diff --git a/atom.sh b/atom.sh
index 53de6a493..6ee2b9990 100755
--- a/atom.sh
+++ b/atom.sh
@@ -32,6 +32,7 @@ done
 
 if [ $EXPECT_OUTPUT ]; then
   $ATOM_BINARY --executed-from="$(pwd)" --pid=$$ $@
+  exit $?
 else
   open -a $ATOM_PATH -n --args --executed-from="$(pwd)" --pid=$$ $@
 fi
diff --git a/benchmark/benchmark-bootstrap.coffee b/benchmark/benchmark-bootstrap.coffee
index 5d74df7de..8d9a0ba4e 100644
--- a/benchmark/benchmark-bootstrap.coffee
+++ b/benchmark/benchmark-bootstrap.coffee
@@ -1,5 +1,9 @@
+require '../src/window'
 Atom = require '../src/atom'
-window.atom = new Atom()
+atom = new Atom()
+atom.show() unless atom.getLoadSettings().exitWhenDone
+window.atom = atom
+
 {runSpecSuite} = require '../spec/jasmine-helper'
 
 atom.openDevTools()
diff --git a/benchmark/benchmark-helper.coffee b/benchmark/benchmark-helper.coffee
index aa91f76d7..5b94da991 100644
--- a/benchmark/benchmark-helper.coffee
+++ b/benchmark/benchmark-helper.coffee
@@ -1,11 +1,9 @@
 require '../spec/spec-helper'
 
-$ = require 'jquery'
-_ = require 'underscore'
-{Point} = require 'telepath'
-Project = require 'project'
-fsUtils = require 'fs-utils'
-TokenizedBuffer = require 'tokenized-buffer'
+{$, _, Point, fs} = require 'atom'
+Project = require '../src/project'
+fsUtils = require '../src/fs-utils'
+TokenizedBuffer = require '../src/tokenized-buffer'
 
 defaultCount = 100
 window.pbenchmark = (args...) -> window.benchmark(args..., profile: true)
@@ -13,7 +11,7 @@ window.fbenchmark = (args...) -> window.benchmark(args..., focused: true)
 window.fpbenchmark = (args...) -> window.benchmark(args..., profile: true, focused: true)
 window.pfbenchmark = window.fpbenchmark
 
-window.benchmarkFixturesProject = new Project(fsUtils.resolveOnLoadPath('benchmark/fixtures'))
+window.benchmarkFixturesProject = new Project(fsUtils.resolveOnLoadPath('../benchmark/fixtures'))
 
 beforeEach ->
   window.project = window.benchmarkFixturesProject
diff --git a/benchmark/benchmark-suite.coffee b/benchmark/benchmark-suite.coffee
index 7a15c846c..b5401d385 100644
--- a/benchmark/benchmark-suite.coffee
+++ b/benchmark/benchmark-suite.coffee
@@ -1,8 +1,6 @@
 require './benchmark-helper'
-$ = require 'jquery'
-_ = require 'underscore'
-TokenizedBuffer = require 'tokenized-buffer'
-RootView = require 'root-view'
+{$, _, RootView} = require 'atom'
+TokenizedBuffer = require '../src/tokenized-buffer'
 
 describe "editor.", ->
   editor = null
@@ -12,7 +10,6 @@ describe "editor.", ->
     window.rootView = new RootView
     window.rootView.attachToDom()
 
-
     rootView.width(1024)
     rootView.height(768)
     rootView.open() # open blank editor
@@ -62,6 +59,116 @@ describe "editor.", ->
         editor.insertText('"')
         editor.backspace()
 
+    describe "empty-vs-set-innerHTML.", ->
+      [firstRow, lastRow] = []
+      beforeEach ->
+        firstRow = editor.getFirstVisibleScreenRow()
+        lastRow = editor.getLastVisibleScreenRow()
+
+      benchmark "build-gutter-html.", 1000, ->
+        editor.gutter.renderLineNumbers(null, firstRow, lastRow)
+
+      benchmark "set-innerHTML.", 1000, ->
+        editor.gutter.renderLineNumbers(null, firstRow, lastRow)
+        editor.gutter.lineNumbers[0].innerHtml = ''
+
+      benchmark "empty.", 1000, ->
+        editor.gutter.renderLineNumbers(null, firstRow, lastRow)
+        editor.gutter.lineNumbers.empty()
+
+    describe "positionLeftForLineAndColumn.", ->
+      line = null
+      beforeEach ->
+        editor.scrollTop(2000)
+        editor.resetDisplay()
+        line = editor.lineElementForScreenRow(106)[0]
+
+      describe "one-line.", ->
+        beforeEach ->
+          editor.clearCharacterWidthCache()
+
+        benchmark "uncached", 5000, ->
+          editor.positionLeftForLineAndColumn(line, 106, 82)
+          editor.clearCharacterWidthCache()
+
+        benchmark "cached", 5000, ->
+          editor.positionLeftForLineAndColumn(line, 106, 82)
+
+      describe "multiple-lines.", ->
+        [firstRow, lastRow] = []
+        beforeEach ->
+          firstRow = editor.getFirstVisibleScreenRow()
+          lastRow = editor.getLastVisibleScreenRow()
+
+        benchmark "cache-entire-visible-area", 100, ->
+          for i in [firstRow..lastRow]
+            line = editor.lineElementForScreenRow(i)[0]
+            editor.positionLeftForLineAndColumn(line, i, Math.max(0, editor.lineLengthForBufferRow(i)))
+
+    describe "text-rendering.", ->
+      beforeEach ->
+        editor.scrollTop(2000)
+
+      benchmark "resetDisplay", 50, ->
+        editor.resetDisplay()
+
+      benchmark "htmlForScreenRows", 1000, ->
+        lastRow = editor.getLastScreenRow()
+        editor.htmlForScreenRows(0, lastRow)
+
+      benchmark "htmlForScreenRows.htmlParsing", 50, ->
+        lastRow = editor.getLastScreenRow()
+        html = editor.htmlForScreenRows(0, lastRow)
+
+        div = document.createElement('div')
+        div.innerHTML = html
+
+    describe "gutter-api.", ->
+      describe "getLineNumberElementsForClass.", ->
+        beforeEach ->
+          editor.gutter.addClassToLine(20, 'omgwow')
+          editor.gutter.addClassToLine(40, 'omgwow')
+
+        benchmark "DOM", 20000, ->
+          editor.gutter.getLineNumberElementsForClass('omgwow')
+
+      benchmark "getLineNumberElement.DOM", 20000, ->
+        editor.gutter.getLineNumberElement(12)
+
+      benchmark "toggle-class", 2000, ->
+        editor.gutter.addClassToLine(40, 'omgwow')
+        editor.gutter.removeClassFromLine(40, 'omgwow')
+
+      describe "find-then-unset.", ->
+        classes = ['one', 'two', 'three', 'four']
+
+        benchmark "single-class", 200, ->
+          editor.gutter.addClassToLine(30, 'omgwow')
+          editor.gutter.addClassToLine(40, 'omgwow')
+          editor.gutter.removeClassFromAllLines('omgwow')
+
+        benchmark "multiple-class", 200, ->
+          editor.gutter.addClassToLine(30, 'one')
+          editor.gutter.addClassToLine(30, 'two')
+
+          editor.gutter.addClassToLine(40, 'two')
+          editor.gutter.addClassToLine(40, 'three')
+          editor.gutter.addClassToLine(40, 'four')
+
+          for klass in classes
+            editor.gutter.removeClassFromAllLines(klass)
+
+    describe "line-htmlification.", ->
+      div = null
+      html = null
+      beforeEach ->
+        lastRow = editor.getLastScreenRow()
+        html = editor.htmlForScreenRows(0, lastRow)
+        div = document.createElement('div')
+
+      benchmark "setInnerHTML", 1, ->
+        div.innerHTML = html
+
   describe "9000-line-file.", ->
     benchmark "opening.", 5, ->
       rootView.open('huge.js')
diff --git a/package.json b/package.json
index 144bd0651..c0ec3ea0e 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "atom",
-  "version": "29.0.0",
+  "version": "31.0.0",
   "main": "./src/main.js",
   "repository": {
     "type": "git",
@@ -16,7 +16,7 @@
     "coffee-script": "1.6.2",
     "coffeestack": "0.6.0",
     "first-mate": "0.2.0",
-    "git-utils": "0.25.0",
+    "git-utils": "0.26.0",
     "guid": "0.0.10",
     "jasmine-focused": "~0.14.0",
     "mkdirp": "0.3.5",
@@ -46,17 +46,17 @@
     "archive-view": "0.8.0",
     "autocomplete": "0.6.0",
     "autoflow": "0.3.0",
-    "bookmarks": "0.4.0",
-    "bracket-matcher": "0.5.0",
-    "collaboration": "0.19.0",
+    "bookmarks": "0.5.0",
+    "bracket-matcher": "0.6.0",
+    "collaboration": "0.21.0",
     "command-logger": "0.4.0",
     "command-palette": "0.4.0",
     "editor-stats": "0.3.0",
-    "exception-reporting": "0.3.0",
+    "exception-reporting": "0.4.0",
     "find-and-replace": "0.24.0",
     "fuzzy-finder": "0.7.0",
     "gfm": "0.5.0",
-    "git-diff": "0.4.0",
+    "git-diff": "0.5.0",
     "gists": "0.3.0",
     "github-sign-in": "0.7.0",
     "go-to-line": "0.4.0",
@@ -66,7 +66,7 @@
     "markdown-preview": "0.6.0",
     "metrics": "0.8.0",
     "package-generator": "0.10.0",
-    "release-notes": "0.2.0",
+    "release-notes": "0.3.0",
     "settings-view": "0.27.0",
     "snippets": "0.6.0",
     "spell-check": "0.6.0",
@@ -75,9 +75,9 @@
     "tabs": "0.5.0",
     "terminal": "0.10.0",
     "timecop": "0.5.0",
-    "to-the-hubs": "0.4.0",
+    "to-the-hubs": "0.6.0",
     "toml": "0.3.0",
-    "tree-view": "0.8.0",
+    "tree-view": "0.10.0",
     "ui-demo": "0.8.0",
     "whitespace": "0.5.0",
     "wrap-guide": "0.3.0",
diff --git a/spec/editor-spec.coffee b/spec/editor-spec.coffee
index 820d56654..48de79f12 100644
--- a/spec/editor-spec.coffee
+++ b/spec/editor-spec.coffee
@@ -119,21 +119,21 @@ describe "Editor", ->
 
