diff --git a/benchmark/benchmark-bootstrap.coffee b/benchmark/benchmark-bootstrap.coffee
index 18d030e62..5d74df7de 100644
--- a/benchmark/benchmark-bootstrap.coffee
+++ b/benchmark/benchmark-bootstrap.coffee
@@ -1,4 +1,5 @@
-require '../src/atom'
+Atom = require '../src/atom'
+window.atom = new Atom()
 {runSpecSuite} = require '../spec/jasmine-helper'
 
 atom.openDevTools()
diff --git a/spec/atom-spec.coffee b/spec/atom-spec.coffee
index a5643443e..26ceea45c 100644
--- a/spec/atom-spec.coffee
+++ b/spec/atom-spec.coffee
@@ -6,29 +6,6 @@ describe "the `atom` global", ->
   beforeEach ->
     window.rootView = new RootView
 
-  describe "base stylesheet loading", ->
-    beforeEach ->
-      rootView.append $$ -> @div class: 'editor'
-      rootView.attachToDom()
-      atom.themes.load()
-      atom.watchThemes()
-
-    afterEach ->
-      atom.themes.unload()
-      config.set('core.themes', [])
-      atom.reloadBaseStylesheets()
-
-    it "loads the correct values from the theme's ui-variables file", ->
-      config.set('core.themes', ['theme-with-ui-variables'])
-
-      # an override loaded in the base css
-      expect(rootView.css("background-color")).toBe "rgb(0, 0, 255)"
-
-      # from within the theme itself
-      expect($(".editor").css("padding-top")).toBe "150px"
-      expect($(".editor").css("padding-right")).toBe "150px"
-      expect($(".editor").css("padding-bottom")).toBe "150px"
-
   describe "package lifecycle methods", ->
     describe ".loadPackage(name)", ->
       describe "when the package has deferred deserializers", ->
@@ -205,15 +182,15 @@ describe "the `atom` global", ->
               one = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/1.css")
               two = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/2.less")
               three = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/3.css")
-              expect(stylesheetElementForId(one)).not.toExist()
-              expect(stylesheetElementForId(two)).not.toExist()
-              expect(stylesheetElementForId(three)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(one)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(two)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(three)).not.toExist()
 
               atom.activatePackage("package-with-stylesheets-manifest")
 
-              expect(stylesheetElementForId(one)).toExist()
-              expect(stylesheetElementForId(two)).toExist()
-              expect(stylesheetElementForId(three)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(one)).toExist()
+              expect(atom.themes.stylesheetElementForId(two)).toExist()
+              expect(atom.themes.stylesheetElementForId(three)).not.toExist()
               expect($('#jasmine-content').css('font-size')).toBe '1px'
 
           describe "when the metadata does not contain a 'stylesheets' manifest", ->
@@ -221,14 +198,14 @@ describe "the `atom` global", ->
               one = require.resolve("./fixtures/packages/package-with-stylesheets/stylesheets/1.css")
               two = require.resolve("./fixtures/packages/package-with-stylesheets/stylesheets/2.less")
               three = require.resolve("./fixtures/packages/package-with-stylesheets/stylesheets/3.css")
-              expect(stylesheetElementForId(one)).not.toExist()
-              expect(stylesheetElementForId(two)).not.toExist()
-              expect(stylesheetElementForId(three)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(one)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(two)).not.toExist()
+              expect(atom.themes.stylesheetElementForId(three)).not.toExist()
 
               atom.activatePackage("package-with-stylesheets")
-              expect(stylesheetElementForId(one)).toExist()
-              expect(stylesheetElementForId(two)).toExist()
-              expect(stylesheetElementForId(three)).toExist()
+              expect(atom.themes.stylesheetElementForId(one)).toExist()
+              expect(atom.themes.stylesheetElementForId(two)).toExist()
+              expect(atom.themes.stylesheetElementForId(three)).toExist()
               expect($('#jasmine-content').css('font-size')).toBe '3px'
 
         describe "grammar loading", ->
@@ -298,8 +275,8 @@ describe "the `atom` global", ->
           atom.activatePackage('package-with-serialize-error',  immediate: true)
           atom.activatePackage('package-with-serialization', immediate: true)
           atom.deactivatePackages()
-          expect(atom.packageStates['package-with-serialize-error']).toBeUndefined()
-          expect(atom.packageStates['package-with-serialization']).toEqual someNumber: 1
+          expect(atom.packages.packageStates['package-with-serialize-error']).toBeUndefined()
+          expect(atom.packages.packageStates['package-with-serialization']).toEqual someNumber: 1
           expect(console.error).toHaveBeenCalled()
 
         it "removes the package's grammars", ->
@@ -320,9 +297,9 @@ describe "the `atom` global", ->
           one = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/1.css")
           two = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/2.less")
           three = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/3.css")
-          expect(stylesheetElementForId(one)).not.toExist()
-          expect(stylesheetElementForId(two)).not.toExist()
-          expect(stylesheetElementForId(three)).not.toExist()
+          expect(atom.themes.stylesheetElementForId(one)).not.toExist()
+          expect(atom.themes.stylesheetElementForId(two)).not.toExist()
+          expect(atom.themes.stylesheetElementForId(three)).not.toExist()
 
         it "removes the package's scoped-properties", ->
           atom.activatePackage("package-with-scoped-properties")
diff --git a/spec/deserializer-manager-spec.coffee b/spec/deserializer-manager-spec.coffee
new file mode 100644
index 000000000..84bc4b9d0
--- /dev/null
+++ b/spec/deserializer-manager-spec.coffee
@@ -0,0 +1,33 @@
+DeserializerManager = require '../src/deserializer-manager'
+
+describe ".deserialize(state)", ->
+  deserializer = null
+
+  class Foo
+    @deserialize: ({name}) -> new Foo(name)
+    constructor: (@name) ->
+
+  beforeEach ->
+    deserializer = new DeserializerManager()
+    deserializer.registerDeserializer(Foo)
+
+  it "calls deserialize on the deserializer for the given state object, or returns undefined if one can't be found", ->
+    spyOn(console, 'warn')
+    object = deserializer.deserialize({ deserializer: 'Foo', name: 'Bar' })
+    expect(object.name).toBe 'Bar'
+    expect(deserializer.deserialize({ deserializer: 'Bogus' })).toBeUndefined()
+
+  describe "when the deserializer has a version", ->
+    beforeEach ->
+      Foo.version = 2
+
+    describe "when the deserialized state has a matching version", ->
+      it "attempts to deserialize the state", ->
+        object = deserializer.deserialize({ deserializer: 'Foo', version: 2, name: 'Bar' })
+        expect(object.name).toBe 'Bar'
+
+    describe "when the deserialized state has a non-matching version", ->
+      it "returns undefined", ->
+        expect(deserializer.deserialize({ deserializer: 'Foo', version: 3, name: 'Bar' })).toBeUndefined()
+        expect(deserializer.deserialize({ deserializer: 'Foo', version: 1, name: 'Bar' })).toBeUndefined()
+        expect(deserializer.deserialize({ deserializer: 'Foo', name: 'Bar' })).toBeUndefined()
diff --git a/spec/spec-bootstrap.coffee b/spec/spec-bootstrap.coffee
index 97a4d8471..d4df9c3cd 100644
--- a/spec/spec-bootstrap.coffee
+++ b/spec/spec-bootstrap.coffee
@@ -1,7 +1,8 @@
 try
-  require '../src/atom'
   require '../src/window'
-  atom.show()
+  Atom = require '../src/atom'
+  window.atom = new Atom()
+  window.atom.show()
   {runSpecSuite} = require './jasmine-helper'
 
   document.title = "Spec Suite"
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index 74155a915..38db81e8c 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -14,12 +14,11 @@ TokenizedBuffer = require '../src/tokenized-buffer'
 pathwatcher = require 'pathwatcher'
 clipboard = require 'clipboard'
 
