diff --git a/README.md b/README.md
index 4fd06f851..7ebdf9252 100644
--- a/README.md
+++ b/README.md
@@ -24,18 +24,8 @@ Atom will automatically update when a new release is available.
 You can also download an `atom-windows.zip` file from the [releases page](https://github.com/atom/atom/releases/latest).
 The `.zip` version will not automatically update.
 
-#### Uninstalling Chocolatey Version
-
-The recommended installation of Atom on Windows used to be using [Chocolatey](https://chocolatey.org/packages/Atom/).
-This is no longer recommended now that the Atom Windows installer & auto-updater
-exists.
-
-To switch from Chocolatey to the new installer:
-  * Upgrade to Atom 0.155 or above by running `cup Atom`
-  * Run `cuninst Atom` to uninstall the Chocolatey version of Atom
-    * This will not delete any of your installed packages or Atom config files.
-  * Download the latest [AtomSetup.exe installer](https://github.com/atom/atom/releases/latest).
-  * Double-click the downloaded file to install Atom
+Using [chocolatey](https://chocolatey.org/)? Run `cinst Atom` to install
+the latest version of Atom.
 
 ### Debian Linux (Ubuntu)
 
diff --git a/apm/package.json b/apm/package.json
index b90f3a05e..c070e36c3 100644
--- a/apm/package.json
+++ b/apm/package.json
@@ -6,6 +6,6 @@
     "url": "https://github.com/atom/atom.git"
   },
   "dependencies": {
-    "atom-package-manager": "0.134.0"
+    "atom-package-manager": "0.135.0"
   }
 }
diff --git a/atom.sh b/atom.sh
index 2f3d59c82..ecd7da052 100755
--- a/atom.sh
+++ b/atom.sh
@@ -75,9 +75,9 @@ elif [ $OS == 'Linux' ]; then
   SCRIPT=$(readlink -f "$0")
   USR_DIRECTORY=$(readlink -f $(dirname $SCRIPT)/..)
   ATOM_PATH="$USR_DIRECTORY/share/atom/atom"
-  DOT_ATOM_DIR="$HOME/.atom"
+  ATOM_HOME="${ATOM_HOME:-$HOME/.atom}"
 
-  mkdir -p "$DOT_ATOM_DIR"
+  mkdir -p "$ATOM_HOME"
 
   : ${TMPDIR:=/tmp}
 
@@ -88,9 +88,9 @@ elif [ $OS == 'Linux' ]; then
     exit $?
   else
     (
-    nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$DOT_ATOM_DIR/nohup.out" 2>&1
+    nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1
     if [ $? -ne 0 ]; then
-      cat "$DOT_ATOM_DIR/nohup.out"
+      cat "$ATOM_HOME/nohup.out"
       exit $?
     fi
     ) &
diff --git a/build/tasks/build-task.coffee b/build/tasks/build-task.coffee
index f49e1ac49..fcb1eb6a8 100644
--- a/build/tasks/build-task.coffee
+++ b/build/tasks/build-task.coffee
@@ -160,6 +160,9 @@ module.exports = (grunt) ->
       cp path.join('resources', 'win', 'atom.js'), path.join(shellAppDir, 'resources', 'cli', 'atom.js')
       cp path.join('resources', 'win', 'apm.sh'), path.join(shellAppDir, 'resources', 'cli', 'apm.sh')
 
+    if process.platform is 'linux'
+      cp path.join('resources', 'linux', 'icons'), path.join(buildDir, 'icons')
+
     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'
diff --git a/build/tasks/install-task.coffee b/build/tasks/install-task.coffee
index ec99ad967..5131f512c 100644
--- a/build/tasks/install-task.coffee
+++ b/build/tasks/install-task.coffee
@@ -47,9 +47,9 @@ module.exports = (grunt) ->
 
         {description} = grunt.file.readJSON('package.json')
         iconName = path.join(shareDir, 'resources', 'app', 'resources', 'atom.png')
-        installDir = path.join(installDir, '.') # To prevent "Exec=/usr/local//share/atom/atom"
+        executable = path.join(shareDir, 'atom')
         template = _.template(String(fs.readFileSync(desktopFile)))
-        filled = template({description, installDir, iconName})
+        filled = template({description, iconName, executable})
 
         grunt.file.write(desktopInstallFile, filled)
 
diff --git a/build/tasks/mkdeb-task.coffee b/build/tasks/mkdeb-task.coffee
index cfe04f429..9fb8c7e4b 100644
--- a/build/tasks/mkdeb-task.coffee
+++ b/build/tasks/mkdeb-task.coffee
@@ -36,8 +36,9 @@ module.exports = (grunt) ->
     maintainer = 'GitHub <atom@github.com>'
     installDir = '/usr'
     iconName = 'atom'
+    executable = path.join(installDir, 'share', 'atom', 'atom')
     getInstalledSize buildDir, (error, installedSize) ->
-      data = {name, version, description, section, arch, maintainer, installDir, iconName, installedSize}
+      data = {name, version, description, section, arch, maintainer, installDir, iconName, installedSize, executable}
       controlFilePath = fillTemplate(path.join('resources', 'linux', 'debian', 'control'), data)
       desktopFilePath = fillTemplate(path.join('resources', 'linux', 'atom.desktop'), data)
       icon = path.join('resources', 'atom.png')
diff --git a/build/tasks/mkrpm-task.coffee b/build/tasks/mkrpm-task.coffee
index 8590049b5..8436fea7a 100644
--- a/build/tasks/mkrpm-task.coffee
+++ b/build/tasks/mkrpm-task.coffee
@@ -32,9 +32,10 @@ module.exports = (grunt) ->
 
     installDir = grunt.config.get('atom.installDir')
     shareDir = path.join(installDir, 'share', 'atom')
-    iconName = path.join(shareDir, 'resources', 'app', 'resources', 'atom.png')
+    iconName = 'atom'
+    executable = 'atom'
 
-    data = {name, version, description, installDir, iconName}
+    data = {name, version, description, installDir, iconName, executable}
     specFilePath = fillTemplate(path.join('resources', 'linux', 'redhat', 'atom.spec'), data)
     desktopFilePath = fillTemplate(path.join('resources', 'linux', 'atom.desktop'), data)
 
diff --git a/docs/advanced/keymaps.md b/docs/advanced/keymaps.md
index 43d0c0e96..ee966a45d 100644
--- a/docs/advanced/keymaps.md
+++ b/docs/advanced/keymaps.md
@@ -16,7 +16,7 @@ keystrokes pass through `atom-text-editor` elements:
   'ctrl-shift-e': 'editor:select-to-end-of-line'
   'cmd-left': 'editor:move-to-first-character-of-line'
 
-'atom-text-editor:not([mini])'
+'atom-text-editor:not([mini])':
   'cmd-alt-[': 'editor:fold-current-row'
   'cmd-alt-]': 'editor:unfold-current-row'
 ```
diff --git a/docs/customizing-atom.md b/docs/customizing-atom.md
index d2151f350..d56bd640a 100644
--- a/docs/customizing-atom.md
+++ b/docs/customizing-atom.md
@@ -100,6 +100,14 @@ namespaces: `core` and `editor`.
