Add missing s in comspec

Closes atom/settings-view#288

apm/package.json

@@ -6,6 +6,6 @@
     "url": "https://github.com/atom/atom.git"
   },
   "dependencies": {
-    "atom-package-manager": "0.114.0"
+    "atom-package-manager": "0.116.0"
   }
 }

build/tasks/build-task.coffee

@@ -21,7 +21,9 @@ module.exports = (grunt) ->
 
     mkdir appDir
 
-    cp 'atom.sh', path.join(appDir, 'atom.sh')
+    if process.platform isnt 'win32'
+      cp 'atom.sh', path.join(appDir, 'atom.sh')
+
     cp 'package.json', path.join(appDir, 'package.json')
 
     packageDirectories = []
@@ -149,10 +151,10 @@ module.exports = (grunt) ->
           grunt.file.copy(sourcePath, path.resolve(appDir, '..', subDirectory, filename))
 
     if process.platform is 'win32'
-      # Set up chocolatey ignore and gui files
-      fs.writeFileSync path.join(appDir, 'apm', 'node_modules', 'atom-package-manager', 'bin', 'node.exe.ignore'), ''
-      fs.writeFileSync path.join(appDir, 'node_modules', 'symbols-view', 'vendor', 'ctags-win32.exe.ignore'), ''
-      fs.writeFileSync path.join(shellAppDir, 'atom.exe.gui'), ''
+      cp path.join('resources', 'win', 'atom.cmd'), path.join(shellAppDir, 'resources', 'cli', 'atom.cmd')
+      cp path.join('resources', 'win', 'atom.sh'), path.join(shellAppDir, 'resources', 'cli', 'atom.sh')
+      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')
 
     dependencies = ['compile', 'generate-license:save', 'generate-module-cache', 'compile-packages-slug']
     dependencies.push('copy-info-plist') if process.platform is 'darwin'

build/tasks/spec-task.coffee

@@ -11,6 +11,13 @@ module.exports = (grunt) ->
 
   packageSpecQueue = null
 
+  logDeprecations = (label, {stderr}={}) ->
+    if process.env.JANKY_SHA1 and stderr?.indexOf('Calls to deprecated functions') isnt -1
+      grunt.log.error(label)
+      stderr = stderr.replace(/^\[.*\] "/g, '')
+      stderr = stderr.replace(/source: .*$/g, '')
+      grunt.log.error(stderr)
+
   getAppPath = ->
     contentsDir = grunt.config.get('atom.contentsDir')
     switch process.platform
@@ -54,6 +61,7 @@ module.exports = (grunt) ->
           fs.unlinkSync(path.join(packagePath, 'ci.log'))
 
         failedPackages.push path.basename(packagePath) if error
+        logDeprecations("#{path.basename(packagePath)} Specs", results)
         callback()
 
     modulesDirectory = path.resolve('node_modules')
@@ -87,6 +95,7 @@ module.exports = (grunt) ->
       else
         # TODO: Restore concurrency on Windows
         packageSpecQueue.concurrency = concurrency
+        logDeprecations('Core Specs', results)
 
       callback(null, error)
 

docs/creating-a-theme.md

@@ -59,6 +59,8 @@ window in dev mode. To open a Dev Mode Atom window run `atom --dev .` in the
 terminal, use `cmd-shift-o` or use the _View > Developer > Open in Dev Mode_
 menu. When you edit your theme, changes will instantly be reflected!
 
+> Note: It's advised to _not_ specify a `font-family` in your syntax theme because it will override the Font Family field in Atom's settings. If you still like to recommend a font that goes well with your theme, we recommend you do so in your README.
+
 ## Creating an Interface Theme
 
 Interface themes **must** provide a `ui-variables.less` file which contains all

docs/customizing-atom.md

@@ -105,6 +105,7 @@ You can open this file in an editor from the _Atom > Open Your Config_ menu.
 - `core`
   - `disabledPackages`: An array of package names to disable
   - `excludeVcsIgnoredPaths`: Don't search within files specified by _.gitignore_
+  - `followSymlinks`: Follow symlinks when searching and scanning root directory
   - `ignoredNames`: File names to ignore across all of Atom
   - `projectHome`: The directory where projects are assumed to be located
   - `themes`: An array of theme names to load, in cascading order

menus/darwin.cson

@@ -202,7 +202,7 @@
 ]
 
 'context-menu':
-  '.overlayer': [
+  'atom-text-editor, .overlayer': [
     {label: 'Undo', command: 'core:undo'}
     {label: 'Redo', command: 'core:redo'}
     {type: 'separator'}

menus/linux.cson

@@ -160,7 +160,7 @@
 ]
 
 'context-menu':
-  '.overlayer': [
+  'atom-text-editor, .overlayer': [
     {label: 'Undo', command: 'core:undo'}
     {label: 'Redo', command: 'core:redo'}
     {type: 'separator'}

menus/win32.cson

@@ -181,7 +181,7 @@
 ]
 
 'context-menu':
-  '.overlayer': [
+  'atom-text-editor, .overlayer': [
     {label: 'Undo', command: 'core:undo'}
     {label: 'Redo', command: 'core:redo'}
     {type: 'separator'}

package.json

@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "0.158.0",
+  "version": "0.165.0",
   "description": "A hackable text editor for the 21st Century.",
   "main": "./src/browser/main.js",
   "repository": {
@@ -32,7 +32,7 @@
     "fs-plus": "^2.3.2",
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
-    "git-utils": "^2.1.5",
+    "git-utils": "^2.2",
     "grim": "0.12.0",
     "guid": "0.0.10",
     "jasmine-json": "~0.0",
@@ -53,7 +53,7 @@
     "reactionary-atom-fork": "^1.0.0",
     "runas": "1.0.1",
     "scandal": "1.0.3",
-    "scoped-property-store": "^0.15.0",
+    "scoped-property-store": "^0.15.4",
     "scrollbar-style": "^1.0.2",
     "season": "^1.0.2",
     "semver": "2.2.1",
@@ -63,7 +63,7 @@
     "temp": "0.7.0",
     "text-buffer": "^3.8.2",
     "theorist": "^1.0.2",
-    "underscore-plus": "^1.6.1",
+    "underscore-plus": "^1.6.6",
     "vm-compatibility-layer": "0.1.0"
   },
   "packageDependencies": {
@@ -73,56 +73,56 @@
     "atom-light-ui": "0.36.0",
     "base16-tomorrow-dark-theme": "0.22.0",
     "base16-tomorrow-light-theme": "0.5.0",
-    "solarized-dark-syntax": "0.26.0",
+    "solarized-dark-syntax": "0.29.0",
     "solarized-light-syntax": "0.13.0",
     "archive-view": "0.40.0",
     "autocomplete": "0.34.0",
-    "autoflow": "0.19.0",
+    "autoflow": "0.20.0",
     "autosave": "0.19.0",
     "background-tips": "0.18.0",
     "bookmarks": "0.31.0",
     "bracket-matcher": "0.64.0",
     "command-palette": "0.30.0",
-    "deprecation-cop": "0.19.0",
-    "dev-live-reload": "0.35.0",
-    "encoding-selector": "0.10.0",
+    "deprecation-cop": "0.20.0",
+    "dev-live-reload": "0.36.0",
+    "encoding-selector": "0.12.0",
     "exception-reporting": "0.21.0",
     "find-and-replace": "0.152.0",
     "fuzzy-finder": "0.62.0",
     "git-diff": "0.45.0",
     "go-to-line": "0.27.0",
-    "grammar-selector": "0.37.0",
-    "image-view": "0.43.0",
-    "incompatible-packages": "0.15.0",
-    "keybinding-resolver": "0.23.0",
+    "grammar-selector": "0.40.0",
+    "image-view": "0.44.0",
+    "incompatible-packages": "0.16.0",
+    "keybinding-resolver": "0.24.0",
     "link": "0.28.0",
     "markdown-preview": "0.112.0",
-    "metrics": "0.39.0",
-    "notifications": "0.16.0",
+    "metrics": "0.40.0",
+    "notifications": "0.21.0",
     "open-on-github": "0.31.0",
-    "package-generator": "0.33.0",
-    "release-notes": "0.36.0",
+    "package-generator": "0.34.0",
+    "release-notes": "0.43.0",
     "settings-view": "0.161.0",
-    "snippets": "0.58.0",
-    "spell-check": "0.44.0",
-    "status-bar": "0.53.0",
-    "styleguide": "0.35.0",
+    "snippets": "0.60.0",
+    "spell-check": "0.45.0",
+    "status-bar": "0.54.0",
+    "styleguide": "0.36.0",
     "symbols-view": "0.70.0",
-    "tabs": "0.57.0",
+    "tabs": "0.58.0",
     "timecop": "0.24.0",
-    "tree-view": "0.138.0",
+    "tree-view": "0.139.0",
     "update-package-dependencies": "0.7.0",
     "welcome": "0.21.0",
     "whitespace": "0.27.0",
-    "wrap-guide": "0.26.0",
+    "wrap-guide": "0.27.0",
     "language-c": "0.33.0",
     "language-clojure": "0.9.0",
     "language-coffee-script": "0.38.1",
-    "language-css": "0.23.1",
+    "language-css": "0.24.0",
     "language-gfm": "0.55.0",
     "language-git": "0.9.0",
     "language-go": "0.19.1",
-    "language-html": "0.26.1",
+    "language-html": "0.27.0",
     "language-hyperlink": "0.12.2",
     "language-java": "0.13.0",
     "language-javascript": "0.51.0",
@@ -135,14 +135,14 @@
     "language-php": "0.18.0",
     "language-property-list": "0.7.0",
     "language-python": "0.26.0",
-    "language-ruby": "0.44.0",
+    "language-ruby": "0.45.0",
     "language-ruby-on-rails": "0.18.0",
-    "language-sass": "0.28.0",
+    "language-sass": "0.29.0",
     "language-shellscript": "0.10.1",
     "language-source": "0.8.0",
     "language-sql": "0.11.0",
     "language-text": "0.6.0",
-    "language-todo": "0.14.0",
+    "language-todo": "0.15.0",
     "language-toml": "0.14.1",
     "language-xml": "0.25.0",
     "language-yaml": "0.21.0"

