diff --git a/menus/base.cson b/menus/base.cson
index 7a991d552..64a45e615 100644
--- a/menus/base.cson
+++ b/menus/base.cson
@@ -7,12 +7,11 @@
       { label: "Install update", command: 'application:install-update', visible: false }
       { type: 'separator' }
       { label: 'Preferences...', command: 'application:show-settings' }
+      { type: 'separator' }
       { label: 'Hide Atom', command: 'application:hide' }
       { label: 'Hide Others', command: 'application:hide-other-applications' }
       { label: 'Show All', command: 'application:unhide-all-applications' }
       { type: 'separator' }
-      { label: 'Run Atom Specs', command: 'application:run-all-specs' }
-      { type: 'separator' }
       { label: 'Quit', command: 'application:quit' }
     ]
   }
@@ -21,10 +20,15 @@
     submenu: [
       { label: 'New Window', command: 'application:new-window' }
       { label: 'New File', command: 'application:new-file' }
-      { type: 'separator' }
       { label: 'Open...', command: 'application:open' }
-      { label: 'Open In Dev Mode...', command: 'application:open-dev' }
+      { label: 'Reopen Last Item', command: 'pane:reopen-closed-item' }
       { type: 'separator' }
+      { label: 'Save', command: 'core:save' }
+      { label: 'Save As...', command: 'core:save-as' }
+      { label: 'Save All', command: 'window:save-all' }
+      { type: 'separator' }
+      { label: 'Close Buffer', command: 'core:close' }
+      { label: 'Close All Buffers', command: 'pane:close' }
       { label: 'Close Window', command: 'window:close' }
     ]
   }
@@ -37,8 +41,10 @@
       { type: 'separator' }
       { label: 'Cut', command: 'core:cut' }
       { label: 'Copy', command: 'core:copy' }
+      { label: 'Copy Path', command: 'editor:copy-path' }
       { label: 'Paste', command: 'core:paste' }
       { label: 'Select All', command: 'core:select-all' }
+      { type: 'separator' }
     ]
   }
 
@@ -47,7 +53,17 @@
     submenu: [
       { label: 'Reload', command: 'window:reload' }
       { label: 'Toggle Full Screen', command: 'window:toggle-full-screen' }
-      { label: 'Toggle Developer Tools', command: 'window:toggle-dev-tools' }
+      {
+        label: 'Developer'
+        submenu: [
+          { label: 'Open In Dev Mode...', command: 'application:open-dev' }
+          { label: 'Run Atom Specs', command: 'application:run-all-specs' }
+          { label: 'Run Package Specs', command: 'window:run-package-specs' }
+          { label: 'Toggle Developer Tools', command: 'window:toggle-dev-tools' }
+        ]
+      }
+      { type: 'separator' }
+      { label: 'Toggle Soft Wrap', command: 'editor:toggle-soft-wrap' }
     ]
   }
 
@@ -60,4 +76,13 @@
       { label: 'Bring All to Front', command: 'application:bring-all-windows-to-front' }
     ]
   }
+
+  {
+    label: 'Help'
+    submenu: [
+      { label: 'Documentation', command: 'application:open-documentation' }
+      { label: 'Report an Issue', command: 'application:report-issue' }
+      { type: 'separator' }
+    ]
+  }
 ]
diff --git a/package.json b/package.json
index 19b1526da..5a7c3eeeb 100644
--- a/package.json
+++ b/package.json
@@ -50,41 +50,41 @@
 
     "archive-view": "0.11.0",
     "autocomplete": "0.10.0",
-    "autoflow": "0.4.0",
-    "bookmarks": "0.7.0",
+    "autoflow": "0.5.0",
+    "bookmarks": "0.8.0",
     "bracket-matcher": "0.7.0",
     "collaboration": "0.26.0",
-    "command-logger": "0.5.0",
+    "command-logger": "0.6.0",
     "command-palette": "0.5.0",
-    "dev-live-reload": "0.7.0",
-    "editor-stats": "0.4.0",
+    "dev-live-reload": "0.8.0",
+    "editor-stats": "0.5.0",
     "exception-reporting": "0.4.0",
-    "find-and-replace": "0.28.0",
-    "fuzzy-finder": "0.14.0",
+    "find-and-replace": "0.29.0",
+    "fuzzy-finder": "0.15.0",
     "gfm": "0.5.0",
     "git-diff": "0.11.0",
-    "gists": "0.4.0",
-    "github-sign-in": "0.7.0",
-    "go-to-line": "0.7.0",
-    "grammar-selector": "0.6.0",
+    "gists": "0.5.0",
+    "github-sign-in": "0.8.0",
+    "go-to-line": "0.8.0",
+    "grammar-selector": "0.7.0",
     "image-view": "0.7.0",
     "link": "0.6.0",
-    "markdown-preview": "0.8.0",
+    "markdown-preview": "0.9.0",
     "metrics": "0.8.0",
-    "package-generator": "0.12.0",
-    "release-notes": "0.4.0",
+    "package-generator": "0.13.0",
+    "release-notes": "0.6.0",
     "settings-view": "0.29.0",
-    "snippets": "0.9.0",
+    "snippets": "0.10.0",
     "spell-check": "0.7.0",
     "status-bar": "0.14.0",
-    "styleguide": "0.8.0",
-    "symbols-view": "0.11.0",
+    "styleguide": "0.9.0",
+    "symbols-view": "0.12.0",
     "tabs": "0.7.0",
-    "terminal": "0.12.0",
-    "timecop": "0.5.0",
-    "to-the-hubs": "0.7.0",
+    "terminal": "0.13.0",
+    "timecop": "0.6.0",
+    "to-the-hubs": "0.8.0",
     "toml": "0.3.0",
-    "tree-view": "0.18.0",
+    "tree-view": "0.19.0",
     "whitespace": "0.7.0",
     "wrap-guide": "0.4.0",
 
