diff --git a/.python-version b/.python-version
index 4712731cc..ecc17b8e9 100644
--- a/.python-version
+++ b/.python-version
@@ -1 +1 @@
-2.7.12
+2.7.13
diff --git a/.travis.yml b/.travis.yml
index 1e768e76a..87559ea3a 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,7 +19,9 @@ install:
   - npm install -g npm
   - script/build --create-debian-package --create-rpm-package --compress-artifacts
 
-script: script/test
+script:
+  - script/lint
+  - script/test
 
 cache:
   directories:
diff --git a/appveyor.yml b/appveyor.yml
index 242b19f74..29606fb4e 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -27,6 +27,7 @@ build_script:
   - script\build.cmd --code-sign --create-windows-installer --compress-artifacts
 
 test_script:
+  - script\lint.cmd
   - script\test.cmd
 
 deploy: off
diff --git a/benchmarks/text-editor-large-file-construction.bench.js b/benchmarks/text-editor-large-file-construction.bench.js
index 694729724..64c6f4d94 100644
--- a/benchmarks/text-editor-large-file-construction.bench.js
+++ b/benchmarks/text-editor-large-file-construction.bench.js
@@ -26,7 +26,7 @@ export default async function ({test}) {
     console.log(text.length / 1024)
 
     let t0 = window.performance.now()
-    const buffer = new TextBuffer(text)
+    const buffer = new TextBuffer({text})
     const editor = new TextEditor({buffer, largeFileMode: true})
     atom.workspace.getActivePane().activateItem(editor)
     let t1 = window.performance.now()
diff --git a/benchmarks/text-editor-long-lines.bench.js b/benchmarks/text-editor-long-lines.bench.js
new file mode 100644
index 000000000..a99220d4e
--- /dev/null
+++ b/benchmarks/text-editor-long-lines.bench.js
@@ -0,0 +1,97 @@
+/** @babel */
+
+import path from 'path'
+import fs from 'fs'
+import {TextEditor, TextBuffer} from 'atom'
+
+const SIZES_IN_KB = [
+  512,
+  1024,
+  2048
+]
+const REPEATED_TEXT = fs.readFileSync(path.join(__dirname, '..', 'spec', 'fixtures', 'sample.js'), 'utf8').replace(/\n/g, '')
+const TEXT = REPEATED_TEXT.repeat(Math.ceil(SIZES_IN_KB[SIZES_IN_KB.length - 1] * 1024 / REPEATED_TEXT.length))
+
+export default async function ({test}) {
+  const data = []
+
+  const workspaceElement = atom.views.getView(atom.workspace)
+  document.body.appendChild(workspaceElement)
+
+  atom.packages.loadPackages()
+  await atom.packages.activate()
+
+  console.log(atom.getLoadSettings().resourcePath);
+
+  for (let pane of atom.workspace.getPanes()) {
+    pane.destroy()
+  }
+
+  for (const sizeInKB of SIZES_IN_KB) {
+    const text = TEXT.slice(0, sizeInKB * 1024)
+    console.log(text.length / 1024)
+
+    let t0 = window.performance.now()
+    const buffer = new TextBuffer({text})
+    const editor = new TextEditor({buffer, largeFileMode: true})
+    editor.setGrammar(atom.grammars.grammarForScopeName('source.js'))
+    atom.workspace.getActivePane().activateItem(editor)
+    let t1 = window.performance.now()
+
+    data.push({
+      name: 'Opening a large single-line file',
+      x: sizeInKB,
+      duration: t1 - t0
+    })
+
+    const tickDurations = []
+    for (let i = 0; i < 20; i++) {
+      await timeout(50)
+      t0 = window.performance.now()
+      await timeout(0)
+      t1 = window.performance.now()
+      tickDurations[i] = t1 - t0
+    }
+
+    data.push({
+      name: 'Max time event loop was blocked after opening a large single-line file',
+      x: sizeInKB,
+      duration: Math.max(...tickDurations)
+    })
+
+    t0 = window.performance.now()
+    editor.setCursorScreenPosition(editor.element.screenPositionForPixelPosition({
+      top: 100,
+      left: 30
+    }))
+    t1 = window.performance.now()
+
+    data.push({
+      name: 'Clicking the editor after opening a large single-line file',
+      x: sizeInKB,
+      duration: t1 - t0
+    })
+
+    t0 = window.performance.now()
+    editor.element.setScrollTop(editor.element.getScrollTop() + 100)
+    t1 = window.performance.now()
+
+    data.push({
+      name: 'Scrolling down after opening a large single-line file',
+      x: sizeInKB,
+      duration: t1 - t0
+    })
+
+    editor.destroy()
+    buffer.destroy()
+    await timeout(10000)
+  }
+
+  workspaceElement.remove()
+
+  return data
+}
+
+function timeout (duration) {
+  return new Promise((resolve) => setTimeout(resolve, duration))
+}
diff --git a/docs/build-instructions/linux.md b/docs/build-instructions/linux.md
index 5f0211c0d..1caf740ba 100644
--- a/docs/build-instructions/linux.md
+++ b/docs/build-instructions/linux.md
@@ -7,7 +7,7 @@ Ubuntu LTS 12.04 64-bit is the recommended platform.
 * OS with 64-bit or 32-bit architecture
 * C++11 toolchain
 * Git
-* Node.js 4.4.x or later (we recommend installing it via [nvm](https://github.com/creationix/nvm))
+* Node.js 6.x (we recommend installing it via [nvm](https://github.com/creationix/nvm))
 * npm 3.10.x or later (run `npm install -g npm`)
 * Ensure node-gyp uses python2 (run `npm config set python /usr/bin/python2 -g`, use `sudo` if you didn't install node via nvm)
 * Development headers for [GNOME Keyring](https://wiki.gnome.org/Projects/GnomeKeyring).
diff --git a/docs/build-instructions/macOS.md b/docs/build-instructions/macOS.md
index 18169435f..0d9335eea 100644
--- a/docs/build-instructions/macOS.md
+++ b/docs/build-instructions/macOS.md
@@ -3,7 +3,7 @@
 ## Requirements
 
   * macOS 10.8 or later
-  * Node.js 4.4.x or later (we recommend installing it via [nvm](https://github.com/creationix/nvm))
+  * Node.js 6.x (we recommend installing it via [nvm](https://github.com/creationix/nvm))
   * npm 3.10.x or later (run `npm install -g npm`)
   * Command Line Tools for [Xcode](https://developer.apple.com/xcode/downloads/) (run `xcode-select --install` to install)
 
diff --git a/docs/build-instructions/windows.md b/docs/build-instructions/windows.md
index 5c8c189ef..2c231b2dc 100644
--- a/docs/build-instructions/windows.md
+++ b/docs/build-instructions/windows.md
@@ -2,7 +2,7 @@
 
 ## Requirements
 
-* Node.js 4.4.x or later (the architecture of node available to the build system will determine whether you build 32-bit or 64-bit Atom)
+* Node.js 6.x (the architecture of node available to the build system will determine whether you build 32-bit or 64-bit Atom)
 * Python v2.7.x
   * The python.exe must be available at `%SystemDrive%\Python27\python.exe`. If it is installed elsewhere create a symbolic link to the directory containing the python.exe using: `mklink /d %SystemDrive%\Python27 D:\elsewhere\Python27`
 * 7zip (7z.exe available from the command line) - for creating distribution zip files
diff --git a/package.json b/package.json
index 312828b68..0a799e71e 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "1.15.0-dev",
+  "version": "1.16.0-dev",
   "description": "A hackable text editor for the 21st Century.",
   "main": "./src/main-process/main.js",
   "repository": {
@@ -15,10 +15,21 @@
   "electronVersion": "1.3.13",
   "dependencies": {
     "async": "0.2.6",
-    "atom-keymap": "7.1.19",
-    "atom-select-list": "0.0.6",
+    "atom-keymap": "7.1.20",
+    "atom-select-list": "0.0.12",
     "atom-ui": "0.4.1",
-    "babel-core": "5.8.38",
+    "babel-core": "6.22.1",
+    "babel-plugin-add-module-exports": "0.2.1",
+    "babel-plugin-transform-async-to-generator": "6.22.0",
+    "babel-plugin-transform-class-properties": "6.23.0",
+    "babel-plugin-transform-decorators-legacy": "1.3.4",
+    "babel-plugin-transform-do-expressions": "6.22.0",
+    "babel-plugin-transform-es2015-modules-commonjs": "6.23.0",
+    "babel-plugin-transform-export-extensions": "6.22.0",
+    "babel-plugin-transform-flow-strip-types": "6.22.0",
+    "babel-plugin-transform-function-bind": "6.22.0",
+    "babel-plugin-transform-object-rest-spread": "6.23.0",
+    "babel-plugin-transform-react-jsx": "6.23.0",
     "cached-run-in-this-context": "0.4.1",
     "chai": "3.5.0",
     "chart.js": "^2.3.0",
@@ -65,7 +76,7 @@
     "sinon": "1.17.4",
     "source-map-support": "^0.3.2",
     "temp": "0.8.1",
-    "text-buffer": "10.2.5",
+    "text-buffer": "10.3.12",
     "typescript-simple": "1.0.0",
     "underscore-plus": "^1.6.6",
     "winreg": "^1.2.1",
@@ -82,85 +93,86 @@
     "one-light-ui": "1.9.1",
     "one-dark-syntax": "1.7.1",
     "one-light-syntax": "1.7.1",
-    "solarized-dark-syntax": "1.1.1",
-    "solarized-light-syntax": "1.1.1",
+    "solarized-dark-syntax": "1.1.2",
+    "solarized-light-syntax": "1.1.2",
     "about": "1.7.2",
     "archive-view": "0.62.2",
     "autocomplete-atom-api": "0.10.0",
-    "autocomplete-css": "0.14.2",
+    "autocomplete-css": "0.15.0",
     "autocomplete-html": "0.7.2",
     "autocomplete-plus": "2.34.2",
     "autocomplete-snippets": "1.11.0",
     "autoflow": "0.29.0",
     "autosave": "0.24.0",
     "background-tips": "0.26.1",
-    "bookmarks": "0.44.0",
-    "bracket-matcher": "0.85.2",
-    "command-palette": "0.40.0",
-    "deprecation-cop": "0.56.1",
+    "bookmarks": "0.44.1",
+    "bracket-matcher": "0.85.3",
+    "command-palette": "0.40.2",
+    "dalek": "0.2.0",
+    "deprecation-cop": "0.56.2",
     "dev-live-reload": "0.47.0",
-    "encoding-selector": "0.23.0",
-    "exception-reporting": "0.40.2",
-    "find-and-replace": "0.206.0",
+    "encoding-selector": "0.23.1",
+    "exception-reporting": "0.41.1",
+    "find-and-replace": "0.206.3",
     "fuzzy-finder": "1.4.1",
-    "git-diff": "1.3.0",
+    "git-diff": "1.3.1",
     "go-to-line": "0.32.0",
-    "grammar-selector": "0.49.0",
-    "image-view": "0.60.0",
-    "incompatible-packages": "0.26.1",
-    "keybinding-resolver": "0.36.0",
-    "line-ending-selector": "0.6.0",
+    "grammar-selector": "0.49.2",
+    "image-view": "0.61.0",
+    "incompatible-packages": "0.27.0",
+    "keybinding-resolver": "0.36.1",
+    "line-ending-selector": "0.6.1",
     "link": "0.31.2",
-    "markdown-preview": "0.159.3",
-    "metrics": "1.1.3",
+    "markdown-preview": "0.159.7",
+    "metrics": "1.2.1",
     "notifications": "0.66.2",
     "open-on-github": "1.2.1",
     "package-generator": "1.1.0",
-    "settings-view": "0.246.0",
+    "settings-view": "0.247.0",
     "snippets": "1.0.5",
-    "spell-check": "0.70.2",
+    "spell-check": "0.71.0",
     "status-bar": "1.8.1",
-    "styleguide": "0.49.0",
+    "styleguide": "0.49.2",
     "symbols-view": "0.114.0",
     "tabs": "0.104.1",
-    "timecop": "0.34.0",
-    "tree-view": "0.213.2",
+    "timecop": "0.36.0",
+    "tree-view": "0.214.1",
     "update-package-dependencies": "0.10.0",
-    "welcome": "0.36.0",
-    "whitespace": "0.36.1",
-    "wrap-guide": "0.39.0",
-    "language-c": "0.54.1",
-    "language-clojure": "0.22.1",
-    "language-coffee-script": "0.48.2",
-    "language-csharp": "0.14.1",
+    "welcome": "0.36.1",
+    "whitespace": "0.36.2",
+    "wrap-guide": "0.39.1",
+    "language-c": "0.56.0",
+    "language-clojure": "0.22.2",
+    "language-coffee-script": "0.48.4",
+    "language-csharp": "0.14.2",
     "language-css": "0.42.0",
     "language-gfm": "0.88.0",
     "language-git": "0.19.0",
     "language-go": "0.43.1",
-    "language-html": "0.47.1",
+    "language-html": "0.47.2",
     "language-hyperlink": "0.16.1",
-    "language-java": "0.25.0",
-    "language-javascript": "0.125.1",
+    "language-java": "0.26.0",
+    "language-javascript": "0.126.0",
     "language-json": "0.18.3",
     "language-less": "0.30.1",
     "language-make": "0.22.3",
     "language-mustache": "0.13.1",
     "language-objective-c": "0.15.1",
     "language-perl": "0.37.0",
-    "language-php": "0.37.3",
+    "language-php": "0.37.4",
     "language-property-list": "0.9.0",
-    "language-python": "0.45.1",
-    "language-ruby": "0.70.4",
-    "language-ruby-on-rails": "0.25.1",
+    "language-python": "0.45.2",
+    "language-ruby": "0.70.5",
+    "language-ruby-on-rails": "0.25.2",
     "language-sass": "0.57.1",
     "language-shellscript": "0.25.0",
     "language-source": "0.9.0",
-    "language-sql": "0.25.2",
+    "language-sql": "0.25.3",
     "language-text": "0.7.1",
     "language-todo": "0.29.1",
     "language-toml": "0.18.1",
-    "language-xml": "0.34.15",
-    "language-yaml": "0.27.2"
+    "language-xml": "0.34.16",
+    "language-yaml": "0.28.0"
   },
   "private": true,
   "scripts": {
diff --git a/resources/win/apm.sh b/resources/win/apm.sh
index 99ccfec69..3a479f53d 100644
--- a/resources/win/apm.sh
+++ b/resources/win/apm.sh
@@ -1,3 +1,3 @@
 #!/bin/sh
 
