diff --git a/build/Gruntfile.coffee b/build/Gruntfile.coffee
index 63afc2fd7..60d5916b8 100644
--- a/build/Gruntfile.coffee
+++ b/build/Gruntfile.coffee
@@ -38,7 +38,6 @@ module.exports = (grunt) ->
   buildDir = grunt.option('build-dir')
   buildDir ?= path.join(os.tmpdir(), 'atom-build')
   buildDir = path.resolve(buildDir)
-  disableAutoUpdate = grunt.option('no-auto-update') ? false
 
   channel = grunt.option('channel')
   releasableBranches = ['stable', 'beta']
@@ -181,7 +180,7 @@ module.exports = (grunt) ->
     pkg: grunt.file.readJSON('package.json')
 
     atom: {
-      appName, channel, metadata, disableAutoUpdate,
+      appName, channel, metadata,
       appFileName, apmFileName,
       appDir, buildDir, contentsDir, installDir, shellAppDir, symbolsDir,
     }
@@ -257,7 +256,7 @@ module.exports = (grunt) ->
       outputDir: 'electron'
       downloadDir: electronDownloadDir
       rebuild: true  # rebuild native modules after electron is updated
-      token: process.env.ATOM_ACCESS_TOKEN
+      token: process.env.ATOM_ACCESS_TOKEN ? 'da809a6077bb1b0aa7c5623f7b2d5f1fec2faae4'
 