 
 You can open this file in an editor from the _Atom > Open Your Config_ menu.
 
+### Custom Configuration Location
+
+You can override the location that Atom stores configuration files and folders
+in by setting the `ATOM_HOME` environment variable. The `ATOM_HOME` path will be
+used instead of `~/.atom` when it is set.
+
+This option can be useful when you want to make Atom portable across machines.
+
 ### Configuration Key Reference
 
 - `core`
diff --git a/docs/index.md b/docs/index.md
index 87e198e09..e034e5784 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -25,5 +25,6 @@
 
 ### Upgrading to 1.0 APIs
 
+* [Upgrading Your Package](upgrading/upgrading-your-package.md)
 * [Upgrading Your UI Theme Or Package Selectors](upgrading/upgrading-your-ui-theme.md)
 * [Upgrading Your Syntax Theme](upgrading/upgrading-your-syntax-theme.md)
diff --git a/docs/upgrading/upgrading-your-package.md b/docs/upgrading/upgrading-your-package.md
index 9bde475ef..e7d603a36 100644
--- a/docs/upgrading/upgrading-your-package.md
+++ b/docs/upgrading/upgrading-your-package.md
@@ -1,4 +1,4 @@
-# Upgrading your package to 1.0 APIs
+# Upgrading Your Package
 
 Atom is rapidly approaching 1.0. Much of the effort leading up to the 1.0 has been cleaning up APIs in an attempt to future proof, and make a more pleasant experience developing packages.
 
@@ -63,7 +63,7 @@ When you are deprecation free and all done converting, upgrade the `engines` fie
 ```json
 {
   "engines": {
-    "atom": ">=0.174.0, <2.0.0"
+    "atom": ">=0.174.0 <2.0.0"
   }
 }
 ```
@@ -603,7 +603,7 @@ atom.workspaceView.command 'core:close core:cancel', ->
 
 ## Upgrading your stylesheet's selectors
 
-Many selectors have changed, and we have introduced the [Shadow DOM][shadowdom] to the editor. See [Upgrading Your Package Selectors guide][upgrading-selectors] for more information in upgrading your package stylesheets.
+Many selectors have changed, and we have introduced the [Shadow DOM][shadowdom] to the editor. See the [Upgrading Your UI Theme And Package Selectors guide][upgrading-selectors] for more information in upgrading your package stylesheets.
 
 ## Help us improve this guide!
 
@@ -620,6 +620,6 @@ Did you hit something painful that wasn't in here? Want to reword some bit of it
 [texteditor]:https://atom.io/docs/api/latest/TextEditor
 [disposable]:https://atom.io/docs/api/latest/Disposable
 [commands-add]:https://atom.io/docs/api/latest/CommandRegistry#instance-add
-[upgrading-selectors]:upgrading-your-ui-theme
+[upgrading-selectors]:https://atom.io/docs/latest/upgrading/upgrading-your-ui-theme
 [shadowdom]:http://blog.atom.io/2014/11/18/avoiding-style-pollution-with-the-shadow-dom.html
 [guide]:https://github.com/atom/atom/blob/master/docs/upgrading/upgrading-your-package.md
diff --git a/package.json b/package.json
index f1db49733..3cb32c233 100644
--- a/package.json
+++ b/package.json
@@ -31,7 +31,7 @@
     "emissary": "^1.3.1",
     "event-kit": "^1.0.2",
     "first-mate": "^3.0.0",
-    "fs-plus": "^2.3.2",
+    "fs-plus": "^2.5",
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
     "git-utils": "^3.0.0",
@@ -71,20 +71,20 @@
   },
   "packageDependencies": {
     "atom-dark-syntax": "0.26.0",
-    "atom-dark-ui": "0.46.0",
+    "atom-dark-ui": "0.47.0",
     "atom-light-syntax": "0.26.0",
-    "atom-light-ui": "0.40.0",
+    "atom-light-ui": "0.41.0",
     "base16-tomorrow-dark-theme": "0.25.0",
     "base16-tomorrow-light-theme": "0.8.0",
-    "one-dark-ui": "0.3.0",
+    "one-dark-ui": "0.4.0",
     "one-dark-syntax": "0.3.0",
     "one-light-syntax": "0.3.0",
-    "one-light-ui": "0.2.0",
+    "one-light-ui": "0.3.0",
     "solarized-dark-syntax": "0.32.0",
     "solarized-light-syntax": "0.19.0",
     "archive-view": "0.46.0",
     "autocomplete": "0.44.0",
-    "autoflow": "0.21.0",
+    "autoflow": "0.22.0",
     "autosave": "0.20.0",
     "background-tips": "0.22.0",
     "bookmarks": "0.35.0",
@@ -103,8 +103,8 @@
     "incompatible-packages": "0.21.0",
     "keybinding-resolver": "0.27.0",
     "link": "0.30.0",
-    "markdown-preview": "0.132.0",
-    "metrics": "0.41.0",
+    "markdown-preview": "0.134.0",
+    "metrics": "0.42.0",
     "notifications": "0.26.0",
     "open-on-github": "0.32.0",
     "package-generator": "0.37.0",
@@ -116,20 +116,21 @@
     "styleguide": "0.43.0",
     "symbols-view": "0.81.0",
     "tabs": "0.64.0",
-    "timecop": "0.28.0",
+    "timecop": "0.29.0",
     "tree-view": "0.154.0",
     "update-package-dependencies": "0.8.0",
     "welcome": "0.21.0",
     "whitespace": "0.28.0",
     "wrap-guide": "0.31.0",
     "language-c": "0.38.0",
-    "language-clojure": "0.10.0",
+    "language-clojure": "0.11.0",
     "language-coffee-script": "0.39.0",
-    "language-css": "0.27.0",
+    "language-csharp": "0.5.0",
+    "language-css": "0.28.0",
     "language-gfm": "0.63.0",
     "language-git": "0.10.0",
     "language-go": "0.21.0",
-    "language-html": "0.28.0",
+    "language-html": "0.29.0",
     "language-hyperlink": "0.12.2",
     "language-java": "0.14.0",
     "language-javascript": "0.56.0",
@@ -142,9 +143,9 @@
     "language-php": "0.20.0",
     "language-property-list": "0.8.0",
     "language-python": "0.30.0",