     it "updates the rendered lines, cursors, selections, scroll position, and event subscriptions to match the given edit session", ->
       editor.attachToDom(heightInLines: 5, widthInChars: 30)
-      editor.setCursorBufferPosition([3, 5])
+      editor.setCursorBufferPosition([6, 13])
       editor.scrollToBottom()
       editor.scrollLeft(150)
       previousScrollHeight = editor.verticalScrollbar.prop('scrollHeight')
       previousScrollTop = editor.scrollTop()
       previousScrollLeft = editor.scrollLeft()
 
-      newEditSession.setScrollTop(120)
+      newEditSession.setScrollTop(900)
       newEditSession.setSelectedBufferRange([[40, 0], [43, 1]])
 
       editor.edit(newEditSession)
       { firstRenderedScreenRow, lastRenderedScreenRow } = editor
       expect(editor.lineElementForScreenRow(firstRenderedScreenRow).text()).toBe newBuffer.lineForRow(firstRenderedScreenRow)
       expect(editor.lineElementForScreenRow(lastRenderedScreenRow).text()).toBe newBuffer.lineForRow(editor.lastRenderedScreenRow)
-      expect(editor.scrollTop()).toBe 120
+      expect(editor.scrollTop()).toBe 900
       expect(editor.scrollLeft()).toBe 0
       expect(editor.getSelectionView().regions[0].position().top).toBe 40 * editor.lineHeight
       editor.insertText("hello")
@@ -146,9 +146,9 @@ describe "Editor", ->
       expect(editor.verticalScrollbar.prop('scrollHeight')).toBe previousScrollHeight
       expect(editor.scrollTop()).toBe previousScrollTop
       expect(editor.scrollLeft()).toBe previousScrollLeft
-      expect(editor.getCursorView().position()).toEqual { top: 3 * editor.lineHeight, left: 5 * editor.charWidth }
+      expect(editor.getCursorView().position()).toEqual { top: 6 * editor.lineHeight, left: 13 * editor.charWidth }
       editor.insertText("goodbye")
-      expect(editor.lineElementForScreenRow(3).text()).toMatch /^    vgoodbyear/
+      expect(editor.lineElementForScreenRow(6).text()).toMatch /^      currentgoodbye/
 
     it "triggers alert if edit session's buffer goes into conflict with changes on disk", ->
       filePath = "/tmp/atom-changed-file.txt"
@@ -904,7 +904,8 @@ describe "Editor", ->
 
       it "moves the hiddenInput to the same position with cursor's view", ->
         editor.setCursorScreenPosition(row: 2, column: 2)
-        expect(editor.getCursorView().offset()).toEqual(editor.hiddenInput.offset())
+        expect(editor.getCursorView()[0].style.left).toEqual(editor.hiddenInput[0].style.left)
+        expect(editor.getCursorView()[0].style.top).toEqual(editor.hiddenInput[0].style.top)
 
       describe "when the editor is using a variable-width font", ->
         beforeEach ->
@@ -1107,8 +1108,8 @@ describe "Editor", ->
         expect(span0.children('span:eq(2)')).toMatchSelector '.meta.brace.curly.js'
         expect(span0.children('span:eq(2)').text()).toBe "{"
 
-        line12 = editor.renderedLines.find('.line:eq(11)')
-        expect(line12.find('span:eq(2)')).toMatchSelector '.keyword'
+        line12 = editor.renderedLines.find('.line:eq(11)').children('span:eq(0)')
+        expect(line12.children('span:eq(1)')).toMatchSelector '.keyword'
 
       it "wraps hard tabs in a span", ->
         editor.setText('\t<- hard tab')
@@ -1123,12 +1124,13 @@ describe "Editor", ->
         expect(span0_0).toMatchSelector '.leading-whitespace'
         expect(span0_0.text()).toBe '  '
 
-      it "wraps trailing whitespace in a span", ->
-        editor.setText('trailing whitespace ->   ')
-        line0 = editor.renderedLines.find('.line:first')
-        span0_last = line0.children('span:eq(0)').children('span:last')
-        expect(span0_last).toMatchSelector '.trailing-whitespace'
-        expect(span0_last.text()).toBe '   '
+      describe "when the line has trailing whitespace", ->
+        it "wraps trailing whitespace in a span", ->
+          editor.setText('trailing whitespace ->   ')
+          line0 = editor.renderedLines.find('.line:first')
+          span0_last = line0.children('span:eq(0)').children('span:last')
+          expect(span0_last).toMatchSelector '.trailing-whitespace'
+          expect(span0_last.text()).toBe '   '
 
       describe "when lines are updated in the buffer", ->
         it "syntax highlights the updated lines", ->
@@ -1878,13 +1880,55 @@ describe "Editor", ->
         # doesn't allow regular editors to set grammars
         expect(-> editor.setGrammar()).toThrow()
 
-
     describe "when config.editor.showLineNumbers is false", ->
       it "doesn't render any line numbers", ->
         expect(editor.gutter.lineNumbers).toBeVisible()
         config.set("editor.showLineNumbers", false)
         expect(editor.gutter.lineNumbers).not.toBeVisible()
 
