Save the state before the browser window is closed

src/browser/atom-application.coffee

@@ -208,7 +208,6 @@ class AtomApplication
     @openPathOnEvent('application:open-license', path.join(process.resourcesPath, 'LICENSE.md'))
 
     app.on 'before-quit', =>
-      @saveState(false)
       @quitting = true
 
     app.on 'will-quit', =>

src/browser/atom-window.coffee

@@ -119,6 +119,9 @@ class AtomWindow
         false
 
   handleEvents: ->
+    @browserWindow.on 'close', ->
+      global.atomApplication.saveState(false)
+
     @browserWindow.on 'closed', =>
       global.atomApplication.removeWindow(this)