-    "language-ruby": "0.47.0",
+    "language-ruby": "0.48.0",
     "language-ruby-on-rails": "0.18.0",
-    "language-sass": "0.31.0",
+    "language-sass": "0.33.0",
     "language-shellscript": "0.12.0",
     "language-source": "0.9.0",
     "language-sql": "0.14.0",
diff --git a/resources/linux/atom.desktop.in b/resources/linux/atom.desktop.in
index db28e7395..1969e3f26 100644
--- a/resources/linux/atom.desktop.in
+++ b/resources/linux/atom.desktop.in
@@ -2,7 +2,7 @@
 Name=Atom
 Comment=<%= description %>
 GenericName=Text Editor
-Exec=<%= installDir %>/share/atom/atom %U
+Exec=<%= executable %> %U
 Icon=<%= iconName %>
 Type=Application
 StartupNotify=true
diff --git a/resources/linux/icons/1024.png b/resources/linux/icons/1024.png
new file mode 100644
index 000000000..a09f04805
Binary files /dev/null and b/resources/linux/icons/1024.png differ
diff --git a/resources/linux/icons/128.png b/resources/linux/icons/128.png
new file mode 100644
index 000000000..78948fb24
Binary files /dev/null and b/resources/linux/icons/128.png differ
diff --git a/resources/linux/icons/16.png b/resources/linux/icons/16.png
new file mode 100644
index 000000000..52df06fa2
Binary files /dev/null and b/resources/linux/icons/16.png differ
diff --git a/resources/linux/icons/24.png b/resources/linux/icons/24.png
new file mode 100644
index 000000000..0bf12cbb0
Binary files /dev/null and b/resources/linux/icons/24.png differ
diff --git a/resources/linux/icons/256.png b/resources/linux/icons/256.png
new file mode 100644
index 000000000..a98caeb7b
Binary files /dev/null and b/resources/linux/icons/256.png differ
diff --git a/resources/linux/icons/32.png b/resources/linux/icons/32.png
new file mode 100644
index 000000000..a960acf00
Binary files /dev/null and b/resources/linux/icons/32.png differ
diff --git a/resources/linux/icons/48.png b/resources/linux/icons/48.png
new file mode 100644
index 000000000..196717e27
Binary files /dev/null and b/resources/linux/icons/48.png differ
diff --git a/resources/linux/icons/512.png b/resources/linux/icons/512.png
new file mode 100644
index 000000000..f1d35d951
Binary files /dev/null and b/resources/linux/icons/512.png differ
diff --git a/resources/linux/icons/64.png b/resources/linux/icons/64.png
new file mode 100644
index 000000000..b9fcf78ab
Binary files /dev/null and b/resources/linux/icons/64.png differ
diff --git a/resources/linux/redhat/atom.spec.in b/resources/linux/redhat/atom.spec.in
index 42c06970d..369aeea70 100644
--- a/resources/linux/redhat/atom.spec.in
+++ b/resources/linux/redhat/atom.spec.in
@@ -1,27 +1,35 @@
 Name:           <%= name %>
 Version:        <%= version %>
 Release:        0.1%{?dist}
-Summary:        Atom is a hackable text editor for the 21st century
+Summary:        <%= description %>
 License:        MIT
 URL:            https://atom.io/
 AutoReqProv:    no # Avoid libchromiumcontent.so missing dependency
-Prefix:         /usr/local
+Prefix:         <%= installDir %>
 
 %description
 <%= description %>
 
 %install
-mkdir -p %{buildroot}/usr/local/share/atom
-cp -r /tmp/atom-build/Atom/* %{buildroot}/usr/local/share/atom
-mkdir -p %{buildroot}/usr/local/bin/
-ln -sf ../share/atom/resources/app/apm/node_modules/.bin/apm %{buildroot}/usr/local/bin/apm
-cp atom.sh %{buildroot}/usr/local/bin/atom
-chmod 755 atom.sh
-mkdir -p %{buildroot}/usr/local/share/applications/
-mv atom.desktop %{buildroot}/usr/local/share/applications/
+mkdir -p %{buildroot}/<%= installDir %>/share/atom/
+cp -r Atom/* %{buildroot}/<%= installDir %>/share/atom/
+mkdir -p %{buildroot}/<%= installDir %>/bin/
+ln -sf ../share/atom/resources/app/apm/node_modules/.bin/apm %{buildroot}/<%= installDir %>/bin/apm
+cp atom.sh %{buildroot}/<%= installDir %>/bin/atom
+chmod 755 %{buildroot}/<%= installDir %>/bin/atom
+mkdir -p %{buildroot}/<%= installDir %>/share/applications/
+cp atom.desktop %{buildroot}/<%= installDir %>/share/applications/
+
+# copy over icons in sizes that most desktop environments like
+for i in 1024 512 256 128 64 48 32 24 16
+do
+    mkdir -p %{buildroot}/<%= installDir %>/share/icons/hicolor/${i}x${i}/apps
+    cp icons/${i}.png %{buildroot}/<%= installDir %>/share/icons/hicolor/${i}x${i}/apps/atom.png
+done
 
 %files
-/usr/local/bin/atom
-/usr/local/bin/apm
-/usr/local/share/atom/
-/usr/local/share/applications/atom.desktop
+<%= installDir %>/bin/atom
+<%= installDir %>/bin/apm
+<%= installDir %>/share/atom/
+<%= installDir %>/share/applications/atom.desktop
+<%= installDir %>/share/icons/hicolor/
diff --git a/script/mkrpm b/script/mkrpm
index 356f0bfc4..c9ba2d7f7 100755
--- a/script/mkrpm
+++ b/script/mkrpm
@@ -11,7 +11,8 @@ ARCH=`uname -m`
 
 rpmdev-setuptree
 
-cp -r $BUILD_DIRECTORY/Atom/* $RPM_BUILD_ROOT/BUILD
+cp -r $BUILD_DIRECTORY/Atom $RPM_BUILD_ROOT/BUILD
+cp -r $BUILD_DIRECTORY/icons $RPM_BUILD_ROOT/BUILD
 cp $SPEC_FILE $RPM_BUILD_ROOT/SPECS
 cp ./atom.sh $RPM_BUILD_ROOT/BUILD
 cp $DESKTOP_FILE $RPM_BUILD_ROOT/BUILD
diff --git a/script/rpmbuild b/script/rpmbuild
index 9405fd585..0e0f4882c 100755
--- a/script/rpmbuild
+++ b/script/rpmbuild
@@ -3,4 +3,4 @@
 set -e
 
 script/build
-script/grunt mkrpm publish-build --stack
+script/grunt mkrpm publish-build --stack --install-dir /usr