     'create-windows-installer':
       installer:
diff --git a/build/tasks/build-task.coffee b/build/tasks/build-task.coffee
index 213aa0da4..a86c7c1f4 100644
--- a/build/tasks/build-task.coffee
+++ b/build/tasks/build-task.coffee
@@ -186,5 +186,4 @@ module.exports = (grunt) ->
     dependencies = ['compile', 'generate-license:save', 'generate-module-cache', 'compile-packages-slug']
     dependencies.push('copy-info-plist') if process.platform is 'darwin'
     dependencies.push('set-exe-icon') if process.platform is 'win32'
-    dependencies.push('disable-autoupdate') if grunt.config.get('atom.disableAutoUpdate')
     grunt.task.run(dependencies...)
diff --git a/build/tasks/disable-autoupdate-task.coffee b/build/tasks/disable-autoupdate-task.coffee
deleted file mode 100644
index 7517543da..000000000
--- a/build/tasks/disable-autoupdate-task.coffee
+++ /dev/null
@@ -1,12 +0,0 @@
-fs = require 'fs'
-path = require 'path'
-
-module.exports = (grunt) ->
-
-  grunt.registerTask 'disable-autoupdate', 'Set up disableAutoUpdate field in package.json file', ->
-    appDir = fs.realpathSync(grunt.config.get('atom.appDir'))
-
-    metadata = grunt.file.readJSON(path.join(appDir, 'package.json'))
-    metadata._disableAutoUpdate = grunt.config.get('atom.disableAutoUpdate')
-
-    grunt.file.write(path.join(appDir, 'package.json'), JSON.stringify(metadata))
diff --git a/dot-atom/.gitignore b/dot-atom/.gitignore
index 81af3f689..e5c80ce23 100644
--- a/dot-atom/.gitignore
+++ b/dot-atom/.gitignore
@@ -1,5 +1,6 @@
-storage
+blob-store
 compile-cache
 dev
-.npm
+storage
 .node-gyp
+.npm
diff --git a/menus/darwin.cson b/menus/darwin.cson
index 52b7a5bc8..0195bde71 100644
--- a/menus/darwin.cson
+++ b/menus/darwin.cson
@@ -139,7 +139,6 @@
   {
     label: 'View'
     submenu: [
-      { label: 'Reload', command: 'window:reload' }
       { label: 'Toggle Full Screen', command: 'window:toggle-full-screen' }
       {
         label: 'Panes'
@@ -164,6 +163,7 @@
         label: 'Developer'
         submenu: [
           { label: 'Open In Dev Mode…', command: 'application:open-dev' }
+          { label: 'Reload Window', command: 'window:reload' }
           { label: 'Run Package Specs', command: 'window:run-package-specs' }
           { label: 'Toggle Developer Tools', command: 'window:toggle-dev-tools' }
         ]
diff --git a/menus/linux.cson b/menus/linux.cson
index fa831b4a4..9f251d67f 100644
--- a/menus/linux.cson
+++ b/menus/linux.cson
@@ -95,7 +95,6 @@
   {
     label: '&View'
     submenu: [
-      { label: '&Reload', command: 'window:reload' }
       { label: 'Toggle &Full Screen', command: 'window:toggle-full-screen' }
       { label: 'Toggle Menu Bar', command: 'window:toggle-menu-bar' }
       {
@@ -121,6 +120,7 @@
         label: 'Developer'
         submenu: [
           { label: 'Open In &Dev Mode…', command: 'application:open-dev' }
+          { label: '&Reload Window', command: 'window:reload' }
           { label: 'Run Package &Specs', command: 'window:run-package-specs' }
           { label: 'Toggle Developer &Tools', command: 'window:toggle-dev-tools' }
         ]
diff --git a/menus/win32.cson b/menus/win32.cson
index 04da3d388..ad0461898 100644
--- a/menus/win32.cson
+++ b/menus/win32.cson
@@ -94,7 +94,6 @@
   {
     label: '&View'
     submenu: [
-      { label: '&Reload', command: 'window:reload' }
       { label: 'Toggle &Full Screen', command: 'window:toggle-full-screen' }
       { label: 'Toggle Menu Bar', command: 'window:toggle-menu-bar' }
       {
@@ -120,6 +119,7 @@
         label: 'Developer'
         submenu: [
           { label: 'Open In &Dev Mode…', command: 'application:open-dev' }
+          { label: '&Reload Window', command: 'window:reload' }
           { label: 'Run Package &Specs', command: 'window:run-package-specs' }
           { label: 'Toggle Developer &Tools', command: 'window:toggle-dev-tools' }
         ]
diff --git a/package.json b/package.json
index aef164c39..3b67d6a5d 100644
--- a/package.json
+++ b/package.json
@@ -52,7 +52,7 @@
     "service-hub": "^0.7.0",
     "source-map-support": "^0.3.2",
     "temp": "0.8.1",
-    "text-buffer": "8.1.3",
+    "text-buffer": "8.1.4",
     "typescript-simple": "1.0.0",
     "underscore-plus": "^1.6.6",
     "yargs": "^3.23.0"
@@ -65,9 +65,9 @@
     "base16-tomorrow-dark-theme": "1.1.0",
     "base16-tomorrow-light-theme": "1.1.1",
     "one-dark-ui": "1.1.9",
-    "one-dark-syntax": "1.1.1",
-    "one-light-syntax": "1.1.1",
     "one-light-ui": "1.1.9",
+    "one-dark-syntax": "1.1.2",
+    "one-light-syntax": "1.1.2",
     "solarized-dark-syntax": "0.39.0",
     "solarized-light-syntax": "0.23.0",
     "about": "1.1.0",
@@ -128,7 +128,7 @@
     "language-hyperlink": "0.16.0",
     "language-java": "0.17.0",
     "language-javascript": "0.105.0",
-    "language-json": "0.17.2",
+    "language-json": "0.17.3",
     "language-less": "0.29.0",
     "language-make": "0.21.0",
     "language-mustache": "0.13.0",
@@ -136,7 +136,7 @@
     "language-perl": "0.32.0",
     "language-php": "0.36.0",
     "language-property-list": "0.8.0",
-    "language-python": "0.42.1",
+    "language-python": "0.43.0",
     "language-ruby": "0.67.0",
     "language-ruby-on-rails": "0.25.0",
     "language-sass": "0.45.0",
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index eab2f6f04..c431fea5f 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -872,6 +872,26 @@ describe "Config", ->
           atom.config.loadUserConfig()
           expect(atom.config.get("foo.bar")).toBe "baz"
 
