diff --git a/apm/package.json b/apm/package.json
index 423e31a12..1dce7e90b 100644
--- a/apm/package.json
+++ b/apm/package.json
@@ -6,6 +6,6 @@
     "url": "https://github.com/atom/atom.git"
   },
   "dependencies": {
-    "atom-package-manager": "0.166.0"
+    "atom-package-manager": "0.167.0"
   }
 }
diff --git a/package.json b/package.json
index 026c5dfbb..cf4634cf6 100644
--- a/package.json
+++ b/package.json
@@ -37,7 +37,7 @@
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
     "git-utils": "^3.0.0",
-    "grim": "1.4.0",
+    "grim": "1.4.1",
     "jasmine-json": "~0.0",
     "jasmine-tagged": "^1.1.4",
     "jquery": "^2.1.1",
@@ -84,19 +84,24 @@
     "solarized-dark-syntax": "0.35.0",
     "solarized-light-syntax": "0.21.0",
     "archive-view": "0.57.0",
-    "autocomplete": "0.47.0",
+    "autocomplete-atom-api": "0.9.0",
+    "autocomplete-css": "0.7.2",
+    "autocomplete-emojis": "2.2.2",
+    "autocomplete-html": "0.7.2",
+    "autocomplete-plus": "2.15.2",
+    "autocomplete-snippets": "1.6.1",
     "autoflow": "0.23.0",
     "autosave": "0.20.0",
     "background-tips": "0.24.0",
     "bookmarks": "0.35.0",
     "bracket-matcher": "0.74.0",
     "command-palette": "0.35.0",
-    "deprecation-cop": "0.46.0",
+    "deprecation-cop": "0.47.0",
     "dev-live-reload": "0.46.0",
     "encoding-selector": "0.20.0",
     "exception-reporting": "0.24.0",
-    "find-and-replace": "0.161.0",
-    "fuzzy-finder": "0.83.0",
+    "find-and-replace": "0.162.0",
+    "fuzzy-finder": "0.84.0",
     "git-diff": "0.55.0",
     "go-to-line": "0.30.0",
     "grammar-selector": "0.47.0",
@@ -105,15 +110,15 @@
     "keybinding-resolver": "0.32.0",
     "link": "0.30.0",
     "markdown-preview": "0.148.0",
-    "metrics": "0.45.0",
-    "notifications": "0.43.0",
+    "metrics": "0.47.0",
+    "notifications": "0.44.0",
     "open-on-github": "0.36.0",
     "package-generator": "0.39.0",
     "release-notes": "0.52.0",
     "settings-view": "0.199.0",
     "snippets": "0.89.0",
     "spell-check": "0.58.0",
-    "status-bar": "0.71.0",
+    "status-bar": "0.72.0",
     "styleguide": "0.44.0",
     "symbols-view": "0.96.0",
     "tabs": "0.68.0",
@@ -128,7 +133,7 @@
     "language-coffee-script": "0.40.0",
     "language-csharp": "0.5.0",
     "language-css": "0.29.0",
-    "language-gfm": "0.73.0",
+    "language-gfm": "0.74.0",
     "language-git": "0.10.0",
     "language-go": "0.26.0",
     "language-html": "0.37.0",
diff --git a/spec/package-manager-spec.coffee b/spec/package-manager-spec.coffee
index 92dc21a13..1244ab984 100644
--- a/spec/package-manager-spec.coffee
+++ b/spec/package-manager-spec.coffee
@@ -824,3 +824,37 @@ describe "PackageManager", ->
           expect(atom.config.get('core.themes')).not.toContain packageName
           expect(atom.config.get('core.themes')).not.toContain packageName
           expect(atom.config.get('core.disabledPackages')).not.toContain packageName
+
+  describe "deleting non-bundled autocomplete packages", ->
+    [autocompleteCSSPath, autocompletePlusPath] = []
+    fs = require 'fs-plus'
+    path = require 'path'
+
+    beforeEach ->
+      fixturePath = path.resolve(__dirname, './fixtures/packages')
+      autocompleteCSSPath = path.join(fixturePath, 'autocomplete-css')
+      autocompletePlusPath = path.join(fixturePath, 'autocomplete-plus')
+
+      try
+        fs.mkdirSync(autocompleteCSSPath)
+        fs.writeFileSync(path.join(autocompleteCSSPath, 'package.json'), '{}')
+        fs.symlinkSync(path.join(fixturePath, 'package-with-main'), autocompletePlusPath, 'dir')
+
+      expect(fs.isDirectorySync(autocompleteCSSPath)).toBe true
+      expect(fs.isSymbolicLinkSync(autocompletePlusPath)).toBe true
+
+      jasmine.unspy(atom.packages, 'uninstallAutocompletePlus')
+
+    afterEach ->
+      try
+        fs.unlink autocompletePlusPath, ->
+
+    it "removes the packages", ->
+      atom.packages.loadPackages()
+
+      waitsFor ->
+        not fs.isDirectorySync(autocompleteCSSPath)
+
+      runs ->
+        expect(fs.isDirectorySync(autocompleteCSSPath)).toBe false
+        expect(fs.isSymbolicLinkSync(autocompletePlusPath)).toBe true
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index e21876e8d..15874ff6f 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -140,6 +140,8 @@ beforeEach ->
   spyOn(clipboard, 'writeText').andCallFake (text) -> clipboardContent = text
   spyOn(clipboard, 'readText').andCallFake -> clipboardContent
 
