Only deactivate the RootView once during shutdown

Previously window.shutdown() was called multiple times
if window.close() was called since the shutdown handler
was also fired in the native window controller.

This prevented proper serialization of the RootView
from occurring when then window was closed via meta-w or
meta-W since it was called a second time when already
empty of packages and editors.

spec/app/window-spec.coffee

@@ -2,8 +2,11 @@ $ = require 'jquery'
 fs = require 'fs'
 
 describe "Window", ->
+  [rootView] = []
+
   beforeEach ->
     window.attachRootView(require.resolve('fixtures'))
+    rootView = window.rootView
 
   afterEach ->
     window.shutdown()
@@ -68,7 +71,7 @@ describe "Window", ->
       expect(atom.getRootViewStateForPath(window.rootView.project.getPath())).toBeUndefined()
       expectedState = JSON.parse(JSON.stringify(window.rootView.serialize())) # JSON.stringify removes keys with undefined values
       $(window).trigger 'beforeunload'
-      expect(atom.getRootViewStateForPath(window.rootView.project.getPath())).toEqual expectedState
+      expect(atom.getRootViewStateForPath(rootView.project.getPath())).toEqual expectedState
 
     it "unsubscribes from all buffers", ->
       rootView.open('sample.js')
@@ -79,3 +82,12 @@ describe "Window", ->
       $(window).trigger 'beforeunload'
 
       expect(editor1.getBuffer().subscriptionCount()).toBe 0
+
+  describe ".shutdown()", ->
+    it "only deactivates the RootView the first time it is called", ->
+      deactivateSpy = spyOn(rootView, "deactivate").andCallThrough()
+      window.shutdown()
+      expect(rootView.deactivate).toHaveBeenCalled()
+      deactivateSpy.reset()
+      window.shutdown()
+      expect(rootView.deactivate).not.toHaveBeenCalled()

src/app/window.coffee

@@ -47,7 +47,8 @@ windowAdditions =
       false
 
   shutdown: ->
-    @rootView.deactivate()
+    @rootView?.deactivate()
+    @rootView = null
     $(window).unbind('focus')
     $(window).unbind('blur')
     $(window).off('before')