-"$(dirname "$0")/../app/apm/apm.sh" "$@"
+"$(dirname "$0")/../app/apm/bin/apm" "$@"
diff --git a/script/lib/code-sign-on-mac.js b/script/lib/code-sign-on-mac.js
index 7d70e2b6b..5e4c67707 100644
--- a/script/lib/code-sign-on-mac.js
+++ b/script/lib/code-sign-on-mac.js
@@ -5,16 +5,17 @@ const path = require('path')
 const spawnSync = require('./spawn-sync')
 
 module.exports = function (packagedAppPath) {
-  if (!process.env.ATOM_MAC_CODE_SIGNING_CERT_DOWNLOAD_URL) {
+  if (!process.env.ATOM_MAC_CODE_SIGNING_CERT_DOWNLOAD_URL && !process.env.ATOM_MAC_CODE_SIGNING_CERT_PATH) {
     console.log('Skipping code signing because the ATOM_MAC_CODE_SIGNING_CERT_DOWNLOAD_URL environment variable is not defined'.gray)
     return
   }
 
-  // This declaration is outside of the try block because it is also used for the finally block
-  const certPath = path.join(os.tmpdir(), 'mac.p12')
-  try {
+  let certPath = process.env.ATOM_MAC_CODE_SIGNING_CERT_PATH;
+  if (!certPath) {
+    certPath = path.join(os.tmpdir(), 'mac.p12')
     downloadFileFromGithub(process.env.ATOM_MAC_CODE_SIGNING_CERT_DOWNLOAD_URL, certPath)
-
+  }
+  try {
     console.log(`Unlocking keychain ${process.env.ATOM_MAC_CODE_SIGNING_KEYCHAIN}`)
     const unlockArgs = ['unlock-keychain']
     // For signing on local workstations, password could be entered interactively
@@ -32,6 +33,18 @@ module.exports = function (packagedAppPath) {
       '-T', '/usr/bin/codesign'
     ])
 
+
+    console.log('Running incantation to suppress dialog when signing on macOS Sierra')
+    try {
+      spawnSync('security', [
+        'set-key-partition-list', '-S', 'apple-tool:,apple:', '-s',
+        '-k', process.env.ATOM_MAC_CODE_SIGNING_KEYCHAIN_PASSWORD,
+        process.env.ATOM_MAC_CODE_SIGNING_KEYCHAIN
+      ])
+    } catch (e) {
+      console.log('Incantation failed... maybe this isn\'t Sierra?');
+    }
+
     console.log(`Code-signing application at ${packagedAppPath}`)
     spawnSync('codesign', [
       '--deep', '--force', '--verbose',
@@ -39,7 +52,9 @@ module.exports = function (packagedAppPath) {
       '--sign', 'Developer ID Application: GitHub', packagedAppPath
     ], {stdio: 'inherit'})
   } finally {
-    console.log(`Deleting certificate at ${certPath}`)
-    fs.removeSync(certPath)
+    if (!process.env.ATOM_MAC_CODE_SIGNING_CERT_PATH) {
+      console.log(`Deleting certificate at ${certPath}`)
+      fs.removeSync(certPath)
+    }
   }
 }
diff --git a/script/lib/create-windows-installer.js b/script/lib/create-windows-installer.js
index fbf3630a3..f3271f198 100644
--- a/script/lib/create-windows-installer.js
+++ b/script/lib/create-windows-installer.js
@@ -18,15 +18,19 @@ module.exports = function (packagedAppPath, codeSign) {
     iconUrl: `https://raw.githubusercontent.com/atom/atom/master/resources/app-icons/${CONFIG.channel}/atom.ico`,
     loadingGif: path.join(CONFIG.repositoryRootPath, 'resources', 'win', 'loading.gif'),
     outputDirectory: CONFIG.buildOutputPath,
-    remoteReleases: `https://atom.io/api/updates${archSuffix}`,
+    remoteReleases: `https://atom.io/api/updates${archSuffix}?version=${CONFIG.appMetadata.version}`,
     setupIcon: path.join(CONFIG.repositoryRootPath, 'resources', 'app-icons', CONFIG.channel, 'atom.ico')
   }
 
-  const certPath = path.join(os.tmpdir(), 'win.p12')
-  const signing = codeSign && process.env.ATOM_WIN_CODE_SIGNING_CERT_DOWNLOAD_URL
+  const signing = codeSign && (process.env.ATOM_WIN_CODE_SIGNING_CERT_DOWNLOAD_URL || process.env.ATOM_WIN_CODE_SIGNING_CERT_PATH)
+  let certPath = process.env.ATOM_WIN_CODE_SIGNING_CERT_PATH;
 
   if (signing) {
-    downloadFileFromGithub(process.env.ATOM_WIN_CODE_SIGNING_CERT_DOWNLOAD_URL, certPath)
+    if (!certPath) {
+      certPath = path.join(os.tmpdir(), 'win.p12')
+      downloadFileFromGithub(process.env.ATOM_WIN_CODE_SIGNING_CERT_DOWNLOAD_URL, certPath)
+    }
+
     var signParams = []
     signParams.push(`/f ${certPath}`) // Signing cert file
     signParams.push(`/p ${process.env.ATOM_WIN_CODE_SIGNING_CERT_PASSWORD}`) // Signing cert password
@@ -39,7 +43,7 @@ module.exports = function (packagedAppPath, codeSign) {
   }
 
   const cleanUp = function () {
-    if (fs.existsSync(certPath)) {
+    if (fs.existsSync(certPath) && !process.env.ATOM_WIN_CODE_SIGNING_CERT_PATH) {
       console.log(`Deleting certificate at ${certPath}`)
       fs.removeSync(certPath)
     }
diff --git a/script/package.json b/script/package.json
index 1284fd83c..87c43f261 100644
--- a/script/package.json
+++ b/script/package.json
@@ -3,7 +3,6 @@
   "description": "Atom build scripts",
   "dependencies": {
     "async": "2.0.1",
-    "babel-core": "5.8.38",
     "coffeelint": "1.15.7",
     "colors": "1.1.2",
     "csslint": "1.0.2",
diff --git a/spec/atom-environment-spec.coffee b/spec/atom-environment-spec.coffee
index 9b9715a07..d967fb97b 100644
--- a/spec/atom-environment-spec.coffee
+++ b/spec/atom-environment-spec.coffee
@@ -142,6 +142,11 @@ describe "AtomEnvironment", ->
           atom.assert(false, "a == b", (e) -> error = e)
           expect(error).toBe errors[0]
 
+      describe "if passed metadata", ->
+        it "assigns the metadata on the assertion failure's error object", ->
+          atom.assert(false, "a == b", {foo: 'bar'})
+          expect(errors[0].metadata).toEqual {foo: 'bar'}
+
     describe "if the condition is true", ->
       it "does nothing", ->
         result = atom.assert(true, "a == b")
diff --git a/spec/atom-reporter.coffee b/spec/atom-reporter.coffee
index 1600da9d7..a91059efe 100644
--- a/spec/atom-reporter.coffee
+++ b/spec/atom-reporter.coffee
@@ -1,4 +1,5 @@
 path = require 'path'
+process = require 'process'
 _ = require 'underscore-plus'
 grim = require 'grim'
 marked = require 'marked'
@@ -20,12 +21,15 @@ formatStackTrace = (spec, message='', stackTrace) ->
   lines.shift() if message.trim() is errorMatch?[1]?.trim()
 
   for line, index in lines
-    # Remove prefix of lines matching: at [object Object].<anonymous> (path:1:2)
-    prefixMatch = line.match(/at \[object Object\]\.<anonymous> \(([^)]+)\)/)
+    # Remove prefix of lines matching: at .<anonymous> (path:1:2)
+    prefixMatch = line.match(/at \.<anonymous> \(([^)]+)\)/)
     line = "at #{prefixMatch[1]}" if prefixMatch
 
