diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index ab19877b4..2afb8ac19 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -30,7 +30,7 @@ in the proper package's repository.
   * Follow the [CoffeeScript](#coffeescript-styleguide),
     [JavaScript](https://github.com/styleguide/javascript),
     and [CSS](https://github.com/styleguide/css) styleguides
-  * Include thoughtfully worded [Jasmine](http://pivotal.github.com/jasmine/)
+  * Include thoughtfully worded [Jasmine](http://pivotal.github.com/jasmine)
     specs
   * Avoid placing files in `vendor`. 3rd-party packages should be added as a
     `package.json` dependency.
@@ -61,3 +61,32 @@ in the proper package's repository.
 
 * Set parameter defaults without spaces around the equal sign
   * `clear = (count=1) ->` instead of `clear = (count = 1) ->`
+
+## Documentation Styleguide
+
+* Use [TomDoc](http://tomdoc.org).
+* Use [Markdown](https://daringfireball.net/projects/markdown).
+* Reference classes with `{ClassName}` style notation.
+* Reference methods with `{ClassName.methodName}` style notation.
+* Delegate to comments elsewhere with `{Delegates to: ClassName.methodName}`
+  style notation.
+
+### Example
+
+```coffee
+# Public: Disable the package with the given name.
+#
+# This method emits multiple events:
+#
+# * `package-will-be-disabled` - before the package is disabled.
+# * `package-disabled`         - after the package is disabled.
+#
+# name     - The {String} name of the package to disable.
+# options  - The {Object} with disable options (default: {}):
+#   :trackTime - `true` to track the amount of time disabling took.
+#   :ignoreErrors - `true` to catch and ignore errors thrown.
+# callback - The {Function} to call after the package has been disabled.
+#
+# Returns `undefined`.
+disablePackage: (name, options, callback) ->
+```
diff --git a/build/package.json b/build/package.json
index 8fe89a79e..3e967318a 100644
--- a/build/package.json
+++ b/build/package.json
@@ -7,7 +7,7 @@
   },
   "dependencies": {
     "async": "~0.2.9",
-    "biscotto": "git://github.com/atom/biscotto.git#12188bfbe5f7303fa9f1aa3c4f8662d40ce3c3be",
+    "biscotto": "0.6.0",
     "first-mate": "1.x",
     "formidable": "~1.0.14",
     "fs-plus": "1.x",
@@ -25,15 +25,13 @@
     "grunt-peg": "~1.1.0",
     "grunt-shell": "~0.3.1",
     "harmony-collections": "~0.3.8",
-    "js-yaml": "~2.1.0",
     "json-front-matter": "~0.1.3",
     "rcedit": "~0.1.2",
     "request": "~2.27.0",
     "rimraf": "~2.2.2",
-    "runas": "~0.3.0",
+    "runas": "0.5.x",
     "underscore-plus": "1.x",
     "unzip": "~0.1.9",
-    "vm-compatibility-layer": "~0.1.0",
-    "walkdir": "0.0.7"
+    "vm-compatibility-layer": "~0.1.0"
   }
 }
diff --git a/build/tasks/build-task.coffee b/build/tasks/build-task.coffee
index 0e1d47e61..bcbcd47aa 100644
--- a/build/tasks/build-task.coffee
+++ b/build/tasks/build-task.coffee
@@ -21,7 +21,6 @@ module.exports = (grunt) ->
 
     cp 'atom.sh', path.join(appDir, 'atom.sh')
     cp 'package.json', path.join(appDir, 'package.json')
-    cp 'apm', path.join(appDir, 'apm')
 
     packageDirectories = []
     nonPackageDirectories = [
@@ -47,8 +46,12 @@ module.exports = (grunt) ->
       path.join('less', 'dist')
       path.join('less', 'test')
       path.join('bootstrap', 'docs')
+      path.join('bootstrap', 'examples')
       path.join('spellchecker', 'vendor')
       path.join('xmldom', 'test')
+      path.join('jasmine-reporters', 'ext')
+      path.join('build', 'Release', 'obj.target')
+      path.join('build', 'Release', '.deps')
       path.join('vendor', 'apm')
       path.join('resources', 'mac')
       path.join('resources', 'win')
@@ -64,6 +67,7 @@ module.exports = (grunt) ->
     cp 'spec', path.join(appDir, 'spec')
     cp 'src', path.join(appDir, 'src'), filter: /.+\.(cson|coffee)$/
     cp 'static', path.join(appDir, 'static')
+    cp 'apm', path.join(appDir, 'apm'), filter: nodeModulesFilter
 