-atom.loadBaseStylesheets()
-requireStylesheet '../static/jasmine'
+atom.themes.loadBaseStylesheets()
+atom.themes.requireStylesheet '../static/jasmine'
 
 fixturePackagesPath = path.resolve(__dirname, './fixtures/packages')
-config.packageDirPaths.unshift(fixturePackagesPath)
-keymap.loadBundledKeymaps()
+atom.keymap.loadBundledKeymaps()
 [bindingSetsToRestore, bindingSetsByFirstKeystrokeToRestore] = []
 
 $(window).on 'core:close', -> window.close()
@@ -36,20 +35,22 @@ specProjectPath = path.join(specDirectory, 'fixtures')
 
 beforeEach ->
   $.fx.off = true
-  window.project = new Project(specProjectPath)
+  atom.project = new Project(specProjectPath)
+  window.project = atom.project
 
   window.resetTimeouts()
-  atom.packageStates = {}
+  atom.packages.packageStates = {}
   spyOn(atom, 'saveWindowState')
-  syntax.clearGrammarOverrides()
-  syntax.clearProperties()
+  atom.syntax.clearGrammarOverrides()
+  atom.syntax.clearProperties()
 
   # used to reset keymap after each spec
   bindingSetsToRestore = _.clone(keymap.bindingSets)
   bindingSetsByFirstKeystrokeToRestore = _.clone(keymap.bindingSetsByFirstKeystroke)
 
   # reset config before each spec; don't load or save from/to `config.json`
-  window.config = new Config()
+  config = new Config()
+  config.packageDirPaths.unshift(fixturePackagesPath)
   spyOn(config, 'load')
   spyOn(config, 'save')
   config.set "editor.fontFamily", "Courier"
@@ -57,6 +58,8 @@ beforeEach ->
   config.set "editor.autoIndent", false
   config.set "core.disabledPackages", ["package-that-throws-an-exception"]
   config.save.reset()
+  atom.config = config
+  window.config = config
 
   # make editor display updates synchronous
   spyOn(Editor.prototype, 'requestDisplayUpdate').andCallFake -> @updateDisplay()
diff --git a/spec/theme-manager-spec.coffee b/spec/theme-manager-spec.coffee
index 43f8185e6..d5d5cc1b3 100644
--- a/spec/theme-manager-spec.coffee
+++ b/spec/theme-manager-spec.coffee
@@ -1,4 +1,5 @@
-{$} = require 'atom'
+path = require 'path'
+{$, $$, fs, RootView} = require 'atom'
 
 ThemeManager = require '../src/theme-manager'
 AtomPackage = require '../src/atom-package'
@@ -73,3 +74,81 @@ describe "ThemeManager", ->
 
       expect(loadHandler).toHaveBeenCalled()
       expect(loadHandler.mostRecentCall.args[0]).toBeInstanceOf AtomPackage
+
+  describe "requireStylesheet(path)", ->
+    it "synchronously loads css at the given path and installs a style tag for it in the head", ->
+      cssPath = project.resolve('css.css')
+      lengthBefore = $('head style').length
+
+      themeManager.requireStylesheet(cssPath)
+      expect($('head style').length).toBe lengthBefore + 1
+
+      element = $('head style[id*="css.css"]')
+      expect(element.attr('id')).toBe cssPath
+      expect(element.text()).toBe fs.read(cssPath)
+
+      # doesn't append twice
+      themeManager.requireStylesheet(cssPath)
+      expect($('head style').length).toBe lengthBefore + 1
+
+      $('head style[id*="css.css"]').remove()
+
+    it "synchronously loads and parses less files at the given path and installs a style tag for it in the head", ->
+      lessPath = project.resolve('sample.less')
+      lengthBefore = $('head style').length
+      themeManager.requireStylesheet(lessPath)
+      expect($('head style').length).toBe lengthBefore + 1
+
+      element = $('head style[id*="sample.less"]')
+      expect(element.attr('id')).toBe lessPath
+      expect(element.text()).toBe """
+      #header {
+        color: #4d926f;
+      }
+      h2 {
+        color: #4d926f;
+      }
+
+      """
+
+      # doesn't append twice
+      themeManager.requireStylesheet(lessPath)
+      expect($('head style').length).toBe lengthBefore + 1
+      $('head style[id*="sample.less"]').remove()
+
+    it "supports requiring css and less stylesheets without an explicit extension", ->
+      themeManager.requireStylesheet path.join(__dirname, 'fixtures', 'css')
+      expect($('head style[id*="css.css"]').attr('id')).toBe project.resolve('css.css')
+      themeManager.requireStylesheet path.join(__dirname, 'fixtures', 'sample')
+      expect($('head style[id*="sample.less"]').attr('id')).toBe project.resolve('sample.less')
+
+      $('head style[id*="css.css"]').remove()
+      $('head style[id*="sample.less"]').remove()
+
+  describe ".removeStylesheet(path)", ->
+    it "removes styling applied by given stylesheet path", ->
+      cssPath = require.resolve('./fixtures/css.css')
+
+      expect($(document.body).css('font-weight')).not.toBe("bold")
+      themeManager.requireStylesheet(cssPath)
+      expect($(document.body).css('font-weight')).toBe("bold")
+      themeManager.removeStylesheet(cssPath)
+      expect($(document.body).css('font-weight')).not.toBe("bold")
+
+  describe "base stylesheet loading", ->
+    beforeEach ->
+      window.rootView = new RootView
+      rootView.append $$ -> @div class: 'editor'
+      rootView.attachToDom()
+      themeManager.load()
+
+    it "loads the correct values from the theme's ui-variables file", ->
+      config.set('core.themes', ['theme-with-ui-variables'])
+
+      # an override loaded in the base css
+      expect(rootView.css("background-color")).toBe "rgb(0, 0, 255)"
+
+      # from within the theme itself
+      expect($(".editor").css("padding-top")).toBe "150px"
+      expect($(".editor").css("padding-right")).toBe "150px"
+      expect($(".editor").css("padding-bottom")).toBe "150px"
diff --git a/spec/window-spec.coffee b/spec/window-spec.coffee
index 1522d6ec4..a536d0ca6 100644
--- a/spec/window-spec.coffee
+++ b/spec/window-spec.coffee
@@ -75,66 +75,6 @@ describe "Window", ->
         expect(window.onbeforeunload(new Event('beforeunload'))).toBeFalsy()
         expect(atom.confirmSync).toHaveBeenCalled()
 