     # Relativize locations to spec directory
-    lines[index] = line.replace("at #{spec.specDirectory}#{path.sep}", 'at ')
+    if process.platform is 'win32'
+      line = line.replace('file:///', '').replace(///#{path.posix.sep}///g, path.win32.sep)
+    line = line.replace("at #{spec.specDirectory}#{path.sep}", 'at ')
+    lines[index] = line.replace("(#{spec.specDirectory}#{path.sep}", '(') # at step (path:1:2)
 
   lines = lines.map (line) -> line.trim()
   lines.join('\n').trim()
diff --git a/spec/decoration-manager-spec.coffee b/spec/decoration-manager-spec.coffee
index 44da440d9..e57660a57 100644
--- a/spec/decoration-manager-spec.coffee
+++ b/spec/decoration-manager-spec.coffee
@@ -1,13 +1,14 @@
 DecorationManager = require '../src/decoration-manager'
 
 describe "DecorationManager", ->
-  [decorationManager, buffer, defaultMarkerLayer] = []
+  [decorationManager, buffer, displayLayer, markerLayer1, markerLayer2] = []
 
   beforeEach ->
     buffer = atom.project.bufferForPathSync('sample.js')
     displayLayer = buffer.addDisplayLayer()
-    defaultMarkerLayer = displayLayer.addMarkerLayer()
-    decorationManager = new DecorationManager(displayLayer, defaultMarkerLayer)
+    markerLayer1 = displayLayer.addMarkerLayer()
+    markerLayer2 = displayLayer.addMarkerLayer()
+    decorationManager = new DecorationManager(displayLayer)
 
     waitsForPromise ->
       atom.packages.activatePackage('language-javascript')
@@ -17,38 +18,53 @@ describe "DecorationManager", ->
     buffer.release()
 
   describe "decorations", ->
-    [marker, decoration, decorationProperties] = []
+    [layer1Marker, layer2Marker, layer1MarkerDecoration, layer2MarkerDecoration, decorationProperties] = []
     beforeEach ->
-      marker = defaultMarkerLayer.markBufferRange([[2, 13], [3, 15]])
+      layer1Marker = markerLayer1.markBufferRange([[2, 13], [3, 15]])
       decorationProperties = {type: 'line-number', class: 'one'}
-      decoration = decorationManager.decorateMarker(marker, decorationProperties)
+      layer1MarkerDecoration = decorationManager.decorateMarker(layer1Marker, decorationProperties)
+      layer2Marker = markerLayer2.markBufferRange([[2, 13], [3, 15]])
+      layer2MarkerDecoration = decorationManager.decorateMarker(layer2Marker, decorationProperties)
 
     it "can add decorations associated with markers and remove them", ->
-      expect(decoration).toBeDefined()
-      expect(decoration.getProperties()).toBe decorationProperties
-      expect(decorationManager.decorationForId(decoration.id)).toBe decoration
-      expect(decorationManager.decorationsForScreenRowRange(2, 3)[marker.id][0]).toBe decoration
+      expect(layer1MarkerDecoration).toBeDefined()
+      expect(layer1MarkerDecoration.getProperties()).toBe decorationProperties
+      expect(decorationManager.decorationForId(layer1MarkerDecoration.id)).toBe layer1MarkerDecoration
+      expect(decorationManager.decorationsForScreenRowRange(2, 3)).toEqual {
+        "#{layer1Marker.id}": [layer1MarkerDecoration],
+        "#{layer2Marker.id}": [layer2MarkerDecoration]
+      }
 
-      decoration.destroy()
-      expect(decorationManager.decorationsForScreenRowRange(2, 3)[marker.id]).not.toBeDefined()
-      expect(decorationManager.decorationForId(decoration.id)).not.toBeDefined()
+      layer1MarkerDecoration.destroy()
+      expect(decorationManager.decorationsForScreenRowRange(2, 3)[layer1Marker.id]).not.toBeDefined()
+      expect(decorationManager.decorationForId(layer1MarkerDecoration.id)).not.toBeDefined()
+      layer2MarkerDecoration.destroy()
+      expect(decorationManager.decorationsForScreenRowRange(2, 3)[layer2Marker.id]).not.toBeDefined()
+      expect(decorationManager.decorationForId(layer2MarkerDecoration.id)).not.toBeDefined()
 
     it "will not fail if the decoration is removed twice", ->
-      decoration.destroy()
-      decoration.destroy()
-      expect(decorationManager.decorationForId(decoration.id)).not.toBeDefined()
+      layer1MarkerDecoration.destroy()
+      layer1MarkerDecoration.destroy()
+      expect(decorationManager.decorationForId(layer1MarkerDecoration.id)).not.toBeDefined()
 
     it "does not allow destroyed markers to be decorated", ->
-      marker.destroy()
+      layer1Marker.destroy()
       expect(->
-        decorationManager.decorateMarker(marker, {type: 'overlay', item: document.createElement('div')})
+        decorationManager.decorateMarker(layer1Marker, {type: 'overlay', item: document.createElement('div')})
       ).toThrow("Cannot decorate a destroyed marker")
       expect(decorationManager.getOverlayDecorations()).toEqual []
 
+    it "does not allow destroyed marker layers to be decorated", ->
+      layer = displayLayer.addMarkerLayer()
+      layer.destroy()
+      expect(->
+        decorationManager.decorateMarkerLayer(layer, {type: 'highlight'})
+      ).toThrow("Cannot decorate a destroyed marker layer")
+
     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()
-        decoration.setProperties type: 'line-number', class: 'two'
+        layer1MarkerDecoration.onDidChangeProperties updatedSpy = jasmine.createSpy()
+        layer1MarkerDecoration.setProperties type: 'line-number', class: 'two'
 
         {oldProperties, newProperties} = updatedSpy.mostRecentCall.args[0]
         expect(oldProperties).toEqual decorationProperties
@@ -56,29 +72,29 @@ describe "DecorationManager", ->
 
     describe "::getDecorations(properties)", ->
       it "returns decorations matching the given optional properties", ->
-        expect(decorationManager.getDecorations()).toEqual [decoration]
+        expect(decorationManager.getDecorations()).toEqual [layer1MarkerDecoration, layer2MarkerDecoration]
         expect(decorationManager.getDecorations(class: 'two').length).toEqual 0
-        expect(decorationManager.getDecorations(class: 'one').length).toEqual 1
+        expect(decorationManager.getDecorations(class: 'one').length).toEqual 2
 
   describe "::decorateMarker", ->
     describe "when decorating gutters", ->
-      [marker] = []
+      [layer1Marker] = []
 
       beforeEach ->
-        marker = defaultMarkerLayer.markBufferRange([[1, 0], [1, 0]])
+        layer1Marker = markerLayer1.markBufferRange([[1, 0], [1, 0]])
 
       it "creates a decoration that is both of 'line-number' and 'gutter' type when called with the 'line-number' type", ->
         decorationProperties = {type: 'line-number', class: 'one'}
-        decoration = decorationManager.decorateMarker(marker, decorationProperties)
-        expect(decoration.isType('line-number')).toBe true
-        expect(decoration.isType('gutter')).toBe true
-        expect(decoration.getProperties().gutterName).toBe 'line-number'
-        expect(decoration.getProperties().class).toBe 'one'
+        layer1MarkerDecoration = decorationManager.decorateMarker(layer1Marker, decorationProperties)
+        expect(layer1MarkerDecoration.isType('line-number')).toBe true
+        expect(layer1MarkerDecoration.isType('gutter')).toBe true
+        expect(layer1MarkerDecoration.getProperties().gutterName).toBe 'line-number'
+        expect(layer1MarkerDecoration.getProperties().class).toBe 'one'
 
       it "creates a decoration that is only of 'gutter' type if called with the 'gutter' type and a 'gutterName'", ->
         decorationProperties = {type: 'gutter', gutterName: 'test-gutter', class: 'one'}
-        decoration = decorationManager.decorateMarker(marker, decorationProperties)
-        expect(decoration.isType('gutter')).toBe true
-        expect(decoration.isType('line-number')).toBe false
-        expect(decoration.getProperties().gutterName).toBe 'test-gutter'
-        expect(decoration.getProperties().class).toBe 'one'
+        layer1MarkerDecoration = decorationManager.decorateMarker(layer1Marker, decorationProperties)
+        expect(layer1MarkerDecoration.isType('gutter')).toBe true
+        expect(layer1MarkerDecoration.isType('line-number')).toBe false
+        expect(layer1MarkerDecoration.getProperties().gutterName).toBe 'test-gutter'
+        expect(layer1MarkerDecoration.getProperties().class).toBe 'one'
diff --git a/spec/default-directory-provider-spec.coffee b/spec/default-directory-provider-spec.coffee
index 821c278ee..bf23195cf 100644
--- a/spec/default-directory-provider-spec.coffee
+++ b/spec/default-directory-provider-spec.coffee
@@ -28,6 +28,15 @@ describe "DefaultDirectoryProvider", ->
       directory = provider.directoryForURISync(nonNormalizedPath)
       expect(directory.getPath()).toEqual tmp
 