+      describe "when the config file fails to load", ->
+        addErrorHandler = null
+
+        beforeEach ->
+          atom.notifications.onDidAddNotification addErrorHandler = jasmine.createSpy()
+          spyOn(fs, "existsSync").andCallFake ->
+            error = new Error()
+            error.code = 'EPERM'
+            throw error
+
+        it "creates a notification and does not try to save later changes to disk", ->
+          load = -> atom.config.loadUserConfig()
+          expect(load).not.toThrow()
+          expect(addErrorHandler.callCount).toBe 1
+
+          atom.config.set("foo.bar", "baz")
+          advanceClock(100)
+          expect(atom.config.save).not.toHaveBeenCalled()
+          expect(atom.config.get("foo.bar")).toBe "baz"
+
     describe ".observeUserConfig()", ->
       updatedHandler = null
 
diff --git a/src/browser/application-menu.coffee b/src/browser/application-menu.coffee
index fef9f90fa..b0a6e3267 100644
--- a/src/browser/application-menu.coffee
+++ b/src/browser/application-menu.coffee
@@ -101,8 +101,6 @@ class ApplicationMenu
     downloadingUpdateItem.visible = false
     installUpdateItem.visible = false
 
-    return if @autoUpdateManager.isDisabled()
-
     switch state
       when 'idle', 'error', 'no-update-available'
         checkForUpdateItem.visible = true
@@ -117,9 +115,10 @@ class ApplicationMenu
   #
   # Returns an Array of menu item Objects.
   getDefaultTemplate: ->
-    template = [
+    [
       label: "Atom"
       submenu: [
+          {label: "Check for Update", metadata: {autoUpdate: true}}
           {label: 'Reload', accelerator: 'Command+R', click: => @focusedWindow()?.reload()}
           {label: 'Close Window', accelerator: 'Command+Shift+W', click: => @focusedWindow()?.close()}
           {label: 'Toggle Dev Tools', accelerator: 'Command+Alt+I', click: => @focusedWindow()?.toggleDevTools()}
@@ -127,10 +126,6 @@ class ApplicationMenu
       ]
     ]
 
-    # Add `Check for Update` button if autoUpdateManager is enabled.
-    template[0].submenu.unshift({label: "Check for Update", metadata: {autoUpdate: true}}) unless @autoUpdateManager.isDisabled()
-    template
-
   focusedWindow: ->
     _.find global.atomApplication.windows, (atomWindow) -> atomWindow.isFocused()
 
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 954eb868d..d68141f5c 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -69,8 +69,7 @@ class AtomApplication
     @pidsToOpenWindows = {}
     @windows = []
 
-    disableAutoUpdate = require(path.join(@resourcePath, 'package.json'))._disableAutoUpdate ? false
-    @autoUpdateManager = new AutoUpdateManager(@version, options.test, disableAutoUpdate)
+    @autoUpdateManager = new AutoUpdateManager(@version, options.test, @resourcePath)
     @applicationMenu = new ApplicationMenu(@version, @autoUpdateManager)
     @atomProtocolHandler = new AtomProtocolHandler(@resourcePath, @safeMode)
 
diff --git a/src/browser/auto-update-manager.coffee b/src/browser/auto-update-manager.coffee
index 63a79b60f..2df338761 100644
--- a/src/browser/auto-update-manager.coffee
+++ b/src/browser/auto-update-manager.coffee
@@ -1,5 +1,6 @@
 autoUpdater = null
 _ = require 'underscore-plus'
+Config = require '../config'
 {EventEmitter} = require 'events'
 path = require 'path'
 
@@ -15,10 +16,13 @@ module.exports =
 class AutoUpdateManager
   _.extend @prototype, EventEmitter.prototype
 
-  constructor: (@version, @testMode, @disabled) ->
+  constructor: (@version, @testMode, resourcePath) ->
     @state = IdleState
     @iconPath = path.resolve(__dirname, '..', '..', 'resources', 'atom.png')
     @feedUrl = "https://atom.io/api/updates?version=#{@version}"
+    @config = new Config({configDirPath: process.env.ATOM_HOME, resourcePath, enablePersistence: true})
+    @config.setSchema null, {type: 'object', properties: _.clone(require('../config-schema'))}
+    @config.load()
     process.nextTick => @setupAutoUpdater()
 
   setupAutoUpdater: ->
@@ -46,9 +50,13 @@ class AutoUpdateManager
       @setState(UpdateAvailableState)
       @emitUpdateAvailableEvent(@getWindows()...)
 