     if process.platform is 'darwin'
       grunt.file.recurse path.join('resources', 'mac'), (sourcePath, rootDirectory, subDirectory='', filename) ->
diff --git a/build/tasks/convert-theme.coffee b/build/tasks/convert-theme.coffee
deleted file mode 100644
index e94370e16..000000000
--- a/build/tasks/convert-theme.coffee
+++ /dev/null
@@ -1,102 +0,0 @@
-path = require 'path'
-
-_ = require 'underscore-plus'
-fs = require 'fs-plus'
-{ScopeSelector} = require 'first-mate'
-
-module.exports = (grunt) ->
-  grunt.registerTask 'convert-theme', 'Convert a TextMate theme to an Atom theme', ->
-    if textMateThemePath = grunt.option('path')
-      textMateThemePath = path.resolve(textMateThemePath)
-      if grunt.file.isFile(textMateThemePath)
-        textMateTheme = new TextMateTheme(textMateThemePath)
-        themeName = path.basename(textMateThemePath, path.extname(textMateThemePath))
-        atomThemePath = path.join(path.dirname(textMateThemePath), "#{themeName.toLowerCase()}-syntax.css")
-        grunt.file.write(atomThemePath, textMateTheme.getStylesheet())
-        grunt.log.ok("Atom theme written to: #{atomThemePath}")
-      else
-        grunt.log.error("No theme file found at: #{textMateThemePath}")
-        false
-    else
-      grunt.log.error('Must specify --path=<path to TextMate theme>')
-      false
-
-class TextMateTheme
-  constructor: (@path) ->
-    @rulesets = []
-    @buildRulesets()
-
-  buildRulesets: ->
-    {settings} = fs.readPlistSync(@path)
-    @buildGlobalSettingsRulesets(settings[0])
-    @buildScopeSelectorRulesets(settings[1..])
-
-  getStylesheet: ->
-    lines = []
-    for {selector, properties} in @getRulesets()
-      lines.push("#{selector} {")
-      lines.push "  #{name}: #{value};" for name, value of properties
-      lines.push("}\n")
-    lines.join('\n')
-
-  getRulesets: -> @rulesets
-
-  buildGlobalSettingsRulesets: ({settings}) ->
-    { background, foreground, caret, selection, lineHighlight } = settings
-
-    @rulesets.push
-      selector: '.editor, .editor .gutter'
-      properties:
-        'background-color': @translateColor(background)
-        'color': @translateColor(foreground)
-
-    @rulesets.push
-      selector: '.editor.is-focused .cursor'
-      properties:
-        'border-color': @translateColor(caret)
-
-    @rulesets.push
-      selector: '.editor.is-focused .selection .region'
-      properties:
-        'background-color': @translateColor(selection)
-
-    @rulesets.push
-      selector: '.editor.is-focused .line-number.cursor-line-no-selection, .editor.is-focused .line.cursor-line'
-      properties:
-        'background-color': @translateColor(lineHighlight)
-
-  buildScopeSelectorRulesets: (scopeSelectorSettings) ->
-    for { name, scope, settings } in scopeSelectorSettings
-      continue unless scope
-      @rulesets.push
-        comment: name
-        selector: @translateScopeSelector(scope)
-        properties: @translateScopeSelectorSettings(settings)
-
-  translateScopeSelector: (textmateScopeSelector) ->
-    new ScopeSelector(textmateScopeSelector).toCssSelector()
-
-  translateScopeSelectorSettings: ({ foreground, background, fontStyle }) ->
-    properties = {}
-
-    if fontStyle
-      fontStyles = fontStyle.split(/\s+/)
-      properties['font-weight'] = 'bold' if _.contains(fontStyles, 'bold')
-      properties['font-style'] = 'italic' if _.contains(fontStyles, 'italic')
-      properties['text-decoration'] = 'underline' if _.contains(fontStyles, 'underline')
-
-    properties['color'] = @translateColor(foreground) if foreground
-    properties['background-color'] = @translateColor(background) if background
-    properties
-
-  translateColor: (textmateColor) ->
-    if textmateColor.length <= 7
-      textmateColor
-    else
-      r = parseInt(textmateColor[1..2], 16)
-      g = parseInt(textmateColor[3..4], 16)
-      b = parseInt(textmateColor[5..6], 16)
-      a = parseInt(textmateColor[7..8], 16)
-      a = Math.round((a / 255.0) * 100) / 100
-
-      "rgba(#{r}, #{g}, #{b}, #{a})"
diff --git a/build/tasks/docs-task.coffee b/build/tasks/docs-task.coffee
index 6f9b3c8b4..53dab4ca7 100644
--- a/build/tasks/docs-task.coffee
+++ b/build/tasks/docs-task.coffee
@@ -15,24 +15,7 @@ module.exports = (grunt) ->
   grunt.registerTask 'build-docs', 'Builds the API docs in src', ->
     done = @async()
 