+    describe "using gutter's api", ->
+      it "can get all the line number elements", ->
+        elements = editor.gutter.getLineNumberElements()
+        len = editor.gutter.lastScreenRow - editor.gutter.firstScreenRow + 1
+        expect(elements).toHaveLength(len)
+
+      it "can get a single line number element", ->
+        element = editor.gutter.getLineNumberElement(3)
+        expect(element).toBeTruthy()
+
+      it "returns falsy when there is no line element", ->
+        expect(editor.gutter.getLineNumberElement(42)).toHaveLength 0
+
+      it "can add and remove classes to all the line numbers", ->
+        wasAdded = editor.gutter.addClassToAllLines('heyok')
+        expect(wasAdded).toBe true
+
+        elements = editor.gutter.getLineNumberElementsForClass('heyok')
+        expect($(elements)).toHaveClass('heyok')
+
+        editor.gutter.removeClassFromAllLines('heyok')
+        expect($(editor.gutter.getLineNumberElements())).not.toHaveClass('heyok')
+
+      it "can add and remove classes from a single line number", ->
+        wasAdded = editor.gutter.addClassToLine(3, 'heyok')
+        expect(wasAdded).toBe true
+
+        element = editor.gutter.getLineNumberElement(2)
+        expect($(element)).not.toHaveClass('heyok')
+
+      it "can fetch line numbers by their class", ->
+        editor.gutter.addClassToLine(1, 'heyok')
+        editor.gutter.addClassToLine(3, 'heyok')
+
+        elements = editor.gutter.getLineNumberElementsForClass('heyok')
+        expect(elements.length).toBe 2
+
+        expect($(elements[0])).toHaveClass 'line-number-1'
+        expect($(elements[0])).toHaveClass 'heyok'
+
+        expect($(elements[1])).toHaveClass 'line-number-3'
+        expect($(elements[1])).toHaveClass 'heyok'
+
   describe "gutter line highlighting", ->
     beforeEach ->
       editor.attachToDom(heightInLines: 5.5)
@@ -2160,10 +2204,21 @@ describe "Editor", ->
         expect(editor.pixelPositionForBufferPosition([2,7])).toEqual top: 0, left: 0
 
     describe "when the editor is attached and visible", ->
-      it "returns the top and left pixel positions", ->
+      beforeEach ->
         editor.attachToDom()
+
+      it "returns the top and left pixel positions", ->
         expect(editor.pixelPositionForBufferPosition([2,7])).toEqual top: 40, left: 70
 
+      it "caches the left position", ->
+        editor.renderedLines.css('font-size', '16px')
+        expect(editor.pixelPositionForBufferPosition([2,8])).toEqual top: 40, left: 80
+
+        # make characters smaller
+        editor.renderedLines.css('font-size', '15px')
+
+        expect(editor.pixelPositionForBufferPosition([2,8])).toEqual top: 40, left: 80
+
   describe "when clicking in the gutter", ->
     beforeEach ->
       editor.attachToDom()
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index a902fc2b4..db907b685 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -18,6 +18,7 @@ atom.themes.loadBaseStylesheets()
 atom.themes.requireStylesheet '../static/jasmine'
 
 fixturePackagesPath = path.resolve(__dirname, './fixtures/packages')
+atom.packages.packageDirPaths.unshift(fixturePackagesPath)
 atom.keymap.loadBundledKeymaps()
 [bindingSetsToRestore, bindingSetsByFirstKeystrokeToRestore] = []
 
@@ -50,7 +51,9 @@ beforeEach ->
   bindingSetsByFirstKeystrokeToRestore = _.clone(keymap.bindingSetsByFirstKeystroke)
 
   # reset config before each spec; don't load or save from/to `config.json`
-  config = new Config()
+  config = new Config
+    resourcePath: window.resourcePath
+    configDirPath: atom.getConfigDirPath()
   config.packageDirPaths.unshift(fixturePackagesPath)
   spyOn(config, 'load')
   spyOn(config, 'save')
diff --git a/src/atom-application.coffee b/src/atom-application.coffee
index d33a9255b..9747fe509 100644
--- a/src/atom-application.coffee
+++ b/src/atom-application.coffee
@@ -51,7 +51,7 @@ class AtomApplication
   version: null
 
   constructor: (options) ->
-    {@resourcePath, @version} = options
+    {@resourcePath, @version, @devMode} = options
     global.atomApplication = this
 
     @pidsToOpenWindows = {}
@@ -147,7 +147,7 @@ class AtomApplication
 
     app.on 'open-url', (event, urlToOpen) =>
       event.preventDefault()
-      @openUrl(urlToOpen)
+      @openUrl({urlToOpen, @devMode})
 
     autoUpdater.on 'ready-for-update-on-quit', (event, version, quitAndUpdateCallback) =>
       event.preventDefault()
@@ -221,9 +221,10 @@ class AtomApplication
   #    + devMode:
   #      Boolean to control the opened window's dev mode.
   openPath: ({pathToOpen, pidToKillWhenClosed, newWindow, devMode}={}) ->
-    [basename, initialLine] = path.basename(pathToOpen).split(':')
-    pathToOpen = "#{path.dirname(pathToOpen)}/#{basename}"
-    initialLine -= 1 if initialLine # Convert line numbers to a base of 0
+    if pathToOpen
+      [basename, initialLine] = path.basename(pathToOpen).split(':')
+      pathToOpen = "#{path.dirname(pathToOpen)}/#{basename}"
+      initialLine -= 1 if initialLine # Convert line numbers to a base of 0
 
     unless devMode
       existingWindow = @windowForPath(pathToOpen) unless pidToKillWhenClosed or newWindow
@@ -251,9 +252,11 @@ class AtomApplication
             console.log("Killing process #{pid} failed: #{error.code}")
         delete @pidsToOpenWindows[pid]
 
-  # Private: Handles an atom:// url.
+  # Private: Open an atom:// url.
   #
-  # Currently only supports atom://session/<session-id> urls.
+  # The host of the URL being opened is assumed to be the package name
+  # responsible for opening the URL.  A new window will be created with
+  # that package's `urlMain` as the bootstrap script.
   #
   # * options
   #    + urlToOpen:
@@ -261,15 +264,25 @@ class AtomApplication
   #    + devMode:
   #      Boolean to control the opened window's dev mode.
   openUrl: ({urlToOpen, devMode}) ->
-    parsedUrl = url.parse(urlToOpen)
-    if parsedUrl.host is 'session'
-      sessionId = parsedUrl.path.split('/')[1]
-      console.log "Joining session #{sessionId}"
-      if sessionId
-        bootstrapScript = 'collaboration/lib/bootstrap'
-        new AtomWindow({bootstrapScript, @resourcePath, sessionId, devMode})
+    unless @packages?
+      PackageManager = require './package-manager'
+      fsUtils = require './fs-utils'
+      @packages = new PackageManager
+        configDirPath: fsUtils.absolute('~/.atom')
+        devMode: devMode
+        resourcePath: @resourcePath
+
+    packageName = url.parse(urlToOpen).host
+    pack = _.find @packages.getAvailablePackageMetadata(), ({name}) -> name is packageName
+    if pack?
+      if pack.urlMain
+        packagePath = @packages.resolvePackagePath(packageName)
+        bootstrapScript = path.resolve(packagePath, pack.urlMain)
+        new AtomWindow({bootstrapScript, @resourcePath, devMode, urlToOpen})
+      else
+        console.log "Package '#{pack.name}' does not have a url main: #{urlToOpen}"
     else
-      console.log "Opening unknown url #{urlToOpen}"
+      console.log "Opening unknown url: #{urlToOpen}"
 
   # Private: Opens up a new {AtomWindow} to run specs within.
   #
diff --git a/src/atom-window.coffee b/src/atom-window.coffee
index 350aac6f5..4cd34b85e 100644
--- a/src/atom-window.coffee
+++ b/src/atom-window.coffee
@@ -30,9 +30,8 @@ class AtomWindow
     loadSettings = _.extend({}, settings)
     loadSettings.windowState ?= ''
     loadSettings.initialPath = pathToOpen
-    try
-      if fs.statSync(pathToOpen).isFile()
-        loadSettings.initialPath = path.dirname(pathToOpen)
+    if fs.statSyncNoException(pathToOpen).isFile?()
+      loadSettings.initialPath = path.dirname(pathToOpen)
 
     @browserWindow.loadSettings = loadSettings
     @browserWindow.once 'window:loaded', => @loaded = true
@@ -55,6 +54,8 @@ class AtomWindow
       false
     else if pathToCheck is initialPath
       true
+    else if fs.statSyncNoException(pathToCheck).isDirectory?()
+      false
     else if pathToCheck.indexOf(path.join(initialPath, path.sep)) is 0
       true
     else
diff --git a/src/atom.coffee b/src/atom.coffee
index 4eb2b34d6..dbf62b991 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -27,6 +27,9 @@ class Atom
   initialize: ->
     @unsubscribe()
 
