diff --git a/CHANGELOG.md b/CHANGELOG.md
index e36b3f59e..8823bd9cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,18 +1 @@
 See https://atom.io/releases
-
-## 1.4.0
-
-* Switching encoding is now fast also with large files.
-* Fixed an issue where disabling and re-enabling a package caused custom keymaps to be overridden.
-* Fixed restoring untitled editors on restart. The new behavior never prompts to save new/changed files when closing a window or quitting Atom.
-
-## 1.3.0
-
-* The tree-view now sorts directory entries more naturally, in a locale-sensitive way.
-* Lines can now be moved up and down with multiple cursors.
-* Improved the performance of marker-dependent code paths such as spell-check and find and replace.
-* Fixed copying and pasting in native input fields.
-* By default, windows with no pane items are now closed via the `core:close` command. The previous behavior can be restored via the `Close Empty Windows` option in settings.
-* Fixed an issue where characters were inserted when toggling the settings view on some keyboard layouts.
-* Modules can now temporarily override `Error.prepareStackTrace`. There is also an `Error.prototype.getRawStack()` method if you just need access to the raw v8 trace structure.
-* Fixed a problem that caused blurry fonts on monitors that have a slightly higher resolution than 96 DPI.
diff --git a/apm/package.json b/apm/package.json
index b8dda21ea..2e6b0b8ea 100644
--- a/apm/package.json
+++ b/apm/package.json
@@ -6,6 +6,6 @@
     "url": "https://github.com/atom/atom.git"
   },
   "dependencies": {
-    "atom-package-manager": "1.5.0"
+    "atom-package-manager": "1.6.0"
   }
 }
diff --git a/build/Gruntfile.coffee b/build/Gruntfile.coffee
index 26d9c2f42..60d5916b8 100644
--- a/build/Gruntfile.coffee
+++ b/build/Gruntfile.coffee
@@ -14,6 +14,8 @@ _ = require 'underscore-plus'
 packageJson = require '../package.json'
 
 module.exports = (grunt) ->
+  require('time-grunt')(grunt)
+
   grunt.loadNpmTasks('grunt-babel')
   grunt.loadNpmTasks('grunt-coffeelint')
   grunt.loadNpmTasks('grunt-lesslint')
@@ -36,7 +38,6 @@ module.exports = (grunt) ->
   buildDir = grunt.option('build-dir')
   buildDir ?= path.join(os.tmpdir(), 'atom-build')
   buildDir = path.resolve(buildDir)
-  disableAutoUpdate = grunt.option('no-auto-update') ? false
 
   channel = grunt.option('channel')
   releasableBranches = ['stable', 'beta']
@@ -179,7 +180,7 @@ module.exports = (grunt) ->
     pkg: grunt.file.readJSON('package.json')
 
     atom: {
-      appName, channel, metadata, disableAutoUpdate,
+      appName, channel, metadata,
       appFileName, apmFileName,
       appDir, buildDir, contentsDir, installDir, shellAppDir, symbolsDir,
     }
@@ -255,7 +256,7 @@ module.exports = (grunt) ->
       outputDir: 'electron'
       downloadDir: electronDownloadDir
       rebuild: true  # rebuild native modules after electron is updated
-      token: process.env.ATOM_ACCESS_TOKEN
+      token: process.env.ATOM_ACCESS_TOKEN ? 'da809a6077bb1b0aa7c5623f7b2d5f1fec2faae4'
 
     'create-windows-installer':
       installer:
diff --git a/build/package.json b/build/package.json
index fd7d29d80..d5c780c08 100644
--- a/build/package.json
+++ b/build/package.json
@@ -37,6 +37,7 @@
     "runas": "^3.1",
     "tello": "1.0.5",
     "temp": "~0.8.1",
+    "time-grunt": "1.2.2",
     "underscore-plus": "1.x",
     "unzip": "~0.1.9",
     "vm-compatibility-layer": "~0.1.0",
diff --git a/build/tasks/build-task.coffee b/build/tasks/build-task.coffee
index 213aa0da4..a86c7c1f4 100644
--- a/build/tasks/build-task.coffee
+++ b/build/tasks/build-task.coffee
@@ -186,5 +186,4 @@ module.exports = (grunt) ->
     dependencies = ['compile', 'generate-license:save', 'generate-module-cache', 'compile-packages-slug']
     dependencies.push('copy-info-plist') if process.platform is 'darwin'
     dependencies.push('set-exe-icon') if process.platform is 'win32'
-    dependencies.push('disable-autoupdate') if grunt.config.get('atom.disableAutoUpdate')
     grunt.task.run(dependencies...)
diff --git a/build/tasks/disable-autoupdate-task.coffee b/build/tasks/disable-autoupdate-task.coffee
deleted file mode 100644
index 7517543da..000000000
--- a/build/tasks/disable-autoupdate-task.coffee
+++ /dev/null
@@ -1,12 +0,0 @@
-fs = require 'fs'
-path = require 'path'
-
-module.exports = (grunt) ->
-
-  grunt.registerTask 'disable-autoupdate', 'Set up disableAutoUpdate field in package.json file', ->
-    appDir = fs.realpathSync(grunt.config.get('atom.appDir'))
-
-    metadata = grunt.file.readJSON(path.join(appDir, 'package.json'))
-    metadata._disableAutoUpdate = grunt.config.get('atom.disableAutoUpdate')
-
-    grunt.file.write(path.join(appDir, 'package.json'), JSON.stringify(metadata))
diff --git a/dot-atom/.gitignore b/dot-atom/.gitignore
index 81af3f689..e5c80ce23 100644
--- a/dot-atom/.gitignore
+++ b/dot-atom/.gitignore
@@ -1,5 +1,6 @@
-storage
+blob-store
 compile-cache
 dev
-.npm
+storage
 .node-gyp
+.npm
diff --git a/keymaps/linux.cson b/keymaps/linux.cson
index 28f43a8fc..536a1d75d 100644
--- a/keymaps/linux.cson
+++ b/keymaps/linux.cson
@@ -13,7 +13,7 @@
   'ctrl-alt-o': 'application:add-project-folder'
   'ctrl-shift-pageup': 'pane:move-item-left'
   'ctrl-shift-pagedown': 'pane:move-item-right'
-  'F11': 'window:toggle-full-screen'
+  'f11': 'window:toggle-full-screen'
 
   # Sublime Parity
   'ctrl-,': 'application:show-settings'
diff --git a/keymaps/win32.cson b/keymaps/win32.cson
index f052a64fc..cb291f493 100644
--- a/keymaps/win32.cson
+++ b/keymaps/win32.cson
@@ -19,7 +19,7 @@
   'ctrl-alt-o': 'application:add-project-folder'
   'ctrl-shift-left': 'pane:move-item-left'
   'ctrl-shift-right': 'pane:move-item-right'
-  'F11': 'window:toggle-full-screen'
+  'f11': 'window:toggle-full-screen'
 
   # Sublime Parity
   'ctrl-,': 'application:show-settings'
diff --git a/menus/darwin.cson b/menus/darwin.cson
index 52b7a5bc8..23f4b6144 100644
--- a/menus/darwin.cson
+++ b/menus/darwin.cson
@@ -110,36 +110,9 @@
     ]
   }
 
