Fix incorrect state save when exiting

src/browser/atom-application.coffee

@@ -105,7 +105,7 @@ class AtomApplication
         app.quit()
         return
     @windows.splice(@windows.indexOf(window), 1)
-    @saveState() unless window.isSpec
+    @saveState(true) unless window.isSpec
 
   # Public: Adds the {AtomWindow} to the global window list.
   addWindow: (window) ->
@@ -116,14 +116,14 @@ class AtomApplication
 
     unless window.isSpec
       focusHandler = => @lastFocusedWindow = window
-      blurHandler = => @saveState()
+      blurHandler = => @saveState(false)
       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()
+      window.browserWindow.webContents.once 'did-finish-load', => @saveState(false)
 
   # Creates server to listen for additional atom application launches.
   #
@@ -213,7 +213,7 @@ class AtomApplication
     @openPathOnEvent('application:open-license', path.join(process.resourcesPath, 'LICENSE.md'))
 
     app.on 'before-quit', =>
-      @saveState() if @hasEditorWindows()
+      @saveState(false)
       @quitting = true
 
     app.on 'will-quit', =>
@@ -221,7 +221,7 @@ class AtomApplication
       @deleteSocketFile()
 
     app.on 'will-exit', =>
-      @saveState() if @hasEditorWindows()
+      @saveState(false)
       @killAllProcesses()
       @deleteSocketFile()
 
@@ -439,14 +439,15 @@ class AtomApplication
         console.log("Killing process #{pid} failed: #{error.code ? error.message}")
     delete @pidsToOpenWindows[pid]
 
-  saveState: ->
+  saveState: (allowEmpty=false) ->
     return if @quitting
     states = []
     for window in @windows
       unless window.isSpec
         if loadSettings = window.getLoadSettings()
           states.push(initialPaths: loadSettings.initialPaths)
-    @storageFolder.store('application.json', states)
+    if states.length > 0 or allowEmpty
+      @storageFolder.store('application.json', states)
 
   hasEditorWindows: ->
     @windows.some (window) -> not window.isSpec