+    {devMode, resourcePath} = atom.getLoadSettings()
+    configDirPath = @getConfigDirPath()
+
     Config = require './config'
     Keymap = require './keymap'
     PackageManager = require './package-manager'
@@ -36,9 +39,9 @@ class Atom
     ContextMenuManager = require './context-menu-manager'
     MenuManager = require './menu-manager'
 
-    @config = new Config()
+    @config = new Config({configDirPath, resourcePath})
     @keymap = new Keymap()
-    @packages = new PackageManager()
+    @packages = new PackageManager({devMode, configDirPath, resourcePath})
 
     #TODO Remove once packages have been updated to not touch atom.packageStates directly
     @__defineGetter__ 'packageStates', => @packages.packageStates
@@ -46,7 +49,7 @@ class Atom
 
     @subscribe @packages, 'loaded', => @watchThemes()
     @themes = new ThemeManager()
-    @contextMenu = new ContextMenuManager(@getLoadSettings().devMode)
+    @contextMenu = new ContextMenuManager(devMode)
     @menu = new MenuManager()
     @pasteboard = new Pasteboard()
     @syntax = deserialize(@getWindowState('syntax')) ? new Syntax()
@@ -215,6 +218,10 @@ class Atom
   getHomeDirPath: ->
     app.getHomeDir()
 
+  # Public: Get the directory path to Atom's configuration area.
+  getConfigDirPath: ->
+    @configDirPath ?= fsUtils.absolute('~/.atom')
+
   getWindowStatePath: ->
     switch @windowMode
       when 'spec'
@@ -246,7 +253,7 @@ class Atom
       documentStateJson = @getLoadSettings().windowState
 
     try
-      documentState = JSON.parse(documentStateJson) if documentStateJson?
+      documentState = JSON.parse(documentStateJson) if documentStateJson
     catch error
       console.warn "Error parsing window state: #{windowStatePath}", error.stack, error
 
diff --git a/src/config.coffee b/src/config.coffee
index 5ee609147..8c9c6e71d 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -7,8 +7,6 @@ path = require 'path'
 async = require 'async'
 pathWatcher = require 'pathwatcher'
 
-configDirPath = fsUtils.absolute("~/.atom")
-
 # Public: Used to access all of Atom's configuration details.
 #
 # A global instance of this class is available to all plugins which can be
@@ -35,28 +33,27 @@ class Config
   configFileHasErrors: null
 
   # Private: Created during initialization, available as `global.config`
-  constructor: ->
-    @configDirPath = configDirPath
-    @bundledKeymapsDirPath = path.join(resourcePath, "keymaps")
+  constructor: ({@configDirPath, @resourcePath}={}) ->
+    @bundledKeymapsDirPath = path.join(@resourcePath, "keymaps")
     @bundledMenusDirPath = path.join(resourcePath, "menus")
-    @nodeModulesDirPath = path.join(resourcePath, "node_modules")
+    @nodeModulesDirPath = path.join(@resourcePath, "node_modules")
     @bundledPackageDirPaths = [@nodeModulesDirPath]
     @lessSearchPaths = [
-      path.join(resourcePath, 'static', 'variables')
-      path.join(resourcePath, 'static')
+      path.join(@resourcePath, 'static', 'variables')
+      path.join(@resourcePath, 'static')
     ]
-    @packageDirPaths = [path.join(configDirPath, "packages")]
+    @packageDirPaths = [path.join(@configDirPath, "packages")]
     if atom.getLoadSettings().devMode
-      @packageDirPaths.unshift(path.join(configDirPath, "dev", "packages"))
+      @packageDirPaths.unshift(path.join(@configDirPath, "dev", "packages"))
     @userPackageDirPaths = _.clone(@packageDirPaths)
-    @userStoragePath = path.join(configDirPath, "storage")
+    @userStoragePath = path.join(@configDirPath, "storage")
 
     @defaultSettings =
       core: _.clone(require('./root-view').configDefaults)
       editor: _.clone(require('./editor').configDefaults)
     @settings = {}
-    @configFilePath = fsUtils.resolve(configDirPath, 'config', ['json', 'cson'])
-    @configFilePath ?= path.join(configDirPath, 'config.cson')
+    @configFilePath = fsUtils.resolve(@configDirPath, 'config', ['json', 'cson'])
+    @configFilePath ?= path.join(@configDirPath, 'config.cson')
 
   # Private:
   initializeConfigDirectory: (done) ->
@@ -68,7 +65,7 @@ class Config
       fsUtils.copy(sourcePath, destinationPath, callback)
     queue.drain = done
 
-    templateConfigDirPath = fsUtils.resolve(window.resourcePath, 'dot-atom')
+    templateConfigDirPath = fsUtils.resolve(@resourcePath, 'dot-atom')
     onConfigDirFile = (sourcePath) =>
       relativePath = sourcePath.substring(templateConfigDirPath.length + 1)
       destinationPath = path.join(@configDirPath, relativePath)
diff --git a/src/cursor-view.coffee b/src/cursor-view.coffee
index 3c15c235d..5cef2af46 100644
--- a/src/cursor-view.coffee
+++ b/src/cursor-view.coffee
@@ -54,6 +54,14 @@ class CursorView extends View
 
     @setVisible(@cursor.isVisible() and not @editor.isFoldedAtScreenRow(screenPosition.row))
 
+  # Override for speed. The base function checks the computedStyle
+  isHidden: ->
+    style = this[0].style
+    if style.display == 'none' or not @isOnDom()
+      true
+    else
+      false
+
   needsAutoscroll: ->
     @cursor.needsAutoscroll
 
diff --git a/src/editor.coffee b/src/editor.coffee
index ee105b165..4ced66eea 100644
--- a/src/editor.coffee
+++ b/src/editor.coffee
@@ -9,11 +9,16 @@ fsUtils = require './fs-utils'
 $ = require './jquery-extensions'
 _ = require './underscore-extensions'
 
+MeasureRange = document.createRange()
+TextNodeFilter = { acceptNode: -> NodeFilter.FILTER_ACCEPT }
+NoScope = ['no-scope']
+
 # Private: Represents the entire visual pane in Atom.
 #
 # The Editor manages the {EditSession}, which manages the file buffers.
 module.exports =
 class Editor extends View
+  @characterWidthCache: {}
   @configDefaults:
     fontSize: 20
     showInvisibles: false
@@ -703,7 +708,12 @@ class Editor extends View
     @on 'cursor:moved', =>
       return unless @isFocused
       cursorView = @getCursorView()
-      @hiddenInput.offset(cursorView.offset()) if cursorView.is(':visible')
+
+      if cursorView.isVisible()
+        # This is an order of magnitude faster than checking .offset().
+        style = cursorView[0].style
+        @hiddenInput[0].style.top = style.top
+        @hiddenInput[0].style.left = style.left
 
     selectedText = null
     @hiddenInput.on 'compositionstart', =>
@@ -961,6 +971,9 @@ class Editor extends View
   # fontSize - A {Number} indicating the font size in pixels.
   setFontSize: (fontSize) ->
     @css('font-size', "#{fontSize}px}")
+
+    @clearCharacterWidthCache()
+
     if @isOnDom()
       @redraw()
     else
@@ -977,6 +990,9 @@ class Editor extends View
   # fontFamily - A {String} identifying the CSS `font-family`,
   setFontFamily: (fontFamily='') ->
     @css('font-family', fontFamily)
+
+    @clearCharacterWidthCache()
+
     @redraw()
 
   # Gets the font family for the editor.
@@ -1133,6 +1149,14 @@ class Editor extends View
       @layerMinWidth = minWidth
       @trigger 'editor:min-width-changed'
 
+  # Override for speed. The base function checks computedStyle, unnecessary here.
+  isHidden: ->
+    style = this[0].style
+    if style.display == 'none' or not @isOnDom()
+      true
+    else
+      false
+
   clearRenderedLines: ->
     @renderedLines.empty()
     @firstRenderedScreenRow = null
@@ -1184,9 +1208,15 @@ class Editor extends View
     for cursorView in @getCursorViews()
       if cursorView.needsRemoval
         cursorView.remove()
-      else if cursorView.needsUpdate
+      else if @shouldUpdateCursor(cursorView)
         cursorView.updateDisplay()
 