-  {
-    label: 'Selection'
-    submenu: [
-      { label: 'Add Selection Above', command: 'editor:add-selection-above' }
-      { label: 'Add Selection Below', command: 'editor:add-selection-below' }
-      { label: 'Single Selection', command: 'editor:consolidate-selections'}
-      { label: 'Split into Lines', command: 'editor:split-selections-into-lines'}
-      { type: 'separator' }
-      { label: 'Select to Top', command: 'core:select-to-top' }
-      { label: 'Select to Bottom', command: 'core:select-to-bottom' }
-      { type: 'separator' }
-      { label: 'Select Line', command: 'editor:select-line' }
-      { label: 'Select Word', command: 'editor:select-word' }
-      { label: 'Select to Beginning of Word', command: 'editor:select-to-beginning-of-word' }
-      { label: 'Select to Beginning of Line', command: 'editor:select-to-beginning-of-line' }
-      { label: 'Select to First Character of Line', command: 'editor:select-to-first-character-of-line' }
-      { label: 'Select to End of Word', command: 'editor:select-to-end-of-word' }
-      { label: 'Select to End of Line', command: 'editor:select-to-end-of-line' }
-    ]
-  }
-
-  {
-    label: 'Find'
-    submenu: []
-  }
-
   {
     label: 'View'
     submenu: [
-      { label: 'Reload', command: 'window:reload' }
       { label: 'Toggle Full Screen', command: 'window:toggle-full-screen' }
       {
         label: 'Panes'
@@ -164,6 +137,7 @@
         label: 'Developer'
         submenu: [
           { label: 'Open In Dev Mode…', command: 'application:open-dev' }
+          { label: 'Reload Window', command: 'window:reload' }
           { label: 'Run Package Specs', command: 'window:run-package-specs' }
           { label: 'Toggle Developer Tools', command: 'window:toggle-dev-tools' }
         ]
@@ -177,6 +151,32 @@
     ]
   }
 
+  {
+    label: 'Selection'
+    submenu: [
+      { label: 'Add Selection Above', command: 'editor:add-selection-above' }
+      { label: 'Add Selection Below', command: 'editor:add-selection-below' }
+      { label: 'Single Selection', command: 'editor:consolidate-selections'}
+      { label: 'Split into Lines', command: 'editor:split-selections-into-lines'}
+      { type: 'separator' }
+      { label: 'Select to Top', command: 'core:select-to-top' }
+      { label: 'Select to Bottom', command: 'core:select-to-bottom' }
+      { type: 'separator' }
+      { label: 'Select Line', command: 'editor:select-line' }
+      { label: 'Select Word', command: 'editor:select-word' }
+      { label: 'Select to Beginning of Word', command: 'editor:select-to-beginning-of-word' }
+      { label: 'Select to Beginning of Line', command: 'editor:select-to-beginning-of-line' }
+      { label: 'Select to First Character of Line', command: 'editor:select-to-first-character-of-line' }
+      { label: 'Select to End of Word', command: 'editor:select-to-end-of-word' }
+      { label: 'Select to End of Line', command: 'editor:select-to-end-of-line' }
+    ]
+  }
+
+  {
+    label: 'Find'
+    submenu: []
+  }
+
   {
     label: 'Packages'
     submenu: []
diff --git a/menus/linux.cson b/menus/linux.cson
index fa831b4a4..9f251d67f 100644
--- a/menus/linux.cson
+++ b/menus/linux.cson
@@ -95,7 +95,6 @@
   {
     label: '&View'
     submenu: [
-      { label: '&Reload', command: 'window:reload' }
       { label: 'Toggle &Full Screen', command: 'window:toggle-full-screen' }
       { label: 'Toggle Menu Bar', command: 'window:toggle-menu-bar' }
       {
@@ -121,6 +120,7 @@
         label: 'Developer'
         submenu: [
           { label: 'Open In &Dev Mode…', command: 'application:open-dev' }
+          { label: '&Reload Window', command: 'window:reload' }
           { label: 'Run Package &Specs', command: 'window:run-package-specs' }
           { label: 'Toggle Developer &Tools', command: 'window:toggle-dev-tools' }
         ]
diff --git a/menus/win32.cson b/menus/win32.cson
index 04da3d388..ad0461898 100644
--- a/menus/win32.cson
+++ b/menus/win32.cson
@@ -94,7 +94,6 @@
   {
     label: '&View'
     submenu: [
-      { label: '&Reload', command: 'window:reload' }
       { label: 'Toggle &Full Screen', command: 'window:toggle-full-screen' }
       { label: 'Toggle Menu Bar', command: 'window:toggle-menu-bar' }
       {
@@ -120,6 +119,7 @@
         label: 'Developer'
         submenu: [
           { label: 'Open In &Dev Mode…', command: 'application:open-dev' }
+          { label: '&Reload Window', command: 'window:reload' }
           { label: 'Run Package &Specs', command: 'window:run-package-specs' }
           { label: 'Toggle Developer &Tools', command: 'window:toggle-dev-tools' }
         ]
diff --git a/package.json b/package.json
index 35a0bcb2d..b13313aee 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "1.5.0-dev",
+  "version": "1.6.0-dev",
   "description": "A hackable text editor for the 21st Century.",
   "main": "./src/browser/main.js",
   "repository": {
@@ -22,17 +22,17 @@
     "clear-cut": "^2.0.1",
     "coffee-script": "1.8.0",
     "color": "^0.7.3",
-    "event-kit": "^1.3.0",
+    "event-kit": "^1.5.0",
     "find-parent-dir": "^0.3.0",
     "first-mate": "^5.1.1",
     "fs-plus": "^2.8.0",
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
-    "git-utils": "^4.0.7",
+    "git-utils": "^4.1.0",
     "grim": "1.5.0",
     "jasmine-json": "~0.0",
     "jasmine-tagged": "^1.1.4",
-    "jquery": "^2.1.1",
+    "jquery": "2.1.4",
     "key-path-helpers": "^0.4.0",
     "less-cache": "0.22",
     "line-top-index": "0.2.0",
@@ -53,7 +53,7 @@
     "service-hub": "^0.7.0",
     "source-map-support": "^0.3.2",
     "temp": "0.8.1",
-    "text-buffer": "8.1.3",
+    "text-buffer": "8.1.4",
     "typescript-simple": "1.0.0",
     "underscore-plus": "^1.6.6",
     "yargs": "^3.23.0"
@@ -66,12 +66,12 @@
     "base16-tomorrow-dark-theme": "1.1.0",
     "base16-tomorrow-light-theme": "1.1.1",
     "one-dark-ui": "1.1.9",
-    "one-dark-syntax": "1.1.1",
-    "one-light-syntax": "1.1.1",
     "one-light-ui": "1.1.9",
+    "one-dark-syntax": "1.1.2",
+    "one-light-syntax": "1.1.2",
     "solarized-dark-syntax": "0.39.0",
     "solarized-light-syntax": "0.23.0",
-    "about": "1.1.0",
+    "about": "1.3.0",
     "archive-view": "0.61.0",
     "autocomplete-atom-api": "0.9.2",
     "autocomplete-css": "0.11.0",
@@ -103,16 +103,15 @@
     "notifications": "0.62.1",
     "open-on-github": "0.40.0",
     "package-generator": "0.41.0",
-    "release-notes": "0.53.0",
-    "settings-view": "0.232.1",
+    "settings-view": "0.232.3",
     "snippets": "1.0.1",
-    "spell-check": "0.63.0",
+    "spell-check": "0.65.0",
     "status-bar": "0.80.0",
     "styleguide": "0.45.0",
     "symbols-view": "0.110.1",
     "tabs": "0.88.0",
     "timecop": "0.33.0",
-    "tree-view": "0.198.0",
+    "tree-view": "0.198.1",
     "update-package-dependencies": "0.10.0",
     "welcome": "0.33.0",
     "whitespace": "0.32.1",
@@ -122,24 +121,24 @@
     "language-coffee-script": "0.46.0",
     "language-csharp": "0.11.0",
     "language-css": "0.36.0",
-    "language-gfm": "0.82.0",
+    "language-gfm": "0.83.0",
     "language-git": "0.11.0",
-    "language-go": "0.41.0",
-    "language-html": "0.43.1",
+    "language-go": "0.42.0",
+    "language-html": "0.44.0",
     "language-hyperlink": "0.16.0",
     "language-java": "0.17.0",
-    "language-javascript": "0.104.0",
-    "language-json": "0.17.2",
+    "language-javascript": "0.105.0",
+    "language-json": "0.17.3",
     "language-less": "0.29.0",
     "language-make": "0.21.0",
     "language-mustache": "0.13.0",
     "language-objective-c": "0.15.1",
     "language-perl": "0.32.0",
-    "language-php": "0.34.0",
+    "language-php": "0.36.0",
     "language-property-list": "0.8.0",
-    "language-python": "0.42.1",
-    "language-ruby": "0.65.0",
-    "language-ruby-on-rails": "0.24.0",
+    "language-python": "0.43.0",
+    "language-ruby": "0.68.0",
+    "language-ruby-on-rails": "0.25.0",
     "language-sass": "0.45.0",
     "language-shellscript": "0.21.0",
     "language-source": "0.9.0",
diff --git a/script/bootstrap b/script/bootstrap
index 8314b9cb0..5f9241a3d 100755
--- a/script/bootstrap
+++ b/script/bootstrap
@@ -5,8 +5,16 @@ var verifyRequirements = require('./utils/verify-requirements');
 var safeExec = require('./utils/child-process-wrapper.js').safeExec;
 var path = require('path');
 
