diff --git a/spec/atom-environment-spec.coffee b/spec/atom-environment-spec.coffee
index 3e6536681..127659cf7 100644
--- a/spec/atom-environment-spec.coffee
+++ b/spec/atom-environment-spec.coffee
@@ -151,7 +151,7 @@ describe "AtomEnvironment", ->
       [dir1, dir2] = [temp.mkdirSync("dir1-"), temp.mkdirSync("dir2-")]
 
       loadSettings = _.extend atom.getLoadSettings(),
-        initialPaths: [dir1]
+        projectDirectoryPaths: [dir1]
         windowState: null
 
       spyOn(atom, 'getLoadSettings').andCallFake -> loadSettings
@@ -165,7 +165,7 @@ describe "AtomEnvironment", ->
       atom.loadStateSync()
       expect(atom.state.stuff).toBeUndefined()
 
-      loadSettings.initialPaths = [dir2, dir1]
+      loadSettings.projectDirectoryPaths = [dir2, dir1]
       atom.state = {}
       atom.loadStateSync()
       expect(atom.state.stuff).toBe("cool")
@@ -173,7 +173,7 @@ describe "AtomEnvironment", ->
   describe "openInitialEmptyEditorIfNecessary", ->
     describe "when there are no paths set", ->
       beforeEach ->
-        spyOn(atom, 'getLoadSettings').andReturn(initialPaths: [])
+        spyOn(atom, 'getLoadSettings').andReturn(projectDirectoryPaths: [])
 
       it "opens an empty buffer", ->
         spyOn(atom.workspace, 'open')
@@ -191,7 +191,7 @@ describe "AtomEnvironment", ->
 
     describe "when the project has a path", ->
       beforeEach ->
-        spyOn(atom, 'getLoadSettings').andReturn(initialPaths: ['something'])
+        spyOn(atom, 'getLoadSettings').andReturn(projectDirectoryPaths: ['something'])
         spyOn(atom.workspace, 'open')
 
       it "does not open an empty buffer", ->
diff --git a/src/application-delegate.coffee b/src/application-delegate.coffee
index 1e05b3dbb..0ea0bdafd 100644
--- a/src/application-delegate.coffee
+++ b/src/application-delegate.coffee
@@ -4,7 +4,7 @@ remote = require 'remote'
 shell = require 'shell'
 webFrame = require 'web-frame'
 {Disposable} = require 'event-kit'
-{getWindowLoadSettings, setWindowLoadSettings} = require './window-load-settings-helpers'
+getWindowLoadSettings = require './get-window-load-settings'
 
 module.exports =
 class ApplicationDelegate
@@ -80,10 +80,8 @@ class ApplicationDelegate
   setRepresentedFilename: (filename) ->
     ipc.send("call-window-method", "setRepresentedFilename", filename)
 
-  setRepresentedDirectoryPaths: (paths) ->
-    loadSettings = getWindowLoadSettings()
-    loadSettings['initialPaths'] = paths
-    setWindowLoadSettings(loadSettings)
+  setProjectDirectoryPaths: (paths) ->
+    ipc.send("window-command", "set-project-directory-paths", paths)
 
   setAutoHideWindowMenuBar: (autoHide) ->
     ipc.send("call-window-method", "setAutoHideMenuBar", autoHide)
@@ -124,7 +122,7 @@ class ApplicationDelegate
     else
       params = _.clone(params)
     params.title ?= 'Save File'
-    params.defaultPath ?= getWindowLoadSettings().initialPaths[0]
+    params.defaultPath ?= getWindowLoadSettings().projectDirectoryPaths[0]
     dialog = remote.require('dialog')
     dialog.showSaveDialog remote.getCurrentWindow(), params
 
diff --git a/src/atom-environment.coffee b/src/atom-environment.coffee
index ac76daf04..c1b25abf1 100644
--- a/src/atom-environment.coffee
+++ b/src/atom-environment.coffee
@@ -11,7 +11,7 @@ Model = require './model'
 WindowEventHandler = require './window-event-handler'
 StylesElement = require './styles-element'
 StorageFolder = require './storage-folder'
-{getWindowLoadSettings} = require './window-load-settings-helpers'
+getWindowLoadSettings = require './get-window-load-settings'
 registerDefaultCommands = require './register-default-commands'
 
 DeserializerManager = require './deserializer-manager'
@@ -651,7 +651,7 @@ class AtomEnvironment extends Model
 
   openInitialEmptyEditorIfNecessary: ->
     return unless @config.get('core.openEmptyEditorOnStart')
-    if @getLoadSettings().initialPaths?.length is 0 and @workspace.getPaneItems().length is 0
+    if @getLoadSettings().projectDirectoryPaths?.length is 0 and @workspace.getPaneItems().length is 0
       @workspace.open(null)
 
   installUncaughtErrorHandler: ->
@@ -753,7 +753,7 @@ class AtomEnvironment extends Model
   # Notify the browser project of the window's current project path
   watchProjectPath: ->
     @disposables.add @project.onDidChangePaths =>
-      @applicationDelegate.setRepresentedDirectoryPaths(@project.getPaths())
+      @applicationDelegate.setProjectDirectoryPaths(@project.getPaths())
 
   setDocumentEdited: (edited) ->
     @applicationDelegate.setWindowDocumentEdited?(edited)
@@ -789,7 +789,7 @@ class AtomEnvironment extends Model
 
     startTime = Date.now()
 
-    if stateKey = @getStateKey(@getLoadSettings().initialPaths)
+    if stateKey = @getStateKey(@getLoadSettings().projectDirectoryPaths)
       if state = @getStorageFolder().load(stateKey)
         @state = state
 