-  describe "requireStylesheet(path)", ->
-    it "synchronously loads css at the given path and installs a style tag for it in the head", ->
-      cssPath = project.resolve('css.css')
-      lengthBefore = $('head style').length
-
-      requireStylesheet(cssPath)
-      expect($('head style').length).toBe lengthBefore + 1
-
-      element = $('head style[id*="css.css"]')
-      expect(element.attr('id')).toBe cssPath
-      expect(element.text()).toBe fs.read(cssPath)
-
-      # doesn't append twice
-      requireStylesheet(cssPath)
-      expect($('head style').length).toBe lengthBefore + 1
-
-      $('head style[id*="css.css"]').remove()
-
-    it "synchronously loads and parses less files at the given path and installs a style tag for it in the head", ->
-      lessPath = project.resolve('sample.less')
-      lengthBefore = $('head style').length
-      requireStylesheet(lessPath)
-      expect($('head style').length).toBe lengthBefore + 1
-
-      element = $('head style[id*="sample.less"]')
-      expect(element.attr('id')).toBe lessPath
-      expect(element.text()).toBe """
-      #header {
-        color: #4d926f;
-      }
-      h2 {
-        color: #4d926f;
-      }
-
-      """
-
-      # doesn't append twice
-      requireStylesheet(lessPath)
-      expect($('head style').length).toBe lengthBefore + 1
-      $('head style[id*="sample.less"]').remove()
-
-    it "supports requiring css and less stylesheets without an explicit extension", ->
-      requireStylesheet path.join(__dirname, 'fixtures', 'css')
-      expect($('head style[id*="css.css"]').attr('id')).toBe project.resolve('css.css')
-      requireStylesheet path.join(__dirname, 'fixtures', 'sample')
-      expect($('head style[id*="sample.less"]').attr('id')).toBe project.resolve('sample.less')
-
-      $('head style[id*="css.css"]').remove()
-      $('head style[id*="sample.less"]').remove()
-
-  describe ".removeStylesheet(path)", ->
-    it "removes styling applied by given stylesheet path", ->
-      cssPath = require.resolve('./fixtures/css.css')
-
-      expect($(document.body).css('font-weight')).not.toBe("bold")
-      requireStylesheet(cssPath)
-      expect($(document.body).css('font-weight')).toBe("bold")
-      removeStylesheet(cssPath)
-      expect($(document.body).css('font-weight')).not.toBe("bold")
-
   describe ".unloadEditorWindow()", ->
     it "saves the serialized state of the window so it can be deserialized after reload", ->
       rootViewState = rootView.serialize()
@@ -156,38 +96,6 @@ describe "Window", ->
 
       expect(buffer.subscriptionCount()).toBe 0
 
-  describe ".deserialize(state)", ->
-    class Foo
-      @deserialize: ({name}) -> new Foo(name)
-      constructor: (@name) ->
-
-    beforeEach ->
-      registerDeserializer(Foo)
-
-    afterEach ->
-      unregisterDeserializer(Foo)
-
-    it "calls deserialize on the deserializer for the given state object, or returns undefined if one can't be found", ->
-      spyOn(console, 'warn')
-      object = deserialize({ deserializer: 'Foo', name: 'Bar' })
-      expect(object.name).toBe 'Bar'
-      expect(deserialize({ deserializer: 'Bogus' })).toBeUndefined()
-
-    describe "when the deserializer has a version", ->
-      beforeEach ->
-        Foo.version = 2
-
-      describe "when the deserialized state has a matching version", ->
-        it "attempts to deserialize the state", ->
-          object = deserialize({ deserializer: 'Foo', version: 2, name: 'Bar' })
-          expect(object.name).toBe 'Bar'
-
-      describe "when the deserialized state has a non-matching version", ->
-        it "returns undefined", ->
-          expect(deserialize({ deserializer: 'Foo', version: 3, name: 'Bar' })).toBeUndefined()
-          expect(deserialize({ deserializer: 'Foo', version: 1, name: 'Bar' })).toBeUndefined()
-          expect(deserialize({ deserializer: 'Foo', name: 'Bar' })).toBeUndefined()
-
   describe "drag and drop", ->
     buildDragEvent = (type, files) ->
       dataTransfer =
@@ -206,7 +114,7 @@ describe "Window", ->
       it "opens it", ->
         spyOn(atom, "open")
         event = buildDragEvent("drop", [ {path: "/fake1"}, {path: "/fake2"} ])
-        window.onDrop(event)
+        $(document).trigger(event)
         expect(atom.open.callCount).toBe 1
         expect(atom.open.argsForCall[0][0]).toEqual pathsToOpen: ['/fake1', '/fake2']
 
@@ -214,7 +122,7 @@ describe "Window", ->
       it "does nothing", ->
         spyOn(atom, "open")
         event = buildDragEvent("drop", [])
-        window.onDrop(event)
+        $(document).trigger(event)
         expect(atom.open).not.toHaveBeenCalled()
 
   describe "when a link is clicked", ->
diff --git a/src/atom-package.coffee b/src/atom-package.coffee
index 1074eca48..641f67b39 100644
--- a/src/atom-package.coffee
+++ b/src/atom-package.coffee
@@ -83,7 +83,8 @@ class AtomPackage extends Package
 
   activateStylesheets: ->
     type = if @metadata.theme then 'theme' else 'bundled'
-    applyStylesheet(stylesheetPath, content, type) for [stylesheetPath, content] in @stylesheets
+    for [stylesheetPath, content] in @stylesheets
+      atom.themes.applyStylesheet(stylesheetPath, content, type)
 
   activateResources: ->
     keymap.add(keymapPath, map) for [keymapPath, map] in @keymaps
@@ -113,7 +114,8 @@ class AtomPackage extends Package
       fsUtils.listSync(menusDirPath, ['cson', 'json'])
 
   loadStylesheets: ->
-    @stylesheets = @getStylesheetPaths().map (stylesheetPath) -> [stylesheetPath, loadStylesheet(stylesheetPath)]
+    @stylesheets = @getStylesheetPaths().map (stylesheetPath) ->
+      [stylesheetPath, atom.themes.loadStylesheet(stylesheetPath)]
 
   getStylesheetsPath: ->
     path.join(@path, @constructor.stylesheetsDir)
@@ -165,17 +167,17 @@ class AtomPackage extends Package
     syntax.removeGrammar(grammar) for grammar in @grammars
     syntax.removeProperties(scopedPropertiesPath) for [scopedPropertiesPath] in @scopedProperties
     keymap.remove(keymapPath) for [keymapPath] in @keymaps
-    removeStylesheet(stylesheetPath) for [stylesheetPath] in @stylesheets
+    atom.themes.removeStylesheet(stylesheetPath) for [stylesheetPath] in @stylesheets
 
   reloadStylesheets: ->
     oldSheets = _.clone(@stylesheets)
     @loadStylesheets()
-    removeStylesheet(stylesheetPath) for [stylesheetPath] in oldSheets
+    atom.themes.removeStylesheet(stylesheetPath) for [stylesheetPath] in oldSheets
     @reloadStylesheet(stylesheetPath, content) for [stylesheetPath, content] in @stylesheets
 
   reloadStylesheet: (stylesheetPath, content) ->
     type = if @metadata.theme then 'theme' else 'bundled'
-    window.applyStylesheet(stylesheetPath, content, type)
+    atom.themes.applyStylesheet(stylesheetPath, content, type)
 
   requireMainModule: ->
     return @mainModule if @mainModule?
diff --git a/src/atom.coffee b/src/atom.coffee
index 723f9a7f4..3206081c3 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -10,155 +10,140 @@ path = require 'path'
 dialog = remote.require 'dialog'
 app = remote.require 'app'
 {Document} = require 'telepath'
-ThemeManager = require './theme-manager'
-ContextMenuManager = require './context-menu-manager'
+DeserializerManager = require './deserializer-manager'
+Subscriber = require './subscriber'
 
-window.atom =
-  loadedPackages: {}
-  activePackages: {}
-  packageStates: {}
-  themes: new ThemeManager()
-  contextMenu: new ContextMenuManager(remote.getCurrentWindow().loadSettings.devMode)
+# Public: Atom global for dealing with packages, themes, menus, and the window.
+#
+# An instance of this class is always available as the `atom` global.
+module.exports =
+class Atom
+  _.extend @prototype, Subscriber
 
-  getLoadSettings: ->
-    @getCurrentWindow().loadSettings
+  constructor: ->
+    @rootViewParentSelector = 'body'
+    @deserializers = new DeserializerManager()
+
+  initialize: ->
+    @unsubscribe()
+
+    Config = require './config'
+    Keymap = require './keymap'
+    PackageManager = require './package-manager'
+    Pasteboard = require './pasteboard'
+    Syntax = require './syntax'
+    ThemeManager = require './theme-manager'
+    ContextMenuManager = require './context-menu-manager'
+
+    @packages = new PackageManager()
+
+    #TODO Remove once packages have been updated to not touch atom.packageStates directly
+    @__defineGetter__ 'packageStates', => @packages.packageStates
+    @__defineSetter__ 'packageStates', (packageStates) => @packages.packageStates = packageStates
+
+    @subscribe @packages, 'loaded', => @watchThemes()
+    @themes = new ThemeManager()
+    @contextMenu = new ContextMenuManager(@getLoadSettings().devMode)
+    @config = new Config()
+    @pasteboard = new Pasteboard()
+    @keymap = new Keymap()
+    @syntax = deserialize(@getWindowState('syntax')) ? new Syntax()
 
   getCurrentWindow: ->
     remote.getCurrentWindow()
 