+    it "normalizes disk drive letter in path on #win32", ->
+      provider = new DefaultDirectoryProvider()
+      nonNormalizedPath = tmp[0].toLowerCase()+tmp.slice(1)
+      expect(tmp).not.toMatch /^[a-z]:/
+      expect(nonNormalizedPath).toMatch /^[a-z]:/
+
+      directory = provider.directoryForURISync(nonNormalizedPath)
+      expect(directory.getPath()).toEqual tmp
+
     it "creates a Directory for its parent dir when passed a file", ->
       provider = new DefaultDirectoryProvider()
       file = path.join(tmp, "example.txt")
diff --git a/spec/dom-element-pool-spec.coffee b/spec/dom-element-pool-spec.coffee
deleted file mode 100644
index 2efe80beb..000000000
--- a/spec/dom-element-pool-spec.coffee
+++ /dev/null
@@ -1,60 +0,0 @@
-DOMElementPool = require '../src/dom-element-pool'
-{contains} = require 'underscore-plus'
-
-describe "DOMElementPool", ->
-  domElementPool = null
-
-  beforeEach ->
-    domElementPool = new DOMElementPool
-
-  it "builds DOM nodes, recycling them when they are freed", ->
-    [div, span1, span2, span3, span4, span5, textNode] = elements = [
-      domElementPool.buildElement("div")
-      domElementPool.buildElement("span")
-      domElementPool.buildElement("span")
-      domElementPool.buildElement("span")
-      domElementPool.buildElement("span")
-      domElementPool.buildElement("span")
-      domElementPool.buildText("Hello world!")
-    ]
-
-    div.appendChild(span1)
-    span1.appendChild(span2)
-    div.appendChild(span3)
-    span3.appendChild(span4)
-    span4.appendChild(textNode)
-
-    domElementPool.freeElementAndDescendants(div)
-    domElementPool.freeElementAndDescendants(span5)
-
-    expect(contains(elements, domElementPool.buildElement("div"))).toBe(true)
-    expect(contains(elements, domElementPool.buildElement("span"))).toBe(true)
-    expect(contains(elements, domElementPool.buildElement("span"))).toBe(true)
-    expect(contains(elements, domElementPool.buildElement("span"))).toBe(true)
-    expect(contains(elements, domElementPool.buildElement("span"))).toBe(true)
-    expect(contains(elements, domElementPool.buildElement("span"))).toBe(true)
-    expect(contains(elements, domElementPool.buildText("another text"))).toBe(true)
-
-    expect(contains(elements, domElementPool.buildElement("div"))).toBe(false)
-    expect(contains(elements, domElementPool.buildElement("span"))).toBe(false)
-    expect(contains(elements, domElementPool.buildText("unexisting"))).toBe(false)
-
-  it "forgets free nodes after being cleared", ->
-    span = domElementPool.buildElement("span")
-    div = domElementPool.buildElement("div")
-    domElementPool.freeElementAndDescendants(span)
-    domElementPool.freeElementAndDescendants(div)
-
-    domElementPool.clear()
-
-    expect(domElementPool.buildElement("span")).not.toBe(span)
-    expect(domElementPool.buildElement("div")).not.toBe(div)
-
-  it "throws an error when trying to free the same node twice", ->
-    div = domElementPool.buildElement("div")
-    domElementPool.freeElementAndDescendants(div)
-    expect(-> domElementPool.freeElementAndDescendants(div)).toThrow()
-
-  it "throws an error when trying to free an invalid element", ->
-    expect(-> domElementPool.freeElementAndDescendants(null)).toThrow()
-    expect(-> domElementPool.freeElementAndDescendants(undefined)).toThrow()
diff --git a/spec/dom-element-pool-spec.js b/spec/dom-element-pool-spec.js
new file mode 100644
index 000000000..9de932e27
--- /dev/null
+++ b/spec/dom-element-pool-spec.js
@@ -0,0 +1,112 @@
+const DOMElementPool = require ('../src/dom-element-pool')
+
+describe('DOMElementPool', function () {
+  let domElementPool
+
+  beforeEach(() => { domElementPool = new DOMElementPool() })
+
+  it('builds DOM nodes, recycling them when they are freed', function () {
+    let elements
+    const [div, span1, span2, span3, span4, span5, textNode] = Array.from(elements = [
+      domElementPool.buildElement('div', 'foo'),
+      domElementPool.buildElement('span'),
+      domElementPool.buildElement('span'),
+      domElementPool.buildElement('span'),
+      domElementPool.buildElement('span'),
+      domElementPool.buildElement('span'),
+      domElementPool.buildText('Hello world!')
+    ])
+
+    expect(div.className).toBe('foo')
+    div.textContent = 'testing'
+    div.style.backgroundColor = 'red'
+    div.dataset.foo = 'bar'
+
+    expect(textNode.textContent).toBe('Hello world!')
+
+    div.appendChild(span1)
+    span1.appendChild(span2)
+    div.appendChild(span3)
+    span3.appendChild(span4)
+    span4.appendChild(textNode)
+
+    domElementPool.freeElementAndDescendants(div)
+    domElementPool.freeElementAndDescendants(span5)
+
+    expect(elements.includes(domElementPool.buildElement('div'))).toBe(true)
+    expect(elements.includes(domElementPool.buildElement('span'))).toBe(true)
+    expect(elements.includes(domElementPool.buildElement('span'))).toBe(true)
+    expect(elements.includes(domElementPool.buildElement('span'))).toBe(true)
+    expect(elements.includes(domElementPool.buildElement('span'))).toBe(true)
+    expect(elements.includes(domElementPool.buildElement('span'))).toBe(true)
+    expect(elements.includes(domElementPool.buildText('another text'))).toBe(true)
+
+    expect(elements.includes(domElementPool.buildElement('div'))).toBe(false)
+    expect(elements.includes(domElementPool.buildElement('span'))).toBe(false)
+    expect(elements.includes(domElementPool.buildText('unexisting'))).toBe(false)
+
+    expect(div.className).toBe('')
+    expect(div.textContent).toBe('')
+    expect(div.style.backgroundColor).toBe('')
+    expect(div.dataset.foo).toBeUndefined()
+
+    expect(textNode.textContent).toBe('another text')
+  })
+
+  it('forgets free nodes after being cleared', function () {
+    const span = domElementPool.buildElement('span')
+    const div = domElementPool.buildElement('div')
+    domElementPool.freeElementAndDescendants(span)
+    domElementPool.freeElementAndDescendants(div)
+
+    domElementPool.clear()
+
+    expect(domElementPool.buildElement('span')).not.toBe(span)
+    expect(domElementPool.buildElement('div')).not.toBe(div)
+  })
+
+  it('does not attempt to free nodes that were not created by the pool', () => {
+    let assertionFailure
+    atom.onDidFailAssertion((error) => assertionFailure = error)
+
+    const foreignDiv = document.createElement('div')
+    const div = domElementPool.buildElement('div')
+    div.appendChild(foreignDiv)
+    domElementPool.freeElementAndDescendants(div)
+    const span = domElementPool.buildElement('span')
+    span.appendChild(foreignDiv)
+    domElementPool.freeElementAndDescendants(span)
+
+    expect(assertionFailure).toBeUndefined()
+  })
+
+  it('fails an assertion when freeing the same element twice', function () {
+    let assertionFailure
+    atom.onDidFailAssertion((error) => assertionFailure = error)
+
+    const div = domElementPool.buildElement('div')
+    div.textContent = 'testing'
+    domElementPool.freeElementAndDescendants(div)
+    expect(assertionFailure).toBeUndefined()
+    domElementPool.freeElementAndDescendants(div)
+    expect(assertionFailure.message).toBe('Assertion failed: The element has already been freed!')
+    expect(assertionFailure.metadata.content).toBe('<div>testing</div>')
+  })
+
+  it('fails an assertion when freeing the same text node twice', function () {
+    let assertionFailure
+    atom.onDidFailAssertion((error) => assertionFailure = error)
+
+    const node = domElementPool.buildText('testing')
+    domElementPool.freeElementAndDescendants(node)
+    expect(assertionFailure).toBeUndefined()
+    domElementPool.freeElementAndDescendants(node)
+    expect(assertionFailure.message).toBe('Assertion failed: The element has already been freed!')
+    expect(assertionFailure.metadata.content).toBe('testing')
+  })
+
+  it('throws an error when trying to free an invalid element', function () {
+    expect(() => domElementPool.freeElementAndDescendants(null)).toThrow()
+    expect(() => domElementPool.freeElementAndDescendants(undefined)).toThrow()
+  })
+})
diff --git a/spec/main-process/atom-application.test.js b/spec/main-process/atom-application.test.js
index 77d7987a7..d30900b99 100644
--- a/spec/main-process/atom-application.test.js
+++ b/spec/main-process/atom-application.test.js
@@ -196,7 +196,9 @@ describe('AtomApplication', function () {
     it('persists window state based on the project directories', async function () {
       const tempDirPath = makeTempDir()
       const atomApplication = buildAtomApplication()
-      const window1 = atomApplication.launch(parseCommandLine([path.join(tempDirPath, 'new-file')]))
+      const nonExistentFilePath = path.join(tempDirPath, 'new-file')
+
+      const window1 = atomApplication.launch(parseCommandLine([nonExistentFilePath]))
       await evalInWebContents(window1.browserWindow.webContents, function (sendBackToMainProcess) {
         atom.workspace.observeActivePaneItem(function (textEditor) {
           if (textEditor) {
@@ -205,17 +207,31 @@ describe('AtomApplication', function () {
           }
         })
       })
+      await window1.saveState()
       window1.close()
       await window1.closedPromise
 
-      const window2 = atomApplication.launch(parseCommandLine([path.join(tempDirPath)]))
+      // Restore unsaved state when opening the directory itself
+      const window2 = atomApplication.launch(parseCommandLine([tempDirPath]))
+      await window2.loadedPromise
       const window2Text = await evalInWebContents(window2.browserWindow.webContents, function (sendBackToMainProcess) {
-        atom.workspace.observeActivePaneItem(function (textEditor) {
-          if (textEditor) sendBackToMainProcess(textEditor.getText())
-        })
+        const textEditor = atom.workspace.getActiveTextEditor()
+        textEditor.moveToBottom()
+        textEditor.insertText(' How are you?')
+        sendBackToMainProcess(textEditor.getText())
       })
+      assert.equal(window2Text, 'Hello World! How are you?')
+      await window2.saveState()
+      window2.close()
+      await window2.closedPromise
 
-      assert.equal(window2Text, 'Hello World!')
+      // Restore unsaved state when opening a path to a non-existent file in the directory
+      const window3 = atomApplication.launch(parseCommandLine([path.join(tempDirPath, 'another-non-existent-file')]))
+      await window3.loadedPromise
+      const window3Texts = await evalInWebContents(window3.browserWindow.webContents, function (sendBackToMainProcess, nonExistentFilePath) {
+        sendBackToMainProcess(atom.workspace.getTextEditors().map(editor => editor.getText()))
+      })
+      assert.include(window3Texts, 'Hello World! How are you?')
     })
 
     it('shows all directories in the tree view when multiple directory paths are passed to Atom', async function () {
@@ -260,7 +276,7 @@ describe('AtomApplication', function () {
       })
       assert.equal(window1EditorTitle, 'untitled')
 
-      const window2 = atomApplication.launch(parseCommandLine([]))
+      const window2 = atomApplication.openWithOptions(parseCommandLine([]))
       await focusWindow(window2)
       const window2EditorTitle = await evalInWebContents(window1.browserWindow.webContents, function (sendBackToMainProcess) {
         sendBackToMainProcess(atom.workspace.getActiveTextEditor().getTitle())
@@ -472,7 +488,7 @@ describe('AtomApplication', function () {
   }
 
   let channelIdCounter = 0
-  function evalInWebContents (webContents, source) {
+  function evalInWebContents (webContents, source, ...args) {
     const channelId = 'eval-result-' + channelIdCounter++
     return new Promise(function (resolve) {
       electron.ipcMain.on(channelId, receiveResult)
diff --git a/spec/main-process/file-recovery-service.test.js b/spec/main-process/file-recovery-service.test.js
index 862b7f428..4821dbc9b 100644
--- a/spec/main-process/file-recovery-service.test.js
+++ b/spec/main-process/file-recovery-service.test.js
@@ -112,7 +112,7 @@ describe("FileRecoveryService", () => {
       const mockWindow = {}
       const filePath = temp.path()
       fs.writeFileSync(filePath, "content")
-      fs.chmodSync(filePath, 0444)
+      fs.chmodSync(filePath, 0o444)
 
       let logs = []
       this.stub(console, 'log', (message) => logs.push(message))
diff --git a/spec/project-spec.coffee b/spec/project-spec.coffee
index d548255e5..997f6054e 100644
--- a/spec/project-spec.coffee
+++ b/spec/project-spec.coffee
@@ -614,3 +614,7 @@ describe "Project", ->
 
       randomPath = path.join("some", "random", "path")
       expect(atom.project.contains(randomPath)).toBe false
+
+  describe ".resolvePath(uri)", ->
+    it "normalizes disk drive letter in passed path on #win32", ->
+      expect(atom.project.resolvePath("d:\\file.txt")).toEqual "D:\\file.txt"
diff --git a/spec/text-editor-component-spec.js b/spec/text-editor-component-spec.js
index eef49f9f6..b26e64e34 100644
--- a/spec/text-editor-component-spec.js
+++ b/spec/text-editor-component-spec.js
@@ -1747,11 +1747,13 @@ describe('TextEditorComponent', function () {
   })
 
   describe('block decorations rendering', function () {
+    let markerLayer
+
     function createBlockDecorationBeforeScreenRow(screenRow, {className}) {
       let item = document.createElement("div")
       item.className = className || ""
       let blockDecoration = editor.decorateMarker(
-        editor.markScreenPosition([screenRow, 0], {invalidate: "never"}),
+        markerLayer.markScreenPosition([screenRow, 0], {invalidate: "never"}),
         {type: "block", item: item, position: "before"}
       )
       return [item, blockDecoration]
@@ -1761,13 +1763,14 @@ describe('TextEditorComponent', function () {
       let item = document.createElement("div")
       item.className = className || ""
       let blockDecoration = editor.decorateMarker(
-        editor.markScreenPosition([screenRow, 0], {invalidate: "never"}),
+        markerLayer.markScreenPosition([screenRow, 0], {invalidate: "never"}),
         {type: "block", item: item, position: "after"}
       )
       return [item, blockDecoration]
     }
 
     beforeEach(function () {
+      markerLayer = editor.addMarkerLayer()
       wrapperNode.style.height = 5 * lineHeightInPixels + 'px'
       editor.update({autoHeight: false})
       component.measureDimensions()
diff --git a/spec/workspace-spec.coffee b/spec/workspace-spec.coffee
index 08afa6239..153cc5dc3 100644
--- a/spec/workspace-spec.coffee
+++ b/spec/workspace-spec.coffee
@@ -886,8 +886,12 @@ describe "Workspace", ->
 
   describe "document.title", ->
     describe "when there is no item open", ->
-      it "sets the title to 'untitled'", ->
-        expect(document.title).toMatch ///^untitled///
+      it "sets the title to the project path", ->
+        expect(document.title).toMatch escapeStringRegex(fs.tildify(atom.project.getPaths()[0]))
+
+      it "sets the title to 'untitled' if there is no project path", ->
+        atom.project.setPaths([])
+        expect(document.title).toMatch /^untitled/
 
     describe "when the active pane item's path is not inside a project path", ->
       beforeEach ->
@@ -948,10 +952,10 @@ describe "Workspace", ->
           expect(document.title).toMatch ///^#{item.getTitle()}\ \u2014\ #{pathEscaped}///
 
       describe "when the last pane item is removed", ->
-        it "updates the title to be untitled", ->
+        it "updates the title to the project's first path", ->
           atom.workspace.getActivePane().destroy()
           expect(atom.workspace.getActivePaneItem()).toBeUndefined()
-          expect(document.title).toMatch ///^untitled///
+          expect(document.title).toMatch escapeStringRegex(fs.tildify(atom.project.getPaths()[0]))
 
       describe "when an inactive pane's item changes", ->
         it "does not update the title", ->
diff --git a/src/application-delegate.coffee b/src/application-delegate.coffee
index 185db5059..766ba7aa8 100644
--- a/src/application-delegate.coffee
+++ b/src/application-delegate.coffee
@@ -2,10 +2,12 @@ _ = require 'underscore-plus'
 {screen, ipcRenderer, remote, shell, webFrame} = require 'electron'
 ipcHelpers = require './ipc-helpers'
 {Disposable} = require 'event-kit'
-{getWindowLoadSettings, setWindowLoadSettings} = require './window-load-settings-helpers'
+getWindowLoadSettings = require './get-window-load-settings'
 
 module.exports =
 class ApplicationDelegate
+  getWindowLoadSettings: -> getWindowLoadSettings()
+
   open: (params) ->
     ipcRenderer.send('open', params)
 