-    downloadFileFromRepo = ({repo, file}, callback) ->
-      uri = "https://raw2.github.com/atom/#{repo}/master/#{file}"
-      request uri, (error, response, contents) ->
-        return callback(error) if error?
-        downloadPath = path.join('docs', 'includes', repo, file)
-        fs.writeFile downloadPath, contents, (error) ->
-          callback(error, downloadPath)
-
-    includes = [
-      {repo: 'first-mate',  file: 'src/grammar-registry.coffee'}
-      {repo: 'space-pen',   file: 'src/space-pen.coffee'}
-      {repo: 'text-buffer', file: 'src/marker.coffee'}
-      {repo: 'text-buffer', file: 'src/point.coffee'}
-      {repo: 'text-buffer', file: 'src/range.coffee'}
-      {repo: 'theorist',    file: 'src/model.coffee'}
-    ]
-
-    async.map includes, downloadFileFromRepo, (error, includePaths) ->
+    downloadIncludes (error, includePaths) ->
       if error?
         done(error)
       else
@@ -49,13 +32,32 @@ module.exports = (grunt) ->
 
   grunt.registerTask 'lint-docs', 'Generate stats about the doc coverage', ->
     done = @async()
-    args = [commonArgs..., '--noOutput', 'src/']
-    grunt.util.spawn({cmd, args, opts}, done)
+    downloadIncludes (error, includePaths) ->
+      if error?
+        done(error)
+      else
+        args = [
+          commonArgs...
+          '--noOutput'
+          'src/'
+          includePaths...
+        ]
+        grunt.util.spawn({cmd, args, opts}, done)
 
   grunt.registerTask 'missing-docs', 'Generate stats about the doc coverage', ->
     done = @async()
-    args = [commonArgs..., '--noOutput', '--missing', 'src/']
-    grunt.util.spawn({cmd, args, opts}, done)
+    downloadIncludes (error, includePaths) ->
+      if error?
+        done(error)
+      else
+        args = [
+          commonArgs...
+          '--noOutput'
+          '--missing'
+          'src/'
+          includePaths...
+        ]
+        grunt.util.spawn({cmd, args, opts}, done)
 
   grunt.registerTask 'copy-docs', 'Copies over latest API docs to atom-docs', ->
     done = @async()
@@ -129,3 +131,24 @@ module.exports = (grunt) ->
       grunt.util.spawn({cmd, args, opts}, callback)
 
     grunt.util.async.waterfall [fetchTag, stageDocs, fetchSha, commitChanges, pushOrigin, pushHeroku], done
+
+downloadFileFromRepo = ({repo, file}, callback) ->
+  uri = "https://raw.github.com/atom/#{repo}/master/#{file}"
+  request uri, (error, response, contents) ->
+    return callback(error) if error?
+    downloadPath = path.join('docs', 'includes', repo, file)
+    fs.writeFile downloadPath, contents, (error) ->
+      callback(error, downloadPath)
+
+downloadIncludes = (callback) ->
+  includes = [
+    {repo: 'first-mate',  file: 'src/grammar.coffee'}
+    {repo: 'first-mate',  file: 'src/grammar-registry.coffee'}
+    {repo: 'space-pen',   file: 'src/space-pen.coffee'}
+    {repo: 'text-buffer', file: 'src/marker.coffee'}
+    {repo: 'text-buffer', file: 'src/point.coffee'}
+    {repo: 'text-buffer', file: 'src/range.coffee'}
+    {repo: 'theorist',    file: 'src/model.coffee'}
+  ]
+
+  async.map(includes, downloadFileFromRepo, callback)
diff --git a/build/tasks/install-task.coffee b/build/tasks/install-task.coffee
index a2b591734..273e1b5ef 100644
--- a/build/tasks/install-task.coffee
+++ b/build/tasks/install-task.coffee
@@ -1,24 +1,20 @@
 path = require 'path'
+runas = null
 
