath(settings, keyPath, undefined)
           settings = withoutEmptyObjects(settings)
           @set(null, settings, {scopeSelector, source, priority: @priorityForSource(source)}) if settings?
-          @requestSave()
+          if source is @getUserConfigPath() and not @configFileHasErrors and @settingsLoaded
+            @requestSave()
       else
         @scopedSettingsStore.removePropertiesForSourceAndSelector(source, scopeSelector)
         @emitChangeEvent()
@@ -848,21 +864,26 @@ class Config
 
   loadUserConfig: ->
     return if @shouldNotAccessFileSystem()
+    return if @savePending
 
     try
-      unless fs.existsSync(@configFilePath)
-        fs.makeTreeSync(path.dirname(@configFilePath))
-        CSON.writeFileSync(@configFilePath, {})
+      fs.makeTreeSync(path.dirname(@configFilePath))
+      CSON.writeFileSync(@configFilePath, {}, {flag: 'wx'}) # fails if file exists
     catch error
-      @configFileHasErrors = true
-      @notifyFailure("Failed to initialize `#{path.basename(@configFilePath)}`", error.stack)
-      return
+      if error.code isnt 'EEXIST'
+        @configFileHasErrors = true
+        @notifyFailure("Failed to initialize `#{path.basename(@configFilePath)}`", error.stack)
+        return
 
     try
-      unless @savePending
-        userConfig = CSON.readFileSync(@configFilePath)
-        @resetUserSettings(userConfig)
-        @configFileHasErrors = false
+      userConfig = CSON.readFileSync(@configFilePath)
+      userConfig = {} if userConfig is null
+
+      unless isPlainObject(userConfig)
+        throw new Error("`#{path.basename(@configFilePath)}` must contain valid JSON or CSON")
+
+      @resetUserSettings(userConfig)
+      @configFileHasErrors = false
     catch error
       @configFileHasErrors = true
       message = "Failed to load `#{path.basename(@configFilePath)}`"
@@ -880,8 +901,10 @@ class Config
     return if @shouldNotAccessFileSystem()
 
     try
-      @watchSubscription ?= pathWatcher.watch @configFilePath, (eventType) =>
-        @requestLoad() if eventType is 'change' and @watchSubscription?
+      @watchSubscriptionPromise ?= watchPath @configFilePath, {}, (events) =>
+        for {action} in events
+          if action in ['created', 'modified', 'renamed'] and @watchSubscriptionPromise?
+            @requestLoad()
     catch error
       @notifyFailure """
         Unable to watch path: `#{path.basename(@configFilePath)}`. Make sure you have permissions to
@@ -890,9 +913,11 @@ class Config
         [watches]:https://github.com/atom/atom/blob/master/docs/build-instructions/linux.md#typeerror-unable-to-watch-path
       """
 
+    @watchSubscriptionPromise
+
   unobserveUserConfig: ->
-    @watchSubscription?.close()
-    @watchSubscription = null
+    @watchSubscriptionPromise?.then (watcher) -> watcher?.dispose()
+    @watchSubscriptionPromise = null
 
   notifyFailure: (errorMessage, detail) ->
     @notificationManager?.addError(errorMessage, {detail, dismissable: true})
@@ -915,11 +940,6 @@ class Config
   ###
 
   resetUserSettings: (newSettings) ->
-    unless isPlainObject(newSettings)
-      @settings = {}
-      @emitChangeEvent()
-      return
-
     if newSettings.global?
       newSettings['*'] = newSettings.global
       delete newSettings.global
@@ -932,8 +952,11 @@ class Config
 
     @transact =>
       @settings = {}
+      @settingsLoaded = true
       @set(key, value, save: false) for key, value of newSettings
-      return
+      if @pendingOperations.length
+        op() for op in @pendingOperations
+        @pendingOperations = []
 
   getRawValue: (keyPath, options) ->
     unless options?.excludeSources?.indexOf(@getUserConfigPath()) >= 0