@@ -109,10 +111,7 @@ class ApplicationDelegate
     ipcRenderer.send("add-recent-document", filename)
 
   setRepresentedDirectoryPaths: (paths) ->
-    loadSettings = getWindowLoadSettings()
-    loadSettings['initialPaths'] = paths
-    setWindowLoadSettings(loadSettings)
-    ipcRenderer.send("did-change-paths")
+    ipcHelpers.call('window-method', 'setRepresentedDirectoryPaths', paths)
 
   setAutoHideWindowMenuBar: (autoHide) ->
     ipcHelpers.call('window-method', 'setAutoHideMenuBar', autoHide)
@@ -149,13 +148,9 @@ class ApplicationDelegate
   showMessageDialog: (params) ->
 
   showSaveDialog: (params) ->
-    if _.isString(params)
-      params = defaultPath: params
-    else
-      params = _.clone(params)
-    params.title ?= 'Save File'
-    params.defaultPath ?= getWindowLoadSettings().initialPaths[0]
-    remote.dialog.showSaveDialog remote.getCurrentWindow(), params
+    if typeof params is 'string'
+      params = {defaultPath: params}
+    @getCurrentWindow().showSaveDialog(params)
 
   playBeepSound: ->
     shell.beep()
diff --git a/src/atom-environment.coffee b/src/atom-environment.coffee
index a740b22d5..3133b5af8 100644
--- a/src/atom-environment.coffee
+++ b/src/atom-environment.coffee
@@ -11,7 +11,6 @@ Model = require './model'
 WindowEventHandler = require './window-event-handler'
 StateStore = require './state-store'
 StorageFolder = require './storage-folder'
-{getWindowLoadSettings} = require './window-load-settings-helpers'
 registerDefaultCommands = require './register-default-commands'
 {updateProcessEnv} = require './update-process-env'
 
@@ -458,7 +457,7 @@ class AtomEnvironment extends Model
   #
   # Returns an {Object} containing all the load setting key/value pairs.
   getLoadSettings: ->
-    getWindowLoadSettings()
+    @applicationDelegate.getWindowLoadSettings()
 
   ###
   Section: Managing The Atom Window
@@ -695,8 +694,14 @@ class AtomEnvironment extends Model
         @deserialize(state) if state?
         @deserializeTimings.atom = Date.now() - startTime
 
-        if process.platform is 'darwin' and @config.get('core.useCustomTitleBar')
+        if process.platform is 'darwin' and @config.get('core.titleBar') is 'custom'
           @workspace.addHeaderPanel({item: new TitleBar({@workspace, @themes, @applicationDelegate})})
+          @document.body.classList.add('custom-title-bar')
+        if process.platform is 'darwin' and @config.get('core.titleBar') is 'custom-inset'
+          @workspace.addHeaderPanel({item: new TitleBar({@workspace, @themes, @applicationDelegate})})
+          @document.body.classList.add('custom-inset-title-bar')
+        if process.platform is 'darwin' and @config.get('core.titleBar') is 'hidden'
+          @document.body.classList.add('hidden-title-bar')
 
         @document.body.appendChild(@views.getView(@workspace))
         @backgroundStylesheet?.remove()
@@ -822,12 +827,17 @@ class AtomEnvironment extends Model
   Section: Private
   ###
 
-  assert: (condition, message, callback) ->
+  assert: (condition, message, callbackOrMetadata) ->
     return true if condition
 
     error = new Error("Assertion failed: #{message}")
     Error.captureStackTrace(error, @assert)
-    callback?(error)
+
+    if callbackOrMetadata?
+      if typeof callbackOrMetadata is 'function'
+        callbackOrMetadata?(error)
+      else
+        error.metadata = callbackOrMetadata
 
     @emitter.emit 'did-fail-assertion', error
 
diff --git a/src/babel.js b/src/babel.js
index a944f2e8c..d72b29ffd 100644
--- a/src/babel.js
+++ b/src/babel.js
@@ -6,6 +6,7 @@ var defaultOptions = require('../static/babelrc.json')
 
 var babel = null
 var babelVersionDirectory = null
+var options = null
 
 var PREFIXES = [
   '/** @babel */',
@@ -47,16 +48,27 @@ exports.compile = function (sourceCode, filePath) {
     var noop = function () {}
     Logger.prototype.debug = noop
     Logger.prototype.verbose = noop
+
+    options = {ast: false, babelrc: false}
+    for (var key in defaultOptions) {
+      if (key === 'plugins') {
+        const plugins = []
+        for (const [pluginName, pluginOptions] of defaultOptions[key]) {
+          plugins.push([require.resolve(`babel-plugin-${pluginName}`), pluginOptions])
+        }
+        options[key] = plugins
+      } else {
+        options[key] = defaultOptions[key]
+      }
+    }
   }
 
   if (process.platform === 'win32') {
     filePath = 'file:///' + path.resolve(filePath).replace(/\\/g, '/')
   }
 
-  var options = {filename: filePath}
-  for (var key in defaultOptions) {
-    options[key] = defaultOptions[key]
-  }
+  options.filename = filePath
+
   return babel.transform(sourceCode, options).code
 }
 
diff --git a/src/config-schema.js b/src/config-schema.js
index 4dd99d2b4..41b5ecbb6 100644
--- a/src/config-schema.js
+++ b/src/config-schema.js
@@ -68,6 +68,12 @@ const configSchema = {
         default: true,
         description: 'Trigger the system\'s beep sound when certain actions cannot be executed or there are no results.'
       },
+      closeDeletedFileTabs: {
+        type: 'boolean',
+        default: false,
+        title: 'Close Deleted File Tabs',
+        description: 'Close corresponding editors when a file is deleted outside Atom.'
+      },
       destroyEmptyPanes: {
         type: 'boolean',
         default: true,
@@ -492,10 +498,11 @@ if (['win32', 'linux'].includes(process.platform)) {
 }
 
 if (process.platform === 'darwin') {
-  configSchema.core.properties.useCustomTitleBar = {
-    type: 'boolean',
-    default: false,
-    description: 'Use custom, theme-aware title bar.<br>Note: This currently does not include a proxy icon.<br>This setting will require a relaunch of Atom to take effect.'
+  configSchema.core.properties.titleBar = {
+    type: 'string',
+    default: 'native',
+    enum: ['native', 'custom', 'custom-inset', 'hidden'],
+    description: 'Experimental: A `custom` title bar adapts to theme colors. Choosing `custom-inset` adds a bit more padding. The title bar can also be completely `hidden`.<br>Note: Switching to a custom or hidden title bar will compromise some functionality.<br>This setting will require a relaunch of Atom to take effect.'
   }
 }
 
diff --git a/src/config.coffee b/src/config.coffee
index 2dc537dd4..e873a1348 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -336,6 +336,31 @@ ScopeDescriptor = require './scope-descriptor'
 #     order: 2
 # ```
 #
+# ## Manipulating values outside your configuration schema
+#
+# It is possible to manipulate(`get`, `set`, `observe` etc) values that do not
+# appear in your configuration schema. For example, if the config schema of the
+# package 'some-package' is
+#
+# ```coffee
+# config:
+# someSetting:
+#   type: 'boolean'
+#   default: false
+# ```
+#
+# You can still do the following
+#
+# ```coffee
+# let otherSetting  = atom.config.get('some-package.otherSetting')
+# atom.config.set('some-package.stillAnotherSetting', otherSetting * 5)
+# ```
+#
+# In other words, if a function asks for a `key-path`, that path doesn't have to
+# be described in the config schema for the package or any package. However, as
+# highlighted in the best practices section, you are advised against doing the
+# above.
+#
 # ## Best practices
 #
 # * Don't depend on (or write to) configuration keys outside of your keypath.
diff --git a/src/decoration-manager.coffee b/src/decoration-manager.coffee
index e1096f572..05935f018 100644
--- a/src/decoration-manager.coffee
+++ b/src/decoration-manager.coffee
@@ -8,7 +8,7 @@ class DecorationManager extends Model
   didUpdateDecorationsEventScheduled: false
   updatedSynchronously: false
 
-  constructor: (@displayLayer, @defaultMarkerLayer) ->
+  constructor: (@displayLayer) ->
     super
 
     @emitter = new Emitter
@@ -71,9 +71,11 @@ class DecorationManager extends Model
 
   decorationsForScreenRowRange: (startScreenRow, endScreenRow) ->
     decorationsByMarkerId = {}
-    for marker in @defaultMarkerLayer.findMarkers(intersectsScreenRowRange: [startScreenRow, endScreenRow])
-      if decorations = @decorationsByMarkerId[marker.id]
-        decorationsByMarkerId[marker.id] = decorations
+    for layerId of @decorationCountsByLayerId
+      layer = @displayLayer.getMarkerLayer(layerId)
+      for marker in layer.findMarkers(intersectsScreenRowRange: [startScreenRow, endScreenRow])
+        if decorations = @decorationsByMarkerId[marker.id]
+          decorationsByMarkerId[marker.id] = decorations
     decorationsByMarkerId
 
   decorationsStateForScreenRowRange: (startScreenRow, endScreenRow) ->
@@ -104,7 +106,14 @@ class DecorationManager extends Model
     decorationsState
 
   decorateMarker: (marker, decorationParams) ->
-    throw new Error("Cannot decorate a destroyed marker") if marker.isDestroyed()
+    if marker.isDestroyed()
+      error = new Error("Cannot decorate a destroyed marker")
+      error.metadata = {markerLayerIsDestroyed: marker.layer.isDestroyed()}
+      if marker.destroyStackTrace?
+        error.metadata.destroyStackTrace = marker.destroyStackTrace
+      if marker.bufferMarker?.destroyStackTrace?
+        error.metadata.destroyStackTrace = marker.bufferMarker?.destroyStackTrace
+      throw error
     marker = @displayLayer.getMarkerLayer(marker.layer.id).getMarker(marker.id)
     decoration = new Decoration(marker, this, decorationParams)
     @decorationsByMarkerId[marker.id] ?= []
@@ -117,6 +126,7 @@ class DecorationManager extends Model
     decoration
 