resources/linux/debian/control.in

@@ -1,6 +1,6 @@
 Package: <%= name %>
 Version: <%= version %>
-Depends: gconf2, gconf-service, libgtk2.0-0, libudev0 | libudev1, libgcrypt11, libnotify4, libxtst6, libnss3, python, gvfs-bin, xdg-utils
+Depends: git, gconf2, gconf-service, libgtk2.0-0, libudev0 | libudev1, libgcrypt11, libnotify4, libxtst6, libnss3, python, gvfs-bin, xdg-utils
 Suggests: libgnome-keyring0, gir1.2-gnomekeyring-1.0
 Section: <%= section %>
 Priority: optional

resources/win/apm.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+"$0/../../app/apm/node_modules/atom-package-manager/bin/node.exe" "$0/../../app/apm/node_modules/atom-package-manager/lib/cli.js" "$@"

resources/win/atom.cmd

@@ -0,0 +1,22 @@
+@echo off
+
+SET EXPECT_OUTPUT=
+
+FOR %%a IN (%*) DO (
+  IF /I "%%a"=="-f"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--foreground" SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-h"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--help"       SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-t"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--test"       SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-v"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--version"    SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="-w"           SET EXPECT_OUTPUT=YES
+  IF /I "%%a"=="--wait"       SET EXPECT_OUTPUT=YES
+)
+
+IF "%EXPECT_OUTPUT%"=="YES" (
+  "%~dp0\..\..\atom.exe" %*
+) ELSE (
+  "%~dp0\..\app\apm\node_modules\atom-package-manager\bin\node.exe" "%~dp0\atom.js" %*
+)

resources/win/atom.js

@@ -0,0 +1,9 @@
+var path  = require('path');
+var spawn = require('child_process').spawn;
+
+var atomCommandPath = path.resolve(__dirname, '..', '..', 'atom.exe');
+var arguments = process.argv.slice(2);
+arguments.unshift('--executed-from', process.cwd());
+var options = {detached: true, stdio: 'ignore'};
+spawn(atomCommandPath, arguments, options);
+process.exit(0);

resources/win/atom.sh

@@ -0,0 +1,22 @@
+#!/bin/sh
+
+while getopts ":fhtvw-:" opt; do
+  case "$opt" in
+    -)
+      case "${OPTARG}" in
+        foreground|help|test|version|wait)
+          EXPECT_OUTPUT=1
+        ;;
+      esac
+      ;;
+    f|h|t|v|w)
+      EXPECT_OUTPUT=1
+      ;;
+  esac
+done
+
+if [ $EXPECT_OUTPUT ]; then
+  "$0/../../../atom.exe" "$@"
+else
+  "$0/../../app/apm/node_modules/atom-package-manager/bin/node.exe" "$0/../atom.js" "$@"
+fi

script/cibuild-atom-rpm

@@ -4,7 +4,9 @@ set -e
 
 docker build -t atom-rpm .
 docker run \
+ --rm \
  --env JANKY_SHA1="$JANKY_SHA1" \
  --env JANKY_BRANCH="$JANKY_BRANCH" \
  --env ATOM_ACCESS_TOKEN="$BUILD_ATOM_RPM_ACCESS_TOKEN" \
  atom-rpm /atom/script/rpmbuild
+docker rmi atom-rpm

spec/atom-spec.coffee

@@ -54,6 +54,7 @@ describe "the `atom` global", ->
   describe "loading default config", ->
     it 'loads the default core config', ->
       expect(atom.config.get('core.excludeVcsIgnoredPaths')).toBe true
+      expect(atom.config.get('core.followSymlinks')).toBe false
       expect(atom.config.get('editor.showInvisibles')).toBe false
 
   describe "window onerror handler", ->

spec/buffered-process-spec.coffee

@@ -1,3 +1,5 @@
+ChildProcess = require 'child_process'
+path = require 'path'
 BufferedProcess  = require '../src/buffered-process'
 
 describe "BufferedProcess", ->
@@ -40,3 +42,34 @@ describe "BufferedProcess", ->
           expect(window.onerror).toHaveBeenCalled()
           expect(window.onerror.mostRecentCall.args[0]).toContain 'Failed to spawn command `bad-command-nope`'
           expect(window.onerror.mostRecentCall.args[4].name).toBe 'BufferedProcessError'
+
+  describe "on Windows", ->
+    originalPlatform = null
+
+    beforeEach ->
+      # Prevent any commands from actually running and affecting the host
+      originalSpawn = ChildProcess.spawn
+      spyOn(ChildProcess, 'spawn').andCallFake ->
+        # Just spawn something that won't actually modify the host
+        if originalPlatform is 'win32'
+          originalSpawn('dir')
+        else
+          originalSpawn('ls')
+
+      originalPlatform = process.platform
+      Object.defineProperty process, 'platform', value: 'win32'
+
+    afterEach ->
+      Object.defineProperty process, 'platform', value: originalPlatform
+
+    describe "when the explorer command is spawned on Windows", ->
+      it "doesn't quote arguments of the form /root,C...", ->
+        new BufferedProcess({command: 'explorer.exe', args: ['/root,C:\\foo']})
+        expect(ChildProcess.spawn.argsForCall[0][1][2]).toBe '"explorer.exe /root,C:\\foo"'
+
+    it "spawns the command using a cmd.exe wrapper", ->
+      new BufferedProcess({command: 'dir'})
+      expect(path.basename(ChildProcess.spawn.argsForCall[0][0])).toBe 'cmd.exe'
+      expect(ChildProcess.spawn.argsForCall[0][1][0]).toBe '/s'
+      expect(ChildProcess.spawn.argsForCall[0][1][1]).toBe '/c'
+      expect(ChildProcess.spawn.argsForCall[0][1][2]).toBe '"dir"'