diff --git a/spec/buffered-node-process-spec.coffee b/spec/buffered-node-process-spec.coffee
new file mode 100644
index 000000000..1ea6074c5
--- /dev/null
+++ b/spec/buffered-node-process-spec.coffee
@@ -0,0 +1,39 @@
+path = require 'path'
+BufferedNodeProcess  = require '../src/buffered-node-process'
+
+describe "BufferedNodeProcess", ->
+  it "executes the script in a new process", ->
+    exit = jasmine.createSpy('exitCallback')
+    output = ''
+    stdout = (lines) -> output += lines
+    error = ''
+    stderr = (lines) -> error += lines
+    args = ['hi']
+    command = path.join(__dirname, 'fixtures', 'script.js')
+
+    new BufferedNodeProcess({command, args, stdout, stderr, exit})
+
+    waitsFor ->
+      exit.callCount is 1
+
+    runs ->
+      expect(output).toBe 'hi'
+      expect(error).toBe ''
+      expect(args).toEqual ['hi']
+
+  it "suppresses deprecations in the new process", ->
+    exit = jasmine.createSpy('exitCallback')
+    output = ''
+    stdout = (lines) -> output += lines
+    error = ''
+    stderr = (lines) -> error += lines
+    command = path.join(__dirname, 'fixtures', 'script-with-deprecations.js')
+
+    new BufferedNodeProcess({command, stdout, stderr, exit})
+
+    waitsFor ->
+      exit.callCount is 1
+
+    runs ->
+      expect(output).toBe 'hi'
+      expect(error).toBe ''
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 15dc3b8fa..4abd3b0db 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -666,6 +666,23 @@ describe "Config", ->
               foo:
                 bar: 'coffee'
 
+      describe "when an error is thrown writing the file to disk", ->
+        addErrorHandler = null
+        beforeEach ->
+          atom.notifications.onDidAddNotification addErrorHandler = jasmine.createSpy()
+
+        it "creates a notification", ->
+          jasmine.unspy CSON, 'writeFileSync'
+          spyOn(CSON, 'writeFileSync').andCallFake ->
+            error = new Error()
+            error.code = 'EPERM'
+            error.path = atom.config.getUserConfigPath()
+            throw error
+
+          save = -> atom.config.save()
+          expect(save).not.toThrow()
+          expect(addErrorHandler.callCount).toBe 1
+
     describe ".loadUserConfig()", ->
       beforeEach ->
         expect(fs.existsSync(atom.config.configDirPath)).toBeFalsy()
diff --git a/spec/fixtures/script-with-deprecations.js b/spec/fixtures/script-with-deprecations.js
new file mode 100644
index 000000000..4abe4774a
--- /dev/null
+++ b/spec/fixtures/script-with-deprecations.js
@@ -0,0 +1,2 @@
+require('fs').existsSync('hi');
+process.stdout.write('hi');
diff --git a/spec/fixtures/script.js b/spec/fixtures/script.js
new file mode 100644
index 000000000..94972dfb5
--- /dev/null
+++ b/spec/fixtures/script.js
@@ -0,0 +1 @@
+process.stdout.write(process.argv[2]);
diff --git a/spec/pane-spec.coffee b/spec/pane-spec.coffee
index 3477acc52..ac6e1d26f 100644
--- a/spec/pane-spec.coffee
+++ b/spec/pane-spec.coffee
@@ -383,6 +383,25 @@ describe "Pane", ->
           pane.saveActiveItem()
           expect(atom.showSaveDialogSync).not.toHaveBeenCalled()
 
+    describe "when the item's saveAs method throws a well-known IO error", ->
+      notificationSpy = null
+      beforeEach ->
+        atom.notifications.onDidAddNotification notificationSpy = jasmine.createSpy()
+
+      it "creates a notification", ->
+        pane.getActiveItem().saveAs = ->
+          error = new Error("EACCES, permission denied '/foo'")
+          error.path = '/foo'
+          error.code = 'EACCES'
+          throw error
+
+        pane.saveActiveItem()
+        expect(notificationSpy).toHaveBeenCalled()
+        notification = notificationSpy.mostRecentCall.args[0]
+        expect(notification.getType()).toBe 'warning'
+        expect(notification.getMessage()).toContain 'Permission denied'
+        expect(notification.getMessage()).toContain '/foo'
+
   describe "::saveActiveItemAs()", ->
     pane = null
 
@@ -404,6 +423,25 @@ describe "Pane", ->
         pane.saveActiveItemAs()
         expect(atom.showSaveDialogSync).not.toHaveBeenCalled()
 
+    describe "when the item's saveAs method throws a well-known IO error", ->
+      notificationSpy = null
+      beforeEach ->
+        atom.notifications.onDidAddNotification notificationSpy = jasmine.createSpy()
+
+      it "creates a notification", ->
+        pane.getActiveItem().saveAs = ->
+          error = new Error("EACCES, permission denied '/foo'")
+          error.path = '/foo'
+          error.code = 'EACCES'
+          throw error
+
+        pane.saveActiveItemAs()
+        expect(notificationSpy).toHaveBeenCalled()
+        notification = notificationSpy.mostRecentCall.args[0]
+        expect(notification.getType()).toBe 'warning'
+        expect(notification.getMessage()).toContain 'Permission denied'
+        expect(notification.getMessage()).toContain '/foo'
+
   describe "::itemForURI(uri)", ->
     it "returns the item for which a call to .getURI() returns the given uri", ->
       pane = new Pane(items: [new Item("A"), new Item("B"), new Item("C"), new Item("D")])
diff --git a/spec/window-spec.coffee b/spec/window-spec.coffee
index 7e9370d50..1706e042e 100644
