Use relative requires

src/atom-application.coffee

@@ -1,4 +1,4 @@
-AtomWindow = require 'atom-window'
+AtomWindow = require './atom-window'
 BrowserWindow = require 'browser_window'
 Menu = require 'menu'
 app = require 'app'

src/atom-window.coffee

@@ -6,7 +6,7 @@ class AtomWindow
   browserWindow: null
 
   constructor: ({bootstrapScript, resourcePath, @pathToOpen, exitWhenDone, @isSpec}) ->
-    require('atom-application').addWindow(this)
+    require('./atom-application').addWindow(this)
 
     @browserWindow = new BrowserWindow show: false, title: 'Atom'
     @handleEvents()
@@ -19,7 +19,7 @@ class AtomWindow
 
   handleEvents: ->
     @browserWindow.on 'destroyed', =>
-      require('atom-application').removeWindow(this)
+      require('./atom-application').removeWindow(this)
 
     if @isSpec
       # Spec window's web view should always have focus

src/main.coffee

@@ -3,19 +3,16 @@ path = require 'path'
 delegate = require 'atom_delegate'
 optimist = require 'optimist'
 nslog = require('nslog')
+AtomApplication = require('./atom-application')
 
 console.log = (args...) ->
   nslog(args.map((arg) -> JSON.stringify(arg)).join(" "))
 
 require 'coffee-script'
 
-atomApplication = null
-
 delegate.browserMainParts.preMainMessageLoopRun = ->
   commandLineArgs = parseCommandLine()
-  require('module').globalPaths.push(path.join(commandLineArgs.resourcePath, 'src'))
-  AtomApplication = require('atom-application')
-  atomApplication = new AtomApplication(commandLineArgs)
+  new AtomApplication(commandLineArgs)
 
 getHomeDir = ->
   process.env[if process.platform is 'win32' then 'USERPROFILE' else 'HOME']