-  getPackageState: (name) ->
-    @packageStates[name]
+  # Public: Get the dimensions of this window.
+  #
+  # Returns an object with x, y, width, and height keys.
+  getDimensions: ->
+    browserWindow = @getCurrentWindow()
+    [x, y] = browserWindow.getPosition()
+    [width, height] = browserWindow.getSize()
+    {x, y, width, height}
 
-  setPackageState: (name, state) ->
-    @packageStates[name] = state
-
-  activatePackages: ->
-    @activatePackage(pack.name) for pack in @getLoadedPackages()
-
-  activatePackage: (name, options) ->
-    if pack = @loadPackage(name, options)
-      @activePackages[pack.name] = pack
-      pack.activate(options)
-      pack
-
-  deactivatePackages: ->
-    @deactivatePackage(pack.name) for pack in @getActivePackages()
-
-  deactivatePackage: (name) ->
-    if pack = @getActivePackage(name)
-      @setPackageState(pack.name, state) if state = pack.serialize?()
-      pack.deactivate()
-      delete @activePackages[pack.name]
+  # Public: Set the dimensions of the window.
+  #
+  # The window will be centered if either the x or y coordinate is not set
+  # in the dimensions parameter.
+  #
+  # * dimensions:
+  #    + x:
+  #      The new x coordinate.
+  #    + y:
+  #      The new y coordinate.
+  #    + width:
+  #      The new width.
+  #    + height:
+  #      The new height.
+  setDimensions: ({x, y, width, height}) ->
+    browserWindow = @getCurrentWindow()
+    browserWindow.setSize(width, height)
+    if x? and y?
+      browserWindow.setPosition(x, y)
     else
-      throw new Error("No active package for name '#{name}'")
+      browserWindow.center()
 
-  getActivePackage: (name) ->
-    @activePackages[name]
+  restoreDimensions: (defaultDimensions={width: 800, height: 600})->
+    dimensions = @getWindowState().getObject('dimensions')
+    dimensions = defaultDimensions unless dimensions?.width and dimensions?.height
+    @setDimensions(dimensions)
 
-  isPackageActive: (name) ->
-    @getActivePackage(name)?
+  getLoadSettings: ->
+    @getCurrentWindow().loadSettings
 
-  getActivePackages: ->
-    _.values(@activePackages)
+  deserializeProject: ->
+    Project = require './project'
+    state = @getWindowState()
+    @project = deserialize(state.get('project'))
+    unless @project?
+      @project = new Project(@getLoadSettings().initialPath)
+      state.set('project', @project.getState())
 
-  loadPackages: ->
-    # Ensure atom exports is already in the require cache so the load time
-    # of the first package isn't skewed by being the first to require atom
-    require '../exports/atom'
+  deserializeRootView: ->
+    RootView = require './root-view'
+    state = @getWindowState()
+    @rootView = deserialize(state.get('rootView'))
+    unless @rootView?
+      @rootView = new RootView()
+      state.set('rootView', @rootView.getState())
+    $(@rootViewParentSelector).append(@rootView)
 
-    @loadPackage(name) for name in @getAvailablePackageNames() when not @isPackageDisabled(name)
-    @watchThemes()
+  deserializePackageStates: ->
+    state = @getWindowState()
+    @packages.packageStates = state.getObject('packageStates') ? {}
+    state.remove('packageStates')
 
-  loadPackage: (name, options) ->
-    if @isPackageDisabled(name)
-      return console.warn("Tried to load disabled package '#{name}'")
-
-    if packagePath = @resolvePackagePath(name)
-      return pack if pack = @getLoadedPackage(name)
-      pack = Package.load(packagePath, options)
-      if pack.metadata.theme
-        @themes.register(pack)
-      else
-        @loadedPackages[pack.name] = pack
-      pack
-    else
-      throw new Error("Could not resolve '#{name}' to a package path")
-
-  unloadPackage: (name) ->
-    if @isPackageActive(name)
-      throw new Error("Tried to unload active package '#{name}'")
-
-    if pack = @getLoadedPackage(name)
-      delete @loadedPackages[pack.name]
-    else
-      throw new Error("No loaded package for name '#{name}'")
-
-  resolvePackagePath: (name) ->
-    return name if fsUtils.isDirectorySync(name)
-
-    packagePath = fsUtils.resolve(config.packageDirPaths..., name)
-    return packagePath if fsUtils.isDirectorySync(packagePath)
-
-    packagePath = path.join(window.resourcePath, 'node_modules', name)
-    return packagePath if @isInternalPackage(packagePath)
-
-  isInternalPackage: (packagePath) ->
-    {engines} = Package.loadMetadata(packagePath, true)
-    engines?.atom?
-
-  getLoadedPackage: (name) ->
-    @loadedPackages[name]
-
-  isPackageLoaded: (name) ->
-    @getLoadedPackage(name)?
-
-  getLoadedPackages: ->
-    _.values(@loadedPackages)
-
-  isPackageDisabled: (name) ->
-    _.include(config.get('core.disabledPackages') ? [], name)
-
-  getAvailablePackagePaths: ->
-    packagePaths = []
-
-    for packageDirPath in config.packageDirPaths
-      for packagePath in fsUtils.listSync(packageDirPath)
-        packagePaths.push(packagePath) if fsUtils.isDirectorySync(packagePath)
-
-    for packagePath in fsUtils.listSync(path.join(window.resourcePath, 'node_modules'))
-      packagePaths.push(packagePath) if @isInternalPackage(packagePath)
-
-    _.uniq(packagePaths)
-
-  getAvailablePackageNames: ->
-    _.uniq _.map @getAvailablePackagePaths(), (packagePath) -> path.basename(packagePath)
-
-  getAvailablePackageMetadata: ->
-    packages = []
-    for packagePath in atom.getAvailablePackagePaths()
-      name = path.basename(packagePath)
-      metadata = atom.getLoadedPackage(name)?.metadata ? Package.loadMetadata(packagePath, true)
-      packages.push(metadata)
-    packages
+  #TODO Remove theses once packages have been migrated
+  getPackageState: (args...) -> @packages.getPackageState(args...)
+  setPackageState: (args...) -> @packages.setPackageState(args...)
+  activatePackages: (args...) -> @packages.activatePackages(args...)
+  activatePackage: (args...) -> @packages.activatePackage(args...)
+  deactivatePackages: (args...) -> @packages.deactivatePackages(args...)
+  deactivatePackage: (args...) -> @packages.deactivatePackage(args...)
+  getActivePackage: (args...) -> @packages.getActivePackage(args...)
+  isPackageActive: (args...) -> @packages.isPackageActive(args...)
+  getActivePackages: (args...) -> @packages.getActivePackages(args...)
+  loadPackages: (args...) -> @packages.loadPackages(args...)
+  loadPackage: (args...) -> @packages.loadPackage(args...)
+  unloadPackage: (args...) -> @packages.unloadPackage(args...)
+  resolvePackagePath: (args...) -> @packages.resolvePackagePath(args...)
+  isInternalPackage: (args...) -> @packages.isInternalPackage(args...)
+  getLoadedPackage: (args...) -> @packages.getLoadedPackage(args...)
+  isPackageLoaded: (args...) -> @packages.isPackageLoaded(args...)
+  getLoadedPackages: (args...) -> @packages.getLoadedPackages(args...)
+  isPackageDisabled: (args...) -> @packages.isPackageDisabled(args...)
+  getAvailablePackagePaths: (args...) -> @packages.getAvailablePackagePaths(args...)
+  getAvailablePackageNames: (args...) -> @packages.getAvailablePackageNames(args...)
+  getAvailablePackageMetadata: (args...)-> @packages.getAvailablePackageMetadata(args...)
 