--- a/spec/window-spec.coffee
+++ b/spec/window-spec.coffee
@@ -1,5 +1,7 @@
 {$, $$} = require '../src/space-pen-extensions'
 path = require 'path'
+fs = require 'fs-plus'
+temp = require 'temp'
 TextEditor = require '../src/text-editor'
 WindowEventHandler = require '../src/window-event-handler'
 
@@ -54,7 +56,7 @@ describe "Window", ->
       jasmine.unspy(TextEditor.prototype, "shouldPromptToSave")
       beforeUnloadEvent = $.Event(new Event('beforeunload'))
 
-    describe "when pane items are are modified", ->
+    describe "when pane items are modified", ->
       it "prompts user to save and calls atom.workspace.confirmClose", ->
         editor = null
         spyOn(atom.workspace, 'confirmClose').andCallThrough()
@@ -92,6 +94,25 @@ describe "Window", ->
           $(window).trigger(beforeUnloadEvent)
           expect(atom.confirm).toHaveBeenCalled()
 
+      describe "when the same path is modified in multiple panes", ->
+        it "prompts to save the item", ->
+          editor = null
+          filePath = path.join(temp.mkdirSync('atom-file'), 'file.txt')
+          fs.writeFileSync(filePath, 'hello')
+          spyOn(atom.workspace, 'confirmClose').andCallThrough()
+          spyOn(atom, 'confirm').andReturn(0)
+
+          waitsForPromise ->
+            atom.workspace.open(filePath).then (o) -> editor = o
+
+          runs ->
+            atom.workspace.getActivePane().splitRight(copyActiveItem: true)
+            editor.setText('world')
+            $(window).trigger(beforeUnloadEvent)
+            expect(atom.workspace.confirmClose).toHaveBeenCalled()
+            expect(atom.confirm.callCount).toBe 1
+            expect(fs.readFileSync(filePath, 'utf8')).toBe 'world'
+
   describe ".unloadEditorWindow()", ->
     it "saves the serialized state of the window so it can be deserialized after reload", ->
       workspaceState = atom.workspace.serialize()
diff --git a/spec/workspace-spec.coffee b/spec/workspace-spec.coffee
index b9642e17d..82526a299 100644
--- a/spec/workspace-spec.coffee
+++ b/spec/workspace-spec.coffee
@@ -955,9 +955,14 @@ describe "Workspace", ->
           expect(editor.isModified()).toBeTruthy()
 
   describe "::saveActivePaneItem()", ->
+    editor = null
+    beforeEach ->
+      waitsForPromise ->
+        atom.workspace.open('sample.js').then (o) -> editor = o
+
     describe "when there is an error", ->
       it "emits a warning notification when the file cannot be saved", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           throw new Error("'/some/file' is a directory")
 
         atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
@@ -966,7 +971,7 @@ describe "Workspace", ->
         expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
 
       it "emits a warning notification when the directory cannot be written to", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           throw new Error("ENOTDIR, not a directory '/Some/dir/and-a-file.js'")
 
         atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
@@ -975,7 +980,7 @@ describe "Workspace", ->
         expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
 
       it "emits a warning notification when the user does not have permission", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           error = new Error("EACCES, permission denied '/Some/dir/and-a-file.js'")
           error.code = 'EACCES'
           error.path = '/Some/dir/and-a-file.js'
@@ -987,14 +992,14 @@ describe "Workspace", ->
         expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
 
       it "emits a warning notification when the operation is not permitted", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           error = new Error("EPERM, operation not permitted '/Some/dir/and-a-file.js'")
           error.code = 'EPERM'
           error.path = '/Some/dir/and-a-file.js'
           throw error
 
       it "emits a warning notification when the file is already open by another app", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           error = new Error("EBUSY, resource busy or locked '/Some/dir/and-a-file.js'")
           error.code = 'EBUSY'
           error.path = '/Some/dir/and-a-file.js'
@@ -1009,7 +1014,7 @@ describe "Workspace", ->
         expect(notificaiton.getMessage()).toContain 'Unable to save'
 
       it "emits a warning notification when the file system is read-only", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           error = new Error("EROFS, read-only file system '/Some/dir/and-a-file.js'")
           error.code = 'EROFS'
           error.path = '/Some/dir/and-a-file.js'
@@ -1024,7 +1029,7 @@ describe "Workspace", ->
         expect(notification.getMessage()).toContain 'Unable to save'
 
       it "emits a warning notification when the file cannot be saved", ->
-        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+        spyOn(editor, 'save').andCallFake ->
           throw new Error("no one knows")
 
         save = -> atom.workspace.saveActivePaneItem()
diff --git a/src/6to5.coffee b/src/6to5.coffee
index f0e1dc7c1..15059ad62 100644
--- a/src/6to5.coffee
+++ b/src/6to5.coffee
@@ -96,7 +96,7 @@ getCachePath = (sourceCode) ->
 
   unless jsCacheDir?