+var t0, t1
+
 // Executes an array of commands one by one.
 function executeCommands(commands, done, index) {
+  if (index != undefined) {
+    t1 = Date.now()
+    console.log("=> Took " + (t1 - t0) + "ms.");
+    console.log();
+  }
+
   index = (index == undefined ? 0 : index);
   if (index < commands.length) {
     var command = commands[index];
@@ -17,6 +25,7 @@ function executeCommands(commands, done, index) {
       options = command.options;
       command = command.command;
     }
+    t0 = Date.now()
     safeExec(command, options, executeCommands.bind(this, commands, done, index + 1));
   }
   else
@@ -96,7 +105,10 @@ function bootstrap() {
       message: 'Installing apm...',
       options: apmInstallOptions
     },
-    apmPath + ' clean' + apmFlags,
+    {
+      command: apmPath + ' clean' + apmFlags,
+      message: 'Deleting old packages...'
+    },
     moduleInstallCommand,
     dedupeApmCommand + ' ' + packagesToDedupe.join(' '),
   ];
diff --git a/spec/babel-spec.coffee b/spec/babel-spec.coffee
index caaaed9f2..3c4a4fe4b 100644
--- a/spec/babel-spec.coffee
+++ b/spec/babel-spec.coffee
@@ -1,4 +1,26 @@
+# Users may have this environment variable set. Currently, it causes babel to
+# log to stderr, which causes errors on Windows.
+# See https://github.com/atom/electron/issues/2033
+process.env.DEBUG='*'
+
+path = require('path')
+temp = require('temp').track()
+CompileCache = require('../src/compile-cache')
+
 describe "Babel transpiler support", ->
+  originalCacheDir = null
+
+  beforeEach ->
+    originalCacheDir = CompileCache.getCacheDirectory()
+    CompileCache.setCacheDirectory(temp.mkdirSync('compile-cache'))
+    for cacheKey in Object.keys(require.cache)
+      if cacheKey.startsWith(path.join(__dirname, 'fixtures', 'babel'))
+        console.log('deleting', cacheKey)
+        delete require.cache[cacheKey]
+
+  afterEach ->
+    CompileCache.setCacheDirectory(originalCacheDir)
+
   describe 'when a .js file starts with /** @babel */;', ->
     it "transpiles it using babel", ->
       transpiled = require('./fixtures/babel/babel-comment.js')
@@ -17,3 +39,12 @@ describe "Babel transpiler support", ->
   describe "when a .js file does not start with 'use babel';", ->
     it "does not transpile it using babel", ->
       expect(-> require('./fixtures/babel/invalid.js')).toThrow()
+
+    it "does not try to log to stdout or stderr while parsing the file", ->
+      spyOn(process.stderr, 'write')
+      spyOn(process.stdout, 'write')
+
+      transpiled = require('./fixtures/babel/babel-double-quotes.js')
+
+      expect(process.stdout.write).not.toHaveBeenCalled()
+      expect(process.stderr.write).not.toHaveBeenCalled()
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index eab2f6f04..c431fea5f 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -872,6 +872,26 @@ describe "Config", ->
           atom.config.loadUserConfig()
           expect(atom.config.get("foo.bar")).toBe "baz"
 
+      describe "when the config file fails to load", ->
+        addErrorHandler = null
+
+        beforeEach ->
+          atom.notifications.onDidAddNotification addErrorHandler = jasmine.createSpy()
+          spyOn(fs, "existsSync").andCallFake ->
+            error = new Error()
+            error.code = 'EPERM'
+            throw error
+
+        it "creates a notification and does not try to save later changes to disk", ->
+          load = -> atom.config.loadUserConfig()
+          expect(load).not.toThrow()
+          expect(addErrorHandler.callCount).toBe 1
+
+          atom.config.set("foo.bar", "baz")
+          advanceClock(100)
+          expect(atom.config.save).not.toHaveBeenCalled()
+          expect(atom.config.get("foo.bar")).toBe "baz"
+
     describe ".observeUserConfig()", ->
       updatedHandler = null
 
diff --git a/spec/display-buffer-spec.coffee b/spec/display-buffer-spec.coffee
index 8c4adca44..0246008a4 100644
--- a/spec/display-buffer-spec.coffee
+++ b/spec/display-buffer-spec.coffee
@@ -1253,6 +1253,13 @@ describe "DisplayBuffer", ->
       decoration.destroy()
       expect(displayBuffer.decorationForId(decoration.id)).not.toBeDefined()
 
+    it "does not allow destroyed markers to be decorated", ->
+      marker.destroy()
+      expect(->
+        displayBuffer.decorateMarker(marker, {type: 'overlay', item: document.createElement('div')})
+      ).toThrow("Cannot decorate a destroyed marker")
+      expect(displayBuffer.getOverlayDecorations()).toEqual []
+
     describe "when a decoration is updated via Decoration::update()", ->
       it "emits an 'updated' event containing the new and old params", ->
         decoration.onDidChangeProperties updatedSpy = jasmine.createSpy()
diff --git a/spec/fake-lines-yardstick.coffee b/spec/fake-lines-yardstick.coffee
index 888272295..38716ab3e 100644
--- a/spec/fake-lines-yardstick.coffee
+++ b/spec/fake-lines-yardstick.coffee
@@ -19,9 +19,8 @@ class FakeLinesYardstick
   setScopedCharacterWidth: (scopeNames, character, width) ->
     @getScopedCharacterWidths(scopeNames)[character] = width
 
-  pixelPositionForScreenPosition: (screenPosition, clip=true) ->
+  pixelPositionForScreenPosition: (screenPosition) ->
     screenPosition = Point.fromObject(screenPosition)
-    screenPosition = @model.clipScreenPosition(screenPosition) if clip
 
     targetRow = screenPosition.row
     targetColumn = screenPosition.column
diff --git a/spec/integration/startup-spec.coffee b/spec/integration/startup-spec.coffee
index 799c7685f..da4e08ae2 100644
--- a/spec/integration/startup-spec.coffee
+++ b/spec/integration/startup-spec.coffee
@@ -125,6 +125,27 @@ describe "Starting Atom", ->
           .treeViewRootDirectories()
           .then ({value}) -> expect(value).toEqual([otherTempDirPath])
 