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 8bb44349e..7e1f71390 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -437,9 +437,8 @@ class AtomApplication
     return if @quitting
     states = []
     for window in @windows
-      unless window.isSpec
-        if loadSettings = window.getLoadSettings()
-          states.push(initialPaths: loadSettings.initialPaths)
+      if not window.isSpec and window.projectDirectoryPaths?
+        states.push(projectDirectoryPaths: window.projectDirectoryPaths)
     if states.length > 0 or allowEmpty
       @storageFolder.store('application.json', states)
 
@@ -447,7 +446,7 @@ class AtomApplication
     if (states = @storageFolder.load('application.json'))?.length > 0
       for state in states
         @openWithOptions(_.extend(options, {
-          pathsToOpen: state.initialPaths
+          pathsToOpen: state.projectDirectoryPaths
           urlsToOpen: []
           devMode: @devMode
           safeMode: @safeMode
diff --git a/src/browser/atom-window.coffee b/src/browser/atom-window.coffee
index c507b634c..e519d9157 100644
--- a/src/browser/atom-window.coffee
+++ b/src/browser/atom-window.coffee
@@ -55,14 +55,15 @@ class AtomWindow
       @constructor.includeShellLoadTime = false
       loadSettings.shellLoadTime ?= Date.now() - global.shellStartTime
 
-    loadSettings.initialPaths =
+    loadSettings.projectDirectoryPaths =
       for {pathToOpen} in locationsToOpen when pathToOpen
         if fs.statSyncNoException(pathToOpen).isFile?()
           path.dirname(pathToOpen)
         else
           pathToOpen
 
-    loadSettings.initialPaths.sort()
+    loadSettings.projectDirectoryPaths.sort()
+    @setProjectDirectoryPaths(loadSettings.projectDirectoryPaths)
 
     @browserWindow.loadSettings = loadSettings
     @browserWindow.once 'window:loaded', =>
@@ -87,12 +88,9 @@ class AtomWindow
       slashes: true
       hash: encodeURIComponent(JSON.stringify(loadSettings))
 
-  getLoadSettings: ->
-    if @browserWindow.webContents? and not @browserWindow.webContents.isLoading()
-      hash = url.parse(@browserWindow.webContents.getUrl()).hash.substr(1)
-      JSON.parse(decodeURIComponent(hash))
+  setProjectDirectoryPaths: (@projectDirectoryPaths) ->
 
-  hasProjectPath: -> @getLoadSettings().initialPaths?.length > 0
+  hasProjectPath: -> @projectDirectoryPaths?.length > 0
 
   setupContextMenu: ->
     ContextMenu = require './context-menu'
@@ -106,7 +104,7 @@ class AtomWindow
     true
 
   containsPath: (pathToCheck) ->
-    @getLoadSettings()?.initialPaths?.some (projectPath) ->
+    @projectDirectoryPaths?.some (projectPath) ->
       if not projectPath
         false
       else if not pathToCheck
@@ -121,6 +119,8 @@ class AtomWindow
         false
 
   handleEvents: ->
+    @browserWindow.on 'set-project-directory-paths', @setProjectDirectoryPaths.bind(this)
+
     @browserWindow.on 'closed', =>
       global.atomApplication.removeWindow(this)
 
diff --git a/src/window-load-settings-helpers.coffee b/src/get-window-load-settings.coffee
similarity index 74%
rename from src/window-load-settings-helpers.coffee
rename to src/get-window-load-settings.coffee
index 59ee2f382..85e087645 100644
--- a/src/window-load-settings-helpers.coffee
+++ b/src/get-window-load-settings.coffee
@@ -3,7 +3,7 @@ _ = require 'underscore-plus'
 
 windowLoadSettings = null
 
-exports.getWindowLoadSettings = ->
+module.exports = ->
   windowLoadSettings ?= JSON.parse(window.decodeURIComponent(window.location.hash.substr(1)))
   clone = _.deepClone(windowLoadSettings)
 
@@ -14,7 +14,3 @@ exports.getWindowLoadSettings = ->
     remote.getCurrentWindow().loadSettings.windowState = value
 
   clone
-
-exports.setWindowLoadSettings = (settings) ->
-  windowLoadSettings = settings
-  location.hash = encodeURIComponent(JSON.stringify(settings))
diff --git a/src/initialize-application-window.coffee b/src/initialize-application-window.coffee
index 57aa33ce0..4bc50144c 100644
--- a/src/initialize-application-window.coffee
+++ b/src/initialize-application-window.coffee
@@ -2,7 +2,7 @@
 module.exports = ({blobStore}) ->
   path = require 'path'
   require './window'
-  {getWindowLoadSettings} = require './window-load-settings-helpers'
+  getWindowLoadSettings = require './get-window-load-settings'
 
   {resourcePath, isSpec, devMode} = getWindowLoadSettings()
 
diff --git a/src/initialize-test-window.coffee b/src/initialize-test-window.coffee
index 375581a96..97caae276 100644
--- a/src/initialize-test-window.coffee
+++ b/src/initialize-test-window.coffee
@@ -15,7 +15,7 @@ module.exports = ({blobStore}) ->
   try
     path = require 'path'
     ipc = require 'ipc'
-    {getWindowLoadSettings} = require './window-load-settings-helpers'
+    getWindowLoadSettings = require './get-window-load-settings'
     AtomEnvironment = require '../src/atom-environment'
     ApplicationDelegate = require '../src/application-delegate'