+  shouldUpdateCursor: (cursorView) ->
+    return false unless cursorView.needsUpdate
+
+    pos = cursorView.getScreenPosition()
+    pos.row >= @firstRenderedScreenRow and pos.row <= @lastRenderedScreenRow
+
   updateSelectionViews: ->
     if @newSelections.length > 0
       @addSelectionView(selection) for selection in @newSelections when not selection.destroyed
@@ -1195,9 +1225,15 @@ class Editor extends View
     for selectionView in @getSelectionViews()
       if selectionView.needsRemoval
         selectionView.remove()
-      else
+      else if @shouldUpdateSelection(selectionView)
         selectionView.updateDisplay()
 
+  shouldUpdateSelection: (selectionView) ->
+    screenRange = selectionView.getScreenRange()
+    startRow = screenRange.start.row
+    endRow = screenRange.end.row
+    (startRow >= @firstRenderedScreenRow and startRow <= @lastRenderedScreenRow) or (endRow >= @firstRenderedScreenRow and endRow <= @lastRenderedScreenRow)
+
   syncCursorAnimations: ->
     for cursorView in @getCursorViews()
       do (cursorView) -> cursorView.resetBlinking()
@@ -1229,10 +1265,11 @@ class Editor extends View
     if @pendingChanges.length == 0 and @firstRenderedScreenRow and @firstRenderedScreenRow <= renderFrom and renderTo <= @lastRenderedScreenRow
       return
 
-    @gutter.updateLineNumbers(@pendingChanges, renderFrom, renderTo)
-    intactRanges = @computeIntactRanges()
-    @pendingChanges = []
-    @truncateIntactRanges(intactRanges, renderFrom, renderTo)
+    changes = @pendingChanges
+    intactRanges = @computeIntactRanges(renderFrom, renderTo)
+
+    @gutter.updateLineNumbers(changes, renderFrom, renderTo)
+
     @clearDirtyRanges(intactRanges)
     @fillDirtyRanges(intactRanges, renderFrom, renderTo)
     @firstRenderedScreenRow = renderFrom
@@ -1258,7 +1295,7 @@ class Editor extends View
 
     emptyLineChanges
 
-  computeIntactRanges: ->
+  computeIntactRanges: (renderFrom, renderTo) ->
     return [] if !@firstRenderedScreenRow? and !@lastRenderedScreenRow?
 
     intactRanges = [{start: @firstRenderedScreenRow, end: @lastRenderedScreenRow, domStart: 0}]
@@ -1293,6 +1330,9 @@ class Editor extends View
               domStart: range.domStart + change.end + 1 - range.start
             )
       intactRanges = newIntactRanges
+
+    @truncateIntactRanges(intactRanges, renderFrom, renderTo)
+
     @pendingChanges = []
 
     intactRanges
@@ -1312,35 +1352,35 @@ class Editor extends View
     intactRanges.sort (a, b) -> a.domStart - b.domStart
 
   clearDirtyRanges: (intactRanges) ->
-    renderedLines = @renderedLines[0]
-    killLine = (line) ->
-      next = line.nextSibling
-      renderedLines.removeChild(line)
-      next
-
     if intactRanges.length == 0
-      @renderedLines.empty()
-    else if currentLine = renderedLines.firstChild
+      @renderedLines[0].innerHTML = ''
+    else if currentLine = @renderedLines[0].firstChild
       domPosition = 0
       for intactRange in intactRanges
         while intactRange.domStart > domPosition
-          currentLine = killLine(currentLine)
+          currentLine = @clearLine(currentLine)
           domPosition++
         for i in [intactRange.start..intactRange.end]
           currentLine = currentLine.nextSibling
           domPosition++
       while currentLine
-        currentLine = killLine(currentLine)
+        currentLine = @clearLine(currentLine)
+
+  clearLine: (lineElement) ->
+    next = lineElement.nextSibling
+    @renderedLines[0].removeChild(lineElement)
+    next
 
   fillDirtyRanges: (intactRanges, renderFrom, renderTo) ->
-    renderedLines = @renderedLines[0]
-    nextIntact = intactRanges.shift()
-    currentLine = renderedLines.firstChild
+    i = 0
+    nextIntact = intactRanges[i]
+    currentLine = @renderedLines[0].firstChild
 
     row = renderFrom
     while row <= renderTo
       if row == nextIntact?.end + 1
-        nextIntact = intactRanges.shift()
+        nextIntact = intactRanges[++i]
+
       if !nextIntact or row < nextIntact.start
         if nextIntact
           dirtyRangeEnd = nextIntact.start - 1
@@ -1348,7 +1388,7 @@ class Editor extends View
           dirtyRangeEnd = renderTo
 
         for lineElement in @buildLineElementsForScreenRows(row, dirtyRangeEnd)
-          renderedLines.insertBefore(lineElement, currentLine)
+          @renderedLines[0].insertBefore(lineElement, currentLine)
           row++
       else
         currentLine = currentLine.nextSibling
@@ -1369,14 +1409,18 @@ class Editor extends View
   #
   # Returns a {Number}.
   getFirstVisibleScreenRow: ->
-    Math.floor(@scrollTop() / @lineHeight)
+    screenRow = Math.floor(@scrollTop() / @lineHeight)
+    screenRow = 0 if isNaN(screenRow)
+    screenRow
 
   # Retrieves the number of the row that is visible and currently at the bottom of the editor.
   #
   # Returns a {Number}.
   getLastVisibleScreenRow: ->
     calculatedRow = Math.ceil((@scrollTop() + @scrollView.height()) / @lineHeight) - 1
-    Math.max(0, Math.min(@getScreenLineCount() - 1, calculatedRow))
+    screenRow = Math.max(0, Math.min(@getScreenLineCount() - 1, calculatedRow))
+    screenRow = 0 if isNaN(screenRow)
+    screenRow
 
   # Given a row number, identifies if it is currently visible.
   #
@@ -1401,11 +1445,11 @@ class Editor extends View
     new Array(div.children...)
 
   htmlForScreenRows: (startRow, endRow) ->
-    htmlLines = []
+    htmlLines = ''
     screenRow = startRow
     for line in @activeEditSession.linesForScreenRows(startRow, endRow)
-      htmlLines.push(@htmlForScreenLine(line, screenRow++))
-    htmlLines.join('\n\n')
+      htmlLines += @htmlForScreenLine(line, screenRow++)
+    htmlLines
 
   htmlForScreenLine: (screenLine, screenRow) ->
     { tokens, text, lineEnding, fold, isSoftWrapped } =  screenLine
@@ -1496,28 +1540,92 @@ class Editor extends View
     unless existingLineElement
       lineElement = @buildLineElementForScreenRow(actualRow)
       @renderedLines.append(lineElement)
-    left = @positionLeftForLineAndColumn(lineElement, column)
+    left = @positionLeftForLineAndColumn(lineElement, actualRow, column)
     unless existingLineElement
       @renderedLines[0].removeChild(lineElement)
     { top: row * @lineHeight, left }
 
-  positionLeftForLineAndColumn: (lineElement, column) ->
-    return 0 if column is 0
-    delta = 0
-    iterator = document.createNodeIterator(lineElement, NodeFilter.SHOW_TEXT, acceptNode: -> NodeFilter.FILTER_ACCEPT)
-    while textNode = iterator.nextNode()
-      nextDelta = delta + textNode.textContent.length
-      if nextDelta >= column
-        offset = column - delta
-        break
-      delta = nextDelta
+  positionLeftForLineAndColumn: (lineElement, screenRow, column) ->
+    return 0 if column == 0
 
