diff --git a/docs/customizing-atom.md b/docs/customizing-atom.md
index e6ad89305..49d196e50 100644
--- a/docs/customizing-atom.md
+++ b/docs/customizing-atom.md
@@ -112,14 +112,16 @@ namespaces: `core` and `editor`.
 
 ### Quick Personal Hacks
 
-### user.coffee
+### init.coffee
 
-When Atom finishes loading, it will evaluate _user.coffee_ in your _~/.atom_
+When Atom finishes loading, it will evaluate _init.coffee_ in your _~/.atom_
 directory, giving you a chance to run arbitrary personal CoffeeScript code to
 make customizations. You have full access to Atom's API from code in this file.
 If customizations become extensive, consider [creating a
 package][create-a-package].
 
+This file can also be named _init.js_ and contain JavaScript code.
+
 ### styles.css
 
 If you want to apply quick-and-dirty personal styling changes without creating
diff --git a/dot-atom/init.coffee b/dot-atom/init.coffee
new file mode 100644
index 000000000..4d10e775b
--- /dev/null
+++ b/dot-atom/init.coffee
@@ -0,0 +1,14 @@
+# Your init script
+#
+# Atom will evaluate this file each time a new window is opened. It is run
+# after packages are loaded/activated and after the previous editor state
+# has been restored.
+#
+# An example hack to make opened Markdown files always be soft wrapped:
+#
+# path = require 'path'
+#
+# atom.workspaceView.eachEditorView (editorView) ->
+#   editor = editorView.getEditor()
+#   if path.extname(editor.getPath()) is '.md'
+#     editor.setSoftWrap(true)
diff --git a/dot-atom/user.coffee b/dot-atom/user.coffee
deleted file mode 100644
index 60880641d..000000000
--- a/dot-atom/user.coffee
+++ /dev/null
@@ -1 +0,0 @@
-# For more on how to configure atom open `~/github/atom/docs/configuring-and-extending.md`
diff --git a/menus/darwin.cson b/menus/darwin.cson
index 346523299..4ac239e8a 100644
--- a/menus/darwin.cson
+++ b/menus/darwin.cson
@@ -9,6 +9,7 @@
       { type: 'separator' }
       { label: 'Preferences...', command: 'application:show-settings' }
       { label: 'Open Your Config', command: 'application:open-your-config' }
+      { label: 'Open Your Init Script', command: 'application:open-your-init-script' }
       { label: 'Open Your Keymap', command: 'application:open-your-keymap' }
       { label: 'Open Your Snippets', command: 'application:open-your-snippets' }
       { label: 'Open Your Stylesheet', command: 'application:open-your-stylesheet' }
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 77455c5c2..9f8afa408 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -220,6 +220,8 @@ describe "Config", ->
           expect(fs.existsSync(path.join(atom.config.configDirPath, 'packages'))).toBeTruthy()
           expect(fs.isFileSync(path.join(atom.config.configDirPath, 'snippets.cson'))).toBeTruthy()
           expect(fs.isFileSync(path.join(atom.config.configDirPath, 'config.cson'))).toBeTruthy()
+          expect(fs.isFileSync(path.join(atom.config.configDirPath, 'init.coffee'))).toBeTruthy()
+          expect(fs.isFileSync(path.join(atom.config.configDirPath, 'styles.css'))).toBeTruthy()
 
   describe ".loadUserConfig()", ->
     beforeEach ->
diff --git a/src/atom.coffee b/src/atom.coffee
index bc22aa661..9cfffb74a 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -494,8 +494,12 @@ class Atom extends Model
     shell.beep() if @config.get('core.audioBeep')
     @workspaceView.trigger 'beep'
 
+  getUserInitScriptPath: ->
+    initScriptPath = fs.resolve(@getConfigDirPath(), 'init', ['js', 'coffee'])
+    initScriptPath ? path.join(@getConfigDirPath(), 'init.coffee')
+
   requireUserInitScript: ->
-    if userInitScriptPath = fs.resolve(@getConfigDirPath(), 'user', ['js', 'coffee'])
+    if userInitScriptPath = @getUserInitScriptPath()
       try
         require userInitScriptPath
       catch error
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 7966b7cc3..149c6f61c 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -189,6 +189,7 @@ class AtomApplication
 
     @openPathOnEvent('application:show-settings', 'atom://config')
     @openPathOnEvent('application:open-your-config', 'atom://.atom/config')
+    @openPathOnEvent('application:open-your-init-script', 'atom://.atom/init-script')
     @openPathOnEvent('application:open-your-keymap', 'atom://.atom/keymap')
     @openPathOnEvent('application:open-your-snippets', 'atom://.atom/snippets')
     @openPathOnEvent('application:open-your-stylesheet', 'atom://.atom/stylesheet')
diff --git a/src/workspace-view.coffee b/src/workspace-view.coffee
index 7e94f7721..6b62a7829 100644
--- a/src/workspace-view.coffee
+++ b/src/workspace-view.coffee
@@ -107,6 +107,7 @@ class WorkspaceView extends View
     @command 'application:zoom', -> ipc.sendChannel('command', 'application:zoom')
     @command 'application:bring-all-windows-to-front', -> ipc.sendChannel('command', 'application:bring-all-windows-to-front')
     @command 'application:open-your-config', -> ipc.sendChannel('command', 'application:open-your-config')
+    @command 'application:open-your-init-script', -> ipc.sendChannel('command', 'application:open-your-init-script')
     @command 'application:open-your-keymap', -> ipc.sendChannel('command', 'application:open-your-keymap')
     @command 'application:open-your-snippets', -> ipc.sendChannel('command', 'application:open-your-snippets')
     @command 'application:open-your-stylesheet', -> ipc.sendChannel('command', 'application:open-your-stylesheet')
diff --git a/src/workspace.coffee b/src/workspace.coffee
index eec5d88ed..ec5b8fa87 100644
--- a/src/workspace.coffee
+++ b/src/workspace.coffee
@@ -35,6 +35,8 @@ class Workspace extends Model
           @open(atom.keymap.getUserKeymapPath())
         when 'atom://.atom/config'
           @open(atom.config.getUserConfigPath())
+        when 'atom://.atom/init-script'
+          @open(atom.getUserInitScriptPath())
 
   # Called by the Serializable mixin during deserialization
   deserializeParams: (params) ->