+    it "opens the new window offset from the other window", ->
+      runAtom [path.join(tempDirPath, "new-file")], {ATOM_HOME: atomHome}, (client) ->
+        win0Position = null
+        win1Position = null
+        client
+          .waitForWindowCount(1, 10000)
+          .execute -> atom.getPosition()
+          .then ({value}) -> win0Position = value
+          .waitForNewWindow(->
+            @startAnotherAtom([path.join(temp.mkdirSync("a-third-dir"), "a-file")], ATOM_HOME: atomHome)
+          , 5000)
+          .waitForWindowCount(2, 10000)
+          .execute -> atom.getPosition()
+          .then ({value}) -> win1Position = value
+          .then ->
+            expect(win1Position.x).toBeGreaterThan(win0Position.x)
+            # Ideally we'd test the y coordinate too, but if the window's
+            # already as tall as it can be, then OS X won't move it down outside
+            # the screen.
+            # expect(win1Position.y).toBeGreaterThan(win0Position.y)
+
   describe "reopening a directory that was previously opened", ->
     it "remembers the state of the window", ->
       runAtom [tempDirPath], {ATOM_HOME: atomHome}, (client) ->
diff --git a/spec/lines-yardstick-spec.coffee b/spec/lines-yardstick-spec.coffee
index c6b8b2d76..46935510f 100644
--- a/spec/lines-yardstick-spec.coffee
+++ b/spec/lines-yardstick-spec.coffee
@@ -1,6 +1,7 @@
 LinesYardstick = require '../src/lines-yardstick'
 LineTopIndex = require 'line-top-index'
 {toArray} = require 'underscore-plus'
+{Point} = require 'text-buffer'
 
 describe "LinesYardstick", ->
   [editor, mockLineNodesProvider, createdLineNodes, linesYardstick, buildLineNode] = []
@@ -66,12 +67,12 @@ describe "LinesYardstick", ->
       }
       """
 
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 0])).toEqual({left: 0, top: 0})
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 1])).toEqual({left: 7, top: 0})
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 5])).toEqual({left: 37.78125, top: 0})
-      expect(linesYardstick.pixelPositionForScreenPosition([1, 6])).toEqual({left: 43.171875, top: 14})
-      expect(linesYardstick.pixelPositionForScreenPosition([1, 9])).toEqual({left: 72.171875, top: 14})
-      expect(linesYardstick.pixelPositionForScreenPosition([2, Infinity])).toEqual({left: 287.859375, top: 28})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 0))).toEqual({left: 0, top: 0})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 1))).toEqual({left: 7, top: 0})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 5))).toEqual({left: 37.78125, top: 0})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(1, 6))).toEqual({left: 43.171875, top: 14})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(1, 9))).toEqual({left: 72.171875, top: 14})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(2, Infinity))).toEqual({left: 287.859375, top: 28})
 
     it "reuses already computed pixel positions unless it is invalidated", ->
       atom.styles.addStyleSheet """
@@ -81,9 +82,9 @@ describe "LinesYardstick", ->
       }
       """
 
-      expect(linesYardstick.pixelPositionForScreenPosition([1, 2])).toEqual({left: 19.203125, top: 14})
-      expect(linesYardstick.pixelPositionForScreenPosition([2, 6])).toEqual({left: 57.609375, top: 28})
-      expect(linesYardstick.pixelPositionForScreenPosition([5, 10])).toEqual({left: 95.609375, top: 70})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(1, 2))).toEqual({left: 19.203125, top: 14})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(2, 6))).toEqual({left: 57.609375, top: 28})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(5, 10))).toEqual({left: 95.609375, top: 70})
 
       atom.styles.addStyleSheet """
       * {
@@ -91,15 +92,15 @@ describe "LinesYardstick", ->
       }
       """
 
-      expect(linesYardstick.pixelPositionForScreenPosition([1, 2])).toEqual({left: 19.203125, top: 14})
-      expect(linesYardstick.pixelPositionForScreenPosition([2, 6])).toEqual({left: 57.609375, top: 28})
-      expect(linesYardstick.pixelPositionForScreenPosition([5, 10])).toEqual({left: 95.609375, top: 70})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(1, 2))).toEqual({left: 19.203125, top: 14})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(2, 6))).toEqual({left: 57.609375, top: 28})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(5, 10))).toEqual({left: 95.609375, top: 70})
 
       linesYardstick.invalidateCache()
 
-      expect(linesYardstick.pixelPositionForScreenPosition([1, 2])).toEqual({left: 24, top: 14})
-      expect(linesYardstick.pixelPositionForScreenPosition([2, 6])).toEqual({left: 72, top: 28})
-      expect(linesYardstick.pixelPositionForScreenPosition([5, 10])).toEqual({left: 120, top: 70})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(1, 2))).toEqual({left: 24, top: 14})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(2, 6))).toEqual({left: 72, top: 28})
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(5, 10))).toEqual({left: 120, top: 70})
 
     it "correctly handles RTL characters", ->
       atom.styles.addStyleSheet """
@@ -110,13 +111,13 @@ describe "LinesYardstick", ->
       """
 
       editor.setText("السلام عليكم")
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 0]).left).toBe 0
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 1]).left).toBe 8
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 2]).left).toBe 16
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 5]).left).toBe 33
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 7]).left).toBe 50
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 9]).left).toBe 67
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 11]).left).toBe 84
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 0)).left).toBe 0
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 1)).left).toBe 8
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 2)).left).toBe 16
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 5)).left).toBe 33
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 7)).left).toBe 50
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 9)).left).toBe 67
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 11)).left).toBe 84
 
     it "doesn't report a width greater than 0 when the character to measure is at the beginning of a text node", ->
       # This spec documents what seems to be a bug in Chromium, because we'd
@@ -141,9 +142,9 @@ describe "LinesYardstick", ->
 
       editor.setText(text)
 
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 35]).left).toBe 230.90625
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 36]).left).toBe 237.5
-      expect(linesYardstick.pixelPositionForScreenPosition([0, 37]).left).toBe 244.09375
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 35)).left).toBe 230.90625
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 36)).left).toBe 237.5
+      expect(linesYardstick.pixelPositionForScreenPosition(Point(0, 37)).left).toBe 244.09375
 
     describe "::screenPositionForPixelPosition(pixelPosition)", ->
       it "converts pixel positions to screen positions", ->
diff --git a/spec/package-manager-spec.coffee b/spec/package-manager-spec.coffee
index e6848ef03..46d1d11ee 100644
--- a/spec/package-manager-spec.coffee
+++ b/spec/package-manager-spec.coffee
@@ -1026,6 +1026,16 @@ describe "PackageManager", ->
         expect(atom.packages.enablePackage("this-doesnt-exist")).toBeNull()
         expect(console.warn.callCount).toBe 1
 
+      it "does not disable an already disabled package", ->
+        packageName = 'package-with-main'
+        atom.config.pushAtKeyPath('core.disabledPackages', packageName)
+        atom.packages.observeDisabledPackages()
+        expect(atom.config.get('core.disabledPackages')).toContain packageName
+
+        atom.packages.disablePackage(packageName)
+        packagesDisabled = atom.config.get('core.disabledPackages').filter((pack) -> pack is packageName)
+        expect(packagesDisabled.length).toEqual 1
+
     describe "with themes", ->
       didChangeActiveThemesHandler = null
 
diff --git a/spec/pane-spec.coffee b/spec/pane-spec.coffee
index 36803bde6..5c5cd9e95 100644
--- a/spec/pane-spec.coffee
+++ b/spec/pane-spec.coffee
@@ -18,6 +18,8 @@ describe "Pane", ->
     onDidDestroy: (fn) -> @emitter.on('did-destroy', fn)
     destroy: -> @destroyed = true; @emitter.emit('did-destroy')
     isDestroyed: -> @destroyed
+    isPending: -> @pending
+    pending: false
 
   beforeEach ->
     confirm = spyOn(atom.applicationDelegate, 'confirm')
@@ -153,6 +155,26 @@ describe "Pane", ->
       pane.activateItem(pane.itemAtIndex(1))
       expect(observed).toEqual [pane.itemAtIndex(1)]
 