spec/config-spec.coffee

@@ -4,7 +4,6 @@ CSON = require 'season'
 fs = require 'fs-plus'
 
 describe "Config", ->
-  dotAtomPath = path.join(temp.dir, 'dot-atom-dir')
   dotAtomPath = null
 
   beforeEach ->
@@ -407,11 +406,11 @@ describe "Config", ->
       it "fires the callback every time the observed value changes", ->
         observeHandler.reset() # clear the initial call
         atom.config.set('foo.bar.baz', "value 2")
-        expect(observeHandler).toHaveBeenCalledWith({newValue: 'value 2', oldValue: 'value 1', keyPath: 'foo.bar.baz'})
+        expect(observeHandler).toHaveBeenCalledWith({newValue: 'value 2', oldValue: 'value 1'})
         observeHandler.reset()
 
         atom.config.set('foo.bar.baz', "value 1")
-        expect(observeHandler).toHaveBeenCalledWith({newValue: 'value 1', oldValue: 'value 2', keyPath: 'foo.bar.baz'})
+        expect(observeHandler).toHaveBeenCalledWith({newValue: 'value 1', oldValue: 'value 2'})
 
     describe 'when a keyPath is not specified', ->
       beforeEach ->
@@ -425,15 +424,21 @@ describe "Config", ->
       it "fires the callback every time any value changes", ->
         observeHandler.reset() # clear the initial call
         atom.config.set('foo.bar.baz', "value 2")
-        expect(observeHandler).toHaveBeenCalledWith({newValue: 'value 2', oldValue: 'value 1', keyPath: 'foo.bar.baz'})
+        expect(observeHandler).toHaveBeenCalled()
+        expect(observeHandler.mostRecentCall.args[0].newValue.foo.bar.baz).toBe("value 2")
+        expect(observeHandler.mostRecentCall.args[0].oldValue.foo.bar.baz).toBe("value 1")
 
         observeHandler.reset()
         atom.config.set('foo.bar.baz', "value 1")
-        expect(observeHandler).toHaveBeenCalledWith({newValue: 'value 1', oldValue: 'value 2', keyPath: 'foo.bar.baz'})
+        expect(observeHandler).toHaveBeenCalled()
+        expect(observeHandler.mostRecentCall.args[0].newValue.foo.bar.baz).toBe("value 1")
+        expect(observeHandler.mostRecentCall.args[0].oldValue.foo.bar.baz).toBe("value 2")
 
         observeHandler.reset()
         atom.config.set('foo.bar.int', 1)
-        expect(observeHandler).toHaveBeenCalledWith({newValue: 1, oldValue: undefined, keyPath: 'foo.bar.int'})
+        expect(observeHandler).toHaveBeenCalled()
+        expect(observeHandler.mostRecentCall.args[0].newValue.foo.bar.int).toBe(1)
+        expect(observeHandler.mostRecentCall.args[0].oldValue.foo.bar.int).toBe(undefined)
 
   describe ".observe(keyPath)", ->
     [observeHandler, observeSubscription] = []
@@ -455,6 +460,10 @@ describe "Config", ->
       atom.config.set('foo.bar.baz', "value 1")
       expect(observeHandler).toHaveBeenCalledWith("value 1")
 
+      observeHandler.reset()
+      atom.config.loadUserConfig()
+      expect(observeHandler).toHaveBeenCalledWith(undefined)
+
     it "fires the callback when the observed value is deleted", ->
       observeHandler.reset() # clear the initial call
       atom.config.set('foo.bar.baz', undefined)
@@ -483,6 +492,26 @@ describe "Config", ->
       atom.config.set('foo.bar.baz', "value 10")
       expect(bazCatHandler).not.toHaveBeenCalled()
 
+  describe ".transact(callback)", ->
+    changeSpy = null
+
+    beforeEach ->
+      changeSpy = jasmine.createSpy('onDidChange callback')
+      atom.config.onDidChange("foo.bar.baz", changeSpy)
+
+    it "allows only one change event for the duration of the given callback", ->
+      atom.config.transact ->
+        atom.config.set("foo.bar.baz", 1)
+        atom.config.set("foo.bar.baz", 2)
+        atom.config.set("foo.bar.baz", 3)
+
+      expect(changeSpy.callCount).toBe(1)
+      expect(changeSpy.argsForCall[0][0]).toEqual(newValue: 3, oldValue: undefined)
+
+    it "does not emit an event if no changes occur while paused", ->
+      atom.config.transact ->
+      expect(changeSpy).not.toHaveBeenCalled()
+
   describe ".initializeConfigDirectory()", ->
     beforeEach ->
       if fs.existsSync(dotAtomPath)
@@ -1186,25 +1215,25 @@ describe "Config", ->
         atom.config.onDidChange [".source.coffee", ".string.quoted.double.coffee"], keyPath, changeSpy = jasmine.createSpy()
 
         atom.config.set("foo.bar.baz", 12)
-        expect(changeSpy).toHaveBeenCalledWith({oldValue: undefined, newValue: 12, keyPath})
+        expect(changeSpy).toHaveBeenCalledWith({oldValue: undefined, newValue: 12})
         changeSpy.reset()
 
         disposable1 = atom.config.addScopedSettings("a", ".source .string.quoted.double", foo: bar: baz: 22)
-        expect(changeSpy).toHaveBeenCalledWith({oldValue: 12, newValue: 22, keyPath})
+        expect(changeSpy).toHaveBeenCalledWith({oldValue: 12, newValue: 22})
         changeSpy.reset()
 
         disposable2 = atom.config.addScopedSettings("b", ".source.coffee .string.quoted.double.coffee", foo: bar: baz: 42)
-        expect(changeSpy).toHaveBeenCalledWith({oldValue: 22, newValue: 42, keyPath})
+        expect(changeSpy).toHaveBeenCalledWith({oldValue: 22, newValue: 42})
         changeSpy.reset()
 
         disposable2.dispose()
-        expect(changeSpy).toHaveBeenCalledWith({oldValue: 42, newValue: 22, keyPath})
+        expect(changeSpy).toHaveBeenCalledWith({oldValue: 42, newValue: 22})
         changeSpy.reset()
 
         disposable1.dispose()
-        expect(changeSpy).toHaveBeenCalledWith({oldValue: 22, newValue: 12, keyPath})
+        expect(changeSpy).toHaveBeenCalledWith({oldValue: 22, newValue: 12})
         changeSpy.reset()
 
         atom.config.set("foo.bar.baz", undefined)
-        expect(changeSpy).toHaveBeenCalledWith({oldValue: 12, newValue: undefined, keyPath})
+        expect(changeSpy).toHaveBeenCalledWith({oldValue: 12, newValue: undefined})
         changeSpy.reset()

spec/git-spec.coffee

@@ -259,6 +259,10 @@ describe "GitRepository", ->
       editor.getBuffer().emitter.emit 'did-change-path'
       expect(statusHandler.callCount).toBe 1
 
