atom variable holds all global state and is shared across contexts.

src/atom-bootstrap.coffee

@@ -0,0 +1,2 @@
+App = require 'app'
+window.atom = new App(atom.loadPath, atom.native)

src/atom/app.coffee

@@ -1,14 +1,15 @@
 Native = require 'native'
 GlobalKeymap = require 'global-keymap'
 $ = require 'jquery'
+_ = require 'underscore'
 
 module.exports =
 class App
   globalKeymap: null
   native: null
 
-  constructor: ->
-    @native = new Native
+  constructor: (@loadPath, nativeMethods)->
+    @native = new Native(nativeMethods)
     @globalKeymap = new GlobalKeymap
     $(document).on 'keydown', (e) => @globalKeymap.handleKeyEvent(e)
 
@@ -19,11 +20,11 @@ class App
     @globalKeymap.bindKey(selector, pattern, eventName)
 
   open: (url) ->
-    $native.open url
+    @native.open url
 
   quit: ->
-    $native.terminate null
+    @native.terminate null
 
   windows: ->
-		#		controller.jsWindow for controller in OSX.NSApp.controllers
-		[]
+    #    controller.jsWindow for controller in OSX.NSApp.controllers
+    []

src/bootstrap.coffee

@@ -1,7 +1,4 @@
 # Like sands through the hourglass, so are the days of our lives.
-App = require 'app'
-window.atom = new App
-
 require 'window'
 window.startup $pathToOpen
 

src/stdlib/fs.coffee

@@ -9,7 +9,7 @@ module.exports =
   # Make the given path absolute by resolving it against the
   # current working directory.
   absolute: (path) ->
-    $native.absolute(path)
+    atom.native.absolute(path)
 
   # Return the basename of the given path. That is the path with
   # any leading directory components removed. If specified, also
@@ -28,7 +28,7 @@ module.exports =
 
   # Returns true if the file specified by path exists
   exists: (path) ->
-    $native.exists path
+    atom.native.exists path
 
   join: (paths...) ->
     return paths[0] if paths.length == 1
@@ -38,44 +38,44 @@ module.exports =
   # Returns true if the file specified by path exists and is a
   # directory.
   isDirectory: (path) ->
-    $native.isDirectory path
+    atom.native.isDirectory path
 
   # Returns true if the file specified by path exists and is a
   # regular file.
   isFile: (path) ->
-    not $native.isDirectory path
+    not atom.native.isDirectory path
 
   # Returns an array with all the names of files contained
   # in the directory path.
   list: (path) ->
-    $native.list(path, false)
+    atom.native.list(path, false)
 
   listTree: (path) ->
-    $native.list(path, true)
+    atom.native.list(path, true)
 
   # Remove a file at the given path. Throws an error if path is not a
   # file or a symbolic link to a file.
   remove: (path) ->
-    $native.remove path
+    atom.native.remove path
 
   # Open, read, and close a file, returning the file's contents.
   read: (path) ->
-    $native.read(path)
+    atom.native.read(path)
 
   # Open, write, flush, and close a file, writing the given content.
   write: (path, content) ->
-    $native.write(path, content)
+    atom.native.write(path, content)
 
   async:
     list: (path) ->
       deferred = $.Deferred()
-      $native.asyncList path, false, (subpaths) ->
+      atom.native.asyncList path, false, (subpaths) ->
         deferred.resolve subpaths
       deferred
 
     listTree: (path) ->
       deferred = $.Deferred()
-      $native.asyncList path, true, (subpaths) ->
+      atom.native.asyncList path, true, (subpaths) ->
         deferred.resolve subpaths
       deferred
 

src/stdlib/native.coffee

@@ -2,8 +2,11 @@ _ = require 'underscore'
 
 module.exports =
 class Native
+  constructor: (nativeMethods)->
+    _.extend(this, nativeMethods)
+
   alert: (message, detailedMessage, buttons) ->
-	  $native.alert(message, detailedMessage, buttons)
+    atom.native.alert(message, detailedMessage, buttons)
 
   # path - Optional. The String path to the file to base it on.
   newWindow: (path) ->
@@ -29,10 +32,10 @@ class Native
     panel.filenames.lastObject.valueOf()
 
   writeToPasteboard: (text) ->
-    $native.writeToPasteboard text
+    atom.native.writeToPasteboard text
 
   readFromPasteboard: ->
-    $native.readFromPasteboard()
+    atom.native.readFromPasteboard()
 
   resetMainMenu: (menu) ->
     # OSX.NSApp.resetMainMenu

src/stdlib/require.coffee

@@ -1,11 +1,11 @@
 paths = [
-  "#{$atom.loadPath}/spec"
-  "#{$atom.loadPath}/src/stdlib"
-  "#{$atom.loadPath}/src/atom"
-  "#{$atom.loadPath}/src"
-  "#{$atom.loadPath}/extensions"
-  "#{$atom.loadPath}/vendor"
-  "#{$atom.loadPath}/static"
+  "#{atom.loadPath}/spec"
+  "#{atom.loadPath}/src/stdlib"
+  "#{atom.loadPath}/src/atom"
+  "#{atom.loadPath}/src"
+  "#{atom.loadPath}/extensions"
+  "#{atom.loadPath}/vendor"
+  "#{atom.loadPath}/static"
 ]
 
 window.__filename = null
@@ -100,7 +100,7 @@ __expand = (path) ->
   return null
 
 __exists = (path) ->
-  $native.exists path
+  atom.native.exists path
 
 __coffeeCache = (filePath) ->
   {CoffeeScript} = require 'coffee-script'
@@ -108,7 +108,7 @@ __coffeeCache = (filePath) ->
 
 __read = (path) ->
   try
-    $native.read(path)
+    atom.native.read(path)
   catch e
     throw "require: can't read #{path}"