+    it "replaces pending items", ->
+      itemC = new Item("C")
+      itemD = new Item("D")
+      itemC.pending = true
+      itemD.pending = true
+
+      expect(itemC.isPending()).toBe true
+      pane.activateItem(itemC)
+      expect(pane.getItems().length).toBe 3
+      expect(pane.getActiveItem()).toBe pane.itemAtIndex(1)
+
+      expect(itemD.isPending()).toBe true
+      pane.activateItem(itemD)
+      expect(pane.getItems().length).toBe 3
+      expect(pane.getActiveItem()).toBe pane.itemAtIndex(1)
+
+      pane.activateItem(pane.itemAtIndex(2))
+      expect(pane.getItems().length).toBe 2
+      expect(pane.getActiveItem()).toBe pane.itemAtIndex(1)
+
   describe "::activateNextItem() and ::activatePreviousItem()", ->
     it "sets the active item to the next/previous item, looping around at either end", ->
       pane = new Pane(paneParams(items: [new Item("A"), new Item("B"), new Item("C")]))
diff --git a/spec/text-editor-component-spec.js b/spec/text-editor-component-spec.js
index c85e8818e..9663c6222 100644
--- a/spec/text-editor-component-spec.js
+++ b/spec/text-editor-component-spec.js
@@ -4809,6 +4809,13 @@ describe('TextEditorComponent', function () {
     })
   })
 
+  describe('::pixelPositionForScreenPosition()', () => {
+    it('returns the correct horizontal position, even if it is on a row that has not yet been rendered (regression)', () => {
+      editor.setTextInBufferRange([[5, 0], [6, 0]], 'hello world\n')
+      expect(wrapperNode.pixelPositionForScreenPosition([5, Infinity]).left).toBeGreaterThan(0)
+    })
+  })
+
   describe('middle mouse paste on Linux', function () {
     let originalPlatform
 
diff --git a/spec/text-editor-spec.coffee b/spec/text-editor-spec.coffee
index 02d2e4a96..ce84d2c50 100644
--- a/spec/text-editor-spec.coffee
+++ b/spec/text-editor-spec.coffee
@@ -5804,3 +5804,29 @@ describe "TextEditor", ->
           screenRange: marker1.getRange(),
           rangeIsReversed: false
         }
+
+  describe "pending state", ->
+    editor1 = null
+    beforeEach ->
+      waitsForPromise ->
+        atom.workspace.open('sample.txt', pending: true).then (o) -> editor1 = o
+
+    it "should open file in pending state if 'pending' option is true", ->
+      expect(editor1.isPending()).toBe true
+      expect(editor.isPending()).toBe false # By default pending status is false
+
+    it "invokes ::onDidTerminatePendingState observers if pending status is terminated", ->
+      events = []
+      editor1.onDidTerminatePendingState (event) -> events.push(event)
+      editor1.terminatePendingState()
+      expect(editor1.isPending()).toBe false
+      expect(events).toEqual [editor1]
+
+    it "should terminate pending state when buffer is changed", ->
+      events = []
+      editor1.onDidTerminatePendingState (event) -> events.push(event)
+      expect(editor1.isPending()).toBe true
+      editor1.insertText('I\'ll be back!')
+      advanceClock(500)
+      expect(editor1.isPending()).toBe false
+      expect(events).toEqual [editor1]
diff --git a/src/babel.js b/src/babel.js
index f53dbc758..1f450ff96 100644
--- a/src/babel.js
+++ b/src/babel.js
@@ -42,6 +42,10 @@ exports.getCachePath = function (sourceCode) {
 exports.compile = function (sourceCode, filePath) {
   if (!babel) {
     babel = require('babel-core')
+    var Logger = require('babel-core/lib/transformation/file/logger')
+    var noop = function () {}
+    Logger.prototype.debug = noop
+    Logger.prototype.verbose = noop
   }
 
   var options = {filename: filePath}
diff --git a/src/browser/application-menu.coffee b/src/browser/application-menu.coffee
index 27b9df8e1..74da80e43 100644
--- a/src/browser/application-menu.coffee
+++ b/src/browser/application-menu.coffee
@@ -103,8 +103,6 @@ class ApplicationMenu
     downloadingUpdateItem.visible = false
     installUpdateItem.visible = false
 
-    return if @autoUpdateManager.isDisabled()
-
     switch state
       when 'idle', 'error', 'no-update-available'
         checkForUpdateItem.visible = true
@@ -119,9 +117,10 @@ class ApplicationMenu
   #
   # Returns an Array of menu item Objects.
   getDefaultTemplate: ->
-    template = [
+    [
       label: "Atom"
       submenu: [
+          {label: "Check for Update", metadata: {autoUpdate: true}}
           {label: 'Reload', accelerator: 'Command+R', click: => @focusedWindow()?.reload()}
           {label: 'Close Window', accelerator: 'Command+Shift+W', click: => @focusedWindow()?.close()}
           {label: 'Toggle Dev Tools', accelerator: 'Command+Alt+I', click: => @focusedWindow()?.toggleDevTools()}
@@ -129,10 +128,6 @@ class ApplicationMenu
       ]
     ]
 
-    # Add `Check for Update` button if autoUpdateManager is enabled.
-    template[0].submenu.unshift({label: "Check for Update", metadata: {autoUpdate: true}}) unless @autoUpdateManager.isDisabled()
-    template
-
   focusedWindow: ->
     _.find global.atomApplication.windows, (atomWindow) -> atomWindow.isFocused()
 
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index e720597e3..3096fb7c0 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -74,8 +74,7 @@ class AtomApplication
     @pidsToOpenWindows = {}
     @windows = []
 
-    disableAutoUpdate = require(path.join(@resourcePath, 'package.json'))._disableAutoUpdate ? false
-    @autoUpdateManager = new AutoUpdateManager(@version, options.test, disableAutoUpdate)
+    @autoUpdateManager = new AutoUpdateManager(@version, options.test, @resourcePath)
     @applicationMenu = new ApplicationMenu(@version, @autoUpdateManager)
     @atomProtocolHandler = new AtomProtocolHandler(@resourcePath, @safeMode)
 
@@ -167,7 +166,7 @@ class AtomApplication
       safeMode: @focusedWindow()?.safeMode
 
     @on 'application:quit', -> app.quit()
-    @on 'application:new-window', -> @openPath(_.extend(windowDimensions: @focusedWindow()?.getDimensions(), getLoadSettings()))
+    @on 'application:new-window', -> @openPath(getLoadSettings())
     @on 'application:new-file', -> (@focusedWindow() ? this).openPath()
     @on 'application:open', -> @promptForPathToOpen('all', getLoadSettings())
     @on 'application:open-file', -> @promptForPathToOpen('file', getLoadSettings())
@@ -229,7 +228,7 @@ class AtomApplication
       @openUrl({urlToOpen, @devMode, @safeMode})
 
     app.on 'activate-with-no-open-windows', (event) =>
-      event.preventDefault()
+      event?.preventDefault()
       @emit('application:new-window')
 
     # A request from the associated render process to open a new render process.
@@ -360,6 +359,23 @@ class AtomApplication
   focusedWindow: ->
     _.find @windows, (atomWindow) -> atomWindow.isFocused()
 
+  # Get the platform-specific window offset for new windows.
+  getWindowOffsetForCurrentPlatform: ->
+    offsetByPlatform =
+      darwin: 22
+      win32: 26
+    offsetByPlatform[process.platform] ? 0
+
+  # Get the dimensions for opening a new window by cascading as appropriate to
+  # the platform.
+  getDimensionsForNewWindow: ->
+    dimensions = (@focusedWindow() ? @lastFocusedWindow)?.getDimensions()
+    offset = @getWindowOffsetForCurrentPlatform()
+    if dimensions? and offset?
+      dimensions.x += offset
+      dimensions.y += offset
+    dimensions
+
   # Public: Opens a single path, in an existing window if possible.
   #
   # options -
@@ -370,7 +386,7 @@ class AtomApplication
   #   :safeMode - Boolean to control the opened window's safe mode.
   #   :profileStartup - Boolean to control creating a profile of the startup time.
   #   :window - {AtomWindow} to open file paths in.
-  openPath: ({pathToOpen, pidToKillWhenClosed, newWindow, devMode, safeMode, profileStartup, window}) ->
+  openPath: ({pathToOpen, pidToKillWhenClosed, newWindow, devMode, safeMode, profileStartup, window} = {}) ->
     @openPaths({pathsToOpen: [pathToOpen], pidToKillWhenClosed, newWindow, devMode, safeMode, profileStartup, window})
 