   decorateMarkerLayer: (markerLayer, decorationParams) ->
+    throw new Error("Cannot decorate a destroyed marker layer") if markerLayer.isDestroyed()
     decoration = new LayerDecoration(markerLayer, this, decorationParams)
     @layerDecorationsByMarkerLayerId[markerLayer.id] ?= []
     @layerDecorationsByMarkerLayerId[markerLayer.id].push(decoration)
diff --git a/src/default-directory-provider.coffee b/src/default-directory-provider.coffee
index ed4e9ba36..44d5298dd 100644
--- a/src/default-directory-provider.coffee
+++ b/src/default-directory-provider.coffee
@@ -15,7 +15,7 @@ class DefaultDirectoryProvider
   # * {Directory} if the given URI is compatible with this provider.
   # * `null` if the given URI is not compatibile with this provider.
   directoryForURISync: (uri) ->
-    normalizedPath = path.normalize(uri)
+    normalizedPath = @normalizePath(uri)
     {host} = url.parse(uri)
     directoryPath = if host
       uri
@@ -42,3 +42,17 @@ class DefaultDirectoryProvider
   # * `null` if the given URI is not compatibile with this provider.
   directoryForURI: (uri) ->
     Promise.resolve(@directoryForURISync(uri))
+
+  # Public: Normalizes path.
+  #
+  # * `uri` {String} The path that should be normalized.
+  #
+  # Returns a {String} with normalized path.
+  normalizePath: (uri) ->
+    # Normalize disk drive letter on Windows to avoid opening two buffers for the same file
+    pathWithNormalizedDiskDriveLetter =
+      if process.platform is 'win32' and matchData = uri.match(/^([a-z]):/)
+        "#{matchData[1].toUpperCase()}#{uri.slice(1)}"
+      else
+        uri
+    path.normalize(pathWithNormalizedDiskDriveLetter)
diff --git a/src/dom-element-pool.coffee b/src/dom-element-pool.coffee
deleted file mode 100644
index f81a537f3..000000000
--- a/src/dom-element-pool.coffee
+++ /dev/null
@@ -1,55 +0,0 @@
-module.exports =
-class DOMElementPool
-  constructor: ->
-    @freeElementsByTagName = {}
-    @freedElements = new Set
-
-  clear: ->
-    @freedElements.clear()
-    for tagName, freeElements of @freeElementsByTagName
-      freeElements.length = 0
-    return
-
-  build: (tagName, factory, reset) ->
-    element = @freeElementsByTagName[tagName]?.pop()
-    element ?= factory()
-    reset(element)
-    @freedElements.delete(element)
-    element
-
-  buildElement: (tagName, className) ->
-    factory = -> document.createElement(tagName)
-    reset = (element) ->
-      delete element.dataset[dataId] for dataId of element.dataset
-      element.removeAttribute("style")
-      if className?
-        element.className = className
-      else
-        element.removeAttribute("class")
-    @build(tagName, factory, reset)
-
-  buildText: (textContent) ->
-    factory = -> document.createTextNode(textContent)
-    reset = (element) -> element.textContent = textContent
-    @build("#text", factory, reset)
-
-  freeElementAndDescendants: (element) ->
-    @free(element)
-    @freeDescendants(element)
-
-  freeDescendants: (element) ->
-    for descendant in element.childNodes by -1
-      @free(descendant)
-      @freeDescendants(descendant)
-    return
-
-  free: (element) ->
-    throw new Error("The element cannot be null or undefined.") unless element?
-    throw new Error("The element has already been freed!") if @freedElements.has(element)
-
-    tagName = element.nodeName.toLowerCase()
-    @freeElementsByTagName[tagName] ?= []
-    @freeElementsByTagName[tagName].push(element)
-    @freedElements.add(element)
-
-    element.remove()
diff --git a/src/dom-element-pool.js b/src/dom-element-pool.js
new file mode 100644
index 000000000..0fef02dee
--- /dev/null
+++ b/src/dom-element-pool.js
@@ -0,0 +1,89 @@
+module.exports =
+class DOMElementPool {
+  constructor () {
+    this.managedElements = new Set()
+    this.freeElementsByTagName = new Map()
+    this.freedElements = new Set()
+  }
+
+  clear () {
+    this.managedElements.clear()
+    this.freedElements.clear()
+    this.freeElementsByTagName.clear()
+  }
+
+  buildElement (tagName, className) {
+    const elements = this.freeElementsByTagName.get(tagName)
+    let element = elements ? elements.pop() : null
+    if (element) {
+      for (let dataId in element.dataset) { delete element.dataset[dataId] }
+      element.removeAttribute('style')
+      if (className) {
+        element.className = className
+      } else {
+        element.removeAttribute('class')
+      }
+      while (element.firstChild) {
+        element.removeChild(element.firstChild)
+      }
+      this.freedElements.delete(element)
+    } else {
+      element = document.createElement(tagName)
+      if (className) {
+        element.className = className
+      }
+      this.managedElements.add(element)
+    }
+    return element
+  }
+
+  buildText (textContent) {
+    const elements = this.freeElementsByTagName.get('#text')
+    let element = elements ? elements.pop() : null
+    if (element) {
+      element.textContent = textContent
+      this.freedElements.delete(element)
+    } else {
+      element = document.createTextNode(textContent)
+      this.managedElements.add(element)
+    }
+    return element
+  }
+
+  freeElementAndDescendants (element) {
+    this.free(element)
+    element.remove()
+  }
+
+  freeDescendants (element) {
+    while (element.firstChild) {
+      this.free(element.firstChild)
+      element.removeChild(element.firstChild)
+    }
+  }
+
+  free (element) {
+    if (element == null) { throw new Error('The element cannot be null or undefined.') }
+    if (!this.managedElements.has(element)) return
+    if (this.freedElements.has(element)) {
+      atom.assert(false, 'The element has already been freed!', {
+        content: element instanceof window.Text ? element.textContent : element.outerHTML
+      })
+      return
+    }
+
+    const tagName = element.nodeName.toLowerCase()
+    let elements = this.freeElementsByTagName.get(tagName)
+    if (!elements) {
+      elements = []
+      this.freeElementsByTagName.set(tagName, elements)
+    }
+    elements.push(element)
+    this.freedElements.add(element)
+
+    for (let i = element.childNodes.length - 1; i >= 0; i--) {
+      const descendant = element.childNodes[i]
+      this.free(descendant)
+    }
+  }
+}
diff --git a/src/get-window-load-settings.js b/src/get-window-load-settings.js
new file mode 100644
index 000000000..7ee465141
--- /dev/null
+++ b/src/get-window-load-settings.js
@@ -0,0 +1,10 @@
+const {remote} = require('electron')
+
+let windowLoadSettings = null
+
+module.exports = () => {
+  if (!windowLoadSettings) {
+    windowLoadSettings = remote.getCurrentWindow().loadSettings
+  }
+  return windowLoadSettings
+}
diff --git a/src/initialize-application-window.coffee b/src/initialize-application-window.coffee
index 7d3a23db7..be13ce6c6 100644
--- a/src/initialize-application-window.coffee
+++ b/src/initialize-application-window.coffee
@@ -3,7 +3,7 @@ module.exports = ({blobStore}) ->
   {updateProcessEnv} = require('./update-process-env')
   path = require 'path'
   require './window'
-  {getWindowLoadSettings} = require './window-load-settings-helpers'
+  getWindowLoadSettings = require './get-window-load-settings'
   {ipcRenderer} = require 'electron'
   {resourcePath, devMode, env} = getWindowLoadSettings()
   require './electron-shims'
diff --git a/src/initialize-benchmark-window.js b/src/initialize-benchmark-window.js
index 29a210904..a223e0b03 100644
--- a/src/initialize-benchmark-window.js
+++ b/src/initialize-benchmark-window.js
@@ -6,7 +6,7 @@ import ipcHelpers from './ipc-helpers'
 import util from 'util'
 
 export default async function () {
-  const {getWindowLoadSettings} = require('./window-load-settings-helpers')
+  const getWindowLoadSettings = require('./get-window-load-settings')
   const {test, headless, resourcePath, benchmarkPaths} = getWindowLoadSettings()
   try {
     const Clipboard = require('../src/clipboard')
diff --git a/src/initialize-test-window.coffee b/src/initialize-test-window.coffee
index 39a408fea..794db3174 100644
--- a/src/initialize-test-window.coffee
+++ b/src/initialize-test-window.coffee
@@ -18,7 +18,7 @@ module.exports = ({blobStore}) ->
   try
     path = require 'path'
     {ipcRenderer} = require 'electron'
-    {getWindowLoadSettings} = require './window-load-settings-helpers'
+    getWindowLoadSettings = require './get-window-load-settings'
     CompileCache = require './compile-cache'
     AtomEnvironment = require '../src/atom-environment'
     ApplicationDelegate = require '../src/application-delegate'
diff --git a/src/main-process/atom-application.coffee b/src/main-process/atom-application.coffee
index 42358409b..93e9e3395 100644
--- a/src/main-process/atom-application.coffee
+++ b/src/main-process/atom-application.coffee
@@ -84,7 +84,13 @@ class AtomApplication
   initialize: (options) ->
     global.atomApplication = this
 
-    @config.onDidChange 'core.useCustomTitleBar', @promptForRestart.bind(this)
+    # DEPRECATED: This can be removed at some point (added in 1.13)
+    # It converts `useCustomTitleBar: true` to `titleBar: "custom"`
+    if process.platform is 'darwin' and @config.get('core.useCustomTitleBar')
+      @config.unset('core.useCustomTitleBar')
+      @config.set('core.titleBar', 'custom')
+    
+    @config.onDidChange 'core.titleBar', @promptForRestart.bind(this)
 
     @autoUpdateManager = new AutoUpdateManager(
       @version, options.test or options.benchmark or options.benchmarkTest, @resourcePath, @config
@@ -587,8 +593,7 @@ class AtomApplication
     states = []
     for window in @windows
       unless window.isSpec
-        if loadSettings = window.getLoadSettings()
-          states.push(initialPaths: loadSettings.initialPaths)
+        states.push({initialPaths: window.representedDirectoryPaths})
     if states.length > 0 or allowEmpty
       @storageFolder.storeSync('application.json', states)
 
diff --git a/src/main-process/atom-window.coffee b/src/main-process/atom-window.coffee
index 9c937e4f6..03386d31a 100644
--- a/src/main-process/atom-window.coffee
+++ b/src/main-process/atom-window.coffee
@@ -43,12 +43,16 @@ class AtomWindow
     if process.platform is 'linux'
       options.icon = @constructor.iconPath
 
-    if @shouldHideTitleBar()
+    if @shouldAddCustomTitleBar()
       options.titleBarStyle = 'hidden'
 
-    @browserWindow = new BrowserWindow options
-    @atomApplication.addWindow(this)
+    if @shouldAddCustomInsetTitleBar()
+      options.titleBarStyle = 'hidden-inset'
 
+    if @shouldHideTitleBar()
+      options.frame = false
+
+    @browserWindow = new BrowserWindow(options)
     @handleEvents()
 
     loadSettings = Object.assign({}, settings)
@@ -60,11 +64,15 @@ class AtomWindow
     loadSettings.clearWindowState ?= false
     loadSettings.initialPaths ?=
       for {pathToOpen} in locationsToOpen when pathToOpen
-        if fs.statSyncNoException(pathToOpen).isFile?()
-          path.dirname(pathToOpen)
-        else
+        stat = fs.statSyncNoException(pathToOpen) or null
+        if stat?.isDirectory()
           pathToOpen
-
+        else
+          parentDirectory = path.dirname(pathToOpen)
+          if stat?.isFile() or fs.existsSync(parentDirectory)
+            parentDirectory
+          else
+            pathToOpen
     loadSettings.initialPaths.sort()
 