 module.exports = (grunt) ->
-  {cp, mkdir, rm, spawn} = require('./task-helpers')(grunt)
+  {cp, mkdir, rm} = require('./task-helpers')(grunt)
 
   grunt.registerTask 'install', 'Install the built application', ->
     installDir = grunt.config.get('atom.installDir')
     shellAppDir = grunt.config.get('atom.shellAppDir')
     if process.platform is 'win32'
-      done = @async()
-
-      runas = require 'runas'
+      runas ?= require 'runas'
       copyFolder = path.resolve 'script', 'copy-folder.cmd'
-      # cmd /c ""script" "source" "destination""
-      arg = "/c \"\"#{copyFolder}\" \"#{shellAppDir}\" \"#{installDir}\"\""
-      if runas('cmd', [arg], hide: true) isnt 0
-        done("Failed to copy #{shellAppDir} to #{installDir}")
+      if runas('cmd', ['/c', copyFolder, shellAppDir, installDir], admin: true) isnt 0
+        grunt.log.error("Failed to copy #{shellAppDir} to #{installDir}")
 
       createShortcut = path.resolve 'script', 'create-shortcut.cmd'
-      args = ['/c', createShortcut, path.join(installDir, 'atom.exe'), 'Atom']
-      spawn {cmd: 'cmd', args}, done
+      runas('cmd', ['/c', createShortcut, path.join(installDir, 'atom.exe'), 'Atom'])
     else
       rm installDir
       mkdir path.dirname(installDir)
diff --git a/build/tasks/task-helpers.coffee b/build/tasks/task-helpers.coffee
index f83430884..4b388ce63 100644
--- a/build/tasks/task-helpers.coffee
+++ b/build/tasks/task-helpers.coffee
@@ -1,27 +1,41 @@
-fs = require 'fs'
+fs = require 'fs-plus'
 path = require 'path'
-walkdir = require 'walkdir'
 
 module.exports = (grunt) ->
   cp: (source, destination, {filter}={}) ->
     unless grunt.file.exists(source)
       grunt.fatal("Cannot copy non-existent #{source.cyan} to #{destination.cyan}")
 
-    try
-      walkdir.sync source, (sourcePath, stats) ->
-        return if filter?.test(sourcePath)
+    copyFile = (sourcePath, destinationPath) ->
+      return if filter?.test(sourcePath)
 
-        destinationPath = path.join(destination, path.relative(source, sourcePath))
-        if stats.isSymbolicLink()
-          grunt.file.mkdir(path.dirname(destinationPath))
-          fs.symlinkSync(fs.readlinkSync(sourcePath), destinationPath)
-        else if stats.isFile()
-          grunt.file.copy(sourcePath, destinationPath)
+      stats = fs.lstatSync(sourcePath)
+      if stats.isSymbolicLink()
+        grunt.file.mkdir(path.dirname(destinationPath))
+        fs.symlinkSync(fs.readlinkSync(sourcePath), destinationPath)
+      else if stats.isFile()
+        grunt.file.copy(sourcePath, destinationPath)
 
-        if grunt.file.exists(destinationPath)
-          fs.chmodSync(destinationPath, fs.statSync(sourcePath).mode)
-    catch error
-      grunt.fatal(error)
+      if grunt.file.exists(destinationPath)
+        fs.chmodSync(destinationPath, fs.statSync(sourcePath).mode)
+
+    if grunt.file.isFile(source)
+      copyFile(source, destination)
+    else
+      try
+        onFile = (sourcePath) ->
+          destinationPath = path.join(destination, path.relative(source, sourcePath))
+          copyFile(sourcePath, destinationPath)
+        onDirectory = (sourcePath) ->
+          if fs.isSymbolicLinkSync(sourcePath)
+            destinationPath = path.join(destination, path.relative(source, sourcePath))
+            copyFile(sourcePath, destinationPath)
+            false
+          else
+            true
+        fs.traverseTreeSync source, onFile, onDirectory
+      catch error
+        grunt.fatal(error)
 
     grunt.verbose.writeln("Copied #{source.cyan} to #{destination.cyan}.")
 