   # Public: Opens multiple paths, in existing windows if possible.
@@ -417,6 +433,7 @@ class AtomApplication
 
       windowInitializationScript ?= require.resolve('../initialize-application-window')
       resourcePath ?= @resourcePath
+      windowDimensions ?= @getDimensionsForNewWindow()
       openedWindow = new AtomWindow({locationsToOpen, windowInitializationScript, resourcePath, devMode, safeMode, windowDimensions, profileStartup})
 
     if pidToKillWhenClosed?
diff --git a/src/browser/auto-update-manager.coffee b/src/browser/auto-update-manager.coffee
index 55ab2462b..6a008d44d 100644
--- a/src/browser/auto-update-manager.coffee
+++ b/src/browser/auto-update-manager.coffee
@@ -1,5 +1,6 @@
 autoUpdater = null
 _ = require 'underscore-plus'
+Config = require '../config'
 {EventEmitter} = require 'events'
 path = require 'path'
 
@@ -15,10 +16,13 @@ module.exports =
 class AutoUpdateManager
   _.extend @prototype, EventEmitter.prototype
 
-  constructor: (@version, @testMode, @disabled) ->
+  constructor: (@version, @testMode, resourcePath) ->
     @state = IdleState
     @iconPath = path.resolve(__dirname, '..', '..', 'resources', 'atom.png')
     @feedUrl = "https://atom.io/api/updates?version=#{@version}"
+    @config = new Config({configDirPath: process.env.ATOM_HOME, resourcePath, enablePersistence: true})
+    @config.setSchema null, {type: 'object', properties: _.clone(require('../config-schema'))}
+    @config.load()
     process.nextTick => @setupAutoUpdater()
 
   setupAutoUpdater: ->
@@ -46,9 +50,13 @@ class AutoUpdateManager
       @setState(UpdateAvailableState)
       @emitUpdateAvailableEvent(@getWindows()...)
 
-    # Only check for updates periodically if enabled and running in release
-    # version.
-    @scheduleUpdateCheck() unless /\w{7}/.test(@version) or @disabled
+    @config.onDidChange 'core.automaticallyUpdate', ({newValue}) =>
+      if newValue
+        @scheduleUpdateCheck()
+      else
+        @cancelScheduledUpdateCheck()
+
+    @scheduleUpdateCheck() if @config.get 'core.automaticallyUpdate'
 
     switch process.platform
       when 'win32'
@@ -56,9 +64,6 @@ class AutoUpdateManager
       when 'linux'
         @setState(UnsupportedState)
 
-  isDisabled: ->
-    @disabled
-
   emitUpdateAvailableEvent: (windows...) ->
     return unless @releaseVersion?
     for atomWindow in windows
@@ -74,10 +79,18 @@ class AutoUpdateManager
     @state
 
   scheduleUpdateCheck: ->
-    checkForUpdates = => @check(hidePopups: true)
-    fourHours = 1000 * 60 * 60 * 4
-    setInterval(checkForUpdates, fourHours)
-    checkForUpdates()
+    # Only schedule update check periodically if running in release version and
+    # and there is no existing scheduled update check.
+    unless /\w{7}/.test(@version) or @checkForUpdatesIntervalID
+      checkForUpdates = => @check(hidePopups: true)
+      fourHours = 1000 * 60 * 60 * 4
+      @checkForUpdatesIntervalID = setInterval(checkForUpdates, fourHours)
+      checkForUpdates()
+
+  cancelScheduledUpdateCheck: ->
+    if @checkForUpdatesIntervalID
+      clearInterval(@checkForUpdatesIntervalID)
+      @checkForUpdatesIntervalID = null
 
   check: ({hidePopups}={}) ->
     unless hidePopups
diff --git a/src/config-schema.coffee b/src/config-schema.coffee
index d9c0c1d21..88e00c71d 100644
--- a/src/config-schema.coffee
+++ b/src/config-schema.coffee
@@ -104,6 +104,10 @@ module.exports =
         description: 'Automatically open an empty editor on startup.'
         type: 'boolean'
         default: true
+      automaticallyUpdate:
+        description: 'Automatically update Atom when a new release is available.'
+        type: 'boolean'
+        default: true
 
   editor:
     type: 'object'
diff --git a/src/config.coffee b/src/config.coffee
index 2e4387732..2a883a57d 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -779,9 +779,14 @@ class Config
   loadUserConfig: ->
     return if @shouldNotAccessFileSystem()
 
-    unless fs.existsSync(@configFilePath)
-      fs.makeTreeSync(path.dirname(@configFilePath))
-      CSON.writeFileSync(@configFilePath, {})
+    try
+      unless fs.existsSync(@configFilePath)
+        fs.makeTreeSync(path.dirname(@configFilePath))
+        CSON.writeFileSync(@configFilePath, {})
+    catch error
+      @configFileHasErrors = true
+      @notifyFailure("Failed to initialize `#{path.basename(@configFilePath)}`", error.stack)
+      return
 
     try
       unless @savePending
@@ -820,7 +825,7 @@ class Config
     @watchSubscription = null
 
   notifyFailure: (errorMessage, detail) ->
-    @notificationManager.addError(errorMessage, {detail, dismissable: true})
+    @notificationManager?.addError(errorMessage, {detail, dismissable: true})
 
   save: ->
     return if @shouldNotAccessFileSystem()
diff --git a/src/display-buffer.coffee b/src/display-buffer.coffee
index f5a7bd853..8b95656f9 100644
--- a/src/display-buffer.coffee
+++ b/src/display-buffer.coffee
@@ -812,6 +812,7 @@ class DisplayBuffer extends Model
     decorationsState
 
   decorateMarker: (marker, decorationParams) ->
+    throw new Error("Cannot decorate a destroyed marker") if marker.isDestroyed()
     marker = @getMarkerLayer(marker.layer.id).getMarker(marker.id)
     decoration = new Decoration(marker, this, decorationParams)
     @decorationsByMarkerId[marker.id] ?= []
diff --git a/src/git-repository.coffee b/src/git-repository.coffee
index 1663f9ad4..ee27f87a5 100644
--- a/src/git-repository.coffee
+++ b/src/git-repository.coffee
@@ -463,8 +463,12 @@ class GitRepository
   refreshStatus: ->
     @handlerPath ?= require.resolve('./repository-status-handler')
 
+    relativeProjectPaths = @project?.getPaths()
+      .map (path) => @relativize(path)
+      .filter (path) -> path.length > 0
+
     @statusTask?.terminate()
-    @statusTask = Task.once @handlerPath, @getPath(), ({statuses, upstream, branch, submodules}) =>
+    @statusTask = Task.once @handlerPath, @getPath(), relativeProjectPaths, ({statuses, upstream, branch, submodules}) =>
       statusesUnchanged = _.isEqual(statuses, @statuses) and
                           _.isEqual(upstream, @upstream) and
                           _.isEqual(branch, @branch) and
diff --git a/src/lines-yardstick.coffee b/src/lines-yardstick.coffee
index 88a836c60..2373463af 100644
--- a/src/lines-yardstick.coffee
+++ b/src/lines-yardstick.coffee
@@ -77,10 +77,7 @@ class LinesYardstick
     else
       Point(row, column)
 
-  pixelPositionForScreenPosition: (screenPosition, clip=true) ->
-    screenPosition = Point.fromObject(screenPosition)
-    screenPosition = @model.clipScreenPosition(screenPosition) if clip
-
+  pixelPositionForScreenPosition: (screenPosition) ->
     targetRow = screenPosition.row
     targetColumn = screenPosition.column
 