   loadThemes: ->
     @themes.load()
 
   watchThemes: ->
     @themes.on 'reloaded', =>
-      @reloadBaseStylesheets()
-      pack.reloadStylesheets?() for name, pack of @loadedPackages
+      pack.reloadStylesheets?() for name, pack of @getLoadedPackages()
       null
 
-  loadBaseStylesheets: ->
-    requireStylesheet('bootstrap/less/bootstrap')
-    @reloadBaseStylesheets()
-
-  reloadBaseStylesheets: ->
-    requireStylesheet('../static/atom')
-    if nativeStylesheetPath = fsUtils.resolveOnLoadPath(process.platform, ['css', 'less'])
-      requireStylesheet(nativeStylesheetPath)
-
   open: (options) ->
     ipc.sendChannel('open', options)
 
@@ -210,8 +195,7 @@ window.atom =
   close: ->
     @getCurrentWindow().close()
 
-  exit: (status) ->
-    app.exit(status)
+  exit: (status) -> app.exit(status)
 
   toggleFullScreen: ->
     @setFullScreen(!@isFullScreen())
@@ -236,7 +220,7 @@ window.atom =
           filename = "editor-#{sha1}"
 
     if filename
-      path.join(config.userStoragePath, filename)
+      path.join(@config.userStoragePath, filename)
     else
       null
 
@@ -289,8 +273,22 @@ window.atom =
     shell.beep()
 
   requireUserInitScript: ->
-    userInitScriptPath = path.join(config.configDirPath, "user.coffee")
+    userInitScriptPath = path.join(@config.configDirPath, "user.coffee")
     try
       require userInitScriptPath if fsUtils.isFileSync(userInitScriptPath)
     catch error
       console.error "Failed to load `#{userInitScriptPath}`", error.stack, error
+
+  requireWithGlobals: (id, globals={}) ->
+    existingGlobals = {}
+    for key, value of globals
+      existingGlobals[key] = window[key]
+      window[key] = value
+
+    require(id)
+
+    for key, value of existingGlobals
+      if value is undefined
+        delete window[key]
+      else
+        window[key] = value
diff --git a/src/config.coffee b/src/config.coffee
index ffcd24809..1b2466381 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -8,12 +8,6 @@ async = require 'async'
 pathWatcher = require 'pathwatcher'
 
 configDirPath = fsUtils.absolute("~/.atom")
-nodeModulesDirPath = path.join(resourcePath, "node_modules")
-bundledKeymapsDirPath = path.join(resourcePath, "keymaps")
-userPackagesDirPath = path.join(configDirPath, "packages")
-userPackageDirPaths = [userPackagesDirPath]
-userPackageDirPaths.unshift(path.join(configDirPath, "dev", "packages")) if atom.getLoadSettings().devMode
-userStoragePath = path.join(configDirPath, "storage")
 
 # Public: Used to access all of Atom's configuration details.
 #
@@ -36,23 +30,26 @@ module.exports =
 class Config
   _.extend @prototype, EventEmitter
 
-  configDirPath: configDirPath
-  bundledPackageDirPaths: [nodeModulesDirPath]
-  bundledKeymapsDirPath: bundledKeymapsDirPath
-  nodeModulesDirPath: nodeModulesDirPath
-  packageDirPaths: _.clone(userPackageDirPaths)
-  userPackageDirPaths: userPackageDirPaths
-  userStoragePath: userStoragePath
-  lessSearchPaths: [
-    path.join(resourcePath, 'static', 'variables')
-    path.join(resourcePath, 'static')
-  ]
   defaultSettings: null
   settings: null
   configFileHasErrors: null
 
   # Private: Created during initialization, available as `global.config`
   constructor: ->
+    @configDirPath = configDirPath
+    @bundledKeymapsDirPath = path.join(resourcePath, "keymaps")
+    @nodeModulesDirPath = path.join(resourcePath, "node_modules")
+    @bundledPackageDirPaths = [@nodeModulesDirPath]
+    @lessSearchPaths = [
+      path.join(resourcePath, 'static', 'variables')
+      path.join(resourcePath, 'static')
+    ]
+    @packageDirPaths = [path.join(configDirPath, "packages")]
+    if atom.getLoadSettings().devMode
+      @packageDirPaths.unshift(path.join(configDirPath, "dev", "packages"))
+    @userPackageDirPaths = _.clone(@packageDirPaths)
+    @userStoragePath = path.join(configDirPath, "storage")
+
     @defaultSettings =
       core: _.clone(require('./root-view').configDefaults)
       editor: _.clone(require('./editor').configDefaults)
diff --git a/src/deserializer-manager.coffee b/src/deserializer-manager.coffee
new file mode 100644
index 000000000..8fd3bec19
--- /dev/null
+++ b/src/deserializer-manager.coffee
@@ -0,0 +1,38 @@
+{Document} = require 'telepath'
+
+module.exports =
+class DeserializerManager
+  constructor: ->
+    @deserializers = {}
+    @deferredDeserializers = {}
+
+  registerDeserializer: (klasses...) ->
+    @deserializers[klass.name] = klass for klass in klasses
+
+  registerDeferredDeserializer: (name, fn) ->
+    @deferredDeserializers[name] = fn
+
+  unregisterDeserializer: (klasses...) ->
+    delete @deserializers[klass.name] for klass in klasses
+
+  deserialize: (state, params) ->
+    return unless state?
+
+    if deserializer = @getDeserializer(state)
+      stateVersion = state.get?('version') ? state.version
+      return if deserializer.version? and deserializer.version isnt stateVersion
+      if (state instanceof Document) and not deserializer.acceptsDocuments
+        state = state.toObject()
+      deserializer.deserialize(state, params)
+    else
+      console.warn "No deserializer found for", state
+
+  getDeserializer: (state) ->
+    return unless state?
+
+    name = state.get?('deserializer') ? state.deserializer
+    if @deferredDeserializers[name]
+      @deferredDeserializers[name]()
+      delete @deferredDeserializers[name]
+
+    @deserializers[name]
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
new file mode 100644
index 000000000..cc08c6f56
--- /dev/null
+++ b/src/package-manager.coffee
@@ -0,0 +1,129 @@
+EventEmitter = require './event-emitter'
+fsUtils = require './fs-utils'
+_ = require './underscore-extensions'
+Package = require './package'
+path = require 'path'
+
+module.exports =
+class PackageManager
+  _.extend @prototype, EventEmitter
+
+  constructor: ->
+    @loadedPackages = {}
+    @activePackages = {}
+    @packageStates = {}
+
+  getPackageState: (name) ->
+    @packageStates[name]
+
+  setPackageState: (name, state) ->
+    @packageStates[name] = state
+
+  activatePackages: ->
+    @activatePackage(pack.name) for pack in @getLoadedPackages()
+
+  activatePackage: (name, options) ->
+    if pack = @loadPackage(name, options)
+      @activePackages[pack.name] = pack
+      pack.activate(options)
+      pack
+
+  deactivatePackages: ->
+    @deactivatePackage(pack.name) for pack in @getActivePackages()
+
+  deactivatePackage: (name) ->
+    if pack = @getActivePackage(name)
+      @setPackageState(pack.name, state) if state = pack.serialize?()
+      pack.deactivate()
+      delete @activePackages[pack.name]
+    else
+      throw new Error("No active package for name '#{name}'")
+
+  getActivePackage: (name) ->
+    @activePackages[name]
+
+  isPackageActive: (name) ->
+    @getActivePackage(name)?
+
+  getActivePackages: ->
+    _.values(@activePackages)
+
+  loadPackages: ->
+    # Ensure atom exports is already in the require cache so the load time
+    # of the first package isn't skewed by being the first to require atom
+    require '../exports/atom'
+
+    @loadPackage(name) for name in @getAvailablePackageNames() when not @isPackageDisabled(name)
+    @trigger 'loaded'
+
+  loadPackage: (name, options) ->
+    if @isPackageDisabled(name)
+      return console.warn("Tried to load disabled package '#{name}'")
+
+    if packagePath = @resolvePackagePath(name)
+      return pack if pack = @getLoadedPackage(name)
+      pack = Package.load(packagePath, options)
+      if pack.metadata.theme
+        atom.themes.register(pack)
+      else
+        @loadedPackages[pack.name] = pack
+      pack
+    else
+      throw new Error("Could not resolve '#{name}' to a package path")
+
+  unloadPackage: (name) ->
+    if @isPackageActive(name)
+      throw new Error("Tried to unload active package '#{name}'")
+
+    if pack = @getLoadedPackage(name)
+      delete @loadedPackages[pack.name]
+    else
+      throw new Error("No loaded package for name '#{name}'")
+
+  resolvePackagePath: (name) ->
+    return name if fsUtils.isDirectorySync(name)
+
+    packagePath = fsUtils.resolve(config.packageDirPaths..., name)
+    return packagePath if fsUtils.isDirectorySync(packagePath)
+
+    packagePath = path.join(window.resourcePath, 'node_modules', name)
+    return packagePath if @isInternalPackage(packagePath)
+
+  isInternalPackage: (packagePath) ->
+    {engines} = Package.loadMetadata(packagePath, true)
+    engines?.atom?
+
+  getLoadedPackage: (name) ->
+    @loadedPackages[name]
+
+  isPackageLoaded: (name) ->
+    @getLoadedPackage(name)?
+
+  getLoadedPackages: ->
+    _.values(@loadedPackages)
+
+  isPackageDisabled: (name) ->
+    _.include(config.get('core.disabledPackages') ? [], name)
+
+  getAvailablePackagePaths: ->
+    packagePaths = []
+
+    for packageDirPath in config.packageDirPaths
+      for packagePath in fsUtils.listSync(packageDirPath)
+        packagePaths.push(packagePath) if fsUtils.isDirectorySync(packagePath)
+
+    for packagePath in fsUtils.listSync(path.join(window.resourcePath, 'node_modules'))
+      packagePaths.push(packagePath) if @isInternalPackage(packagePath)
+
+    _.uniq(packagePaths)
+
+  getAvailablePackageNames: ->
+    _.uniq _.map @getAvailablePackagePaths(), (packagePath) -> path.basename(packagePath)
+
+  getAvailablePackageMetadata: ->
+    packages = []
+    for packagePath in atom.getAvailablePackagePaths()
+      name = path.basename(packagePath)
+      metadata = atom.getLoadedPackage(name)?.metadata ? Package.loadMetadata(packagePath, true)
+      packages.push(metadata)
+    packages
diff --git a/src/theme-manager.coffee b/src/theme-manager.coffee
index 5ae6ff6f7..3c4b71e48 100644
--- a/src/theme-manager.coffee
+++ b/src/theme-manager.coffee
@@ -4,7 +4,7 @@ Package = require './package'
 AtomPackage = require './atom-package'
 