+  spyOn(atom.packages, 'uninstallAutocompletePlus')
+
   addCustomMatchers(this)
 
 afterEach ->
diff --git a/spec/text-editor-spec.coffee b/spec/text-editor-spec.coffee
index dd6b69f26..d1d311088 100644
--- a/spec/text-editor-spec.coffee
+++ b/spec/text-editor-spec.coffee
@@ -36,23 +36,21 @@ describe "TextEditor", ->
 
     it "preserves the invisibles setting", ->
       atom.config.set('editor.showInvisibles', true)
-      previousInvisibles = editor.displayBuffer.invisibles
+      previousInvisibles = editor.tokenizedLineForScreenRow(0).invisibles
 
       editor2 = editor.testSerialization()
 
-      expect(editor2.displayBuffer.invisibles).toEqual previousInvisibles
-      expect(editor2.displayBuffer.tokenizedBuffer.invisibles).toEqual previousInvisibles
+      expect(previousInvisibles).toBeDefined()
+      expect(editor2.displayBuffer.tokenizedLineForScreenRow(0).invisibles).toEqual previousInvisibles
 
     it "updates invisibles if the settings have changed between serialization and deserialization", ->
       atom.config.set('editor.showInvisibles', true)
-      previousInvisibles = editor.displayBuffer.invisibles
 
       state = editor.serialize()
       atom.config.set('editor.invisibles', eol: '?')
       editor2 = TextEditor.deserialize(state)
 
-      expect(editor2.displayBuffer.invisibles.eol).toBe '?'
-      expect(editor2.displayBuffer.tokenizedBuffer.invisibles.eol).toBe '?'
+      expect(editor.tokenizedLineForScreenRow(0).invisibles.eol).toBe '?'
 
   describe "when the editor is constructed with an initialLine option", ->
     it "positions the cursor on the specified line", ->
diff --git a/spec/tokenized-buffer-spec.coffee b/spec/tokenized-buffer-spec.coffee
index 3cd776c2b..9d92335af 100644
--- a/spec/tokenized-buffer-spec.coffee
+++ b/spec/tokenized-buffer-spec.coffee
@@ -611,7 +611,8 @@ describe "TokenizedBuffer", ->
       tokenizedBuffer = new TokenizedBuffer({buffer})
       fullyTokenize(tokenizedBuffer)
 
-      tokenizedBuffer.setInvisibles(space: 'S', tab: 'T')
+      atom.config.set("editor.showInvisibles", true)
+      atom.config.set("editor.invisibles", space: 'S', tab: 'T')
       fullyTokenize(tokenizedBuffer)
 
       expect(tokenizedBuffer.tokenizedLineForRow(0).text).toBe "SST Sa line with tabsTand T spacesSTS"
@@ -623,7 +624,7 @@ describe "TokenizedBuffer", ->
       tokenizedBuffer = new TokenizedBuffer({buffer})
 
       atom.config.set('editor.showInvisibles', true)
-      tokenizedBuffer.setInvisibles(cr: 'R', eol: 'N')
+      atom.config.set("editor.invisibles", cr: 'R', eol: 'N')
       fullyTokenize(tokenizedBuffer)
 
       expect(tokenizedBuffer.tokenizedLineForRow(0).endOfLineInvisibles).toEqual ['R', 'N']
@@ -634,7 +635,7 @@ describe "TokenizedBuffer", ->
       expect(left.endOfLineInvisibles).toBe null
       expect(right.endOfLineInvisibles).toEqual ['R', 'N']
 
-      tokenizedBuffer.setInvisibles(cr: 'R', eol: false)
+      atom.config.set("editor.invisibles", cr: 'R', eol: false)
       expect(tokenizedBuffer.tokenizedLineForRow(0).endOfLineInvisibles).toEqual ['R']
       expect(tokenizedBuffer.tokenizedLineForRow(1).endOfLineInvisibles).toEqual []
 
@@ -688,7 +689,8 @@ describe "TokenizedBuffer", ->
     it "sets leading and trailing whitespace correctly on a line with invisible characters that is copied", ->
       buffer.setText("  \t a line with tabs\tand \tspaces \t ")
 