     to5Version = require('6to5-core/package.json').version
-    cacheDir = path.join(fs.absolute('~/.atom'), 'compile-cache')
+    cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache')
     jsCacheDir = path.join(cacheDir, 'js', '6to5', create6to5VersionAndOptionsDigest(to5Version, defaultOptions))
 
   path.join(jsCacheDir, "#{digest}.js")
diff --git a/src/atom.coffee b/src/atom.coffee
index a1818b138..0036ba420 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -109,7 +109,7 @@ class Atom extends Model
   #
   # Returns the absolute path to ~/.atom
   @getConfigDirPath: ->
-    @configDirPath ?= fs.absolute('~/.atom')
+    @configDirPath ?= process.env.ATOM_HOME
 
   # Get the path to Atom's storage directory.
   #
@@ -263,9 +263,6 @@ class Atom extends Model
     # Make react.js faster
     process.env.NODE_ENV ?= 'production' unless devMode
 
-    # Set Atom's home so packages don't have to guess it
-    process.env.ATOM_HOME = configDirPath
-
     @config = new Config({configDirPath, resourcePath})
     @keymaps = new KeymapManager({configDirPath, resourcePath})
     @keymap = @keymaps # Deprecated
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index 9e34421d4..bd4303ae9 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -5,7 +5,7 @@ AutoUpdateManager = require './auto-update-manager'
 BrowserWindow = require 'browser-window'
 Menu = require 'menu'
 app = require 'app'
-fs = require 'fs'
+fs = require 'fs-plus'
 ipc = require 'ipc'
 path = require 'path'
 os = require 'os'
@@ -342,6 +342,7 @@ class AtomApplication
   #   :window - {AtomWindow} to open file paths in.
   openPath: ({pathToOpen, pidToKillWhenClosed, newWindow, devMode, safeMode, windowDimensions, window}={}) ->
     {pathToOpen, initialLine, initialColumn} = @locationForPathToOpen(pathToOpen)
+    pathToOpen = fs.normalize(pathToOpen)
 
     unless pidToKillWhenClosed or newWindow
       pathToOpenStat = fs.statSyncNoException(pathToOpen)
@@ -414,9 +415,8 @@ class AtomApplication
   openUrl: ({urlToOpen, devMode, safeMode}) ->
     unless @packages?
       PackageManager = require '../package-manager'
-      fs = require 'fs-plus'
       @packages = new PackageManager
-        configDirPath: fs.absolute('~/.atom')
+        configDirPath: process.env.ATOM_HOME
         devMode: devMode
         resourcePath: @resourcePath
 
diff --git a/src/browser/main.coffee b/src/browser/main.coffee
index 035b34db0..48ff85f3f 100644
--- a/src/browser/main.coffee
+++ b/src/browser/main.coffee
@@ -2,7 +2,7 @@ global.shellStartTime = Date.now()
 
 crashReporter = require 'crash-reporter'
 app = require 'app'
-fs = require 'fs'
+fs = require 'fs-plus'
 path = require 'path'
 optimist = require 'optimist'
 nslog = require 'nslog'
@@ -14,6 +14,7 @@ process.on 'uncaughtException', (error={}) ->
   nslog(error.stack) if error.stack?
 
 start = ->
+  setupAtomHome()
   if process.platform is 'win32'
     SquirrelUpdate = require './squirrel-update'
     squirrelCommand = process.argv[1]
@@ -42,10 +43,11 @@ start = ->
 
     cwd = args.executedFrom?.toString() or process.cwd()
     args.pathsToOpen = args.pathsToOpen.map (pathToOpen) ->
+      pathToOpen = fs.normalize(pathToOpen)
       if cwd
-        path.resolve(cwd, pathToOpen.toString())
+        path.resolve(cwd, pathToOpen)
       else
-        path.resolve(pathToOpen.toString())
+        path.resolve(pathToOpen)
 
     setupCoffeeScript()
     if args.devMode
@@ -73,6 +75,14 @@ setupCoffeeScript = ->
     js = CoffeeScript.compile(coffee, filename: filePath)
     module._compile(js, filePath)
 
+setupAtomHome = ->
+  return if process.env.ATOM_HOME
+
+  atomHome = path.join(app.getHomeDir(), '.atom')
+  try
+    atomHome = fs.realpathSync(atomHome)
+  process.env.ATOM_HOME = atomHome
+
 parseCommandLine = ->
   version = app.getVersion()
   options = optimist(process.argv[1..])
@@ -89,8 +99,12 @@ parseCommandLine = ->
     opened or a new window if it hasn't.
 
     Environment Variables:
-    ATOM_DEV_RESOURCE_PATH  The path from which Atom loads source code in dev mode.
-                            Defaults to `~/github/atom`.
+
+      ATOM_DEV_RESOURCE_PATH  The path from which Atom loads source code in dev mode.
+                              Defaults to `~/github/atom`.
+
+      ATOM_HOME               The root path for all configuration files and folders.
+                              Defaults to `~/.atom`.