 _ = require './underscore-extensions'
-
+$ = require './jquery-extensions'
 fsUtils = require './fs-utils'
 
 # Private: Handles discovering and loading available themes.
@@ -15,6 +15,7 @@ class ThemeManager
   constructor: ->
     @loadedThemes = []
     @activeThemes = []
+    @lessCache = null
 
   # Internal-only:
   register: (theme) ->
@@ -33,9 +34,85 @@ class ThemeManager
   getLoadedThemes: ->
     _.clone(@loadedThemes)
 
+  # Internal-only:
+  loadBaseStylesheets: ->
+    @requireStylesheet('bootstrap/less/bootstrap')
+    @reloadBaseStylesheets()
+
+  # Internal-only:
+  reloadBaseStylesheets: ->
+    @requireStylesheet('../static/atom')
+    if nativeStylesheetPath = fsUtils.resolveOnLoadPath(process.platform, ['css', 'less'])
+      @requireStylesheet(nativeStylesheetPath)
+
+  # Internal-only:
+  stylesheetElementForId: (id) ->
+    $("""head style[id="#{id}"]""")
+
+  # Internal-only:
+  resolveStylesheet: (stylesheetPath) ->
+    if path.extname(stylesheetPath).length > 0
+      fsUtils.resolveOnLoadPath(stylesheetPath)
+    else
+      fsUtils.resolveOnLoadPath(stylesheetPath, ['css', 'less'])
+
+  # Public: resolves and applies the stylesheet specified by the path.
+  #
+  # * stylesheetPath: String. Can be an absolute path or the name of a CSS or
+  #   LESS file in the stylesheets path.
+  #
+  # Returns the absolute path to the stylesheet
+  requireStylesheet: (stylesheetPath) ->
+    if fullPath = @resolveStylesheet(stylesheetPath)
+      content = @loadStylesheet(fullPath)
+      @applyStylesheet(fullPath, content)
+    else
+      throw new Error("Could not find a file at path '#{stylesheetPath}'")
+
+    fullPath
+
+  # Internal-only:
+  loadStylesheet: (stylesheetPath) ->
+    if path.extname(stylesheetPath) is '.less'
+      @loadLessStylesheet(stylesheetPath)
+    else
+      fsUtils.read(stylesheetPath)
+
+  # Internal-only:
+  loadLessStylesheet: (lessStylesheetPath) ->
+    unless lessCache?
+      LessCompileCache = require './less-compile-cache'
+      @lessCache = new LessCompileCache()
+
+    try
+      @lessCache.read(lessStylesheetPath)
+    catch e
+      console.error """
+        Error compiling less stylesheet: #{lessStylesheetPath}
+        Line number: #{e.line}
+        #{e.message}
+      """
+
+  # Internal-only:
+  removeStylesheet: (stylesheetPath) ->
+    unless fullPath = @resolveStylesheet(stylesheetPath)
+      throw new Error("Could not find a file at path '#{stylesheetPath}'")
+    @stylesheetElementForId(fullPath).remove()
+
+  # Internal-only:
+  applyStylesheet: (id, text, ttype = 'bundled') ->
+    styleElement = @stylesheetElementForId(id)
+    if styleElement.length
+      styleElement.text(text)
+    else
+      if $("head style.#{ttype}").length
+        $("head style.#{ttype}:last").after "<style class='#{ttype}' id='#{id}'>#{text}</style>"
+      else
+        $("head").append "<style class='#{ttype}' id='#{id}'>#{text}</style>"
+
   # Internal-only:
   unload: ->
-    removeStylesheet(@userStylesheetPath) if @userStylesheetPath?
+    @removeStylesheet(@userStylesheetPath) if @userStylesheetPath?
     theme.deactivate() while theme = @activeThemes.pop()
 
   # Internal-only:
@@ -50,7 +127,7 @@ class ThemeManager
 
       @activateTheme(themeName) for themeName in themeNames
       @loadUserStylesheet()
-
+      @reloadBaseStylesheets()
       @trigger('reloaded')
 