+    it "stops listening to the buffer when the repository is destroyed (regression)", ->
+      atom.project.getRepositories()[0].destroy()
+      expect(-> editor.save()).not.toThrow()
+
   describe "when a project is deserialized", ->
     [buffer, project2] = []
 

spec/jasmine-helper.coffee

@@ -25,6 +25,9 @@ module.exports.runSpecSuite = (specSuite, logFile, logErrors=true) ->
         log(str)
       onComplete: (runner) ->
         fs.closeSync(logStream) if logStream?
+        if process.env.JANKY_SHA1
+          grim = require 'grim'
+          grim.logDeprecations() if grim.getDeprecationsLength() > 0
         atom.exit(runner.results().failedCount > 0 ? 1 : 0)
   else
     AtomReporter = require './atom-reporter'

spec/squirrel-update-spec.coffee

@@ -0,0 +1,94 @@
+ChildProcess = require 'child_process'
+{EventEmitter} = require 'events'
+fs = require 'fs-plus'
+path = require 'path'
+temp = require 'temp'
+SquirrelUpdate = require '../src/browser/squirrel-update'
+
+describe "Windows squirrel updates", ->
+  tempHomeDirectory = null
+
+  beforeEach ->
+    # Prevent the actually home directory from being manipulated
+    tempHomeDirectory = temp.mkdirSync('atom-temp-home-')
+    spyOn(fs, 'getHomeDirectory').andReturn(tempHomeDirectory)
+
+    # Prevent any commands from actually running and affecting the host
+    originalSpawn = ChildProcess.spawn
+    spyOn(ChildProcess, 'spawn').andCallFake (command, args) ->
+      if path.basename(command) is 'Update.exe' and args?[0] is '--createShortcut'
+        fs.writeFileSync(path.join(tempHomeDirectory, 'Desktop', 'Atom.lnk'), '')
+
+      # Just spawn something that won't actually modify the host
+      if process.platform is 'win32'
+        originalSpawn('dir')
+      else
+        originalSpawn('ls')
+
+  it "quits the app on all squirrel events", ->
+    app = quit: jasmine.createSpy('quit')
+
+    expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-install')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
+    runs ->
+      app.quit.reset()
+      expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-updated')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
+    runs ->
+      app.quit.reset()
+      expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-uninstall')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
+    runs ->
+      app.quit.reset()
+      expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-obsolete')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
+    runs ->
+      expect(SquirrelUpdate.handleStartupEvent(app, '--not-squirrel')).toBe false
+
+  it "keeps the desktop shortcut deleted on updates if it was previously deleted after install", ->
+    desktopShortcutPath = path.join(tempHomeDirectory, 'Desktop', 'Atom.lnk')
+    expect(fs.existsSync(desktopShortcutPath)).toBe false
+
+    app = quit: jasmine.createSpy('quit')
+    expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-install')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
+    runs ->
+      app.quit.reset()
+      expect(fs.existsSync(desktopShortcutPath)).toBe true
+      fs.removeSync(desktopShortcutPath)
+      expect(fs.existsSync(desktopShortcutPath)).toBe false
+      expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-updated')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
+    runs ->
+      expect(fs.existsSync(desktopShortcutPath)).toBe false
+
+  describe ".restartAtom", ->
+    it "quits the app and spawns a new one", ->
+      app = new EventEmitter()
+      app.quit = jasmine.createSpy('quit')
+
+      SquirrelUpdate.restartAtom(app)
+      expect(app.quit.callCount).toBe 1
+
+      expect(ChildProcess.spawn.callCount).toBe 0
+      app.emit('will-quit')
+      expect(ChildProcess.spawn.callCount).toBe 1
+      expect(path.basename(ChildProcess.spawn.argsForCall[0][0])).toBe 'atom.cmd'

spec/text-editor-component-spec.coffee

@@ -1612,6 +1612,22 @@ describe "TextEditorComponent", ->
         expect(nextAnimationFrame).toBe noAnimationFrame
         expect(editor.getSelectedScreenRange()).toEqual [[2, 4], [6, 8]]
 
+      describe "when the editor is destroyed while dragging", ->
+        it "cleans up the handlers for window.mouseup and window.mousemove", ->
+          linesNode.dispatchEvent(buildMouseEvent('mousedown', clientCoordinatesForScreenPosition([2, 4]), which: 1))
+          linesNode.dispatchEvent(buildMouseEvent('mousemove', clientCoordinatesForScreenPosition([6, 8]), which: 1))
+          nextAnimationFrame()
+
+          spyOn(window, 'removeEventListener').andCallThrough()
+
+          linesNode.dispatchEvent(buildMouseEvent('mousemove', clientCoordinatesForScreenPosition([6, 10]), which: 1))
+          editor.destroy()
+          nextAnimationFrame()
+
+          call.args.pop() for call in window.removeEventListener.calls
+          expect(window.removeEventListener).toHaveBeenCalledWith('mouseup')
+          expect(window.removeEventListener).toHaveBeenCalledWith('mousemove')
+
     describe "when a line is folded", ->
       beforeEach ->
         editor.foldBufferRow 4
@@ -2697,26 +2713,35 @@ describe "TextEditorComponent", ->
         expect(line1LeafNodes[1].classList.contains('indent-guide')).toBe false
 
   describe "middle mouse paste on Linux", ->
-    it "pastes the previously selected text", ->
+    originalPlatform = null
+
+    beforeEach ->
+      originalPlatform = process.platform
+      Object.defineProperty process, 'platform', value: 'linux'
+
+    afterEach ->
+      Object.defineProperty process, 'platform', value: originalPlatform
+
+    it "pastes the previously selected text at the clicked location", ->
+      jasmine.unspy(window, 'setTimeout')
+      clipboardWrittenTo = false
       spyOn(require('ipc'), 'send').andCallFake (eventName, selectedText) ->
         if eventName is 'write-text-to-selection-clipboard'
           require('clipboard').writeText(selectedText, 'selection')
+          clipboardWrittenTo = true
 
       atom.clipboard.write('')
-      component.listenForMiddleMousePaste()
-
-      editor.setCursorBufferPosition([10, 0])
-      componentNode.querySelector('.scroll-view').dispatchEvent(buildMouseEvent('mouseup', which: 2))
-
-      expect(atom.clipboard.read()).toBe ''
-      expect(editor.lineTextForBufferRow(10)).toBe ''
-
+      component.trackSelectionClipboard()
       editor.setSelectedBufferRange([[1, 6], [1, 10]])
-      editor.setCursorBufferPosition([10, 0])
-      componentNode.querySelector('.scroll-view').dispatchEvent(buildMouseEvent('mouseup', which: 2))
 
-      expect(atom.clipboard.read()).toBe 'sort'
-      expect(editor.lineTextForBufferRow(10)).toBe 'sort'
+      waitsFor ->
+        clipboardWrittenTo
+
+      runs ->
+        componentNode.querySelector('.scroll-view').dispatchEvent(buildMouseEvent('mousedown', clientCoordinatesForScreenPosition([10, 0]), button: 1))
+        componentNode.querySelector('.scroll-view').dispatchEvent(buildMouseEvent('mouseup', clientCoordinatesForScreenPosition([10, 0]), which: 2))
+        expect(atom.clipboard.read()).toBe 'sort'
+        expect(editor.lineTextForBufferRow(10)).toBe 'sort'
 
   buildMouseEvent = (type, properties...) ->
     properties = extend({bubbles: true, cancelable: true}, properties...)

spec/text-editor-element-spec.coffee

@@ -32,6 +32,31 @@ describe "TextEditorElement", ->
       element.setModel(model)
       expect(element.hasAttribute('mini')).toBe true
 
+  describe "when the editor is attached to the DOM", ->
+    describe "when the editor.useShadowDOM config option is true", ->
+      it "mounts the react component and unmounts when removed from the dom", ->
+        atom.config.set('editor.useShadowDOM', true)
+
+        element = new TextEditorElement
+        jasmine.attachToDOM(element)
+
+        component = element.component
+        expect(component.isMounted()).toBe true
+        element.getModel().destroy()
+        expect(component.isMounted()).toBe false
+
+    describe "when the editor.useShadowDOM config option is false", ->
+      it "mounts the react component and unmounts when removed from the dom", ->
+        atom.config.set('editor.useShadowDOM', false)
+
+        element = new TextEditorElement
+        jasmine.attachToDOM(element)
+
+        component = element.component
+        expect(component.isMounted()).toBe true
+        element.getModel().destroy()
+        expect(component.isMounted()).toBe false
+
   describe "focus and blur handling", ->
     describe "when the editor.useShadowDOM config option is true", ->
       it "proxies focus/blur events to/from the hidden input inside the shadow root", ->

spec/workspace-view-spec.coffee

@@ -3,6 +3,7 @@ Q = require 'q'
 path = require 'path'
 temp = require 'temp'
 TextEditorView = require '../src/text-editor-view'
+Pane = require '../src/pane'
 PaneView = require '../src/pane-view'
 Workspace = require '../src/workspace'
 