-    range = document.createRange()
-    range.setEnd(textNode, offset)
-    range.collapse()
-    leftPixels = range.getClientRects()[0].left - Math.floor(@scrollView.offset().left) + Math.floor(@scrollLeft())
-    range.detach()
-    leftPixels
+    bufferRow = @bufferRowsForScreenRows(screenRow, screenRow)[0] ? screenRow
+    tokenizedLine = @activeEditSession.displayBuffer.tokenizedBuffer.tokenizedLines[bufferRow]
+
+    left = 0
+    index = 0
+    for token in tokenizedLine.tokens
+      for char in token.value
+        return left if index >= column
+
+        val = @getCharacterWidthCache(token.scopes, char)
+        if val?
+          left += val
+        else
+          return @measureToColumn(lineElement, tokenizedLine, column)
+
+        index++
+    left
+
+  scopesForColumn: (tokenizedLine, column) ->
+    index = 0
+    for token in tokenizedLine.tokens
+      for char in token.value
+        return token.scopes if index == column
+        index++
+    null
+
+  measureToColumn: (lineElement, tokenizedLine, column) ->
+    left = oldLeft = index = 0
+    iterator = document.createNodeIterator(lineElement, NodeFilter.SHOW_TEXT, TextNodeFilter)
+
+    returnLeft = null
+
+    while textNode = iterator.nextNode()
+      content = textNode.textContent
+
+      for char, i in content
+
+        # Dont return right away, finish caching the whole line
+        returnLeft = left if index == column
+        oldLeft = left
+
+        scopes = @scopesForColumn(tokenizedLine, index)
+        cachedVal = @getCharacterWidthCache(scopes, char)
+
+        if cachedVal?
+          left = oldLeft + cachedVal
+        else
+          # i + 1 to measure to the end of the current character
+          MeasureRange.setEnd(textNode, i + 1)
+          MeasureRange.collapse()
+          rects = MeasureRange.getClientRects()
+          return 0 if rects.length == 0
+          left = rects[0].left - Math.floor(@scrollView.offset().left) + Math.floor(@scrollLeft())
+
+          @setCharacterWidthCache(scopes, char, left - oldLeft) if scopes?
+
+        index++
+
+    returnLeft ? left
+
+  getCharacterWidthCache: (scopes, char) ->
+    scopes ?= NoScope
+    obj = Editor.characterWidthCache
+    for scope in scopes
+      obj = obj[scope]
+      return null unless obj?
+    obj[char]
+
+  setCharacterWidthCache: (scopes, char, val) ->
+    scopes ?= NoScope
+    obj = Editor.characterWidthCache
+    for scope in scopes
+      obj[scope] ?= {}
+      obj = obj[scope]
+    obj[char] = val
+
+  clearCharacterWidthCache: ->
+    Editor.characterWidthCache = {}
 
   pixelOffsetForScreenPosition: (position) ->
     {top, left} = @pixelPositionForScreenPosition(position)
@@ -1591,30 +1699,9 @@ class Editor extends View
     scopeStack = []
     line = []
 
-    updateScopeStack = (desiredScopes) ->
-      excessScopes = scopeStack.length - desiredScopes.length
-      _.times(excessScopes, popScope) if excessScopes > 0
-
-      # pop until common prefix
-      for i in [scopeStack.length..0]
-        break if _.isEqual(scopeStack[0...i], desiredScopes[0...i])
-        popScope()
-
-      # push on top of common prefix until scopeStack == desiredScopes
-      for j in [i...desiredScopes.length]
-        pushScope(desiredScopes[j])
-
-    pushScope = (scope) ->
-      scopeStack.push(scope)
-      line.push("<span class=\"#{scope.replace(/\./g, ' ')}\">")
-
-    popScope = ->
-      scopeStack.pop()
-      line.push("</span>")
-
-    attributePairs = []
-    attributePairs.push "#{attributeName}=\"#{value}\"" for attributeName, value of attributes
-    line.push("<div #{attributePairs.join(' ')}>")
+    attributePairs = ''
+    attributePairs += " #{attributeName}=\"#{value}\"" for attributeName, value of attributes
+    line.push("<div #{attributePairs}>")
 
     if text == ''
       html = Editor.buildEmptyLineHtml(showIndentGuide, eolInvisibles, htmlEolInvisibles, indentation, activeEditSession, mini)
@@ -1625,39 +1712,64 @@ class Editor extends View
       lineIsWhitespaceOnly = firstTrailingWhitespacePosition is 0
       position = 0
       for token in tokens
-        updateScopeStack(token.scopes)
+        @updateScopeStack(line, scopeStack, token.scopes)
         hasLeadingWhitespace =  position < firstNonWhitespacePosition
         hasTrailingWhitespace = position + token.value.length > firstTrailingWhitespacePosition
         hasIndentGuide = not mini and showIndentGuide and (hasLeadingWhitespace or lineIsWhitespaceOnly)
         line.push(token.getValueAsHtml({invisibles, hasLeadingWhitespace, hasTrailingWhitespace, hasIndentGuide}))
         position += token.value.length
 
-    popScope() while scopeStack.length > 0
+    @popScope(line, scopeStack) while scopeStack.length > 0
     line.push(htmlEolInvisibles) unless text == ''
     line.push("<span class='fold-marker'/>") if fold
 
     line.push('</div>')
     line.join('')
 
+  @updateScopeStack: (line, scopeStack, desiredScopes) ->
+    excessScopes = scopeStack.length - desiredScopes.length
+    if excessScopes > 0
+      @popScope(line, scopeStack) while excessScopes--
+
+    # pop until common prefix
+    for i in [scopeStack.length..0]
+      break if _.isEqual(scopeStack[0...i], desiredScopes[0...i])
+      @popScope(line, scopeStack)
+
+    # push on top of common prefix until scopeStack == desiredScopes
+    for j in [i...desiredScopes.length]
+      @pushScope(line, scopeStack, desiredScopes[j])
+
+    null
+
+  @pushScope: (line, scopeStack, scope) ->
+    scopeStack.push(scope)
+    line.push("<span class=\"#{scope.replace(/\./g, ' ')}\">")
+
+  @popScope: (line, scopeStack) ->
+    scopeStack.pop()
+    line.push("</span>")
+
   @buildEmptyLineHtml: (showIndentGuide, eolInvisibles, htmlEolInvisibles, indentation, activeEditSession, mini) ->
+    indentCharIndex = 0
     if not mini and showIndentGuide
       if indentation > 0
         tabLength = activeEditSession.getTabLength()
-        indentGuideHtml = []
+        indentGuideHtml = ''
         for level in [0...indentation]
-          indentLevelHtml = ["<span class='indent-guide'>"]
+          indentLevelHtml = "<span class='indent-guide'>"
           for characterPosition in [0...tabLength]
-            if invisible = eolInvisibles.shift()
-              indentLevelHtml.push("<span class='invisible-character'>#{invisible}</span>")
+            if invisible = eolInvisibles[indentCharIndex++]
+              indentLevelHtml += "<span class='invisible-character'>#{invisible}</span>"
             else
-              indentLevelHtml.push(' ')
-          indentLevelHtml.push("</span>")
-          indentGuideHtml.push(indentLevelHtml.join(''))
+              indentLevelHtml += ' '
+          indentLevelHtml += "</span>"
+          indentGuideHtml += indentLevelHtml
 
         for invisible in eolInvisibles
-          indentGuideHtml.push("<span class='invisible-character'>#{invisible}</span>")
+          indentGuideHtml += "<span class='invisible-character'>#{invisible}</span>"
 
-        return indentGuideHtml.join('')
+        return indentGuideHtml
 
     if htmlEolInvisibles.length > 0
       htmlEolInvisibles
diff --git a/src/git.coffee b/src/git.coffee
index 14e7620fd..c10e50fb1 100644
--- a/src/git.coffee
+++ b/src/git.coffee
@@ -44,6 +44,7 @@ class Git
   path: null
   statuses: null
   upstream: null
+  branch: null
   statusTask: null
 
   # Private: Creates a new `Git` object.
@@ -142,6 +143,12 @@ class Git
   # Public: Determine if the given path is new.
   isPathNew: (path) -> @isStatusNew(@getPathStatus(path))
 
+  # Public: Is the project at the root of this repository?
+  #
+  # Returns true if at the root, false if in a subfolder of the repository.
+  isProjectAtRoot: ->
+    @projectAtRoot ?= project.relativize(@getWorkingDirectory()) is ''
+
   # Public: Makes a path relative to the repository's working directory.
   relativize: (path) -> @getRepo().relativize(path)
 
@@ -171,6 +178,15 @@ class Git
     @getPathStatus(path) if headCheckedOut
     headCheckedOut
 
+  # Public: Checks out a branch in your repository.
+  #
+  # reference - The {String} reference to checkout
+  # create - A {Boolean} value which, if `true` creates the new reference if it doesn't exist.
+  #
+  # Returns a {Boolean} that's `true` if the method was successful.
+  checkoutReference: (reference, create) ->
+    @getRepo().checkoutReference(reference, create)
+
   # Public: Retrieves the number of lines added and removed to a path.
   #
   # This compares the working directory contents of the path to the `HEAD`
@@ -239,6 +255,12 @@ class Git
   # Public: ?
   getReferenceTarget: (reference) -> @getRepo().getReferenceTarget(reference)
 