-    # Only check for updates periodically if enabled and running in release
-    # version.
-    @scheduleUpdateCheck() unless /\w{7}/.test(@version) or @disabled
+    @config.onDidChange 'core.automaticallyUpdate', ({newValue}) =>
+      if newValue
+        @scheduleUpdateCheck()
+      else
+        @cancelScheduledUpdateCheck()
+
+    @scheduleUpdateCheck() if @config.get 'core.automaticallyUpdate'
 
     switch process.platform
       when 'win32'
@@ -56,9 +64,6 @@ class AutoUpdateManager
       when 'linux'
         @setState(UnsupportedState)
 
-  isDisabled: ->
-    @disabled
-
   emitUpdateAvailableEvent: (windows...) ->
     return unless @releaseVersion?
     for atomWindow in windows
@@ -74,10 +79,18 @@ class AutoUpdateManager
     @state
 
   scheduleUpdateCheck: ->
-    checkForUpdates = => @check(hidePopups: true)
-    fourHours = 1000 * 60 * 60 * 4
-    setInterval(checkForUpdates, fourHours)
-    checkForUpdates()
+    # Only schedule update check periodically if running in release version and
+    # and there is no existing scheduled update check.
+    unless /\w{7}/.test(@version) or @checkForUpdatesIntervalID
+      checkForUpdates = => @check(hidePopups: true)
+      fourHours = 1000 * 60 * 60 * 4
+      @checkForUpdatesIntervalID = setInterval(checkForUpdates, fourHours)
+      checkForUpdates()
+
+  cancelScheduledUpdateCheck: ->
+    if @checkForUpdatesIntervalID
+      clearInterval(@checkForUpdatesIntervalID)
+      @checkForUpdatesIntervalID = null
 
   check: ({hidePopups}={}) ->
     unless hidePopups
diff --git a/src/config-schema.coffee b/src/config-schema.coffee
index d9c0c1d21..88e00c71d 100644
--- a/src/config-schema.coffee
+++ b/src/config-schema.coffee
@@ -104,6 +104,10 @@ module.exports =
         description: 'Automatically open an empty editor on startup.'
         type: 'boolean'
         default: true
+      automaticallyUpdate:
+        description: 'Automatically update Atom when a new release is available.'
+        type: 'boolean'
+        default: true
 
   editor:
     type: 'object'
diff --git a/src/config.coffee b/src/config.coffee
index 2e4387732..2a883a57d 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -779,9 +779,14 @@ class Config
   loadUserConfig: ->
     return if @shouldNotAccessFileSystem()
 
-    unless fs.existsSync(@configFilePath)
-      fs.makeTreeSync(path.dirname(@configFilePath))
-      CSON.writeFileSync(@configFilePath, {})
+    try
+      unless fs.existsSync(@configFilePath)
+        fs.makeTreeSync(path.dirname(@configFilePath))
+        CSON.writeFileSync(@configFilePath, {})
+    catch error
+      @configFileHasErrors = true
+      @notifyFailure("Failed to initialize `#{path.basename(@configFilePath)}`", error.stack)
+      return
 
     try
       unless @savePending
@@ -820,7 +825,7 @@ class Config
     @watchSubscription = null
 
   notifyFailure: (errorMessage, detail) ->
-    @notificationManager.addError(errorMessage, {detail, dismissable: true})
+    @notificationManager?.addError(errorMessage, {detail, dismissable: true})
 
   save: ->
     return if @shouldNotAccessFileSystem()
diff --git a/src/pane.coffee b/src/pane.coffee
index 412fc5251..c006e29fe 100644
--- a/src/pane.coffee
+++ b/src/pane.coffee
@@ -721,30 +721,28 @@ class Pane extends Model
       message = "#{message} '#{itemPath}'" if itemPath
       @notificationManager.addWarning(message, options)
 