@@ -294,3 +295,39 @@ describe "WorkspaceView", ->
 
       modalContainer = workspaceElement.querySelector('atom-panel-container.modal')
       expect(modalContainer.parentNode).toBe workspaceElement
+
+  describe "::saveActivePaneItem()", ->
+    describe "when there is an error", ->
+      it "emits a warning notification when the file cannot be saved", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          throw new Error("'/some/file' is a directory")
+
+        atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
+        atom.workspace.saveActivePaneItem()
+        expect(addedSpy).toHaveBeenCalled()
+        expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
+
+      it "emits a warning notification when the directory cannot be written to", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          throw new Error("ENOTDIR, not a directory '/Some/dir/and-a-file.js'")
+
+        atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
+        atom.workspace.saveActivePaneItem()
+        expect(addedSpy).toHaveBeenCalled()
+        expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
+
+      it "emits a warning notification when the user does not have permission", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          throw new Error("EACCES, permission denied '/Some/dir/and-a-file.js'")
+
+        atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
+        atom.workspace.saveActivePaneItem()
+        expect(addedSpy).toHaveBeenCalled()
+        expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
+
+      it "emits a warning notification when the file cannot be saved", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          throw new Error("no one knows")
+
+        save = -> atom.workspace.saveActivePaneItem()
+        expect(save).toThrow()

src/atom.coffee

@@ -341,6 +341,10 @@ class Atom extends Model
   inDevMode: ->
     @getLoadSettings().devMode
 
+  # Public: Is the current window in safe mode?
+  inSafeMode: ->
+    @getLoadSettings().safeMode
+
   # Public: Is the current window running specs?
   inSpecMode: ->
     @getLoadSettings().isSpec

src/browser/atom-application.coffee

@@ -140,14 +140,18 @@ class AtomApplication
 
   # Registers basic application commands, non-idempotent.
   handleEvents: ->
+    getLoadSettings = =>
+      devMode: @focusedWindow()?.devMode
+      safeMode: @focusedWindow()?.safeMode
+
     @on 'application:run-all-specs', -> @runSpecs(exitWhenDone: false, resourcePath: global.devResourcePath, safeMode: @focusedWindow()?.safeMode)
     @on 'application:run-benchmarks', -> @runBenchmarks()
     @on 'application:quit', -> app.quit()
-    @on 'application:new-window', -> @openPath(windowDimensions: @focusedWindow()?.getDimensions())
+    @on 'application:new-window', -> @openPath(_.extend(windowDimensions: @focusedWindow()?.getDimensions(), getLoadSettings()))
     @on 'application:new-file', -> (@focusedWindow() ? this).openPath()
-    @on 'application:open', -> @promptForPath(type: 'all')
-    @on 'application:open-file', -> @promptForPath(type: 'file')
-    @on 'application:open-folder', -> @promptForPath(type: 'folder')
+    @on 'application:open', -> @promptForPath(_.extend(type: 'all', getLoadSettings()))
+    @on 'application:open-file', -> @promptForPath(_.extend(type: 'file', getLoadSettings()))
+    @on 'application:open-folder', -> @promptForPath(_.extend(type: 'folder', getLoadSettings()))
     @on 'application:open-dev', -> @promptForPath(devMode: true)
     @on 'application:open-safe', -> @promptForPath(safeMode: true)
     @on 'application:inspect', ({x,y, atomWindow}) ->

src/browser/atom-window.coffee

@@ -18,7 +18,7 @@ class AtomWindow
   isSpec: null
 
   constructor: (settings={}) ->
-    {@resourcePath, pathToOpen, initialLine, initialColumn, @isSpec, @exitWhenDone, @safeMode} = settings
+    {@resourcePath, pathToOpen, initialLine, initialColumn, @isSpec, @exitWhenDone, @safeMode, @devMode} = settings
 
     # Normalize to make sure drive letter case is consistent on Windows
     @resourcePath = path.normalize(@resourcePath) if @resourcePath
@@ -38,6 +38,8 @@ class AtomWindow
     loadSettings.windowState ?= '{}'
     loadSettings.appVersion = app.getVersion()
     loadSettings.resourcePath = @resourcePath
+    loadSettings.devMode ?= false
+    loadSettings.safeMode ?= false
 
     # Only send to the first non-spec window created
     if @constructor.includeShellLoadTime and not @isSpec

src/browser/auto-updater-win32.coffee

@@ -9,7 +9,7 @@ class AutoUpdater
 
   quitAndInstall: ->
     if SquirrelUpdate.existsSync()
-      SquirrelUpdate.restartAtom()
+      SquirrelUpdate.restartAtom(require('app'))
     else
       require('auto-updater').quitAndInstall()
 

src/browser/main.coffee

@@ -26,7 +26,8 @@ fs.lstatSyncNoException = (pathToStat) ->
 start = ->
   if process.platform is 'win32'
     SquirrelUpdate = require './squirrel-update'
-    return if SquirrelUpdate.handleStartupEvent()
+    squirrelCommand = process.argv[1]
+    return if SquirrelUpdate.handleStartupEvent(app, squirrelCommand)
 
   args = parseCommandLine()
 

src/browser/squirrel-update.coffee

@@ -1,9 +1,9 @@
-app = require 'app'
 ChildProcess = require 'child_process'
 fs = require 'fs-plus'
 path = require 'path'
 
-rootAtomFolder = path.resolve(process.execPath, '..', '..')
+appFolder = path.resolve(process.execPath, '..')
+rootAtomFolder = path.resolve(appFolder, '..')
 binFolder = path.join(rootAtomFolder, 'bin')
 updateDotExe = path.join(rootAtomFolder, 'Update.exe')
 exeName = path.basename(process.execPath)
@@ -111,22 +111,26 @@ uninstallContextMenu = (callback) ->
 addCommandsToPath = (callback) ->
   installCommands = (callback) ->
     atomCommandPath = path.join(binFolder, 'atom.cmd')
-    relativeExePath = path.relative(binFolder, process.execPath)
-    atomCommand = """
-      @echo off
-      "%~dp0\\#{relativeExePath}" %*
-    """
+    relativeAtomPath = path.relative(binFolder, path.join(appFolder, 'resources', 'cli', 'atom.cmd'))
+    atomCommand = "@echo off\r\n\"%~dp0\\#{relativeAtomPath}\" %*"
+
+    atomShCommandPath = path.join(binFolder, 'atom')
+    relativeAtomShPath = path.relative(binFolder, path.join(appFolder, 'resources', 'cli', 'atom.sh'))
+    atomShCommand = "#!/bin/sh\r\n\"$0/../#{relativeAtomShPath.replace(/\\/g, '/')}\" \"$@\""
 
     apmCommandPath = path.join(binFolder, 'apm.cmd')
     relativeApmPath = path.relative(binFolder, path.join(process.resourcesPath, 'app', 'apm', 'node_modules', 'atom-package-manager', 'bin', 'apm.cmd'))
-    apmCommand = """
-      @echo off
-      "%~dp0\\#{relativeApmPath}" %*
-    """
+    apmCommand = "@echo off\r\n\"%~dp0\\#{relativeApmPath}\" %*"
+
+    apmShCommandPath = path.join(binFolder, 'apm')
+    relativeApmShPath = path.relative(binFolder, path.join(appFolder, 'resources', 'cli', 'apm.sh'))
+    apmShCommand = "#!/bin/sh\r\n\"$0/../#{relativeApmShPath.replace(/\\/g, '/')}\" \"$@\""
 
     fs.writeFile atomCommandPath, atomCommand, ->
-      fs.writeFile apmCommandPath, apmCommand, ->
-        callback()
+      fs.writeFile atomShCommandPath, atomShCommand, ->
+        fs.writeFile apmCommandPath, apmCommand, ->
+          fs.writeFile apmShCommandPath, apmShCommand, ->
+            callback()
 
   addBinToPath = (pathSegments, callback) ->
     pathSegments.push(binFolder)
@@ -161,12 +165,29 @@ removeCommandsFromPath = (callback) ->
 
