Add the "atom://" custom protocol handler.

src/atom-application.coffee

@@ -1,5 +1,6 @@
 AtomWindow = require 'atom-window'
 ApplicationMenu = require 'application-menu'
+AtomProtocolHandler = require 'atom-protocol-handler'
 BrowserWindow = require 'browser-window'
 Menu = require 'menu'
 autoUpdater = require 'auto-updater'
@@ -45,6 +46,7 @@ class AtomApplication
 
   windows: null
   applicationMenu: null
+  atomProtocolHandler: null
   resourcePath: null
   version: null
 
@@ -56,6 +58,7 @@ class AtomApplication
     @windows = []
 
     @applicationMenu = new ApplicationMenu(@version, devMode)
+    @atomProtocolHandler = new AtomProtocolHandler(@resourcePath)
 
     @listenForArgumentsFromNewProcess()
     @setupJavaScriptArguments()

src/atom-protocol-handler.coffee

@@ -0,0 +1,18 @@
+path = require 'path'
+protocol = require 'protocol'
+
+# Private: Handles requests with 'atom' protocol.
+#
+# It's created by {AtomApplication} upon instantiation, and is used to create a
+# custom resource loader by adding the 'atom' custom protocol.
+module.exports =
+class AtomProtocolHandler
+  constructor: (@resourcePath) ->
+    @registerAtomProtocol()
+
+  # Private: Creates the 'atom' custom protocol handler.
+  registerAtomProtocol: ->
+    protocol.registerProtocol 'atom', (request) =>
+      relativePath = path.normalize(request.url.substr(7))
+      filePath = path.join(@resourcePath, 'node_modules', relativePath)
+      return new protocol.RequestFileJob(filePath)