-    if error.code is 'EISDIR' or error.message?.endsWith?('is a directory')
+    customMessage = @getMessageForErrorCode(error.code)
+    if customMessage?
+      addWarningWithPath("Unable to save file: #{customMessage}")
+    else if error.code is 'EISDIR' or error.message?.endsWith?('is a directory')
       @notificationManager.addWarning("Unable to save file: #{error.message}")
-    else if error.code is 'EACCES'
-      addWarningWithPath('Unable to save file: Permission denied')
     else if error.code in ['EPERM', 'EBUSY', 'UNKNOWN', 'EEXIST', 'ELOOP', 'EAGAIN']
       addWarningWithPath('Unable to save file', detail: error.message)
-    else if error.code is 'EROFS'
-      addWarningWithPath('Unable to save file: Read-only file system')
-    else if error.code is 'ENOSPC'
-      addWarningWithPath('Unable to save file: No space left on device')
-    else if error.code is 'ENXIO'
-      addWarningWithPath('Unable to save file: No such device or address')
-    else if error.code is 'ENOTSUP'
-      addWarningWithPath('Unable to save file: Operation not supported on socket')
-    else if error.code is 'EIO'
-      addWarningWithPath('Unable to save file: I/O error writing file')
-    else if error.code is 'EINTR'
-      addWarningWithPath('Unable to save file: Interrupted system call')
-    else if error.code is 'ECONNRESET'
-      addWarningWithPath('Unable to save file: Connection reset')
-    else if error.code is 'ESPIPE'
-      addWarningWithPath('Unable to save file: Invalid seek')
     else if errorMatch = /ENOTDIR, not a directory '([^']+)'/.exec(error.message)
       fileName = errorMatch[1]
       @notificationManager.addWarning("Unable to save file: A directory in the path '#{fileName}' could not be written to")
     else
       throw error
+
+  getMessageForErrorCode: (errorCode) ->
+    switch errorCode
+      when 'EACCES' then 'Permission denied'
+      when 'ECONNRESET' then 'Connection reset'
+      when 'EINTR' then 'Interrupted system call'
+      when 'EIO' then 'I/O error writing file'
+      when 'ENOSPC' then 'No space left on device'
+      when 'ENOTSUP' then 'Operation not supported on socket'
+      when 'ENXIO' then 'No such device or address'
+      when 'EROFS' then 'Read-only file system'
+      when 'ESPIPE' then 'Invalid seek'
+      when 'ETIMEDOUT' then 'Connection timed out'
diff --git a/src/project.coffee b/src/project.coffee
index d59c041cb..714511f9a 100644
--- a/src/project.coffee
+++ b/src/project.coffee
@@ -288,7 +288,7 @@ class Project extends Model
       'atom.repository-provider',
       '^0.1.0',
       (provider) =>
-        @repositoryProviders.push(provider)
+        @repositoryProviders.unshift(provider)
         @setPaths(@getPaths()) if null in @repositories
         new Disposable =>
           @repositoryProviders.splice(@repositoryProviders.indexOf(provider), 1)
diff --git a/src/workspace.coffee b/src/workspace.coffee
index f64f58ee0..07e69cdcf 100644
--- a/src/workspace.coffee
+++ b/src/workspace.coffee
@@ -475,7 +475,7 @@ class Workspace extends Model
         when 'EACCES'
           @notificationManager.addWarning("Permission denied '#{error.path}'")
           return Promise.resolve()
-        when 'EPERM', 'EBUSY', 'ENXIO', 'EIO', 'ENOTCONN', 'UNKNOWN', 'ECONNRESET', 'EINVAL', 'EMFILE', 'ENOTDIR'
+        when 'EPERM', 'EBUSY', 'ENXIO', 'EIO', 'ENOTCONN', 'UNKNOWN', 'ECONNRESET', 'EINVAL', 'EMFILE', 'ENOTDIR', 'EAGAIN'
           @notificationManager.addWarning("Unable to open '#{error.path ? uri}'", detail: error.message)
           return Promise.resolve()
         else