-      tokenizedBuffer.setInvisibles(space: 'S', tab: 'T')
+      atom.config.set("editor.showInvisibles", true)
+      atom.config.set("editor.invisibles", space: 'S', tab: 'T')
       fullyTokenize(tokenizedBuffer)
 
       line = tokenizedBuffer.tokenizedLineForRow(0).copy()
@@ -696,7 +698,8 @@ describe "TokenizedBuffer", ->
       expect(line.tokens[line.tokens.length - 1].firstTrailingWhitespaceIndex).toBe 0
 
     it "sets the ::firstNonWhitespaceIndex and ::firstTrailingWhitespaceIndex correctly when tokens are split for soft-wrapping", ->
-      tokenizedBuffer.setInvisibles(space: 'S')
+      atom.config.set("editor.showInvisibles", true)
+      atom.config.set("editor.invisibles", space: 'S')
       buffer.setText(" token ")
       fullyTokenize(tokenizedBuffer)
       token = tokenizedBuffer.tokenizedLines[0].tokens[0]
diff --git a/src/atom.coffee b/src/atom.coffee
index 1cf63b397..0d029b61d 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -223,6 +223,8 @@ class Atom extends Model
     @disposables?.dispose()
     @disposables = new CompositeDisposable
 
+    @displayWindow() unless @inSpecMode()
+
     @setBodyPlatformClass()
 
     @loadTime = null
@@ -483,22 +485,27 @@ class Atom extends Model
   # Extended: Set the full screen state of the current window.
   setFullScreen: (fullScreen=false) ->
     ipc.send('call-window-method', 'setFullScreen', fullScreen)
-    if fullScreen then document.body.classList.add("fullscreen") else document.body.classList.remove("fullscreen")
+    if fullScreen
+      document.body.classList.add("fullscreen")
+    else
+      document.body.classList.remove("fullscreen")
 
   # Extended: Toggle the full screen state of the current window.
   toggleFullScreen: ->
     @setFullScreen(not @isFullScreen())
 
-  # Schedule the window to be shown and focused on the next tick.
+  # Restore the window to its previous dimensions and show it.
   #
-  # This is done in a next tick to prevent a white flicker from occurring
-  # if called synchronously.
-  displayWindow: ({maximize}={}) ->
+  # Also restores the full screen and maximized state on the next tick to
+  # prevent resize glitches.
+  displayWindow: ->
+    dimensions = @restoreWindowDimensions()
+    @show()
+
     setImmediate =>
-      @show()
       @focus()
-      @setFullScreen(true) if @workspace.fullScreen
-      @maximize() if maximize
+      @setFullScreen(true) if @workspace?.fullScreen
+      @maximize() if dimensions?.maximized and process.platform isnt 'darwin'
 
   # Get the dimensions of this window.
   #
@@ -572,6 +579,13 @@ class Atom extends Model
     dimensions = @getWindowDimensions()
     @state.windowDimensions = dimensions if @isValidDimensions(dimensions)
 
+  storeWindowBackground: ->
+    return if @inSpecMode()
+
+    workspaceElement = @views.getView(@workspace)
+    backgroundColor = window.getComputedStyle(workspaceElement)['background-color']
+    window.localStorage.setItem('atom:window-background-color', backgroundColor)
+
   # Call this method when establishing a real application window.
   startEditorWindow: ->
     {safeMode} = @getLoadSettings()
@@ -582,7 +596,6 @@ class Atom extends Model
     CommandInstaller.installApmCommand false, (error) ->
       console.warn error.message if error?
 
-    dimensions = @restoreWindowDimensions()
     @loadConfig()
     @keymaps.loadBundledKeymaps()
     @themes.loadBaseStylesheets()
@@ -602,12 +615,10 @@ class Atom extends Model
 
     @openInitialEmptyEditorIfNecessary()
 
-    maximize = dimensions?.maximized and process.platform isnt 'darwin'
-    @displayWindow({maximize})
-
   unloadEditorWindow: ->
     return if not @project
 
+    @storeWindowBackground()
     @state.grammars = @grammars.serialize()
     @state.project = @project.serialize()
     @state.workspace = @workspace.serialize()
@@ -747,7 +758,7 @@ class Atom extends Model
       # Only reload stylesheets from non-theme packages
       for pack in @packages.getActivePackages() when pack.getType() isnt 'theme'
         pack.reloadStylesheets?()
-      null
+      return
 
   # Notify the browser project of the window's current project path
   watchProjectPath: ->
diff --git a/src/browser/application-menu.coffee b/src/browser/application-menu.coffee
index a845c682f..74da80e43 100644
--- a/src/browser/application-menu.coffee
+++ b/src/browser/application-menu.coffee
@@ -9,11 +9,10 @@ _ = require 'underscore-plus'
 # and maintain the state of all menu items.
 module.exports =
 class ApplicationMenu
-  constructor: (@version) ->
+  constructor: (@version, @autoUpdateManager) ->
     @windowTemplates = new WeakMap()
     @setActiveTemplate(@getDefaultTemplate())
-    global.atomApplication.autoUpdateManager.on 'state-changed', (state) =>
-      @showUpdateMenuItem(state)
+    @autoUpdateManager.on 'state-changed', (state) => @showUpdateMenuItem(state)
 