diff --git a/spec/atom-spec.coffee b/spec/atom-spec.coffee
index 396a497a1..ed357c0fe 100644
--- a/spec/atom-spec.coffee
+++ b/spec/atom-spec.coffee
@@ -171,6 +171,7 @@ describe "the `atom` global", ->
 
               atom.activatePackage("package-with-menus")
 
+              expect(atom.menu.template.length).toBe 2
               expect(atom.menu.template[0].label).toBe "Second to Last"
               expect(atom.menu.template[1].label).toBe "Last"
               expect(atom.contextMenu.definitionsForElement(element)[0].label).toBe "Menu item 1"
diff --git a/spec/fixtures/packages/package-with-menus/menus/menu-3.cson b/spec/fixtures/packages/package-with-menus/menus/menu-3.cson
index 83b77430a..932cd4d5b 100644
--- a/spec/fixtures/packages/package-with-menus/menus/menu-3.cson
+++ b/spec/fixtures/packages/package-with-menus/menus/menu-3.cson
@@ -1,3 +1,7 @@
+'menu': [
+  { 'label': 'Second to Last' }
+]
+
 'context-menu':
   '.test-1':
     'Menu item 3': 'command-3'
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index 0c4cf377d..2749e9247 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -111,6 +111,7 @@ afterEach ->
   keymap.bindingSets = bindingSetsToRestore
   keymap.bindingSetsByFirstKeystroke = bindingSetsByFirstKeystrokeToRestore
   atom.deactivatePackages()
+  atom.menu.template = []
 
   window.rootView?.remove?()
   atom.rootView?.remove?() if atom.rootView isnt window.rootView
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 7def18e06..d51dd5157 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -4,11 +4,12 @@ AtomProtocolHandler = require './atom-protocol-handler'
 Menu = require 'menu'
 autoUpdater = require 'auto-updater'
 app = require 'app'
-ipc = require 'ipc'
 dialog = require 'dialog'
 fs = require 'fs'
+ipc = require 'ipc'
 path = require 'path'
 net = require 'net'
+shell = require 'shell'
 url = require 'url'
 {EventEmitter} = require 'events'
 _ = require 'underscore-plus'
@@ -136,6 +137,8 @@ class AtomApplication
     @on 'application:zoom', -> Menu.sendActionToFirstResponder('zoom:')
     @on 'application:bring-all-windows-to-front', -> Menu.sendActionToFirstResponder('arrangeInFront:')
     @on 'application:inspect', ({x,y}) -> @focusedWindow().browserWindow.inspectElement(x, y)
+    @on 'application:open-documentation', -> shell.openExternal('https://github-atom-io.herokuapp.com/docs/latest/?app=true')
+    @on 'application:report-issue', -> shell.openExternal('https://github.com/atom/atom/issues/new')
     @on 'application:show-settings', ->
       if @focusedWindow()
         @focusedWindow().openPath("atom://config")
diff --git a/src/menu-manager.coffee b/src/menu-manager.coffee
index 02b521443..7fa1f242a 100644
--- a/src/menu-manager.coffee
+++ b/src/menu-manager.coffee
@@ -42,10 +42,12 @@ class MenuManager
   # Private: Merges an item in a submenu aware way such that new items are always
   # appended to the bottom of existing menus where possible.
   merge: (menu, item) ->
-    if item.submenu? and match = _.find(menu, (o) -> o.submenu? and o.label == item.label)
+    item = _.deepClone(item)
+
+    if item.submenu? and match = _.find(menu, (i) -> i.submenu? and i.label == item.label)
       @merge(match.submenu, i) for i in item.submenu
     else
-      menu.push(item)
+      menu.push(item) unless _.find(menu, (i) -> i.label == item.label)
 
   # Private
   sendToBrowserProcess: (template, keystrokesByCommand) ->