diff --git a/package.json b/package.json
index 4dfe23c0f..28a9821be 100644
--- a/package.json
+++ b/package.json
@@ -88,7 +88,7 @@
     "autocomplete-css": "0.7.2",
     "autocomplete-emojis": "2.2.2",
     "autocomplete-html": "0.7.2",
-    "autocomplete-plus": "2.16.0",
+    "autocomplete-plus": "2.16.1",
     "autocomplete-snippets": "1.6.1",
     "autoflow": "0.23.0",
     "autosave": "0.20.0",
@@ -96,12 +96,12 @@
     "bookmarks": "0.35.0",
     "bracket-matcher": "0.74.0",
     "command-palette": "0.35.0",
-    "deprecation-cop": "0.47.0",
+    "deprecation-cop": "0.48.0",
     "dev-live-reload": "0.46.0",
     "encoding-selector": "0.20.0",
     "exception-reporting": "0.24.0",
     "find-and-replace": "0.162.0",
-    "fuzzy-finder": "0.84.0",
+    "fuzzy-finder": "0.85.0",
     "git-diff": "0.55.0",
     "go-to-line": "0.30.0",
     "grammar-selector": "0.47.0",
@@ -110,7 +110,7 @@
     "keybinding-resolver": "0.32.0",
     "link": "0.30.0",
     "markdown-preview": "0.148.0",
-    "metrics": "0.47.0",
+    "metrics": "0.48.0",
     "notifications": "0.44.0",
     "open-on-github": "0.36.0",
     "package-generator": "0.39.0",
@@ -124,7 +124,7 @@
     "tabs": "0.68.0",
     "timecop": "0.31.0",
     "tree-view": "0.171.0",
-    "update-package-dependencies": "0.9.0",
+    "update-package-dependencies": "0.10.0",
     "welcome": "0.27.0",
     "whitespace": "0.29.0",
     "wrap-guide": "0.33.0",
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index afc811144..d81660a49 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -56,6 +56,7 @@ class AtomApplication
   atomProtocolHandler: null
   resourcePath: null
   version: null
+  quitting: false
 
   exit: (status) -> app.exit(status)
 
@@ -104,7 +105,7 @@ class AtomApplication
       if process.platform in ['win32', 'linux']
         app.quit()
         return
-    @saveState() unless window.isSpec
+    @saveState() unless window.isSpec or @quitting
 
   # Public: Adds the {AtomWindow} to the global window list.
   addWindow: (window) ->
@@ -208,6 +209,9 @@ class AtomApplication
     @openPathOnEvent('application:open-your-stylesheet', 'atom://.atom/stylesheet')
     @openPathOnEvent('application:open-license', path.join(process.resourcesPath, 'LICENSE.md'))
 
+    app.on 'before-quit', =>
+      @quitting = true
+
     app.on 'will-quit', =>
       @killAllProcesses()
       @deleteSocketFile()
diff --git a/static/index.js b/static/index.js
index ef61e8bce..f41d41cd9 100644
--- a/static/index.js
+++ b/static/index.js
@@ -1,3 +1,5 @@
+(function() {
+
 var fs = require('fs');
 var path = require('path');
 
@@ -204,3 +206,5 @@ var setupWindowBackground = function() {
 
 parseLoadSettings();
 setupWindowBackground();
+
+})();