   # Public: Updates the entire menu with the given keybindings.
   #
@@ -33,7 +32,7 @@ class ApplicationMenu
       @menu = Menu.buildFromTemplate(_.deepClone(template))
       Menu.setApplicationMenu(@menu)
 
-    @showUpdateMenuItem(global.atomApplication.autoUpdateManager.getState())
+    @showUpdateMenuItem(@autoUpdateManager.getState())
 
   # Register a BrowserWindow with this application menu.
   addWindow: (window) ->
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 0e7ff9f4d..afc811144 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -71,8 +71,8 @@ class AtomApplication
     @pathsToOpen ?= []
     @windows = []
 
-    @autoUpdateManager = new AutoUpdateManager(@version)
-    @applicationMenu = new ApplicationMenu(@version)
+    @autoUpdateManager = new AutoUpdateManager(@version, options.test)
+    @applicationMenu = new ApplicationMenu(@version, @autoUpdateManager)
     @atomProtocolHandler = new AtomProtocolHandler(@resourcePath, @safeMode)
 
     @listenForArgumentsFromNewProcess()
@@ -99,7 +99,12 @@ class AtomApplication
   # Public: Removes the {AtomWindow} from the global window list.
   removeWindow: (window) ->
     @windows.splice @windows.indexOf(window), 1
-    @applicationMenu?.enableWindowSpecificItems(false) if @windows.length is 0
+    if @windows.length is 0
+      @applicationMenu?.enableWindowSpecificItems(false)
+      if process.platform in ['win32', 'linux']
+        app.quit()
+        return
+    @saveState() unless window.isSpec
 
   # Public: Adds the {AtomWindow} to the global window list.
   addWindow: (window) ->
@@ -110,10 +115,14 @@ class AtomApplication
 
     unless window.isSpec
       focusHandler = => @lastFocusedWindow = window
+      blurHandler = => @saveState()
       window.browserWindow.on 'focus', focusHandler
+      window.browserWindow.on 'blur', blurHandler
       window.browserWindow.once 'closed', =>
         @lastFocusedWindow = null if window is @lastFocusedWindow
         window.browserWindow.removeListener 'focus', focusHandler
+        window.browserWindow.removeListener 'blur', blurHandler
+      window.browserWindow.webContents.once 'did-finish-load', => @saveState()
 
   # Creates server to listen for additional atom application launches.
   #
@@ -176,7 +185,7 @@ class AtomApplication
     @on 'application:report-issue', -> require('shell').openExternal('https://github.com/atom/atom/blob/master/CONTRIBUTING.md#submitting-issues')
     @on 'application:search-issues', -> require('shell').openExternal('https://github.com/issues?q=+is%3Aissue+user%3Aatom')
 
-    @on 'application:install-update', -> @autoUpdateManager.install()
+    @on 'application:install-update', => @autoUpdateManager.install()
     @on 'application:check-for-update', => @autoUpdateManager.check()
 
     if process.platform is 'darwin'
@@ -199,17 +208,12 @@ class AtomApplication
     @openPathOnEvent('application:open-your-stylesheet', 'atom://.atom/stylesheet')
     @openPathOnEvent('application:open-license', path.join(process.resourcesPath, 'LICENSE.md'))
 
-    app.on 'window-all-closed', ->
-      app.quit() if process.platform in ['win32', 'linux']
-
-    app.on 'before-quit', =>
-      @saveState()
-
     app.on 'will-quit', =>
       @killAllProcesses()
       @deleteSocketFile()
 
     app.on 'will-exit', =>
+      @saveState() unless @windows.every (window) -> window.isSpec
       @killAllProcesses()
       @deleteSocketFile()
 
@@ -422,8 +426,8 @@ class AtomApplication
   saveState: ->
     states = []
     for window in @windows
-      if loadSettings = window.getLoadSettings()
-        unless loadSettings.isSpec
+      unless window.isSpec
+        if loadSettings = window.getLoadSettings()
           states.push(initialPaths: loadSettings.initialPaths)
     @storageFolder.store('application.json', states)
 
diff --git a/src/browser/auto-update-manager.coffee b/src/browser/auto-update-manager.coffee
index 358390889..654a8de67 100644
--- a/src/browser/auto-update-manager.coffee
+++ b/src/browser/auto-update-manager.coffee
@@ -15,7 +15,7 @@ module.exports =
 class AutoUpdateManager
   _.extend @prototype, EventEmitter.prototype
 
-  constructor: (@version) ->
+  constructor: (@version, @testMode) ->
     @state = IdleState
     if process.platform is 'win32'
       # Squirrel for Windows can't handle query params
@@ -80,10 +80,10 @@ class AutoUpdateManager
       autoUpdater.once 'update-not-available', @onUpdateNotAvailable
       autoUpdater.once 'error', @onUpdateError
 