 # Create a desktop and start menu shortcut by using the command line API
 # provided by Squirrel's Update.exe
-createShortcut = (callback) ->
+createShortcuts = (callback) ->
   spawnUpdate(['--createShortcut', exeName], callback)
 
+# Update the desktop and start menu shortcuts by using the command line API
+# provided by Squirrel's Update.exe
+updateShortcuts = (callback) ->
+  if homeDirectory = fs.getHomeDirectory()
+    desktopShortcutPath = path.join(homeDirectory, 'Desktop', 'Atom.lnk')
+    # Check if the desktop shortcut has been previously deleted and
+    # and keep it deleted if it was
+    fs.exists desktopShortcutPath, (desktopShortcutExists) ->
+      createShortcuts ->
+        if desktopShortcutExists
+          callback()
+        else
+          # Remove the unwanted desktop shortcut that was recreated
+          fs.unlink(desktopShortcutPath, callback)
+  else
+    createShortcuts(callback)
+
 # Remove the desktop and start menu shortcuts by using the command line API
 # provided by Squirrel's Update.exe
-removeShortcut = (callback) ->
+removeShortcuts = (callback) ->
   spawnUpdate(['--removeShortcut', exeName], callback)
 
 exports.spawn = spawnUpdate
@@ -176,21 +197,29 @@ exports.existsSync = ->
   fs.existsSync(updateDotExe)
 
 # Restart Atom using the version pointed to by the atom.cmd shim
-exports.restartAtom = ->
-  app.once 'will-quit', -> spawn(path.join(binFolder, 'atom.cmd'))
+exports.restartAtom = (app) ->
+  if projectPath = global.atomApplication?.lastFocusedWindow?.projectPath
+    args = [projectPath]
+  app.once 'will-quit', -> spawn(path.join(binFolder, 'atom.cmd'), args)
   app.quit()
 
 # Handle squirrel events denoted by --squirrel-* command line arguments.
-exports.handleStartupEvent = ->
-  switch process.argv[1]
-    when '--squirrel-install', '--squirrel-updated'
-      createShortcut ->
+exports.handleStartupEvent = (app, squirrelCommand) ->
+  switch squirrelCommand
+    when '--squirrel-install'
+      createShortcuts ->
+        installContextMenu ->
+          addCommandsToPath ->
+            app.quit()
+      true
+    when '--squirrel-updated'
+      updateShortcuts ->
         installContextMenu ->
           addCommandsToPath ->
             app.quit()
       true
     when '--squirrel-uninstall'
-      removeShortcut ->
+      removeShortcuts ->
         uninstallContextMenu ->
           removeCommandsFromPath ->
             app.quit()

src/buffered-process.coffee

@@ -1,6 +1,7 @@
 _ = require 'underscore-plus'
 ChildProcess = require 'child_process'
 {Emitter} = require 'event-kit'
+path = require 'path'
 
 # Extended: A wrapper which provides standard error/output line buffering for
 # Node's ChildProcess.
@@ -47,12 +48,12 @@ class BufferedProcess
     @emitter = new Emitter
     options ?= {}
     # Related to joyent/node#2318
-    if process.platform is "win32"
+    if process.platform is 'win32'
       # Quote all arguments and escapes inner quotes
       if args?
         cmdArgs = args.filter (arg) -> arg?
-        cmdArgs = cmdArgs.map (arg) ->
-          if command in ['explorer.exe', 'explorer'] and /^\/[a-zA-Z]+,.*$/.test(arg)
+        cmdArgs = cmdArgs.map (arg) =>
+          if @isExplorerCommand(command) and /^\/[a-zA-Z]+,.*$/.test(arg)
             # Don't wrap /root,C:\folder style arguments to explorer calls in
             # quotes since they will not be interpreted correctly if they are
             arg
@@ -67,7 +68,7 @@ class BufferedProcess
       cmdArgs = ['/s', '/c', "\"#{cmdArgs.join(' ')}\""]
       cmdOptions = _.clone(options)
       cmdOptions.windowsVerbatimArguments = true
-      @process = ChildProcess.spawn(process.env.comspec or 'cmd.exe', cmdArgs, cmdOptions)
+      @process = ChildProcess.spawn(@getCmdPath(), cmdArgs, cmdOptions)
     else
       @process = ChildProcess.spawn(command, args, options)
     @killed = false
@@ -191,6 +192,22 @@ class BufferedProcess
     @process?.kill()
     @process = null
 
+  isExplorerCommand: (command) ->
+    if command is 'explorer.exe' or command is 'explorer'
+      true
+    else if process.env.SystemRoot
+      command is path.join(process.env.SystemRoot, 'explorer.exe') or command is path.join(process.env.SystemRoot, 'explorer')
+    else
+      false
+
+  getCmdPath: ->
+    if process.env.comspec
+      process.env.comspec
+    else if process.env.SystemRoot
+      path.join(process.env.SystemRoot, 'System32', 'cmd.exe')
+    else
+      'cmd.exe'
+
   # Public: Terminate the process.
   kill: ->
     return if @killed

src/config-schema.coffee

@@ -16,6 +16,11 @@ module.exports =
         type: 'boolean'
         default: true
         title: 'Exclude VCS Ignored Paths'
+      followSymlinks:
+        type: 'boolean'
+        default: false
+        title: 'Follow symlinks'
+        description: 'Used when searching and when opening files with the fuzzy finder.'
       disabledPackages:
         type: 'array'
         default: []

src/config.coffee

@@ -6,7 +6,7 @@ CSON = require 'season'
 path = require 'path'
 async = require 'async'
 pathWatcher = require 'pathwatcher'
-{deprecate} = require 'grim'
+Grim = require 'grim'
 
 ScopedPropertyStore = require 'scoped-property-store'
 ScopeDescriptor = require './scope-descriptor'
@@ -318,6 +318,7 @@ class Config
     @configFileHasErrors = false
     @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
     @configFilePath ?= path.join(@configDirPath, 'config.cson')
+    @transactDepth = 0
 
   ###
   Section: Config Subscription
@@ -362,7 +363,7 @@ class Config
 
       message = ""
       message = "`callNow` was set to false. Use ::onDidChange instead. Note that ::onDidChange calls back with different arguments." if options.callNow == false
-      deprecate "Config::observe no longer supports options; see https://atom.io/docs/api/latest/Config. #{message}"
+      Grim.deprecate "Config::observe no longer supports options; see https://atom.io/docs/api/latest/Config. #{message}"
     else
       console.error 'An unsupported form of Config::observe is being used. See https://atom.io/docs/api/latest/Config for details'
       return
@@ -607,37 +608,50 @@ class Config
   # Deprecated: Returns a new {Object} containing all of the global settings and
   # defaults. Returns the scoped settings when a `scopeSelector` is specified.
   getSettings: ->
-    deprecate "Use ::get(keyPath) instead"
-    _.deepExtend(@settings, @defaultSettings)
+    Grim.deprecate "Use ::get(keyPath) instead"
+    _.deepExtend({}, @settings, @defaultSettings)
 