   """
   options.alias('d', 'dev').boolean('d').describe('d', 'Run in development mode.')
   options.alias('f', 'foreground').boolean('f').describe('f', 'Keep the browser process in the foreground.')
diff --git a/src/buffered-node-process.coffee b/src/buffered-node-process.coffee
index e9a3fbee4..bb1a1c655 100644
--- a/src/buffered-node-process.coffee
+++ b/src/buffered-node-process.coffee
@@ -48,5 +48,8 @@ class BufferedNodeProcess extends BufferedProcess
     options.env ?= Object.create(process.env)
     options.env['ATOM_SHELL_INTERNAL_RUN_AS_NODE'] = 1
 
+    args = args?.slice() ? []
     args.unshift(command)
+    args.unshift('--no-deprecation')
+
     super({command: node, args, options, stdout, stderr, exit})
diff --git a/src/coffee-cache.coffee b/src/coffee-cache.coffee
index 15892dd2f..1e06fd4d5 100644
--- a/src/coffee-cache.coffee
+++ b/src/coffee-cache.coffee
@@ -5,7 +5,7 @@ CoffeeScript = require 'coffee-script'
 CSON = require 'season'
 fs = require 'fs-plus'
 
-cacheDir = path.join(fs.absolute('~/.atom'), 'compile-cache')
+cacheDir = path.join(process.env.ATOM_HOME, 'compile-cache')
 
 stats =
   hits: 0
diff --git a/src/config.coffee b/src/config.coffee
index d9695fb55..937bb1307 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -868,7 +868,12 @@ class Config
   save: ->
     allSettings = {'*': @settings}
     allSettings = _.extend allSettings, @scopedSettingsStore.propertiesForSource(@getUserConfigPath())
-    CSON.writeFileSync(@configFilePath, allSettings)
+    try
+      CSON.writeFileSync(@configFilePath, allSettings)
+    catch error
+      message = "Failed to save `#{path.basename(@configFilePath)}`"
+      detail = error.message
+      @notifyFailure(message, detail)
 
   ###
   Section: Private methods managing global settings
diff --git a/src/less-compile-cache.coffee b/src/less-compile-cache.coffee
index e07072637..c70f312ee 100644
--- a/src/less-compile-cache.coffee
+++ b/src/less-compile-cache.coffee
@@ -1,14 +1,10 @@
 path = require 'path'
-fs = require 'fs-plus'
 LessCache = require 'less-cache'
-{Subscriber} = require 'emissary'
 
 # {LessCache} wrapper used by {ThemeManager} to read stylesheets.
 module.exports =
 class LessCompileCache
-  Subscriber.includeInto(this)
-
-  @cacheDir: path.join(require('./coffee-cache').cacheDir, 'less')
+  @cacheDir: path.join(process.env.ATOM_HOME, 'compile-cache', 'less')
 
   constructor: ({resourcePath, importPaths}) ->
     @lessSearchPaths = [
@@ -35,5 +31,3 @@ class LessCompileCache
 
   cssForFile: (stylesheetPath, lessContent) ->
     @cache.cssForFile(stylesheetPath, lessContent)
-
-  destroy: -> @unsubscribe()
diff --git a/src/menu-manager.coffee b/src/menu-manager.coffee
index 35c012936..1991cba95 100644
--- a/src/menu-manager.coffee
+++ b/src/menu-manager.coffee
@@ -109,17 +109,20 @@ class MenuManager
     # Simulate an atom-text-editor element attached to a atom-workspace element attached
     # to a body element that has the same classes as the current body element.
     unless @testEditor?
-      testBody = document.createElement('body')
+      # Use new document so that custom elements don't actually get created
+      testDocument = document.implementation.createDocument(document.namespaceURI, 'html')
+
+      testBody = testDocument.createElement('body')
       testBody.classList.add(@classesForElement(document.body)...)
 
-      testWorkspace = document.createElement('div')
+      testWorkspace = testDocument.createElement('atom-workspace')
       workspaceClasses = @classesForElement(document.body.querySelector('atom-workspace'))
       workspaceClasses = ['workspace'] if workspaceClasses.length is 0
       testWorkspace.classList.add(workspaceClasses...)
 
       testBody.appendChild(testWorkspace)
 
-      @testEditor = document.createElement('div')
+      @testEditor = testDocument.createElement('atom-text-editor')
       @testEditor.classList.add('editor')
       testWorkspace.appendChild(@testEditor)
 
diff --git a/src/pane-container.coffee b/src/pane-container.coffee
index f36169e3b..14fa25a44 100644
--- a/src/pane-container.coffee
+++ b/src/pane-container.coffee
@@ -152,12 +152,12 @@ class PaneContainer extends Model
   saveAll: ->
     pane.saveItems() for pane in @getPanes()
 
-  confirmClose: ->
+  confirmClose: (options) ->
     allSaved = true
 
     for pane in @getPanes()
       for item in pane.getItems()
-        unless pane.promptToSaveItem(item)
+        unless pane.promptToSaveItem(item, options)
           allSaved = false
           break
 
diff --git a/src/pane.coffee b/src/pane.coffee
index e2e61ca95..f1bc34abf 100644
--- a/src/pane.coffee
+++ b/src/pane.coffee
@@ -437,8 +437,8 @@ class Pane extends Model
   destroyInactiveItems: ->
     @destroyItem(item) for item in @getItems() when item isnt @activeItem
 
-  promptToSaveItem: (item) ->
-    return true unless item.shouldPromptToSave?()
+  promptToSaveItem: (item, options={}) ->
+    return true unless item.shouldPromptToSave?(options)
 
     if typeof item.getURI is 'function'
       uri = item.getURI()
@@ -481,7 +481,10 @@ class Pane extends Model
       itemURI = item.getUri()
 
     if itemURI?
