RootView deactivates extensions when it is deactivated

src/app/root-view.coffee

@@ -88,6 +88,11 @@ class RootView extends View
     @extensions[extension.name] = extension
     extension.activate(this, @extensionStates[extension.name])
 
+  deactivate: ->
+    atom.rootViewStates[$windowNumber] = @serialize()
+    extension.deactivate() for name, extension of @extensions
+    @remove()
+
   open: (path) ->
     buffer = @project.open(path)
 

src/app/window.coffee

@@ -31,8 +31,7 @@ windowAdditions =
     atom.windowOpened this
 
   shutdown: ->
-    @saveRootViewState()
-    @rootView.remove()
+    @rootView.deactivate()
     $(window).unbind('focus')
     $(window).unbind('blur')
     $(window).off('before')
@@ -46,9 +45,6 @@ windowAdditions =
       new RootView {pathToOpen}
     $(@rootViewParentSelector).append @rootView
 
-  saveRootViewState: ->
-    atom.rootViewStates[$windowNumber] = @rootView.serialize()
-
   loadUserConfiguration: ->
     try
       require atom.userConfigurationPath if fs.exists(atom.userConfigurationPath)