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index 6772178af..1ecdc5448 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -199,7 +199,10 @@ class PackageManager
   # Returns the {Package} that was disabled or null if it isn't loaded.
   disablePackage: (name) ->
     pack = @loadPackage(name)
-    pack?.disable()
+
+    unless @isPackageDisabled(name)
+      pack?.disable()
+
     pack
 
   # Public: Is the package with the given name disabled?
diff --git a/src/pane.coffee b/src/pane.coffee
index 412fc5251..a9c4d45e2 100644
--- a/src/pane.coffee
+++ b/src/pane.coffee
@@ -337,13 +337,19 @@ class Pane extends Model
   #
   # * `index` {Number}
   activateItemAtIndex: (index) ->
-    @activateItem(@itemAtIndex(index))
+    item = @itemAtIndex(index) or @getActiveItem()
+    @setActiveItem(item)
 
   # Public: Make the given item *active*, causing it to be displayed by
   # the pane's view.
   activateItem: (item) ->
     if item?
-      @addItem(item, @getActiveItemIndex() + 1, false)
+      if @activeItem?.isPending?()
+        index = @getActiveItemIndex()
+        @destroyActiveItem() unless item is @activeItem
+      else
+        index = @getActiveItemIndex() + 1
+      @addItem(item, index, false)
       @setActiveItem(item)
 
   # Public: Add the given item to the pane.
@@ -574,7 +580,6 @@ class Pane extends Model
   # Public: Makes this pane the *active* pane, causing it to gain focus.
   activate: ->
     throw new Error("Pane has been destroyed") if @isDestroyed()
-
     @container?.setActivePane(this)
     @emitter.emit 'did-activate'
 
@@ -721,30 +726,28 @@ class Pane extends Model
       message = "#{message} '#{itemPath}'" if itemPath
       @notificationManager.addWarning(message, options)
 
-    if error.code is 'EISDIR' or error.message?.endsWith?('is a directory')
+    customMessage = @getMessageForErrorCode(error.code)
+    if customMessage?
+      addWarningWithPath("Unable to save file: #{customMessage}")
+    else if error.code is 'EISDIR' or error.message?.endsWith?('is a directory')
       @notificationManager.addWarning("Unable to save file: #{error.message}")
-    else if error.code is 'EACCES'
-      addWarningWithPath('Unable to save file: Permission denied')
     else if error.code in ['EPERM', 'EBUSY', 'UNKNOWN', 'EEXIST', 'ELOOP', 'EAGAIN']
       addWarningWithPath('Unable to save file', detail: error.message)
-    else if error.code is 'EROFS'
-      addWarningWithPath('Unable to save file: Read-only file system')
-    else if error.code is 'ENOSPC'
-      addWarningWithPath('Unable to save file: No space left on device')
-    else if error.code is 'ENXIO'
-      addWarningWithPath('Unable to save file: No such device or address')
-    else if error.code is 'ENOTSUP'
-      addWarningWithPath('Unable to save file: Operation not supported on socket')
-    else if error.code is 'EIO'
-      addWarningWithPath('Unable to save file: I/O error writing file')
-    else if error.code is 'EINTR'
-      addWarningWithPath('Unable to save file: Interrupted system call')
-    else if error.code is 'ECONNRESET'
-      addWarningWithPath('Unable to save file: Connection reset')
-    else if error.code is 'ESPIPE'
-      addWarningWithPath('Unable to save file: Invalid seek')
     else if errorMatch = /ENOTDIR, not a directory '([^']+)'/.exec(error.message)
       fileName = errorMatch[1]
       @notificationManager.addWarning("Unable to save file: A directory in the path '#{fileName}' could not be written to")
     else
       throw error
+
+  getMessageForErrorCode: (errorCode) ->
+    switch errorCode
+      when 'EACCES' then 'Permission denied'
+      when 'ECONNRESET' then 'Connection reset'
+      when 'EINTR' then 'Interrupted system call'
+      when 'EIO' then 'I/O error writing file'
+      when 'ENOSPC' then 'No space left on device'
+      when 'ENOTSUP' then 'Operation not supported on socket'
+      when 'ENXIO' then 'No such device or address'
+      when 'EROFS' then 'Read-only file system'
+      when 'ESPIPE' then 'Invalid seek'
+      when 'ETIMEDOUT' then 'Connection timed out'
diff --git a/src/project.coffee b/src/project.coffee
index d59c041cb..714511f9a 100644
--- a/src/project.coffee
+++ b/src/project.coffee
@@ -288,7 +288,7 @@ class Project extends Model
       'atom.repository-provider',
       '^0.1.0',
       (provider) =>
-        @repositoryProviders.push(provider)
+        @repositoryProviders.unshift(provider)
         @setPaths(@getPaths()) if null in @repositories
         new Disposable =>
           @repositoryProviders.splice(@repositoryProviders.indexOf(provider), 1)
diff --git a/src/register-default-commands.coffee b/src/register-default-commands.coffee
index 159ea1abc..b4649f70e 100644
--- a/src/register-default-commands.coffee
+++ b/src/register-default-commands.coffee
@@ -169,7 +169,8 @@ module.exports = ({commandRegistry, commandInstaller, config}) ->
     'editor:fold-at-indent-level-8': -> @foldAllAtIndentLevel(7)
     'editor:fold-at-indent-level-9': -> @foldAllAtIndentLevel(8)
     'editor:log-cursor-scope': -> @logCursorScope()
-    'editor:copy-path': -> @copyPathToClipboard()
+    'editor:copy-path': -> @copyPathToClipboard(false)
+    'editor:copy-project-path': -> @copyPathToClipboard(true)
     'editor:toggle-indent-guide': -> config.set('editor.showIndentGuide', not config.get('editor.showIndentGuide'))
     'editor:toggle-line-numbers': -> config.set('editor.showLineNumbers', not config.get('editor.showLineNumbers'))
     'editor:scroll-to-cursor': -> @scrollToCursorPosition()
diff --git a/src/repository-status-handler.coffee b/src/repository-status-handler.coffee
index d0763fd5a..2fda9a335 100644
--- a/src/repository-status-handler.coffee
+++ b/src/repository-status-handler.coffee
@@ -1,7 +1,7 @@
 Git = require 'git-utils'
 path = require 'path'
 
-module.exports = (repoPath) ->
+module.exports = (repoPath, paths = []) ->
   repo = Git.open(repoPath)
 
   upstream = {}
@@ -12,7 +12,8 @@ module.exports = (repoPath) ->
   if repo?
     # Statuses in main repo
     workingDirectoryPath = repo.getWorkingDirectory()
-    for filePath, status of repo.getStatus()
+    repoStatus = (if paths.length > 0 then repo.getStatusForPaths(paths) else repo.getStatus())
+    for filePath, status of repoStatus
       statuses[filePath] = status
 
     # Statuses in submodules
diff --git a/src/text-editor-component.coffee b/src/text-editor-component.coffee
index 1fcb21123..1576de4bf 100644
--- a/src/text-editor-component.coffee
+++ b/src/text-editor-component.coffee
@@ -445,12 +445,17 @@ class TextEditorComponent
   getVisibleRowRange: ->
     @presenter.getVisibleRowRange()
 
-  pixelPositionForScreenPosition: (screenPosition, clip) ->
+  pixelPositionForScreenPosition: (screenPosition, clip=true) ->
+    screenPosition = Point.fromObject(screenPosition)
+    screenPosition = @editor.clipScreenPosition(screenPosition) if clip
+
     unless @presenter.isRowVisible(screenPosition.row)
       @presenter.setScreenRowsToMeasure([screenPosition.row])
+
+    unless @linesComponent.lineNodeForLineIdAndScreenRow(@presenter.lineIdForScreenRow(screenPosition.row), screenPosition.row)?
       @updateSyncPreMeasurement()
 