-    autoUpdater.checkForUpdates()
+    autoUpdater.checkForUpdates() unless @testMode
 
   install: ->
-    autoUpdater.quitAndInstall()
+    autoUpdater.quitAndInstall() unless @testMode
 
   onUpdateNotAvailable: =>
     autoUpdater.removeListener 'error', @onUpdateError
diff --git a/src/display-buffer.coffee b/src/display-buffer.coffee
index f4c078b17..d5a893fe3 100644
--- a/src/display-buffer.coffee
+++ b/src/display-buffer.coffee
@@ -24,13 +24,13 @@ class DisplayBuffer extends Model
   horizontalScrollMargin: 6
   scopedCharacterWidthsChangeCount: 0
 
-  constructor: ({tabLength, @editorWidthInChars, @tokenizedBuffer, buffer, @invisibles}={}) ->
+  constructor: ({tabLength, @editorWidthInChars, @tokenizedBuffer, buffer, ignoreInvisibles}={}) ->
     super
 
     @emitter = new Emitter
     @disposables = new CompositeDisposable
 
-    @tokenizedBuffer ?= new TokenizedBuffer({tabLength, buffer, @invisibles})
+    @tokenizedBuffer ?= new TokenizedBuffer({tabLength, buffer, ignoreInvisibles})
     @buffer = @tokenizedBuffer.buffer
     @charWidthsByScope = {}
     @markers = {}
@@ -42,6 +42,7 @@ class DisplayBuffer extends Model
     @disposables.add @buffer.onDidUpdateMarkers @handleBufferMarkersUpdated
     @disposables.add @buffer.onDidCreateMarker @handleBufferMarkerCreated
     @updateAllScreenLines()
+    @foldMarkerAttributes = Object.freeze({class: 'fold', displayBufferId: @id})
     @createFoldForMarker(marker) for marker in @buffer.findMarkers(@getFoldMarkerAttributes())
 
   subscribeToScopedConfigSettings: =>
@@ -86,14 +87,13 @@ class DisplayBuffer extends Model
     scrollTop: @scrollTop
     scrollLeft: @scrollLeft
     tokenizedBuffer: @tokenizedBuffer.serialize()
-    invisibles: _.clone(@invisibles)
 
   deserializeParams: (params) ->
     params.tokenizedBuffer = TokenizedBuffer.deserialize(params.tokenizedBuffer)
     params
 
   copy: ->
-    newDisplayBuffer = new DisplayBuffer({@buffer, tabLength: @getTabLength(), @invisibles})
+    newDisplayBuffer = new DisplayBuffer({@buffer, tabLength: @getTabLength()})
     newDisplayBuffer.setScrollTop(@getScrollTop())
     newDisplayBuffer.setScrollLeft(@getScrollLeft())
 
@@ -428,8 +428,8 @@ class DisplayBuffer extends Model
   setTabLength: (tabLength) ->
     @tokenizedBuffer.setTabLength(tabLength)
 
-  setInvisibles: (@invisibles) ->
-    @tokenizedBuffer.setInvisibles(@invisibles)
+  setIgnoreInvisibles: (ignoreInvisibles) ->
+    @tokenizedBuffer.setIgnoreInvisibles(ignoreInvisibles)
 
   setSoftWrapped: (softWrapped) ->
     if softWrapped isnt @softWrapped
@@ -1075,8 +1075,11 @@ class DisplayBuffer extends Model
   findFoldMarkers: (attributes) ->
     @buffer.findMarkers(@getFoldMarkerAttributes(attributes))
 
-  getFoldMarkerAttributes: (attributes={}) ->
-    _.extend(attributes, class: 'fold', displayBufferId: @id)
+  getFoldMarkerAttributes: (attributes) ->
+    if attributes
+      _.extend(attributes, @foldMarkerAttributes)
+    else
+      @foldMarkerAttributes
 
   pauseMarkerChangeEvents: ->
     marker.pauseChangeEvents() for marker in @getMarkers()
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index 8527188d3..606f72eda 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -303,6 +303,9 @@ class PackageManager
     # of the first package isn't skewed by being the first to require atom
     require '../exports/atom'
 
+    # TODO: remove after a few atom versions.
+    @uninstallAutocompletePlus()
+
     packagePaths = @getAvailablePackagePaths()
     packagePaths = packagePaths.filter (packagePath) => not @isPackageDisabled(path.basename(packagePath))
     packagePaths = _.uniq packagePaths, (packagePath) -> path.basename(packagePath)
@@ -409,6 +412,40 @@ class PackageManager
     message = "Failed to load the #{path.basename(packagePath)} package"
     atom.notifications.addError(message, {stack, detail, dismissable: true})
 