+  # Public: Gets all the local and remote references.
+  #
+  # Returns an object with three keys: `heads`, `remotes`, and `tags`. Each key
+  # can be an array of strings containing the reference names.
+  getReferences: -> @getRepo().getReferences()
+
   # Public: ?
   getAheadBehindCount: (reference) -> @getRepo().getAheadBehindCount(reference)
 
@@ -247,8 +269,9 @@ class Git
 
   # Private:
   refreshStatus: ->
-    @statusTask = Task.once require.resolve('./repository-status-handler'), @getPath(), ({statuses, upstream}) =>
-      statusesUnchanged = _.isEqual(statuses, @statuses) and _.isEqual(upstream, @upstream)
+    @statusTask = Task.once require.resolve('./repository-status-handler'), @getPath(), ({statuses, upstream, branch}) =>
+      statusesUnchanged = _.isEqual(statuses, @statuses) and _.isEqual(upstream, @upstream) and _.isEqual(branch, @branch)
       @statuses = statuses
       @upstream = upstream
+      @branch = branch
       @trigger 'statuses-changed' unless statusesUnchanged
diff --git a/src/gutter.coffee b/src/gutter.coffee
index d1c3ac8b1..1e38daa7a 100644
--- a/src/gutter.coffee
+++ b/src/gutter.coffee
@@ -62,6 +62,76 @@ class Gutter extends View
   setShowLineNumbers: (showLineNumbers) ->
     if showLineNumbers then @lineNumbers.show() else @lineNumbers.hide()
 
+  # Get all the line-number divs.
+  #
+  # Returns a list of {HTMLElement}s.
+  getLineNumberElements: ->
+    @lineNumbers[0].childNodes
+
+  # Get all the line-number divs.
+  #
+  # Returns a list of {HTMLElement}s.
+  getLineNumberElementsForClass: (klass) ->
+    @lineNumbers[0].getElementsByClassName(klass)
+
+  # Get a single line-number div.
+  #
+  # * bufferRow: 0 based line number
+  #
+  # Returns a list of {HTMLElement}s that correspond to the bufferRow. More than
+  # one in the list indicates a wrapped line.
+  getLineNumberElement: (bufferRow) ->
+    @getLineNumberElementsForClass("line-number-#{bufferRow}")
+
+  # Add a class to all line-number divs.
+  #
+  # * klass: string class name
+  #
+  # Returns true if the class was added to any lines
+  addClassToAllLines: (klass)->
+    elements = @getLineNumberElements()
+    el.classList.add(klass) for el in elements
+    !!elements.length
+
+  # Remove a class from all line-number divs.
+  #
+  # * klass: string class name. Can only be one class name. i.e. 'my-class'
+  #
+  # Returns true if the class was removed from any lines
+  removeClassFromAllLines: (klass)->
+    # This is faster than calling $.removeClass on all lines, and faster than
+    # making a new array and iterating through it.
+    elements = @getLineNumberElementsForClass(klass)
+    willRemoveClasses = !!elements.length
+    elements[0].classList.remove(klass) while elements.length > 0
+    willRemoveClasses
+
+  # Add a class to a single line-number div
+  #
+  # * bufferRow: 0 based line number
+  # * klass: string class name
+  #
+  # Returns true if there were lines the class was added to
+  addClassToLine: (bufferRow, klass)->
+    elements = @getLineNumberElement(bufferRow)
+    el.classList.add(klass) for el in elements
+    !!elements.length
+
+  # Remove a class from a single line-number div
+  #
+  # * bufferRow: 0 based line number
+  # * klass: string class name
+  #
+  # Returns true if there were lines the class was removed from
+  removeClassFromLine: (bufferRow, klass)->
+    classesRemoved = false
+    elements = @getLineNumberElement(bufferRow)
+    for el in elements
+      hasClass = el.classList.contains(klass)
+      classesRemoved |= hasClass
+      el.classList.remove(klass) if hasClass
+    classesRemoved
+
   ### Internal ###
 
   updateLineNumbers: (changes, renderFrom, renderTo) ->
@@ -78,30 +148,35 @@ class Gutter extends View
     @renderLineNumbers(renderFrom, renderTo) if performUpdate
 
   renderLineNumbers: (startScreenRow, endScreenRow) ->
-    editor = @getEditor()
-    maxDigits = editor.getLineCount().toString().length
-    rows = editor.bufferRowsForScreenRows(startScreenRow, endScreenRow)
-
-    cursorScreenRow = editor.getCursorScreenPosition().row
-    @lineNumbers[0].innerHTML = $$$ ->
-      for row in rows
-        if row == lastScreenRow
-          rowValue = '•'
-        else
-          rowValue = (row + 1).toString()
-        classes = ['line-number']
-        classes.push('fold') if editor.isFoldedAtBufferRow(row)
-        @div linenumber: row, class: classes.join(' '), =>
-          rowValuePadding = _.multiplyString('&nbsp;', maxDigits - rowValue.length)
-          @raw("#{rowValuePadding}#{rowValue}")
-
-        lastScreenRow = row
-
+    @lineNumbers[0].innerHTML = @buildLineElementsHtml(startScreenRow, endScreenRow)
     @firstScreenRow = startScreenRow
     @lastScreenRow = endScreenRow
     @highlightedRows = null
     @highlightLines()
 
+  buildLineElementsHtml: (startScreenRow, endScreenRow) =>
+    editor = @getEditor()
+    maxDigits = editor.getLineCount().toString().length
+    rows = editor.bufferRowsForScreenRows(startScreenRow, endScreenRow)
+
+    html = ''
+    for row in rows
+      if row == lastScreenRow
+        rowValue = '•'
+      else
+        rowValue = (row + 1).toString()
+
+      classes = "line-number line-number-#{row}"
+      classes += ' fold' if editor.isFoldedAtBufferRow(row)
+
+      rowValuePadding = _.multiplyString('&nbsp;', maxDigits - rowValue.length)
+
+      html += """<div class="#{classes}">#{rowValuePadding}#{rowValue}</div>"""
+
+      lastScreenRow = row
+
+    html
+
   removeLineHighlights: ->
     return unless @highlightedLineNumbers
     for line in @highlightedLineNumbers
diff --git a/src/jquery-extensions.coffee b/src/jquery-extensions.coffee
index c749b1ce5..76ee60178 100644
--- a/src/jquery-extensions.coffee
+++ b/src/jquery-extensions.coffee
@@ -38,18 +38,16 @@ $.fn.isVisible = ->
   !@isHidden()
 
 $.fn.isHidden = ->
-  # Implementation taken from jQuery's `:hidden` expression code:
-  # https://github.com/jquery/jquery/blob/master/src/css/hiddenVisibleSelectors.js
-  #
-  # We were using a pseudo selector: @is(':hidden'). But jQuery's pseudo
-  # selector code checks the element's webkitMatchesSelector, which is always
-  # false, and is really really really slow.
+  # We used to check @is(':hidden'). But this is much faster than the
+  # offsetWidth/offsetHeight check + all the pseudo selector mess in jquery.
+  style = this[0].style
 
-  elem = this[0]
-
-  return null unless elem
-
-  elem.offsetWidth <= 0 and elem.offsetHeight <= 0
+  if style.display == 'none' or not @isOnDom()
+    true
+  else if style.display
+    false
+  else
+    getComputedStyle(this[0]).display == 'none'
 
 $.fn.isDisabled = ->
   !!@attr('disabled')
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index cc08c6f56..a2f026b2d 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -8,7 +8,11 @@ module.exports =
 class PackageManager
   _.extend @prototype, EventEmitter
 
-  constructor: ->
+  constructor: ({configDirPath, devMode, @resourcePath}) ->
+    @packageDirPaths = [path.join(configDirPath, "packages")]
+    if devMode
+      @packageDirPaths.unshift(path.join(configDirPath, "dev", "packages"))
+
     @loadedPackages = {}
     @activePackages = {}
     @packageStates = {}
@@ -83,10 +87,10 @@ class PackageManager
   resolvePackagePath: (name) ->
     return name if fsUtils.isDirectorySync(name)
 