   # Extended: Get the {String} path to the config file being used.
   getUserConfigPath: ->
     @configFilePath
 
+  # Extended: Suppress calls to handler functions registered with {::onDidChange}
+  # and {::observe} for the duration of `callback`. After `callback` executes,
+  # handlers will be called once if the value for their key-path has changed.
+  #
+  # * `callback` {Function} to execute while suppressing calls to handlers.
+  transact: (callback) ->
+    @transactDepth++
+    try
+      callback()
+    finally
+      @transactDepth--
+      @emitChangeEvent()
+
   ###
   Section: Deprecated
   ###
 
   getInt: (keyPath) ->
-    deprecate '''Config::getInt is no longer necessary. Use ::get instead.
+    Grim.deprecate '''Config::getInt is no longer necessary. Use ::get instead.
     Make sure the config option you are accessing has specified an `integer`
     schema. See the schema section of
     https://atom.io/docs/api/latest/Config for more info.'''
     parseInt(@get(keyPath))
 
   getPositiveInt: (keyPath, defaultValue=0) ->
-    deprecate '''Config::getPositiveInt is no longer necessary. Use ::get instead.
+    Grim.deprecate '''Config::getPositiveInt is no longer necessary. Use ::get instead.
     Make sure the config option you are accessing has specified an `integer`
     schema with `minimum: 1`. See the schema section of
     https://atom.io/docs/api/latest/Config for more info.'''
     Math.max(@getInt(keyPath), 0) or defaultValue
 
   toggle: (keyPath) ->
-    deprecate 'Config::toggle is no longer supported. Please remove from your code.'
+    Grim.deprecate 'Config::toggle is no longer supported. Please remove from your code.'
     @set(keyPath, !@get(keyPath))
 
   unobserve: (keyPath) ->
-    deprecate 'Config::unobserve no longer does anything. Call `.dispose()` on the object returned by Config::observe instead.'
+    Grim.deprecate 'Config::unobserve no longer does anything. Call `.dispose()` on the object returned by Config::observe instead.'
 
   ###
   Section: Internal methods used by core
@@ -749,7 +763,7 @@ class Config
   resetUserSettings: (newSettings) ->
     unless isPlainObject(newSettings)
       @settings = {}
-      @emitter.emit 'did-change'
+      @emitChangeEvent()
       return
 
     if newSettings.global?
@@ -800,19 +814,22 @@ class Config
     defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
     value = undefined if _.isEqual(defaultValue, value)
 
-    oldValue = _.clone(@get(keyPath))
     _.setValueForKeyPath(@settings, keyPath, value)
-    newValue = @get(keyPath)
-    @emitter.emit 'did-change', {oldValue, newValue, keyPath} unless _.isEqual(newValue, oldValue)
+    @emitChangeEvent()
 
   observeKeyPath: (keyPath, options, callback) ->
-    callback(_.clone(@get(keyPath))) unless options.callNow == false
-    @emitter.on 'did-change', (event) =>
-      callback(event.newValue) if keyPath? and @isSubKeyPath(keyPath, event?.keyPath)
+    callback(@get(keyPath))
+    @onDidChangeKeyPath keyPath, (event) -> callback(event.newValue)
 
   onDidChangeKeyPath: (keyPath, callback) ->
-    @emitter.on 'did-change', (event) =>
-      callback(event) if not keyPath? or (keyPath? and @isSubKeyPath(keyPath, event?.keyPath))
+    oldValue = @get(keyPath)
+
+    didChange = =>
+      newValue = @get(keyPath)
+      callback({oldValue, newValue}) unless _.isEqual(oldValue, newValue)
+      oldValue = newValue
+
+    @emitter.on 'did-change', didChange
 
   isSubKeyPath: (keyPath, subKeyPath) ->
     return false unless keyPath? and subKeyPath?
@@ -821,10 +838,8 @@ class Config
     _.isEqual(pathTokens, pathSubTokens)
 
   setRawDefault: (keyPath, value) ->
-    oldValue = _.clone(@get(keyPath))
     _.setValueForKeyPath(@defaultSettings, keyPath, value)
-    newValue = @get(keyPath)
-    @emitter.emit 'did-change', {oldValue, newValue, keyPath} unless _.isEqual(newValue, oldValue)
+    @emitChangeEvent()
 
   setDefaults: (keyPath, defaults) ->
     if defaults? and isPlainObject(defaults)
@@ -882,20 +897,23 @@ class Config
   Section: Private Scoped Settings
   ###
 
+  emitChangeEvent: ->
+    @emitter.emit 'did-change' unless @transactDepth > 0
+
   resetUserScopedSettings: (newScopedSettings) ->
     @usersScopedSettings?.dispose()
     @usersScopedSettings = new CompositeDisposable
     @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', newScopedSettings, @usersScopedSettingPriority)
-    @emitter.emit 'did-change'
+    @emitChangeEvent()
 
   addScopedSettings: (source, selector, value, options) ->
     settingsBySelector = {}
     settingsBySelector[selector] = value
     disposable = @scopedSettingsStore.addProperties(source, settingsBySelector, options)
-    @emitter.emit 'did-change'
+    @emitChangeEvent()
     new Disposable =>
       disposable.dispose()
-      @emitter.emit 'did-change'
+      @emitChangeEvent()
 
   setRawScopedValue: (selector, keyPath, value) ->
     if keyPath?
@@ -906,7 +924,7 @@ class Config
     settingsBySelector = {}
     settingsBySelector[selector] = value
     @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', settingsBySelector, @usersScopedSettingPriority)
-    @emitter.emit 'did-change'
+    @emitChangeEvent()
 
   getRawScopedValue: (scopeDescriptor, keyPath) ->
     scopeDescriptor = ScopeDescriptor.fromObject(scopeDescriptor)
@@ -928,7 +946,7 @@ class Config
     oldValue = @get(scopeDescriptor, keyPath)
     didChange = =>
       newValue = @get(scopeDescriptor, keyPath)
-      callback({oldValue, newValue, keyPath}) unless _.isEqual(oldValue, newValue)
+      callback({oldValue, newValue}) unless _.isEqual(oldValue, newValue)
       oldValue = newValue
 
     @emitter.on 'did-change', didChange

src/git-repository.coffee

@@ -412,6 +412,8 @@ class GitRepository
     bufferSubscriptions.add buffer.onDidDestroy =>
       bufferSubscriptions.dispose()
       @subscriptions.remove(bufferSubscriptions)
+    @subscriptions.add(bufferSubscriptions)
+    return
 
   # Subscribes to editor view event.
   checkoutHeadForEditor: (editor) ->

src/package-manager.coffee

@@ -329,7 +329,8 @@ class PackageManager
     @packageActivators.push([activator, types])
 
   activatePackages: (packages) ->
-    @activatePackage(pack.name) for pack in packages
+    atom.config.transact =>
+      @activatePackage(pack.name) for pack in packages
     @observeDisabledPackages()
 
   # Activate a single package by name
@@ -344,7 +345,8 @@ class PackageManager
 
   # Deactivate all packages
   deactivatePackages: ->
-    @deactivatePackage(pack.name) for pack in @getLoadedPackages()
+    atom.config.transact =>
+      @deactivatePackage(pack.name) for pack in @getLoadedPackages()
     @unobserveDisabledPackages()
 
   # Deactivate the package with the given name

src/package.coffee

@@ -156,7 +156,7 @@ class Package
     catch e
       console.warn "Failed to activate package named '#{@name}'", e.stack
 
-    @activationDeferred.resolve()
+    @activationDeferred?.resolve()
 
   activateConfig: ->
     return if @configActivated

src/project.coffee

@@ -195,6 +195,7 @@ class Project extends Model
       includeHidden: true
       excludeVcsIgnores: atom.config.get('core.excludeVcsIgnoredPaths')
       exclusions: atom.config.get('core.ignoredNames')
+      follow: atom.config.get('core.followSymlinks')
 