+  # TODO: remove these autocomplete-plus specific helpers after a few versions.
+  uninstallAutocompletePlus: ->
+    packageDir = null
+    devDir = path.join("dev", "packages")
+    for packageDirPath in @packageDirPaths
+      if not packageDirPath.endsWith(devDir)
+        packageDir = packageDirPath
+        break
+
+    if packageDir?
+      dirsToRemove = [
+        path.join(packageDir, 'autocomplete-plus')
+        path.join(packageDir, 'autocomplete-atom-api')
+        path.join(packageDir, 'autocomplete-css')
+        path.join(packageDir, 'autocomplete-html')
+        path.join(packageDir, 'autocomplete-emojis')
+        path.join(packageDir, 'autocomplete-snippets')
+      ]
+      for dirToRemove in dirsToRemove
+        @uninstallDirectory(dirToRemove)
+    return
+
+  uninstallDirectory: (directory) ->
+    symlinkPromise = new Promise (resolve) ->
+      fs.isSymbolicLink directory, (isSymLink) -> resolve(isSymLink)
+
+    dirPromise = new Promise (resolve) ->
+      fs.isDirectory directory, (isDir) -> resolve(isDir)
+
+    Promise.all([symlinkPromise, dirPromise]).then (values) ->
+      [isSymLink, isDir] = values
+      if not isSymLink and isDir
+        fs.remove directory, ->
+
 if Grim.includeDeprecatedAPIs
   EmitterMixin = require('emissary').Emitter
   EmitterMixin.includeInto(PackageManager)
diff --git a/src/text-editor.coffee b/src/text-editor.coffee
index ac7c7d4f2..d2bd77522 100644
--- a/src/text-editor.coffee
+++ b/src/text-editor.coffee
@@ -84,12 +84,10 @@ class TextEditor extends Model
     @selections = []
 
     buffer ?= new TextBuffer
-    @displayBuffer ?= new DisplayBuffer({buffer, tabLength, softWrapped})
+    @displayBuffer ?= new DisplayBuffer({buffer, tabLength, softWrapped, ignoreInvisibles: @mini})
     @buffer = @displayBuffer.buffer
     @softTabs = @usesSoftTabs() ? @softTabs ? atom.config.get('editor.softTabs') ? true
 
-    @updateInvisibles()
-
     for marker in @findMarkers(@getSelectionMarkerAttributes())
       marker.setProperties(preserveFolds: true)
       @addSelection(marker)
@@ -170,21 +168,9 @@ class TextEditor extends Model
       @subscribe @displayBuffer.onDidAddDecoration (decoration) => @emit 'decoration-added', decoration
       @subscribe @displayBuffer.onDidRemoveDecoration (decoration) => @emit 'decoration-removed', decoration
 
-    @subscribeToScopedConfigSettings()
-
-  subscribeToScopedConfigSettings: ->
-    @scopedConfigSubscriptions?.dispose()
-    @scopedConfigSubscriptions = subscriptions = new CompositeDisposable
-
-    scopeDescriptor = @getRootScopeDescriptor()
-
-    subscriptions.add atom.config.onDidChange 'editor.showInvisibles', scope: scopeDescriptor, => @updateInvisibles()
-    subscriptions.add atom.config.onDidChange 'editor.invisibles', scope: scopeDescriptor, => @updateInvisibles()
-
   destroyed: ->
     @unsubscribe() if includeDeprecatedAPIs
     @disposables.dispose()
-    @scopedConfigSubscriptions.dispose()
     selection.destroy() for selection in @getSelections()
     @buffer.release()
     @displayBuffer.destroy()
@@ -488,7 +474,7 @@ class TextEditor extends Model
   setMini: (mini) ->
     if mini isnt @mini
       @mini = mini
-      @updateInvisibles()
+      @displayBuffer.setIgnoreInvisibles(@mini)
       @emitter.emit 'did-change-mini', @mini
     @mini
 
@@ -2779,15 +2765,6 @@ class TextEditor extends Model
   shouldAutoIndentOnPaste: ->
     atom.config.get("editor.autoIndentOnPaste", scope: @getRootScopeDescriptor())
 
-  shouldShowInvisibles: ->
-    not @mini and atom.config.get('editor.showInvisibles', scope: @getRootScopeDescriptor())
-
-  updateInvisibles: ->
-    if @shouldShowInvisibles()
-      @displayBuffer.setInvisibles(atom.config.get('editor.invisibles', scope: @getRootScopeDescriptor()))
-    else
-      @displayBuffer.setInvisibles(null)
-
   ###
   Section: Event Handlers
   ###
@@ -2796,8 +2773,6 @@ class TextEditor extends Model
     @softTabs = @usesSoftTabs() ? @softTabs
 
   handleGrammarChange: ->
-    @updateInvisibles()
-    @subscribeToScopedConfigSettings()
     @unfoldAll()
     @emit 'grammar-changed' if includeDeprecatedAPIs
     @emitter.emit 'did-change-grammar', @getGrammar()
diff --git a/src/tokenized-buffer.coffee b/src/tokenized-buffer.coffee
index d9f1bcba7..6d8f0c018 100644
--- a/src/tokenized-buffer.coffee
+++ b/src/tokenized-buffer.coffee
@@ -20,8 +20,9 @@ class TokenizedBuffer extends Model
   chunkSize: 50
   invalidRows: null
   visible: false
+  configSettings: null
 