-    pixelPosition = @linesYardstick.pixelPositionForScreenPosition(screenPosition, clip)
+    pixelPosition = @linesYardstick.pixelPositionForScreenPosition(screenPosition)
     @presenter.clearScreenRowsToMeasure()
     pixelPosition
 
diff --git a/src/text-editor-presenter.coffee b/src/text-editor-presenter.coffee
index aad660d57..b13bf9036 100644
--- a/src/text-editor-presenter.coffee
+++ b/src/text-editor-presenter.coffee
@@ -459,7 +459,7 @@ class TextEditorPresenter
       else
         screenPosition = decoration.getMarker().getHeadScreenPosition()
 
-      pixelPosition = @pixelPositionForScreenPosition(screenPosition, true)
+      pixelPosition = @pixelPositionForScreenPosition(screenPosition)
 
       top = pixelPosition.top + @lineHeight
       left = pixelPosition.left + @gutterWidth
@@ -681,8 +681,10 @@ class TextEditorPresenter
   updateHorizontalDimensions: ->
     if @baseCharacterWidth?
       oldContentWidth = @contentWidth
-      clip = @model.tokenizedLineForScreenRow(@model.getLongestScreenRow())?.isSoftWrapped()
-      @contentWidth = @pixelPositionForScreenPosition([@model.getLongestScreenRow(), @model.getMaxScreenLineLength()], clip).left
+      rightmostPosition = Point(@model.getLongestScreenRow(), @model.getMaxScreenLineLength())
+      if @model.tokenizedLineForScreenRow(rightmostPosition.row)?.isSoftWrapped()
+        rightmostPosition = @model.clipScreenPosition(rightmostPosition)
+      @contentWidth = @pixelPositionForScreenPosition(rightmostPosition).left
       @contentWidth += @scrollLeft
       @contentWidth += 1 unless @model.isSoftWrapped() # account for cursor width
 
@@ -1007,9 +1009,9 @@ class TextEditorPresenter
   hasPixelPositionRequirements: ->
     @lineHeight? and @baseCharacterWidth?
 
-  pixelPositionForScreenPosition: (screenPosition, clip=true) ->
+  pixelPositionForScreenPosition: (screenPosition) ->
     position =
-      @linesYardstick.pixelPositionForScreenPosition(screenPosition, clip, true)
+      @linesYardstick.pixelPositionForScreenPosition(screenPosition)
     position.top -= @getScrollTop()
     position.left -= @getScrollLeft()
 
@@ -1028,14 +1030,14 @@ class TextEditorPresenter
     lineHeight = @model.getLineHeightInPixels()
 
     if screenRange.end.row > screenRange.start.row
-      top = @linesYardstick.pixelPositionForScreenPosition(screenRange.start, true).top
+      top = @linesYardstick.pixelPositionForScreenPosition(screenRange.start).top
       left = 0
       height = (screenRange.end.row - screenRange.start.row + 1) * lineHeight
       width = @getScrollWidth()
     else
-      {top, left} = @linesYardstick.pixelPositionForScreenPosition(screenRange.start, false)
+      {top, left} = @linesYardstick.pixelPositionForScreenPosition(screenRange.start)
       height = lineHeight
-      width = @linesYardstick.pixelPositionForScreenPosition(screenRange.end, false).left - left
+      width = @linesYardstick.pixelPositionForScreenPosition(screenRange.end).left - left
 
     {top, left, width, height}
 
@@ -1217,8 +1219,8 @@ class TextEditorPresenter
 
   buildHighlightRegions: (screenRange) ->
     lineHeightInPixels = @lineHeight
-    startPixelPosition = @pixelPositionForScreenPosition(screenRange.start, false)
-    endPixelPosition = @pixelPositionForScreenPosition(screenRange.end, false)
+    startPixelPosition = @pixelPositionForScreenPosition(screenRange.start)
+    endPixelPosition = @pixelPositionForScreenPosition(screenRange.end)
     spannedRows = screenRange.end.row - screenRange.start.row + 1
 
     regions = []
@@ -1520,3 +1522,6 @@ class TextEditorPresenter
 
   isRowVisible: (row) ->
     @startRow <= row < @endRow
+
+  lineIdForScreenRow: (screenRow) ->
+    @model.tokenizedLineForScreenRow(screenRow)?.id
diff --git a/src/text-editor.coffee b/src/text-editor.coffee
index a3cb1c812..e132b5500 100644
--- a/src/text-editor.coffee
+++ b/src/text-editor.coffee
@@ -92,7 +92,7 @@ class TextEditor extends Model
       softWrapped, @displayBuffer, @selectionsMarkerLayer, buffer, suppressCursorCreation,
       @mini, @placeholderText, lineNumberGutterVisible, largeFileMode, @config,
       @notificationManager, @packageManager, @clipboard, @viewRegistry, @grammarRegistry,
-      @project, @assert, @applicationDelegate
+      @project, @assert, @applicationDelegate, @pending
     } = params
 
     throw new Error("Must pass a config parameter when constructing TextEditors") unless @config?
@@ -161,6 +161,9 @@ class TextEditor extends Model
     @disposables.add @buffer.onDidChangeEncoding =>
       @emitter.emit 'did-change-encoding', @getEncoding()
     @disposables.add @buffer.onDidDestroy => @destroy()
+    if @pending
+      @disposables.add @buffer.onDidChangeModified =>
+        @terminatePendingState() if @buffer.isModified()
 
     @preserveCursorPositionOnBufferReload()
 
@@ -569,6 +572,13 @@ class TextEditor extends Model
   getEditorWidthInChars: ->
     @displayBuffer.getEditorWidthInChars()
 
+  onDidTerminatePendingState: (callback) ->
+    @emitter.on 'did-terminate-pending-state', callback
+
+  terminatePendingState: ->
+    @pending = false
+    @emitter.emit 'did-terminate-pending-state', this
+
   ###
   Section: File Details
   ###
@@ -652,9 +662,13 @@ class TextEditor extends Model
   # Essential: Returns {Boolean} `true` if this editor has no content.
   isEmpty: -> @buffer.isEmpty()
 
+  # Returns {Boolean} `true` if this editor is pending and `false` if it is permanent.
+  isPending: -> Boolean(@pending)
+
   # Copies the current file path to the native clipboard.
-  copyPathToClipboard: ->
+  copyPathToClipboard: (relative = false) ->
     if filePath = @getPath()
+      filePath = atom.project.relativize(filePath) if relative
       @clipboard.write(filePath)
 
   ###
@@ -3043,7 +3057,7 @@ class TextEditor extends Model
 
   # Essential: Scrolls the editor to the given screen position.
   #
-  # * `screenPosition` An object that represents a buffer position. It can be either
+  # * `screenPosition` An object that represents a screen position. It can be either
   #    an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
   # * `options` (optional) {Object}
   #   * `center` Center the editor around the position if possible. (default: false)
diff --git a/src/workspace.coffee b/src/workspace.coffee
index f64f58ee0..07e69cdcf 100644
--- a/src/workspace.coffee
+++ b/src/workspace.coffee
@@ -475,7 +475,7 @@ class Workspace extends Model
         when 'EACCES'
           @notificationManager.addWarning("Permission denied '#{error.path}'")
           return Promise.resolve()
-        when 'EPERM', 'EBUSY', 'ENXIO', 'EIO', 'ENOTCONN', 'UNKNOWN', 'ECONNRESET', 'EINVAL', 'EMFILE', 'ENOTDIR'
+        when 'EPERM', 'EBUSY', 'ENXIO', 'EIO', 'ENOTCONN', 'UNKNOWN', 'ECONNRESET', 'EINVAL', 'EMFILE', 'ENOTDIR', 'EAGAIN'
           @notificationManager.addWarning("Unable to open '#{error.path ? uri}'", detail: error.message)
           return Promise.resolve()
         else