   # Private:
@@ -118,5 +195,5 @@ class ThemeManager
   loadUserStylesheet: ->
     if userStylesheetPath = @getUserStylesheetPath()
       @userStylesheetPath = userStylesheetPath
-      userStylesheetContents = loadStylesheet(userStylesheetPath)
-      applyStylesheet(userStylesheetPath, userStylesheetContents, 'userTheme')
+      userStylesheetContents = @loadStylesheet(userStylesheetPath)
+      @applyStylesheet(userStylesheetPath, userStylesheetContents, 'userTheme')
diff --git a/src/window-bootstrap.coffee b/src/window-bootstrap.coffee
index bccf2ee92..15da3237e 100644
--- a/src/window-bootstrap.coffee
+++ b/src/window-bootstrap.coffee
@@ -1,9 +1,10 @@
 # Like sands through the hourglass, so are the days of our lives.
 startTime = new Date().getTime()
 
-require './atom'
 require './window'
 
+Atom = require './atom'
+window.atom = new Atom()
 window.setUpEnvironment('editor')
 window.startEditorWindow()
 console.log "Window load time: #{new Date().getTime() - startTime}ms"
diff --git a/src/window-event-handler.coffee b/src/window-event-handler.coffee
index 33b6f2cd5..60e157b6d 100644
--- a/src/window-event-handler.coffee
+++ b/src/window-event-handler.coffee
@@ -1,7 +1,7 @@
 $ = require './jquery-extensions'
 _ = require './underscore-extensions'
 ipc = require 'ipc'
-remote = require 'remote'
+shell = require 'shell'
 Subscriber = require './subscriber'
 fsUtils = require './fs-utils'
 
@@ -20,27 +20,43 @@ class WindowEventHandler
       $(atom.contextMenu.activeElement).trigger(command, args...)
 
     @subscribe $(window), 'focus', -> $("body").removeClass('is-blurred')
+
     @subscribe $(window), 'blur',  -> $("body").addClass('is-blurred')
+
     @subscribe $(window), 'window:open-path', (event, {pathToOpen, initialLine}) ->
-      rootView?.open(pathToOpen, {initialLine}) unless fsUtils.isDirectorySync(pathToOpen)
+      atom.rootView?.open(pathToOpen, {initialLine}) unless fsUtils.isDirectorySync(pathToOpen)
+
     @subscribe $(window), 'beforeunload', =>
-      confirmed = rootView?.confirmClose()
-      atom.hide() if confirmed and not @reloadRequested and remote.getCurrentWindow().isWebViewFocused()
+      confirmed = atom.rootView?.confirmClose()
+      atom.hide() if confirmed and not @reloadRequested and atom.getCurrentWindow().isWebViewFocused()
       @reloadRequested = false
       confirmed
+
+    @subscribe $(window), 'unload', ->
+      atom.getWindowState().set('dimensions', atom.getDimensions())
+
     @subscribeToCommand $(window), 'window:toggle-full-screen', => atom.toggleFullScreen()
+
     @subscribeToCommand $(window), 'window:close', => atom.close()
+
     @subscribeToCommand $(window), 'window:reload', =>
       @reloadRequested = true
       atom.reload()
+
     @subscribeToCommand $(window), 'window:toggle-dev-tools', => atom.toggleDevTools()
 
     @subscribeToCommand $(document), 'core:focus-next', @focusNext
+
     @subscribeToCommand $(document), 'core:focus-previous', @focusPrevious
 
-    @subscribe $(document), 'keydown', keymap.handleKeyEvent
+    @subscribe $(document), 'keydown', atom.keymap.handleKeyEvent
+
+    @subscribe $(document), 'drop', (e) ->
+      e.preventDefault()
+      e.stopPropagation()
+      pathsToOpen = _.pluck(e.originalEvent.dataTransfer.files, 'path')
+      atom.open({pathsToOpen}) if pathsToOpen.length > 0
 
-    @subscribe $(document), 'drop', onDrop
     @subscribe $(document), 'dragover', (e) ->
       e.preventDefault()
       e.stopPropagation()
@@ -54,7 +70,7 @@ class WindowEventHandler
   openLink: (event) =>
     location = $(event.target).attr('href')
     if location and location[0] isnt '#' and /^https?:\/\//.test(location)
-      require('shell').openExternal(location)
+      shell.openExternal(location)
     false
 
   eachTabIndexedElement: (callback) ->
diff --git a/src/window.coffee b/src/window.coffee
index 337a3704b..72c29d1ec 100644
--- a/src/window.coffee
+++ b/src/window.coffee
@@ -1,17 +1,9 @@
-fsUtils = require './fs-utils'
 path = require 'path'
-telepath = require 'telepath'
 $ = require './jquery-extensions'
 _ = require './underscore-extensions'
-remote = require 'remote'
 ipc = require 'ipc'
 WindowEventHandler = require './window-event-handler'
 
-deserializers = {}
-deferredDeserializers = {}
-defaultWindowDimensions = {width: 800, height: 600}
-lessCache = null
-
 ### Internal ###
 
 windowEventHandler = null
@@ -28,19 +20,13 @@ displayWindow = ->
 # This method is called in any window needing a general environment, including specs
 window.setUpEnvironment = (windowMode) ->
   atom.windowMode = windowMode
-  window.resourcePath = remote.getCurrentWindow().loadSettings.resourcePath
-
-  Config = require './config'
-  Syntax = require './syntax'
-  Pasteboard = require './pasteboard'
-  Keymap = require './keymap'
-
-  window.rootViewParentSelector = 'body'
-  window.config = new Config
-  window.syntax = deserialize(atom.getWindowState('syntax')) ? new Syntax
-  window.pasteboard = new Pasteboard
-  window.keymap = new Keymap()
-
+  window.resourcePath = atom.getLoadSettings().resourcePath
+  atom.initialize()
+  #TODO remove once all packages use the atom global
+  window.config = atom.config
+  window.syntax = atom.syntax
+  window.pasteboard = atom.pasteboard
+  window.keymap = atom.keymap
 
 # Set up the default event handlers and menus for a non-editor windows.
 #
@@ -50,8 +36,8 @@ window.setUpEnvironment = (windowMode) ->
 # This should only be called after setUpEnvironment() has been called.
 window.setUpDefaultEvents = ->
   windowEventHandler = new WindowEventHandler
-  keymap.loadBundledKeymaps()
-  ipc.sendChannel 'update-application-menu', keymap.keystrokesByCommandForSelector('body')
+  atom.keymap.loadBundledKeymaps()
+  ipc.sendChannel 'update-application-menu', atom.keymap.keystrokesByCommandForSelector('body')
 
 # This method is only called when opening a real application window
 window.startEditorWindow = ->
@@ -60,16 +46,16 @@ window.startEditorWindow = ->
 
   windowEventHandler = new WindowEventHandler
   restoreDimensions()
-  config.load()
-  keymap.loadBundledKeymaps()
-  atom.loadBaseStylesheets()
-  atom.loadPackages()
-  atom.loadThemes()
+  atom.config.load()
+  atom.keymap.loadBundledKeymaps()
+  atom.themes.loadBaseStylesheets()
+  atom.packages.loadPackages()
+  atom.themes.load()
   deserializeEditorWindow()
-  atom.activatePackages()
-  keymap.loadUserKeymaps()
+  atom.packages.activatePackages()
+  atom.keymap.loadUserKeymaps()
   atom.requireUserInitScript()
-  ipc.sendChannel 'update-application-menu', keymap.keystrokesByCommandForSelector('body')
+  ipc.sendChannel 'update-application-menu', atom.keymap.keystrokesByCommandForSelector('body')
   $(window).on 'unload', ->
     $(document.body).hide()
     unloadEditorWindow()
@@ -78,188 +64,58 @@ window.startEditorWindow = ->
   displayWindow()
 
 window.unloadEditorWindow = ->
-  return if not project and not rootView
+  return if not atom.project and not atom.rootView
   windowState = atom.getWindowState()
-  windowState.set('project', project.serialize())
-  windowState.set('syntax', syntax.serialize())
-  windowState.set('rootView', rootView.serialize())
-  atom.deactivatePackages()
-  windowState.set('packageStates', atom.packageStates)
+  windowState.set('project', atom.project.serialize())
+  windowState.set('syntax', atom.syntax.serialize())
+  windowState.set('rootView', atom.rootView.serialize())
+  atom.packages.deactivatePackages()
+  windowState.set('packageStates', atom.packages.packageStates)
   atom.saveWindowState()
-  rootView.remove()
-  project.destroy()
+  atom.rootView.remove()
+  atom.project.destroy()
   windowEventHandler?.unsubscribe()
-  lessCache?.destroy()
   window.rootView = null
   window.project = null
 