-  constructor: ({@buffer, @tabLength, @invisibles}) ->
+  constructor: ({@buffer, @tabLength, @ignoreInvisibles}) ->
     @emitter = new Emitter
     @disposables = new CompositeDisposable
 
@@ -39,7 +40,7 @@ class TokenizedBuffer extends Model
   serializeParams: ->
     bufferPath: @buffer.getPath()
     tabLength: @tabLength
-    invisibles: _.clone(@invisibles)
+    ignoreInvisibles: @ignoreInvisibles
 
   deserializeParams: (params) ->
     params.buffer = atom.project.bufferForPathSync(params.bufferPath)
@@ -76,13 +77,25 @@ class TokenizedBuffer extends Model
     @grammarUpdateDisposable = @grammar.onDidUpdate => @retokenizeLines()
     @disposables.add(@grammarUpdateDisposable)
 
-    @configSettings = tabLength: atom.config.get('editor.tabLength', scope: @rootScopeDescriptor)
+    scopeOptions = {scope: @rootScopeDescriptor}
+    @configSettings =
+      tabLength: atom.config.get('editor.tabLength', scopeOptions)
+      invisibles: atom.config.get('editor.invisibles', scopeOptions)
+      showInvisibles: atom.config.get('editor.showInvisibles', scopeOptions)
 
-    @grammarTabLengthSubscription?.dispose()
-    @grammarTabLengthSubscription = atom.config.onDidChange 'editor.tabLength', scope: @rootScopeDescriptor, ({newValue}) =>
+    if @configSubscriptions?
+      @configSubscriptions.dispose()
+      @disposables.remove(@configSubscriptions)
+    @configSubscriptions = new CompositeDisposable
+    @configSubscriptions.add atom.config.onDidChange 'editor.tabLength', scopeOptions, ({newValue}) =>
       @configSettings.tabLength = newValue
       @retokenizeLines()
-    @disposables.add(@grammarTabLengthSubscription)
+    ['invisibles', 'showInvisibles'].forEach (key) =>
+      @configSubscriptions.add atom.config.onDidChange "editor.#{key}", scopeOptions, ({newValue}) =>
+        oldInvisibles = @getInvisiblesToShow()
+        @configSettings[key] = newValue
+        @retokenizeLines() unless _.isEqual(@getInvisiblesToShow(), oldInvisibles)
+    @disposables.add(@configSubscriptions)
 
     @retokenizeLines()
 
@@ -123,10 +136,11 @@ class TokenizedBuffer extends Model
     @tabLength = tabLength
     @retokenizeLines()
 
-  setInvisibles: (invisibles) ->
-    unless _.isEqual(invisibles, @invisibles)
-      @invisibles = invisibles
-      @retokenizeLines()
+  setIgnoreInvisibles: (ignoreInvisibles) ->
+    if ignoreInvisibles isnt @ignoreInvisibles
+      @ignoreInvisibles = ignoreInvisibles
+      if @configSettings.showInvisibles and @configSettings.invisibles?
+        @retokenizeLines()
 
   tokenizeInBackground: ->
     return if not @visible or @pendingChunk or not @isAlive()
@@ -302,7 +316,7 @@ class TokenizedBuffer extends Model
     tabLength = @getTabLength()
     indentLevel = @indentLevelForRow(row)
     lineEnding = @buffer.lineEndingForRow(row)
-    new TokenizedLine({tokens, tabLength, indentLevel, @invisibles, lineEnding})
+    new TokenizedLine({tokens, tabLength, indentLevel, invisibles: @getInvisiblesToShow(), lineEnding})
 
   buildTokenizedLineForRow: (row, ruleStack) ->
     @buildTokenizedLineForRowWithText(row, @buffer.lineForRow(row), ruleStack)
@@ -312,7 +326,13 @@ class TokenizedBuffer extends Model
     tabLength = @getTabLength()
     indentLevel = @indentLevelForRow(row)
     {tokens, ruleStack} = @grammar.tokenizeLine(line, ruleStack, row is 0)
-    new TokenizedLine({tokens, ruleStack, tabLength, lineEnding, indentLevel, @invisibles})
+    new TokenizedLine({tokens, ruleStack, tabLength, lineEnding, indentLevel, invisibles: @getInvisiblesToShow()})
+
+  getInvisiblesToShow: ->
+    if @configSettings.showInvisibles and not @ignoreInvisibles
+      @configSettings.invisibles
+    else
+      null
 
   tokenizedLineForRow: (bufferRow) ->
     @tokenizedLines[bufferRow]
diff --git a/static/index.html b/static/index.html
index 5559058dc..84e8d57d4 100644
--- a/static/index.html
+++ b/static/index.html
@@ -1,8 +1,6 @@
 <!DOCTYPE html>
-<html style="background: #fff">
+<html>
 <head>
-  <title></title>
-
   <meta http-equiv="Content-Security-Policy" content="default-src *; script-src 'self'; style-src 'self' 'unsafe-inline';">
 