     # Only send to the first non-spec window created
@@ -72,33 +80,31 @@ class AtomWindow
       @constructor.includeShellLoadTime = false
       loadSettings.shellLoadTime ?= Date.now() - global.shellStartTime
 
+    @representedDirectoryPaths = loadSettings.initialPaths
+    @env = loadSettings.env if loadSettings.env?
+
     @browserWindow.loadSettings = loadSettings
 
     @browserWindow.on 'window:loaded', =>
       @emit 'window:loaded'
       @resolveLoadedPromise()
 
-    @setLoadSettings(loadSettings)
-    @env = loadSettings.env if loadSettings.env?
+    @browserWindow.loadURL url.format
+      protocol: 'file'
+      pathname: "#{@resourcePath}/static/index.html"
+      slashes: true
+
+    @browserWindow.showSaveDialog = @showSaveDialog.bind(this)
+
     @browserWindow.focusOnWebView() if @isSpec
     @browserWindow.temporaryState = {windowDimensions} if windowDimensions?
 
     hasPathToOpen = not (locationsToOpen.length is 1 and not locationsToOpen[0].pathToOpen?)
     @openLocations(locationsToOpen) if hasPathToOpen and not @isSpecWindow()
 
-  setLoadSettings: (loadSettings) ->
-    @browserWindow.loadURL url.format
-      protocol: 'file'
-      pathname: "#{@resourcePath}/static/index.html"
-      slashes: true
-      hash: encodeURIComponent(JSON.stringify(loadSettings))
+    @atomApplication.addWindow(this)
 
-  getLoadSettings: ->
-    if @browserWindow.webContents? and not @browserWindow.webContents.isLoading()
-      hash = url.parse(@browserWindow.webContents.getURL()).hash.substr(1)
-      JSON.parse(decodeURIComponent(hash))
-
-  hasProjectPath: -> @getLoadSettings().initialPaths?.length > 0
+  hasProjectPath: -> @representedDirectoryPaths.length > 0
 
   setupContextMenu: ->
     ContextMenu = require './context-menu'
@@ -112,7 +118,7 @@ class AtomWindow
     true
 
   containsPath: (pathToCheck) ->
-    @getLoadSettings()?.initialPaths?.some (projectPath) ->
+    @representedDirectoryPaths.some (projectPath) ->
       if not projectPath
         false
       else if not pathToCheck
@@ -226,10 +232,20 @@ class AtomWindow
     [width, height] = @browserWindow.getSize()
     {x, y, width, height}
 
+  shouldAddCustomTitleBar: ->
+    not @isSpec and
+    process.platform is 'darwin' and
+    @atomApplication.config.get('core.titleBar') is 'custom'
+
+  shouldAddCustomInsetTitleBar: ->
+    not @isSpec and
+    process.platform is 'darwin' and
+    @atomApplication.config.get('core.titleBar') is 'custom-inset'
+
   shouldHideTitleBar: ->
     not @isSpec and
     process.platform is 'darwin' and
-    @atomApplication.config.get('core.useCustomTitleBar')
+    @atomApplication.config.get('core.titleBar') is 'hidden'
 
   close: -> @browserWindow.close()
 
@@ -265,6 +281,13 @@ class AtomWindow
     @saveState().then => @browserWindow.reload()
     @loadedPromise
 
+  showSaveDialog: (params) ->
+    params = Object.assign({
+      title: 'Save File',
+      defaultPath: @representedDirectoryPaths[0]
+    }, params)
+    dialog.showSaveDialog(this, params)
+
   toggleDevTools: -> @browserWindow.toggleDevTools()
 
   openDevTools: -> @browserWindow.openDevTools()
@@ -275,4 +298,8 @@ class AtomWindow
 
   setRepresentedFilename: (representedFilename) -> @browserWindow.setRepresentedFilename(representedFilename)
 
+  setRepresentedDirectoryPaths: (@representedDirectoryPaths) ->
+    @representedDirectoryPaths.sort()
+    @atomApplication.saveState()
+
   copy: -> @browserWindow.copy()
diff --git a/src/main-process/auto-update-manager.coffee b/src/main-process/auto-update-manager.coffee
index 8fdba844d..ff29dd3d6 100644
--- a/src/main-process/auto-update-manager.coffee
+++ b/src/main-process/auto-update-manager.coffee
@@ -22,7 +22,7 @@ class AutoUpdateManager
   setupAutoUpdater: ->
     if process.platform is 'win32'
       archSuffix = if process.arch is 'ia32' then '' else '-' + process.arch
-      @feedUrl = "https://atom.io/api/updates#{archSuffix}"
+      @feedUrl = "https://atom.io/api/updates#{archSuffix}?version=#{@version}"
       autoUpdater = require './auto-updater-win32'
     else
       @feedUrl = "https://atom.io/api/updates?version=#{@version}"
diff --git a/src/main-process/parse-command-line.js b/src/main-process/parse-command-line.js
index 4227b63ba..3f9f2523a 100644
--- a/src/main-process/parse-command-line.js
+++ b/src/main-process/parse-command-line.js
@@ -106,14 +106,14 @@ module.exports = function parseCommandLine (processArgs) {
 
   if (args['resource-path']) {
     devMode = true
-    resourcePath = args['resource-path']
+    devResourcePath = args['resource-path']
   }
 
   if (test) {
     devMode = true
   }
 
-  if (devMode && !resourcePath) {
+  if (devMode) {
     resourcePath = devResourcePath
   }
 
diff --git a/src/project.coffee b/src/project.coffee
index 522fbfbc7..a02f27dac 100644
--- a/src/project.coffee
+++ b/src/project.coffee
@@ -21,7 +21,6 @@ class Project extends Model
   constructor: ({@notificationManager, packageManager, config, @applicationDelegate}) ->
     @emitter = new Emitter
     @buffers = []
-    @paths = []
     @rootDirectories = []
     @repositories = []
     @directoryProviders = []
@@ -32,7 +31,9 @@ class Project extends Model
 
   destroyed: ->
     buffer.destroy() for buffer in @buffers
-    @setPaths([])
+    repository?.destroy() for repository in @repositories
+    @rootDirectories = []
+    @repositories = []
 
   reset: (packageManager) ->
     @emitter.dispose()
@@ -62,6 +63,9 @@ class Project extends Model
           fs.closeSync(fs.openSync(bufferState.filePath, 'r'))
         catch error
           return unless error.code is 'ENOENT'
+      unless bufferState.shouldDestroyOnFileDelete?
+        bufferState.shouldDestroyOnFileDelete =
+          -> atom.config.get('core.closeDeletedFileTabs')
       TextBuffer.deserialize(bufferState)
 
     @subscribeToBuffer(buffer) for buffer in @buffers
@@ -205,7 +209,7 @@ class Project extends Model
   removePath: (projectPath) ->
     # The projectPath may be a URI, in which case it should not be normalized.
     unless projectPath in @getPaths()
-      projectPath = path.normalize(projectPath)
+      projectPath = @defaultDirectoryProvider.normalizePath(projectPath)
 
     indexToRemove = null
     for directory, i in @rootDirectories
@@ -233,11 +237,10 @@ class Project extends Model
       uri
     else
       if fs.isAbsolute(uri)
-        path.normalize(fs.resolveHome(uri))
-
+        @defaultDirectoryProvider.normalizePath(fs.resolveHome(uri))
       # TODO: what should we do here when there are multiple directories?
       else if projectPath = @getPaths()[0]
-        path.normalize(fs.resolveHome(path.join(projectPath, uri)))
+        @defaultDirectoryProvider.normalizePath(fs.resolveHome(path.join(projectPath, uri)))
       else
         undefined
 
@@ -360,9 +363,14 @@ class Project extends Model
     else
       @buildBuffer(absoluteFilePath)
 
+  shouldDestroyBufferOnFileDelete: ->
+    atom.config.get('core.closeDeletedFileTabs')
+
   # Still needed when deserializing a tokenized buffer
   buildBufferSync: (absoluteFilePath) ->
-    buffer = new TextBuffer({filePath: absoluteFilePath})
+    buffer = new TextBuffer({
+      filePath: absoluteFilePath
+      shouldDestroyOnFileDelete: @shouldDestroyBufferOnFileDelete})
     @addBuffer(buffer)
     buffer.loadSync()
     buffer
@@ -374,7 +382,9 @@ class Project extends Model
   #
   # Returns a {Promise} that resolves to the {TextBuffer}.
   buildBuffer: (absoluteFilePath) ->
-    buffer = new TextBuffer({filePath: absoluteFilePath})
+    buffer = new TextBuffer({
+      filePath: absoluteFilePath
+      shouldDestroyOnFileDelete: @shouldDestroyBufferOnFileDelete})
     @addBuffer(buffer)
     buffer.load()
       .then((buffer) -> buffer)
diff --git a/src/text-editor-element.coffee b/src/text-editor-element.coffee
index 8c9792916..26e3bae12 100644
--- a/src/text-editor-element.coffee
+++ b/src/text-editor-element.coffee
@@ -108,7 +108,10 @@ class TextEditorElement extends HTMLElement
 
   buildModel: ->
     @setModel(@workspace.buildTextEditor(
-      buffer: new TextBuffer(@textContent)
+      buffer: new TextBuffer({
+        text: @textContent
+        shouldDestroyOnFileDelete:
+          -> atom.config.get('core.closeDeletedFileTabs')})
       softWrapped: false
       tabLength: 2
       softTabs: true
diff --git a/src/text-editor-presenter.coffee b/src/text-editor-presenter.coffee
index 3c4739ca5..1106cee09 100644
--- a/src/text-editor-presenter.coffee
+++ b/src/text-editor-presenter.coffee
@@ -622,6 +622,18 @@ class TextEditorPresenter
     return unless @scrollTop? and @lineHeight?
 
     @startRow = Math.max(0, @lineTopIndex.rowForPixelPosition(@scrollTop))
+    atom.assert(
+      Number.isFinite(@startRow),
+      'Invalid start row',
+      (error) =>
+        error.metadata = {
+          startRow: @startRow?.toString(),
+          scrollTop: @scrollTop?.toString(),
+          scrollHeight: @scrollHeight?.toString(),
+          clientHeight: @clientHeight?.toString(),
+          lineHeight: @lineHeight?.toString()
+        }
+    )
 
   updateEndRow: ->
     return unless @scrollTop? and @lineHeight? and @height?
diff --git a/src/text-editor.coffee b/src/text-editor.coffee
index 2ebd106e6..13b8a0bfa 100644
--- a/src/text-editor.coffee
+++ b/src/text-editor.coffee
@@ -16,12 +16,11 @@ TextEditorElement = require './text-editor-element'
 {isDoubleWidthCharacter, isHalfWidthCharacter, isKoreanCharacter, isWrapBoundary} = require './text-utils'
 
 ZERO_WIDTH_NBSP = '\ufeff'
+MAX_SCREEN_LINE_LENGTH = 500
 
 # Essential: This class represents all essential editing state for a single
 # {TextBuffer}, including cursor and selection positions, folds, and soft wraps.
-# If you're manipulating the state of an editor, use this class. If you're
-# interested in the visual appearance of editors, use {TextEditorElement}
-# instead.
+# If you're manipulating the state of an editor, use this class.
 #
 # A single {TextBuffer} can belong to multiple editors. For example, if the
 # same file is open in two different panes, Atom creates a separate editor for
@@ -162,7 +161,8 @@ class TextEditor extends Model
     @softWrapAtPreferredLineLength ?= false
     @preferredLineLength ?= 80
 
