Now storing a window's state based on its rootDirectory (instead of on windowNumber)

src/app/atom.coffee

@@ -2,5 +2,20 @@ fs = require('fs')
 
 atom.configDirPath = fs.absolute("~/.atom")
 atom.configFilePath = fs.join(atom.configDirPath, "atom.coffee")
-atom.open = (args...) -> @sendMessageToBrowserProcess('open', args)
-atom.newWindow = (args...) -> @sendMessageToBrowserProcess('newWindow', args)
+
+atom.open = (args...) ->
+  @sendMessageToBrowserProcess('open', args)
+
+atom.newWindow = (args...) ->
+  @sendMessageToBrowserProcess('newWindow', args)
+
+atom.getRootViewStateForPath = (path) ->
+  if json = localStorage[path]
+    JSON.parse(json)
+
+atom.setRootViewStateForPath = (path, state) ->
+  return unless path
+  if state?
+    localStorage[path] = JSON.stringify(state)
+  else
+    delete localStorage[path]

src/app/root-view.coffee

@@ -94,7 +94,7 @@ class RootView extends View
     delete @extensions[extension.name]
 
   deactivate: ->
-    # atom.rootViewStates[$windowNumber] = JSON.stringify(@serialize()) # TODO: Reinstate
+    atom.setRootViewStateForPath(@project.getPath(), @serialize())
     @deactivateExtension(extension) for name, extension of @extensions
     @remove()
 

src/app/window.coffee

@@ -25,14 +25,12 @@ windowAdditions =
       @shutdown()
       false
     $(window).focus()
-    # atom.windowOpened this # TODO: Reinstate this!
 
   shutdown: ->
     @rootView.deactivate()
     $(window).unbind('focus')
     $(window).unbind('blur')
     $(window).off('before')
-    # atom.windowClosed this # TODO: Reinstate this!
 
   setUpKeymap: ->
     Keymap = require 'keymap'
@@ -47,8 +45,8 @@ windowAdditions =
   # Note: RootView assigns itself on window on initialization so that
   # window.rootView is available when loading user configuration
   attachRootView: (pathToOpen) ->
-    if rootViewState = atom.rootViewStates?[$windowNumber]
-      RootView.deserialize(JSON.parse(rootViewState))
+    if rootViewState = atom.getRootViewStateForPath(pathToOpen)
+      RootView.deserialize(rootViewState)
     else
       new RootView(pathToOpen)
       @rootView.open() unless pathToOpen