Made App a fake singleton. It only has class methods and variables.

src/app.coffee

@@ -1,43 +1,24 @@
 _ = require 'underscore'
+Window = require 'window'
+Plugins = require 'plugins'
 
-module.exports = App =
-  windows: []
-  root: OSX.NSBundle.mainBundle.resourcePath
+module.exports =
+class App
+  @windows: []
+  @root: OSX.NSBundle.mainBundle.resourcePath
 
-  activeWindow: null
+  @activeWindow: null
 
-  setActiveWindow: (window) ->
+  @setup: ->
+    @setActiveWindow new Window controller : WindowController
+
+    # Move this someone more approriate
+    if localStorage.lastOpenedFilename
+      @activeWindow.open(localStorage.lastOpenedFilename)
+
+    Plugins.load()
+    @activeWindow.document.ace._emit "loaded"
+
+  @setActiveWindow: (window) ->
     @activeWindow = window
     @windows.push window if window not in @windows
-
-  # path - Optional. The String path to the file to base it on.
-  newWindow: (path) ->
-    c = OSX.AtomWindowController.alloc.initWithWindowNibName "AtomWindow"
-    c.window
-    c.window.makeKeyAndOrderFront null
-
-  # Returns null or a file path.
-  openPanel: ->
-    panel = OSX.NSOpenPanel.openPanel
-    panel.setCanChooseDirectories true
-    if panel.runModal isnt OSX.NSFileHandlingPanelOKButton
-      return null
-    filename = panel.filenames.lastObject
-    localStorage.lastOpenedFilename = filename
-    filename
-
-  openURL: (url) ->
-    window.location = url
-    @activeWindow.setTitle _.last url.replace(/\/$/,'').split '/'
-
-  # Returns null or a file path.
-  savePanel: ->
-    panel = OSX.NSSavePanel.savePanel
-    if panel.runModal isnt OSX.NSFileHandlingPanelOKButton
-      return null
-    panel.filenames.lastObject
-
-  writeToPasteboard: (text) ->
-    pb = OSX.NSPasteboard.generalPasteboard
-    pb.declareTypes_owner [OSX.NSStringPboardType], null
-    pb.setString_forType text, OSX.NSStringPboardType

src/editor.coffee

@@ -1,9 +1,8 @@
 _ = require 'underscore'
 
 File = require 'fs'
-App  = require 'app'
+Chrome = require 'chrome'
 Pane = require 'pane'
-activeWindow = App.activeWindow
 
 ace = require 'ace/ace'
 
@@ -36,6 +35,8 @@ class Editor extends Pane
   sessions: {}
 
   initialize: ->
+    window.r = require 'app'
+
     @ace = ace.edit "editor"
     @ace.setTheme require "ace/theme/twilight"
     @ace.getSession().setUseSoftTabs true
@@ -45,7 +46,8 @@ class Editor extends Pane
     @ace.setPrintMarginColumn 78
 
     @ace.getSession().on 'change', ->
-      activeWindow.setDirty true
+      App = require 'app' # Get rid of this!
+      App.activeWindow.setDirty true
 
     el = document.body
     el.addEventListener 'DOMNodeInsertedIntoDocument', =>
@@ -59,27 +61,29 @@ class Editor extends Pane
     @removeTrailingWhitespace()
     File.write @filename, @code()
     @sessions[@filename] = @ace.getSession()
-    activeWindow.setDirty false
+    .setDirty false
     @ace._emit 'save', { @filename }
 
   open: (path) ->
-    path = App.openPanel() if not path
+    App = require 'app' # Get rid of this!
+    path = Chrome.openPanel() if not path
     return if not path
     @filename = path
 
     if File.isDirectory @filename
       File.changeWorkingDirectory @filename
-      activeWindow.setTitle _.last @filename.split '/'
+      window.x = App
+      App.activeWindow.setTitle _.last @filename.split '/'
       @ace.setSession @newSession()
-      activeWindow.setDirty false
+      App.activeWindow.setDirty false
     else
       if /png|jpe?g|gif/i.test @filename
-        App.openURL @filename
+        Chrome.openURL @filename
       else
-        activeWindow.setTitle _.last @filename.split '/'
+        App.activeWindow.setTitle _.last @filename.split '/'
         @sessions[@filename] or= @newSession File.read @filename
         @ace.setSession @sessions[@filename]
-        activeWindow.setDirty false
+        App.activeWindow.setDirty false
     @ace._emit 'open', { @filename }
 
   close: (path) ->
@@ -87,9 +91,9 @@ class Editor extends Pane
     @ace._emit 'close', { filename : path }
 
   saveAs: ->
-    if file = App.savePanel()
+    if file = Chrome.savePanel()
       @filename = file
-      activeWindow.setTitle _.last @filename.split '/'
+      App.activeWindow.setTitle _.last @filename.split '/'
       @save()
 
   code: ->
@@ -137,12 +141,12 @@ class Editor extends Pane
   copy: ->
     editor = @ace
     text = editor.getSession().doc.getTextRange editor.getSelectionRange()
-    App.writeToPasteboard text
+    Chrome.writeToPasteboard text
 
   cut: ->
     editor = @ace
     text = editor.getSession().doc.getTextRange editor.getSelectionRange()
-    App.writeToPasteboard text
+    Chrome.writeToPasteboard text
     editor.session.remove editor.getSelectionRange()
 
   eval: ->

src/plugins.coffee

@@ -2,10 +2,11 @@ $ = require 'jquery'
 _ = require 'underscore'
 
 File = require 'fs'
-App  = require 'app'
 
-_.map File.list(App.root + "/plugins"), (plugin) ->
-  require plugin
+exports.load = ->
+  App  = require 'app'
+  _.map File.list(App.root + "/plugins"), (plugin) ->
+    require plugin
 
-_.map File.list("~/.atomicity/"), (path) ->
-  require path
+  _.map File.list("~/.atomicity/"), (path) ->
+    require path

src/startup.coffee

@@ -1,14 +1,3 @@
 # yay!
 App = require 'app'
-Window = require 'window'
-App.setActiveWindow new Window controller: WindowController
-
-Editor = require 'editor'
-App.activeWindow.document = new Editor
-
-if localStorage.lastOpenedFilename
-  App.activeWindow.open(localStorage.lastOpenedFilename)
-
-require 'plugins'
-
-App.activeWindow.document.ace._emit "loaded"
+App.setup()

src/window.coffee

@@ -1,6 +1,6 @@
 $ = require 'jquery'
 
-App  = require 'app'
+Chrome = require 'chrome'
 Pane = require 'pane'
 
 module.exports =
@@ -17,6 +17,12 @@ class Window extends Pane
     'Command-Ctrl-K'  : 'showConsole'
     'Command-Ctrl-R'  : 'reload'
 
+  constructor: (options={}) ->
+    super options
+
+    Editor = require 'editor'
+    @document = new Editor
+
   initialize: ->
     @nswindow = @controller?.window
 
@@ -44,7 +50,7 @@ class Window extends Pane
     @controller.close()
 
   reload: ->
-    App.newWindow()
+    Chrome.newWindow()
     @close()
 
   isDirty: ->
@@ -58,14 +64,15 @@ class Window extends Pane
     @_inspector ?= WindowController.webView.inspector
 
   new: ->
-    App.newWindow()
+    Chrome.newWindow()
 
   open: (path) ->
     @document?.open path
 
   openURL: (url) ->
     if url = prompt "Enter URL:"
-      App.openURL url
+      Chrome = require 'app'
+      Chrome.openURL url
 
   showConsole: ->
     @inspector().showConsole(1)