Rename App.coffee to Atom.coffee. This also required moving src/atom,spec/atom to src/app,spec/app

src/app/atom.coffee

@@ -6,7 +6,7 @@ _ = require 'underscore'
 require 'underscore-extensions'
 
 module.exports =
-class App
+class Atom
   keymap: null
   windows: null
   tabText: null

src/atom-bootstrap.coffee

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

src/stdlib/require.coffee

@@ -2,7 +2,7 @@ paths = [
   "#{atom.loadPath}/spec"
   "#{atom.loadPath}/benchmark"
   "#{atom.loadPath}/src/stdlib"
-  "#{atom.loadPath}/src/atom"
+  "#{atom.loadPath}/src/app"
   "#{atom.loadPath}/src"
   "#{atom.loadPath}/vendor"
   "#{atom.loadPath}/static"
@@ -110,7 +110,8 @@ __read = (path) ->
   try
     $native.read(path)
   catch e
-    throw "require: can't read #{path}"
+    console.error "Failed to read `#{path}`"
+    throw e
 
 __modules = { loaded : {} }
 __defines = []
@@ -127,4 +128,4 @@ this.require.nameToUrl = (path) -> "#{path}.js"
 this.require.__modules = __modules
 
 # issue #17
-this.require.noWorker = true
+this.require.noWorker = true