-window.installAtomCommand = (callback) ->
+installAtomCommand = (callback) ->
   commandPath = path.join(window.resourcePath, 'atom.sh')
   require('./command-installer').install(commandPath, callback)
 
-window.installApmCommand = (callback) ->
+installApmCommand = (callback) ->
   commandPath = path.join(window.resourcePath, 'node_modules', '.bin', 'apm')
   require('./command-installer').install(commandPath, callback)
 
-window.onDrop = (e) ->
-  e.preventDefault()
-  e.stopPropagation()
-  pathsToOpen = _.pluck(e.originalEvent.dataTransfer.files, 'path')
-  atom.open({pathsToOpen}) if pathsToOpen.length > 0
-
 window.deserializeEditorWindow = ->
-  RootView = require './root-view'
-  Project = require './project'
+  atom.deserializePackageStates()
+  atom.deserializeProject()
+  window.project = atom.project
+  atom.deserializeRootView()
+  window.rootView = atom.rootView
 
-  windowState = atom.getWindowState()
+window.getDimensions = -> atom.getDimensions()
 
-  atom.packageStates = windowState.getObject('packageStates') ? {}
-  windowState.remove('packageStates')
+window.setDimensions = (args...) -> atom.setDimensions(args...)
 
-  window.project = deserialize(windowState.get('project'))
-  unless window.project?
-    window.project = new Project(atom.getLoadSettings().initialPath)
-    windowState.set('project', window.project.getState())
-
-  window.rootView = deserialize(windowState.get('rootView'))
-  unless window.rootView?
-    window.rootView = new RootView()
-    windowState.set('rootView', window.rootView.getState())
-
-  $(rootViewParentSelector).append(rootView)
-
-  project.on 'path-changed', ->
-    projectPath = project.getPath()
-    atom.getLoadSettings().initialPath = projectPath
-
-window.stylesheetElementForId = (id) ->
-  $("""head style[id="#{id}"]""")
-
-window.resolveStylesheet = (stylesheetPath) ->
-  if path.extname(stylesheetPath).length > 0
-    fsUtils.resolveOnLoadPath(stylesheetPath)
-  else
-    fsUtils.resolveOnLoadPath(stylesheetPath, ['css', 'less'])
-
-# Public: resolves and applies the stylesheet specified by the path.
-#
-# * stylesheetPath: String. Can be an absolute path or the name of a CSS or
-#   LESS file in the stylesheets path.
-#
-# Returns the absolute path to the stylesheet
-window.requireStylesheet = (stylesheetPath) ->
-  if fullPath = window.resolveStylesheet(stylesheetPath)
-    content = window.loadStylesheet(fullPath)
-    window.applyStylesheet(fullPath, content)
-  else
-    throw new Error("Could not find a file at path '#{stylesheetPath}'")
-
-  fullPath
-
-window.loadStylesheet = (stylesheetPath) ->
-  if path.extname(stylesheetPath) is '.less'
-    loadLessStylesheet(stylesheetPath)
-  else
-    fsUtils.read(stylesheetPath)
-
-window.loadLessStylesheet = (lessStylesheetPath) ->
-  unless lessCache?
-    LessCompileCache = require './less-compile-cache'
-    lessCache = new LessCompileCache()
-
-  try
-    lessCache.read(lessStylesheetPath)
-  catch e
-    console.error """
-      Error compiling less stylesheet: #{lessStylesheetPath}
-      Line number: #{e.line}
-      #{e.message}
-    """
-
-window.removeStylesheet = (stylesheetPath) ->
-  unless fullPath = window.resolveStylesheet(stylesheetPath)
-    throw new Error("Could not find a file at path '#{stylesheetPath}'")
-  window.stylesheetElementForId(fullPath).remove()
-
-window.applyStylesheet = (id, text, ttype = 'bundled') ->
-  styleElement = window.stylesheetElementForId(id)
-  if styleElement.length
-    styleElement.text(text)
-  else
-    if $("head style.#{ttype}").length
-      $("head style.#{ttype}:last").after "<style class='#{ttype}' id='#{id}'>#{text}</style>"
-    else
-      $("head").append "<style class='#{ttype}' id='#{id}'>#{text}</style>"
-
-window.getDimensions = ->
-  browserWindow = remote.getCurrentWindow()
-  [x, y] = browserWindow.getPosition()
-  [width, height] = browserWindow.getSize()
-  {x, y, width, height}
-
-window.setDimensions = ({x, y, width, height}) ->
-  browserWindow = remote.getCurrentWindow()
-  browserWindow.setSize(width, height)
-  if x? and y?
-    browserWindow.setPosition(x, y)
-  else
-    browserWindow.center()
-
-window.restoreDimensions = ->
-  dimensions = atom.getWindowState().getObject('dimensions')
-  dimensions = defaultWindowDimensions unless dimensions?.width and dimensions?.height
-  window.setDimensions(dimensions)
-  $(window).on 'unload', -> atom.getWindowState().set('dimensions', window.getDimensions())
+window.restoreDimensions = (args...) -> atom.restoreDimensions(args...)
 
 window.onerror = ->
   atom.openDevTools()
 
 window.registerDeserializers = (args...) ->
-  registerDeserializer(arg) for arg in args
-
-window.registerDeserializer = (klass) ->
-  deserializers[klass.name] = klass
-
-window.registerDeferredDeserializer = (name, fn) ->
-  deferredDeserializers[name] = fn
-
-window.unregisterDeserializer = (klass) ->
-  delete deserializers[klass.name]
-
-window.deserialize = (state, params) ->
-  return unless state?
-  if deserializer = getDeserializer(state)
-    stateVersion = state.get?('version') ? state.version
-    return if deserializer.version? and deserializer.version isnt stateVersion
-    if (state instanceof telepath.Document) and not deserializer.acceptsDocuments
-      state = state.toObject()
-    deserializer.deserialize(state, params)
-  else
-    console.warn "No deserializer found for", state
-
-window.getDeserializer = (state) ->
-  return unless state?
-
-  name = state.get?('deserializer') ? state.deserializer
-  if deferredDeserializers[name]
-    deferredDeserializers[name]()
-    delete deferredDeserializers[name]
-
-  deserializers[name]
-
-window.requireWithGlobals = (id, globals={}) ->
-  existingGlobals = {}
-  for key, value of globals
-    existingGlobals[key] = window[key]
-    window[key] = value
-
-  require(id)
-
-  for key, value of existingGlobals
-    if value is undefined
-      delete window[key]
-    else
-      window[key] = value
+  atom.deserializers.registerDeserializer(args...)
+window.registerDeserializer = (args...) ->
+  atom.deserializers.registerDeserializer(args...)
+window.registerDeferredDeserializer = (args...) ->
+  atom.deserializers.registerDeferredDeserializer(args...)
+window.unregisterDeserializer = (args...) ->
+  atom.deserializers.unregisterDeserializer(args...)
+window.deserialize = (args...) ->
+  atom.deserializers.deserialize(args...)
+window.getDeserializer = (args...) ->
+  atom.deserializer.getDeserializer(args...)
+window.requireWithGlobals = (args...) ->
+  atom.requireWithGlobals(args...)
 
 window.measure = (description, fn) ->
   start = new Date().getTime()