   <script src="index.js"></script>
diff --git a/static/index.js b/static/index.js
index 0a377044e..ef61e8bce 100644
--- a/static/index.js
+++ b/static/index.js
@@ -1,6 +1,9 @@
 var fs = require('fs');
 var path = require('path');
 
+var loadSettings = null;
+var loadSettingsError = null;
+
 window.onload = function() {
   try {
     var startTime = Date.now();
@@ -12,30 +15,19 @@ window.onload = function() {
     // Ensure ATOM_HOME is always set before anything else is required
     setupAtomHome();
 
-    var cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache');
-    // Use separate compile cache when sudo'ing as root to avoid permission issues
-    if (process.env.USER === 'root' && process.env.SUDO_USER && process.env.SUDO_USER !== process.env.USER) {
-      cacheDir = path.join(cacheDir, 'root');
-    }
-
-    var rawLoadSettings = decodeURIComponent(location.hash.substr(1));
-    var loadSettings;
-    try {
-      loadSettings = JSON.parse(rawLoadSettings);
-    } catch (error) {
-      console.error("Failed to parse load settings: " + rawLoadSettings);
-      throw error;
-    }
-
     // Normalize to make sure drive letter case is consistent on Windows
     process.resourcesPath = path.normalize(process.resourcesPath);
 
+    if (loadSettingsError) {
+      throw loadSettingsError;
+    }
+
     var devMode = loadSettings.devMode || !loadSettings.resourcePath.startsWith(process.resourcesPath + path.sep);
 
     if (loadSettings.profileStartup) {
-      profileStartup(cacheDir, loadSettings, Date.now() - startTime);
+      profileStartup(loadSettings, Date.now() - startTime);
     } else {
-      setupWindow(cacheDir, loadSettings);
+      setupWindow(loadSettings);
       setLoadTime(Date.now() - startTime);
     }
   } catch (error) {
@@ -43,6 +35,15 @@ window.onload = function() {
   }
 }
 
+var getCacheDirectory = function() {
+  var cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache');
+  // Use separate compile cache when sudo'ing as root to avoid permission issues
+  if (process.env.USER === 'root' && process.env.SUDO_USER && process.env.SUDO_USER !== process.env.USER) {
+    cacheDir = path.join(cacheDir, 'root');
+  }
+  return cacheDir;
+}
+
 var setLoadTime = function(loadTime) {
   if (global.atom) {
     global.atom.loadTime = loadTime;
@@ -59,7 +60,9 @@ var handleSetupError = function(error) {
   console.error(error.stack || error);
 }
 
-var setupWindow = function(cacheDir, loadSettings) {
+var setupWindow = function(loadSettings) {
+  var cacheDir = getCacheDirectory();
+
   setupCoffeeCache(cacheDir);
 
   ModuleCache = require('../src/module-cache');
@@ -133,16 +136,17 @@ var setupSourceMapCache = function(cacheDir) {
 
 var setupVmCompatibility = function() {
   var vm = require('vm');
-  if (!vm.Script.createContext)
+  if (!vm.Script.createContext) {
     vm.Script.createContext = vm.createContext;
+  }
 }
 
-var profileStartup = function(cacheDir, loadSettings, initialTime) {
+var profileStartup = function(loadSettings, initialTime) {
   var profile = function() {
     console.profile('startup');
     try {
       var startTime = Date.now()
-      setupWindow(cacheDir, loadSettings);
+      setupWindow(loadSettings);
       setLoadTime(Date.now() - startTime + initialTime);
     } catch (error) {
       handleSetupError(error);
@@ -162,3 +166,41 @@ var profileStartup = function(cacheDir, loadSettings, initialTime) {
     });
   }
 }
+
+var parseLoadSettings = function() {
+  var rawLoadSettings = decodeURIComponent(location.hash.substr(1));
+  try {
+    loadSettings = JSON.parse(rawLoadSettings);
+  } catch (error) {
+    console.error("Failed to parse load settings: " + rawLoadSettings);
+    loadSettingsError = error;
+  }
+}
+
+var setupWindowBackground = function() {
+  if (loadSettings && loadSettings.isSpec) {
+    return;
+  }
+
+  var backgroundColor = window.localStorage.getItem('atom:window-background-color');
+  if (!backgroundColor) {
+    return;
+  }
+
+  var backgroundStylesheet = document.createElement('style');
+  backgroundStylesheet.type = 'text/css';
+  backgroundStylesheet.innerText = 'html, body { background: ' + backgroundColor + '; }';
+  document.head.appendChild(backgroundStylesheet);
+
+  // Remove once the page loads
+  window.addEventListener("load", function loadWindow() {
+    window.removeEventListener("load", loadWindow, false);
+    setTimeout(function() {
+      backgroundStylesheet.remove();
+      backgroundStylesheet = null;
+    }, 1000);
+  }, false);
+}
+
+parseLoadSettings();
+setupWindowBackground();