     # TODO: need to support all paths in @getPaths()
     task = Task.once require.resolve('./scan-handler'), @getPaths()[0], regex.source, searchOptions, ->

src/task.coffee

@@ -1,5 +1,5 @@
 _ = require 'underscore-plus'
-child_process = require 'child_process'
+{fork} = require 'child_process'
 {Emitter} = require 'emissary'
 
 # Extended: Run a node script in a separate process.
@@ -98,7 +98,7 @@ class Task
     taskPath = taskPath.replace(/\\/g, "\\\\")
 
     env = _.extend({}, process.env, {taskPath, userAgent: navigator.userAgent})
-    @childProcess = child_process.fork '--eval', [bootstrap], {env, cwd: __dirname}
+    @childProcess = fork '--eval', [bootstrap], {env, cwd: __dirname}
 
     @on "task:log", -> console.log(arguments...)
     @on "task:warn", -> console.warn(arguments...)

src/text-editor-component.coffee

@@ -404,7 +404,7 @@ TextEditorComponent = React.createClass
     window.addEventListener 'resize', @requestHeightAndWidthMeasurement
 
     @listenForIMEEvents()
-    @listenForMiddleMousePaste() if process.platform is 'linux'
+    @trackSelectionClipboard() if process.platform is 'linux'
 
   listenForIMEEvents: ->
     node = @getDOMNode()
@@ -432,21 +432,21 @@ TextEditorComponent = React.createClass
       editor.insertText(selectedText, select: true, undo: 'skip')
       event.target.value = ''
 
-  listenForMiddleMousePaste: ->
-    clipboard = require 'clipboard'
-
-    @refs.scrollView.getDOMNode().addEventListener 'mouseup', ({which}) =>
-      return unless which is 2
-
-      if selection = clipboard.readText('selection')
-        @props.editor.insertText(selection)
-
-    @subscribe @props.editor.onDidChangeSelectionRange =>
-      if selectedText = @props.editor.getSelectedText()
+  # Listen for selection changes and store the currently selected text
+  # in the selection clipboard. This is only applicable on Linux.
+  trackSelectionClipboard: ->
+    timeoutId = null
+    {editor} = @props
+    writeSelectedTextToSelectionClipboard = =>
+      return if editor.isDestroyed()
+      if selectedText = editor.getSelectedText()
         # This uses ipc.send instead of clipboard.writeText because
         # clipboard.writeText is a sync ipc call on Linux and that
         # will slow down selections.
         ipc.send('write-text-to-selection-clipboard', selectedText)
+    @subscribe editor.onDidChangeSelectionRange ->
+      clearTimeout(timeoutId)
+      timeoutId = setTimeout(writeSelectedTextToSelectionClipboard)
 
   observeConfig: ->
     @subscribe atom.config.observe 'editor.useHardwareAcceleration', @setUseHardwareAcceleration
@@ -560,7 +560,11 @@ TextEditorComponent = React.createClass
       scrollViewNode.scrollLeft = 0
 
   onMouseDown: (event) ->
-    return unless event.button is 0 # only handle the left mouse button
+    unless event.button is 0 or (event.button is 1 and process.platform is 'linux')
+      # Only handle mouse down events for left mouse button on all platforms
+      # and middle mouse button on Linux since it pastes the selection clipboard
+      return
+
     return if event.target?.classList.contains('horizontal-scrollbar')
 
     {editor} = @props
@@ -750,10 +754,12 @@ TextEditorComponent = React.createClass
     lastMousePosition = {}
     animationLoop = =>
       @requestAnimationFrame =>
-        if dragging
+        if dragging and @isMounted()
           screenPosition = @screenPositionForMouseEvent(lastMousePosition)
           dragHandler(screenPosition)
           animationLoop()
+        else if not @isMounted()
+          stopDragging()
 
     onMouseMove = (event) ->
       lastMousePosition.clientX = event.clientX
@@ -767,11 +773,20 @@ TextEditorComponent = React.createClass
       # Stop dragging when cursor enters dev tools because we can't detect mouseup
       onMouseUp() if event.which is 0
 
-    onMouseUp = ->
+    onMouseUp = (event) ->
+      stopDragging()
+      editor.finalizeSelections()
+      pasteSelectionClipboard(event)
+
+    stopDragging = ->
       dragging = false
       window.removeEventListener('mousemove', onMouseMove)
       window.removeEventListener('mouseup', onMouseUp)
-      editor.finalizeSelections()
+
+    pasteSelectionClipboard = (event) ->
+      if event?.which is 2 and process.platform is 'linux'
+        if selection = require('clipboard').readText('selection')
+          editor.insertText(selection)
 
     window.addEventListener('mousemove', onMouseMove)
     window.addEventListener('mouseup', onMouseUp)

src/text-editor-element.coffee

@@ -123,7 +123,7 @@ class TextEditorElement extends HTMLElement
   unmountComponent: ->
     return unless @component?.isMounted()
     callRemoveHooks(this)
-    React.unmountComponentAtNode(this)
+    React.unmountComponentAtNode(@rootElement)
     @component = null
 
   focused: ->

src/workspace-element.coffee

@@ -112,6 +112,10 @@ class WorkspaceElement extends HTMLElement
 
   focusPaneViewOnRight: -> @paneContainer.focusPaneViewOnRight()
 
+  runPackageSpecs: ->
+    [projectPath] = atom.project.getPaths()
+    ipc.send('run-package-specs', path.join(projectPath, 'spec')) if projectPath
+
 atom.commands.add 'atom-workspace',
   'window:increase-font-size': -> @getModel().increaseFontSize()
   'window:decrease-font-size': -> @getModel().decreaseFontSize()
@@ -141,7 +145,7 @@ atom.commands.add 'atom-workspace',
   'application:open-your-snippets': -> ipc.send('command', 'application:open-your-snippets')
   'application:open-your-stylesheet': -> ipc.send('command', 'application:open-your-stylesheet')
   'application:open-license': -> @getModel().openLicense()
-  'window:run-package-specs': -> ipc.send('run-package-specs', path.join(atom.project.getPath(), 'spec'))
+  'window:run-package-specs': -> @runPackageSpecs()
   'window:focus-next-pane': -> @getModel().activateNextPane()
   'window:focus-previous-pane': -> @getModel().activatePreviousPane()
   'window:focus-pane-above': -> @focusPaneViewAbove()

src/workspace.coffee

@@ -459,8 +459,6 @@ class Workspace extends Model
         @emit "uri-opened"
         @emitter.emit 'did-open', {uri, pane, item, index}
         item
-      .catch (error) ->
-        console.error(error.stack ? error)
 
   # Public: Asynchronously reopens the last-closed item's URI if it hasn't already been
   # reopened.
@@ -557,7 +555,7 @@ class Workspace extends Model
   # {::saveActivePaneItemAs} # will be called instead. This method does nothing
   # if the active item does not implement a `.save` method.
   saveActivePaneItem: ->
-    @getActivePane().saveActiveItem()
+    @saveActivePaneItemAndReportErrors('saveActiveItem')
 
   # Prompt the user for a path and save the active pane item to it.
   #
@@ -565,7 +563,21 @@ 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: ->
-    @getActivePane().saveActiveItemAs()
+    @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.message.startsWith('EACCES,')
+        atom.notifications.addWarning("Unable to save file: #{error.message.replace('EACCES, ', '')}")
+      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
 
   # Destroy (close) the active pane item.
   #

static/variables/ui-variables.less

@@ -82,4 +82,4 @@
 
 // Other
 
-@font-family: 'Lucida Grande', 'Segoe UI', sans-serif;
+@font-family: 'Lucida Grande', 'Segoe UI', Ubuntu, Cantarell, sans-serif;