diff --git a/package.json b/package.json
index 09d76509b..3b4089d07 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "version": "31.0.0",
-  "main": "./src/main.js",
+  "main": "./src/browser/main.js",
   "repository": {
     "type": "git",
     "url": "https://github.com/atom/atom.git"
diff --git a/src/application-menu.coffee b/src/browser/application-menu.coffee
similarity index 100%
rename from src/application-menu.coffee
rename to src/browser/application-menu.coffee
diff --git a/src/atom-application.coffee b/src/browser/atom-application.coffee
similarity index 96%
rename from src/atom-application.coffee
rename to src/browser/atom-application.coffee
index b3fc70596..aad19da63 100644
--- a/src/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -1,6 +1,6 @@
-AtomWindow = require 'atom-window'
-ApplicationMenu = require 'application-menu'
-AtomProtocolHandler = require 'atom-protocol-handler'
+AtomWindow = require './atom-window'
+ApplicationMenu = require './application-menu'
+AtomProtocolHandler = require './atom-protocol-handler'
 Menu = require 'menu'
 autoUpdater = require 'auto-updater'
 app = require 'app'
@@ -251,7 +251,7 @@ class AtomApplication
         bootstrapScript = require.resolve(path.join(global.devResourcePath, 'src', 'window-bootstrap'))
       else
         resourcePath = @resourcePath
-        bootstrapScript = require.resolve('./window-bootstrap')
+        bootstrapScript = require.resolve('../window-bootstrap')
       openedWindow = new AtomWindow({pathToOpen, initialLine, bootstrapScript, resourcePath, devMode, initialSize})
 
     if pidToKillWhenClosed?
@@ -279,8 +279,8 @@ class AtomApplication
   #      Boolean to control the opened window's dev mode.
   openUrl: ({urlToOpen, devMode}) ->
     unless @packages?
-      PackageManager = require './package-manager'
-      fsUtils = require './fs-utils'
+      PackageManager = require '../package-manager'
+      fsUtils = require '../fs-utils'
       @packages = new PackageManager
         configDirPath: fsUtils.absolute('~/.atom')
         devMode: devMode
@@ -314,7 +314,7 @@ class AtomApplication
     try
       bootstrapScript = require.resolve(path.resolve(global.devResourcePath, 'spec', 'spec-bootstrap'))
     catch error
-      bootstrapScript = require.resolve(path.resolve(__dirname, '..', 'spec', 'spec-bootstrap'))
+      bootstrapScript = require.resolve(path.resolve(__dirname, '..', '..', 'spec', 'spec-bootstrap'))
 
     isSpec = true
     devMode = true
@@ -324,9 +324,9 @@ class AtomApplication
     try
       bootstrapScript = require.resolve(path.resolve(global.devResourcePath, 'benchmark', 'benchmark-bootstrap'))
     catch error
-      bootstrapScript = require.resolve(path.resolve(__dirname, '..', 'benchmark', 'benchmark-bootstrap'))
+      bootstrapScript = require.resolve(path.resolve(__dirname, '..', '..', 'benchmark', 'benchmark-bootstrap'))
 
-    isSpec = true # Needed because this flag adds the spec directory to the NODE_PATH
+    isSpec = true
     new AtomWindow({bootstrapScript, @resourcePath, isSpec})
 
   # Private: Opens a native dialog to prompt the user for a path.
diff --git a/src/atom-protocol-handler.coffee b/src/browser/atom-protocol-handler.coffee
similarity index 100%
rename from src/atom-protocol-handler.coffee
rename to src/browser/atom-protocol-handler.coffee
diff --git a/src/atom-window.coffee b/src/browser/atom-window.coffee
similarity index 97%
rename from src/atom-window.coffee
rename to src/browser/atom-window.coffee
index 81de39f38..031fcd68d 100644
--- a/src/atom-window.coffee
+++ b/src/browser/atom-window.coffee
@@ -1,7 +1,6 @@
 BrowserWindow = require 'browser-window'
 Menu = require 'menu'
-MenuItem = require 'menu-item'
-ContextMenu = require 'context-menu'
+ContextMenu = require './context-menu'
 dialog = require 'dialog'
 ipc = require 'ipc'
 path = require 'path'
@@ -84,7 +83,7 @@ class AtomWindow
         when 1 then @browserWindow.restart()
 
     @browserWindow.on 'context-menu', (menuTemplate) =>
-      new ContextMenu(menuTemplate)
+      new ContextMenu(menuTemplate, @browserWindow)
 
     if @isSpec
       # Spec window's web view should always have focus
diff --git a/src/context-menu.coffee b/src/browser/context-menu.coffee
similarity index 83%
rename from src/context-menu.coffee
rename to src/browser/context-menu.coffee
index f60a7709e..6abc6a801 100644
--- a/src/context-menu.coffee
+++ b/src/browser/context-menu.coffee
@@ -1,12 +1,11 @@
 Menu = require 'menu'
-BrowserWindow =  require 'browser-window'
 
 module.exports =
 class ContextMenu
-  constructor: (template) ->
+  constructor: (template, browserWindow) ->
     template = @createClickHandlers(template)
     menu = Menu.buildFromTemplate(template)
-    menu.popup(BrowserWindow.getFocusedWindow())
+    menu.popup(browserWindow)
 
   # Private: It's necessary to build the event handlers in this process, otherwise
   # closures are drug across processes and failed to be garbage collected
diff --git a/src/main.coffee b/src/browser/main.coffee
similarity index 91%
rename from src/main.coffee
rename to src/browser/main.coffee
index f6c5bf165..e2490b97c 100644
--- a/src/main.coffee
+++ b/src/browser/main.coffee
@@ -14,6 +14,10 @@ dialog = require 'dialog'
 console.log = (args...) ->
   nslog(args.map((arg) -> JSON.stringify(arg)).join(" "))
 
+process.on 'uncaughtException', (error={}) ->
+  nslog(error.message) if error.message?
+  nslog(error.stack) if error.stack?
+
 delegate.browserMainParts.preMainMessageLoopRun = ->
   args = parseCommandLine()
 
@@ -47,12 +51,9 @@ delegate.browserMainParts.preMainMessageLoopRun = ->
     require('coffee-script')
     if args.devMode
       require(path.join(args.resourcePath, 'src', 'coffee-cache')).register()
-      module.globalPaths.push(path.join(args.resourcePath, 'src'))
+      AtomApplication = require path.join(args.resourcePath, 'src', 'browser', 'atom-application')
     else
-      appSrcPath = path.resolve(process.argv[0], "../../Resources/app/src")
-      module.globalPaths.push(appSrcPath)
-
-    AtomApplication = require 'atom-application'
+      AtomApplication = require './atom-application'
 
     AtomApplication.open(args)
     console.log("App load time: #{new Date().getTime() - startTime}ms")
@@ -112,6 +113,6 @@ parseCommandLine = ->
     fs.statSync resourcePath
   catch e
     devMode = false
-    resourcePath = path.dirname(__dirname)
+    resourcePath = path.dirname(path.dirname(__dirname))
 
   {resourcePath, pathsToOpen, executedFrom, test, version, pidToKillWhenClosed, devMode, newWindow, specDirectory}