-      item.save?()
+      try
+        item.save?()
+      catch error
+        @handleSaveError(error)
       nextAction?()
     else
       @saveItemAs(item, nextAction)
@@ -498,7 +501,10 @@ class Pane extends Model
     itemPath = item.getPath?()
     newItemPath = atom.showSaveDialogSync(itemPath)
     if newItemPath
-      item.saveAs(newItemPath)
+      try
+        item.saveAs(newItemPath)
+      catch error
+        @handleSaveError(error)
       nextAction?()
 
   # Public: Save all items.
@@ -667,3 +673,18 @@ class Pane extends Model
     for item in @getItems()
       return false unless @promptToSaveItem(item)
     true
+
+  handleSaveError: (error) ->
+    if error.message.endsWith('is a directory')
+      atom.notifications.addWarning("Unable to save file: #{error.message}")
+    else if error.code is 'EACCES' and error.path?
+      atom.notifications.addWarning("Unable to save file: Permission denied '#{error.path}'")
+    else if error.code in ['EPERM', 'EBUSY', 'UNKNOWN'] and error.path?
+      atom.notifications.addWarning("Unable to save file '#{error.path}'", detail: error.message)
+    else if error.code is 'EROFS' and error.path?
+      atom.notifications.addWarning("Unable to save file: Read-only file system '#{error.path}'")
+    else if errorMatch = /ENOTDIR, not a directory '([^']+)'/.exec(error.message)
+      fileName = errorMatch[1]
+      atom.notifications.addWarning("Unable to save file: A directory in the path '#{fileName}' could not be written to")
+    else
+      throw error
diff --git a/src/text-editor.coffee b/src/text-editor.coffee
index dbd1075c5..b86b97d17 100644
--- a/src/text-editor.coffee
+++ b/src/text-editor.coffee
@@ -641,7 +641,11 @@ class TextEditor extends Model
 
   # Determine whether the user should be prompted to save before closing
   # this editor.
-  shouldPromptToSave: -> @isModified() and not @buffer.hasMultipleEditors()
+  shouldPromptToSave: ({windowCloseRequested}={}) ->
+    if windowCloseRequested
+      @isModified()
+    else
+      @isModified() and not @buffer.hasMultipleEditors()
 
   ###
   Section: Reading Text
diff --git a/src/window-event-handler.coffee b/src/window-event-handler.coffee
index 37c04670b..d2a79b2a4 100644
--- a/src/window-event-handler.coffee
+++ b/src/window-event-handler.coffee
@@ -52,7 +52,7 @@ class WindowEventHandler
     @subscribe $(window), 'blur', -> document.body.classList.add('is-blurred')
 
     @subscribe $(window), 'beforeunload', =>
-      confirmed = atom.workspace?.confirmClose()
+      confirmed = atom.workspace?.confirmClose(windowCloseRequested: true)
       atom.hide() if confirmed and not @reloadRequested and atom.getCurrentWindow().isWebViewFocused()
       @reloadRequested = false
 
diff --git a/src/workspace.coffee b/src/workspace.coffee
index fc2a12cdb..b2fc6fbf1 100644
--- a/src/workspace.coffee
+++ b/src/workspace.coffee
@@ -599,8 +599,8 @@ class Workspace extends Model
   saveAll: ->
     @paneContainer.saveAll()
 
-  confirmClose: ->
-    @paneContainer.confirmClose()
+  confirmClose: (options) ->
+    @paneContainer.confirmClose(options)
 
   # Save the active pane item.
   #
@@ -609,7 +609,7 @@ class Workspace extends Model
   # {::saveActivePaneItemAs} # will be called instead. This method does nothing
   # if the active item does not implement a `.save` method.
   saveActivePaneItem: ->
-    @saveActivePaneItemAndReportErrors('saveActiveItem')
+    @getActivePane().saveActiveItem()
 
   # Prompt the user for a path and save the active pane item to it.
   #
@@ -617,27 +617,7 @@ class Workspace extends Model
   # `.saveAs` on the item with the selected path. This method does nothing if
   # the active item does not implement a `.saveAs` method.
   saveActivePaneItemAs: ->
-    @saveActivePaneItemAndReportErrors('saveActiveItemAs')
-
-  saveActivePaneItemAndReportErrors: (method) ->
-    try
-      @getActivePane()[method]()
-    catch error
-      if error.message.endsWith('is a directory')
-        atom.notifications.addWarning("Unable to save file: #{error.message}")
-      else if error.code is 'EACCES' and error.path?
-        atom.notifications.addWarning("Unable to save file: Permission denied '#{error.path}'")
-      else if error.code is 'EPERM' and error.path?
-        atom.notifications.addWarning("Unable to save file '#{error.path}'", detail: error.message)
-      else if error.code is 'EBUSY' and error.path?
-        atom.notifications.addWarning("Unable to save file '#{error.path}'", detail: error.message)
-      else if error.code is 'EROFS' and error.path?
-        atom.notifications.addWarning("Unable to save file: Read-only file system '#{error.path}'")
-      else if errorMatch = /ENOTDIR, not a directory '([^']+)'/.exec(error.message)
-        fileName = errorMatch[1]
-        atom.notifications.addWarning("Unable to save file: A directory in the path '#{fileName}' could not be written to")
-      else
-        throw error
+    @getActivePane().saveActiveItemAs()
 
   # Destroy (close) the active pane item.
   #
diff --git a/static/index.js b/static/index.js
index 12b149699..e5f84f794 100644
--- a/static/index.js
+++ b/static/index.js
@@ -13,6 +13,23 @@ window.onload = function() {
     var fs = require('fs');
     var path = require('path');
 
+    // Ensure ATOM_HOME is always set before anything else is required
+    if (!process.env.ATOM_HOME) {
+      var home;
+      if (process.platform === 'win32') {
+        home = process.env.USERPROFILE;
+      } else {
+        home = process.env.HOME;
+      }
+      var atomHome = path.join(home, '.atom');
+      try {
+        atomHome = fs.realpathSync(atomHome);
+      } catch (error) {
+        // Ignore since the path might just not exist yet.
+      }
+      process.env.ATOM_HOME = atomHome;
+    }
+
     // Skip "?loadSettings=".
     var rawLoadSettings = decodeURIComponent(location.search.substr(14));
     var loadSettings;