-    packagePath = fsUtils.resolve(config.packageDirPaths..., name)
+    packagePath = fsUtils.resolve(@packageDirPaths..., name)
     return packagePath if fsUtils.isDirectorySync(packagePath)
 
-    packagePath = path.join(window.resourcePath, 'node_modules', name)
+    packagePath = path.join(@resourcePath, 'node_modules', name)
     return packagePath if @isInternalPackage(packagePath)
 
   isInternalPackage: (packagePath) ->
@@ -108,11 +112,11 @@ class PackageManager
   getAvailablePackagePaths: ->
     packagePaths = []
 
-    for packageDirPath in config.packageDirPaths
+    for packageDirPath in @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'))
+    for packagePath in fsUtils.listSync(path.join(@resourcePath, 'node_modules'))
       packagePaths.push(packagePath) if @isInternalPackage(packagePath)
 
     _.uniq(packagePaths)
@@ -122,8 +126,8 @@ class PackageManager
 
   getAvailablePackageMetadata: ->
     packages = []
-    for packagePath in atom.getAvailablePackagePaths()
+    for packagePath in @getAvailablePackagePaths()
       name = path.basename(packagePath)
-      metadata = atom.getLoadedPackage(name)?.metadata ? Package.loadMetadata(packagePath, true)
+      metadata = @getLoadedPackage(name)?.metadata ? Package.loadMetadata(packagePath, true)
       packages.push(metadata)
     packages
diff --git a/src/repository-status-handler.coffee b/src/repository-status-handler.coffee
index 9eda7e2f6..0a9c08f7c 100644
--- a/src/repository-status-handler.coffee
+++ b/src/repository-status-handler.coffee
@@ -9,9 +9,11 @@ module.exports = (repoPath) ->
     for filePath, status of repo.getStatus()
       statuses[path.join(workingDirectoryPath, filePath)] = status
     upstream = repo.getAheadBehindCount()
+    branch = repo.getHead()
     repo.release()
   else
     upstream = {}
     statuses = {}
+    branch = null
 
-  {statuses, upstream}
+  {statuses, upstream, branch}
diff --git a/src/token.coffee b/src/token.coffee
index 141e6a756..81b5b2556 100644
--- a/src/token.coffee
+++ b/src/token.coffee
@@ -1,7 +1,14 @@
 _ = require './underscore-extensions'
 textUtils = require './text-utils'
 
-whitespaceRegexesByTabLength = {}
+WhitespaceRegexesByTabLength = {}
+LeadingWhitespaceRegex = /^[ ]+/
+TrailingWhitespaceRegex = /[ ]+$/
+EscapeRegex = /[&"'<>]/g
+CharacterRegex = /./g
+StartCharacterRegex = /^./
+StartDotRegex = /^\.?/
+WhitespaceRegex = /\S/
 
 # Private: Represents a single unit of text as selected by a grammar.
 module.exports =
@@ -33,7 +40,7 @@ class Token
     [new Token(value: value1, scopes: @scopes), new Token(value: value2, scopes: @scopes)]
 
   whitespaceRegexForTabLength: (tabLength) ->
-    whitespaceRegexesByTabLength[tabLength] ?= new RegExp("([ ]{#{tabLength}})|(\t)|([^\t]+)", "g")
+    WhitespaceRegexesByTabLength[tabLength] ?= new RegExp("([ ]{#{tabLength}})|(\t)|([^\t]+)", "g")
 
   breakOutAtomicTokens: (tabLength, breakOutLeadingWhitespace) ->
     if @hasSurrogatePair
@@ -112,10 +119,10 @@ class Token
     )
 
   isOnlyWhitespace: ->
-    not /\S/.test(@value)
+    not WhitespaceRegex.test(@value)
 
   matchesScopeSelector: (selector) ->
-    targetClasses = selector.replace(/^\.?/, '').split('.')
+    targetClasses = selector.replace(StartDotRegex, '').split('.')
     _.any @scopes, (scope) ->
       scopeClasses = scope.split('.')
       _.isSubset(targetClasses, scopeClasses)
@@ -123,39 +130,59 @@ class Token
   getValueAsHtml: ({invisibles, hasLeadingWhitespace, hasTrailingWhitespace, hasIndentGuide})->
     invisibles ?= {}
     html = @value
-      .replace(/&/g, '&amp;')
-      .replace(/"/g, '&quot;')
-      .replace(/'/g, '&#39;')
-      .replace(/</g, '&lt;')
-      .replace(/>/g, '&gt;')
 
     if @isHardTab
-      classes = []
-      classes.push('indent-guide') if hasIndentGuide
-      classes.push('invisible-character') if invisibles.tab
-      classes.push('hard-tab')
-      classes = classes.join(' ')
-      html = html.replace /^./, (match) ->
+      classes = 'hard-tab'
+      classes += ' indent-guide' if hasIndentGuide
+      classes += ' invisible-character' if invisibles.tab
+      html = html.replace StartCharacterRegex, (match) =>
         match = invisibles.tab ? match
-        "<span class='#{classes}'>#{match}</span>"
+        "<span class='#{classes}'>#{@escapeString(match)}</span>"
     else
-      if hasLeadingWhitespace
-        classes = []
-        classes.push('indent-guide') if hasIndentGuide
-        classes.push('invisible-character') if invisibles.space
-        classes.push('leading-whitespace')
-        classes = classes.join(' ')
-        html = html.replace /^[ ]+/, (match) ->
-          match = match.replace(/./g, invisibles.space) if invisibles.space
-          "<span class='#{classes}'>#{match}</span>"
-      if hasTrailingWhitespace
-        classes = []
-        classes.push('indent-guide') if hasIndentGuide and not hasLeadingWhitespace
-        classes.push('invisible-character') if invisibles.space
-        classes.push('trailing-whitespace')
-        classes = classes.join(' ')
-        html = html.replace /[ ]+$/, (match) ->
-          match = match.replace(/./g, invisibles.space) if invisibles.space
-          "<span class='#{classes}'>#{match}</span>"
+      startIndex = 0
+      endIndex = html.length
+
+      leadingHtml = ''
+      trailingHtml = ''
+
+      if hasLeadingWhitespace and match = LeadingWhitespaceRegex.exec(html)
+        classes = 'leading-whitespace'
+        classes += ' indent-guide' if hasIndentGuide
+        classes += ' invisible-character' if invisibles.space
+
+        match[0] = match[0].replace(CharacterRegex, invisibles.space) if invisibles.space
+        leadingHtml = "<span class='#{classes}'>#{match[0]}</span>"
+
+        startIndex = match[0].length
+
+      if hasTrailingWhitespace and match = TrailingWhitespaceRegex.exec(html)
+        classes = 'trailing-whitespace'
+        classes += ' indent-guide' if hasIndentGuide and not hasLeadingWhitespace
+        classes += ' invisible-character' if invisibles.space
+
+        match[0] = match[0].replace(CharacterRegex, invisibles.space) if invisibles.space
+        trailingHtml = "<span class='#{classes}'>#{match[0]}</span>"
+
+        endIndex = match.index
+
+      html = leadingHtml + @escapeString(html, startIndex, endIndex) + trailingHtml
 
     html
+
+  escapeString: (str, startIndex, endIndex) ->
+    strLength = str.length
+
+    startIndex ?= 0
+    endIndex ?= strLength
+
+    str = str.slice(startIndex, endIndex) if startIndex > 0 or endIndex < strLength
+    str.replace(EscapeRegex, @escapeStringReplace)
+
+  escapeStringReplace: (match) ->
+    switch match
+      when '&' then '&amp;'
+      when '"' then '&quot;'
+      when "'" then '&#39;'
+      when '<' then '&lt;'
+      when '>' then '&gt;'
+      else match
diff --git a/vendor/apm b/vendor/apm
index 162824eb1..fcb19e296 160000
--- a/vendor/apm
+++ b/vendor/apm
@@ -1 +1 @@
-Subproject commit 162824eb1a73c154e3bf823c591fa42f8ebcaa37
+Subproject commit fcb19e296ca8979a28d2d503c2650f4ef381c8be