-    @buffer ?= new TextBuffer
+    @buffer ?= new TextBuffer({shouldDestroyOnFileDelete: ->
+      atom.config.get('core.closeDeletedFileTabs')})
     @tokenizedBuffer ?= new TokenizedBuffer({
       grammar, tabLength, @buffer, @largeFileMode, @assert
     })
@@ -193,8 +193,9 @@ class TextEditor extends Model
     @displayLayer.setTextDecorationLayer(@tokenizedBuffer)
     @defaultMarkerLayer = @displayLayer.addMarkerLayer()
     @selectionsMarkerLayer ?= @addMarkerLayer(maintainHistory: true, persistent: true)
+    @selectionsMarkerLayer.trackDestructionInOnDidCreateMarkerCallbacks = true
 
-    @decorationManager = new DecorationManager(@displayLayer, @defaultMarkerLayer)
+    @decorationManager = new DecorationManager(@displayLayer)
     @decorateMarkerLayer(@displayLayer.foldsMarkerLayer, {type: 'line-number', class: 'folded'})
 
     for marker in @selectionsMarkerLayer.getMarkers()
@@ -2965,7 +2966,7 @@ class TextEditor extends Model
       else
         @getEditorWidthInChars()
     else
-      Infinity
+      MAX_SCREEN_LINE_LENGTH
 
   ###
   Section: Indentation
diff --git a/src/tokenized-buffer.coffee b/src/tokenized-buffer.coffee
index 234f82be9..77221f52e 100644
--- a/src/tokenized-buffer.coffee
+++ b/src/tokenized-buffer.coffee
@@ -8,6 +8,8 @@ ScopeDescriptor = require './scope-descriptor'
 TokenizedBufferIterator = require './tokenized-buffer-iterator'
 NullGrammar = require './null-grammar'
 
+MAX_LINE_LENGTH_TO_TOKENIZE = 500
+
 module.exports =
 class TokenizedBuffer extends Model
   grammar: null
@@ -251,6 +253,8 @@ class TokenizedBuffer extends Model
 
   buildTokenizedLineForRowWithText: (row, text, ruleStack = @stackForRow(row - 1), openScopes = @openScopesForRow(row)) ->
     lineEnding = @buffer.lineEndingForRow(row)
+    if text.length > MAX_LINE_LENGTH_TO_TOKENIZE
+      text = text.slice(0, MAX_LINE_LENGTH_TO_TOKENIZE)
     {tags, ruleStack} = @grammar.tokenizeLine(text, ruleStack, row is 0, false)
     new TokenizedLine({openScopes, text, tags, ruleStack, lineEnding, @tokenIterator})
 
diff --git a/src/window-load-settings-helpers.coffee b/src/window-load-settings-helpers.coffee
deleted file mode 100644
index 639dc751d..000000000
--- a/src/window-load-settings-helpers.coffee
+++ /dev/null
@@ -1,8 +0,0 @@
-windowLoadSettings = null
-
-exports.getWindowLoadSettings = ->
-  windowLoadSettings ?= JSON.parse(window.decodeURIComponent(window.location.hash.substr(1)))
-
-exports.setWindowLoadSettings = (settings) ->
-  windowLoadSettings = settings
-  location.hash = encodeURIComponent(JSON.stringify(settings))
diff --git a/src/workspace.coffee b/src/workspace.coffee
index 9871db224..2a46ce57a 100644
--- a/src/workspace.coffee
+++ b/src/workspace.coffee
@@ -182,7 +182,7 @@ class Workspace extends Model
       projectPath = _.find projectPaths, (projectPath) ->
         itemPath is projectPath or itemPath?.startsWith(projectPath + path.sep)
     itemTitle ?= "untitled"
-    projectPath ?= if itemPath then path.dirname(itemPath) else null
+    projectPath ?= if itemPath then path.dirname(itemPath) else projectPaths[0]
     if projectPath?
       projectPath = fs.tildify(projectPath)
 
diff --git a/static/babelrc.json b/static/babelrc.json
index 26b70dc41..11474dd8d 100644
--- a/static/babelrc.json
+++ b/static/babelrc.json
@@ -1,7 +1,16 @@
 {
-  "breakConfig": true,
   "sourceMap": "inline",
-  "blacklist": ["es6.forOf", "useStrict"],
-  "optional": ["asyncToGenerator"],
-  "stage": 0
+  "plugins": [
+    ["add-module-exports", {}],
+    ["transform-async-to-generator", {}],
+    ["transform-decorators-legacy", {}],
+    ["transform-class-properties", {}],
+    ["transform-es2015-modules-commonjs", {"strictMode": false}],
+    ["transform-export-extensions", {}],
+    ["transform-do-expressions", {}],
+    ["transform-function-bind", {}],
+    ["transform-object-rest-spread", {}],
+    ["transform-flow-strip-types", {}],
+    ["transform-react-jsx", {}]
+  ]
 }
diff --git a/static/index.js b/static/index.js
index 2966eafdf..aa57a594a 100644
--- a/static/index.js
+++ b/static/index.js
@@ -2,9 +2,8 @@
   var path = require('path')
   var FileSystemBlobStore = require('../src/file-system-blob-store')
   var NativeCompileCache = require('../src/native-compile-cache')
+  var getWindowLoadSettings = require('../src/get-window-load-settings')
 
-  var loadSettings = null
-  var loadSettingsError = null
   var blobStore = null
 
   window.onload = function () {
@@ -25,20 +24,16 @@
       // Normalize to make sure drive letter case is consistent on Windows
       process.resourcesPath = path.normalize(process.resourcesPath)
 
-      if (loadSettingsError) {
-        throw loadSettingsError
-      }
-
-      var devMode = loadSettings.devMode || !loadSettings.resourcePath.startsWith(process.resourcesPath + path.sep)
+      var devMode = getWindowLoadSettings().devMode || !getWindowLoadSettings().resourcePath.startsWith(process.resourcesPath + path.sep)
 
       if (devMode) {
         setupDeprecatedPackages()
       }
 
-      if (loadSettings.profileStartup) {
-        profileStartup(loadSettings, Date.now() - startTime)
+      if (getWindowLoadSettings().profileStartup) {
+        profileStartup(Date.now() - startTime)
       } else {
-        setupWindow(loadSettings)
+        setupWindow()
         setLoadTime(Date.now() - startTime)
       }
     } catch (error) {
@@ -61,23 +56,23 @@
     console.error(error.stack || error)
   }
 
-  function setupWindow (loadSettings) {
+  function setupWindow () {
     var CompileCache = require('../src/compile-cache')
     CompileCache.setAtomHomeDirectory(process.env.ATOM_HOME)
 
     var ModuleCache = require('../src/module-cache')
-    ModuleCache.register(loadSettings)
-    ModuleCache.add(loadSettings.resourcePath)
+    ModuleCache.register(getWindowLoadSettings())
+    ModuleCache.add(getWindowLoadSettings().resourcePath)
 
     // By explicitly passing the app version here, we could save the call
     // of "require('remote').require('app').getVersion()".
     var startCrashReporter = require('../src/crash-reporter-start')
-    startCrashReporter({_version: loadSettings.appVersion})
+    startCrashReporter({_version: getWindowLoadSettings().appVersion})
 
     setupVmCompatibility()
     setupCsonCache(CompileCache.getCacheDirectory())
 
-    var initialize = require(loadSettings.windowInitializationScript)
+    var initialize = require(getWindowLoadSettings().windowInitializationScript)
     return initialize({blobStore: blobStore}).then(function () {
       require('electron').ipcRenderer.send('window-command', 'window:loaded')
     })
@@ -105,11 +100,11 @@
     }
   }
 
-  function profileStartup (loadSettings, initialTime) {
+  function profileStartup (initialTime) {
     function profile () {
       console.profile('startup')
       var startTime = Date.now()
-      setupWindow(loadSettings).then(function () {
+      setupWindow().then(function () {
         setLoadTime(Date.now() - startTime + initialTime)
         console.profileEnd('startup')
         console.log('Switch to the Profiles tab to view the created startup profile')
@@ -125,16 +120,6 @@
     }
   }
 
-  function parseLoadSettings () {
-    var rawLoadSettings = decodeURIComponent(window.location.hash.substr(1))
-    try {
-      loadSettings = JSON.parse(rawLoadSettings)
-    } catch (error) {
-      console.error('Failed to parse load settings: ' + rawLoadSettings)
-      loadSettingsError = error
-    }
-  }
-
   var setupAtomHome = function () {
     if (process.env.ATOM_HOME) {
       return
@@ -143,11 +128,10 @@
     // Ensure ATOM_HOME is always set before anything else is required
     // This is because of a difference in Linux not inherited between browser and render processes
     // https://github.com/atom/atom/issues/5412
-    if (loadSettings && loadSettings.atomHome) {
-      process.env.ATOM_HOME = loadSettings.atomHome
+    if (getWindowLoadSettings() && getWindowLoadSettings().atomHome) {
+      process.env.ATOM_HOME = getWindowLoadSettings().atomHome
     }
   }
 
-  parseLoadSettings()
   setupAtomHome()
 })()
diff --git a/static/title-bar.less b/static/title-bar.less
index 8191bc278..3eb2c4022 100644
--- a/static/title-bar.less
+++ b/static/title-bar.less
@@ -1,30 +1,32 @@
 @import "ui-variables";
 
+@title-bar-height:           22px;
+@traffic-lights-width:       68px;
+
+@inset-title-bar-height:     38px;
+@inset-traffic-lights-width: 78px;
+
 @title-bar-text-size: 13px;
-@title-bar-height: 23px;
 @title-bar-background-color: @base-background-color;
 @title-bar-border-color: @base-border-color;
 
-body.fullscreen .title-bar {
-  margin-top: -@title-bar-height;
-}
+
+// Title Bar -------------------------------
 
 .title-bar {
-  height: @title-bar-height;
-  transition: margin-top 160ms;
-
-  flex-shrink: 0;
   display: flex;
+  flex-shrink: 0;
   align-items: center;
   justify-content: center;
-
+  overflow: hidden;
+  box-sizing: content-box;
   font-size: @title-bar-text-size;
+  background-color: @title-bar-background-color;
+  border-bottom: 1px solid @title-bar-border-color;
+  transition: margin-top 160ms;
   -webkit-user-select: none;
   -webkit-app-region: drag;
 
-  padding: 0 70px;
-  overflow: hidden;
-
   .title {
     flex: 0 1 auto;
     overflow: hidden;
@@ -32,10 +34,54 @@ body.fullscreen .title-bar {
     text-overflow: ellipsis;
   }
 
-  background-color: @title-bar-background-color;
-  border-bottom: 1px solid @title-bar-border-color;
-
   .is-blurred & {
     color: @text-color-subtle;
   }
 }
+
+
+// Custom -------------------------------
+
+.custom-title-bar {
+  .title-bar {
+    height: @title-bar-height;
+    padding-left: @traffic-lights-width;
+    padding-right: @traffic-lights-width;
+  }
+
+  &.fullscreen .title-bar {
+    margin-top: -@title-bar-height; // hide title bar in fullscreen mode
+  }
+
+  atom-panel.modal {
+    top: @title-bar-height; // Move modals down
+  }
+}
+
+
+// Custom Inset -------------------------------
+
+.custom-inset-title-bar {
+  .title-bar {
+    height: @inset-title-bar-height;
+    padding-left: @inset-traffic-lights-width;
+    padding-right: @inset-traffic-lights-width;
+  }
+
+  &.fullscreen .title-bar {
+    margin-top: -@inset-title-bar-height; // hide title bar in fullscreen mode
+  }
+
+  atom-panel.modal {
+    top: @inset-title-bar-height; // Move modals down
+  }
+}
+
+
+// Hidden -------------------------------
+
+.hidden-title-bar {
+  .status-bar {
+    -webkit-app-region: drag; // Enable dragging
+  }
+}