diff --git a/build/tasks/update-octicons-task.coffee b/build/tasks/update-octicons-task.coffee
new file mode 100644
index 000000000..bdc56e8f5
--- /dev/null
+++ b/build/tasks/update-octicons-task.coffee
@@ -0,0 +1,22 @@
+path = require 'path'
+
+module.exports = (grunt) ->
+  grunt.registerTask 'update-octicons', 'Update octicon font and LESS variables', ->
+    pathToOcticons = path.resolve('..', 'octicons')
+    if grunt.file.isDir(pathToOcticons)
+      # Copy font-file
+      fontSrc = path.join(pathToOcticons, 'octicons', 'octicons.woff')
+      fontDest = path.resolve('static', 'octicons.woff')
+      grunt.file.copy(fontSrc, fontDest)
+
+      # Update Octicon UTF codes
+      glyphsSrc = path.join(pathToOcticons, 'data', 'glyphs.yml')
+      output = []
+      for {css, code} in grunt.file.readYAML(glyphsSrc)
+        output.push "@#{css}: \"\\#{code}\";"
+
+      octiconUtfDest = path.resolve('static', 'variables', 'octicon-utf-codes.less')
+      grunt.file.write(octiconUtfDest, "#{output.join('\n')}\n")
+    else
+      grunt.log.error("octicons repo must be cloned to #{pathToOcticons}")
+      false
diff --git a/docs/advanced/serialization.md b/docs/advanced/serialization.md
index ce1d7a78e..282d9e358 100644
--- a/docs/advanced/serialization.md
+++ b/docs/advanced/serialization.md
@@ -71,27 +71,3 @@ will only attempt to call deserialize if the two versions match, and otherwise
 return undefined. We plan on implementing a migration system in the future, but
 this at least protects you from improperly deserializing old state. If you find
 yourself in dire need of the migration system, let us know.
-
-### Deferred Package Deserializers
-
-If your package defers loading on startup with an `activationEvents` property in
-its `package.cson`, your deserializers won't be loaded until your package is
-activated. If you want to deserialize an object from your package on startup,
-this could be a problem.
-
-The solution is to also supply a `deferredDeserializers` array in your
-`package.cson` with the names of all your deserializers. When Atom attempts to
-deserialize some state whose `deserializer` matches one of these names, it will
-load your package first so it can register any necessary deserializers before
-proceeding.
-
-For example, the markdown preview package doesn't fully load until a preview is
-triggered. But if you refresh a window with a preview pane, it loads the
-markdown package early so Atom can deserialize the view correctly.
-
-```coffee-script
-# markdown-preview/package.cson
-'activationEvents': 'markdown-preview:toggle': '.editor'
-'deferredDeserializers': ['MarkdownPreviewView']
-...
-```
diff --git a/docs/converting-a-text-mate-bundle.md b/docs/converting-a-text-mate-bundle.md
new file mode 100644
index 000000000..f3a5da4b8
--- /dev/null
+++ b/docs/converting-a-text-mate-bundle.md
@@ -0,0 +1,52 @@
+## Converting a TextMate Bundle
+
+This guide will show you how to convert a [TextMate][TextMate] bundle to an
+Atom package.
+
+Converting a TextMate bundle will allow you to use its editor preferences,
+snippets, and colorization inside Atom.
+
+### Install apm
+
+The `apm` command line utility that ships with Atom supports converting
+a TextMate bundle to an Atom package.
+
+Check that you have `apm` installed by running the following command in your
+terminal:
+
+```sh
+apm help init
+```
+
+You should see a message print out with details about the `apm init` command.
+
+If you do not, launch Atom and run the _Atom > Install Shell Commmands_ menu
+to install the `apm` and `atom` commands.
+
+### Convert the Package
+
+Let's convert the TextMate bundle for the [R][R] programming language. You can find other existing TextMate bundles [here][TextMateOrg].
+
+You can convert the R bundle with the following command:
+
+```sh
+apm init --package ~/.atom/packages/language-r --convert https://github.com/textmate/r.tmbundle
+```
+
+You can now browse to `~/.atom/packages/language-r` to see the converted bundle.
+
+:tada: Your new package is now ready to use, launch Atom and open a `.r` file in
+the editor to see it in action!
+
+### Further Reading
+
+* Check out [Publishing a Package](publish-a-package.html) for more information
+  on publishing the package you just created to [atom.io][atomio].
+
+[atomio]: https://atom.io
+[CSS]: http://en.wikipedia.org/wiki/Cascading_Style_Sheets
+[LESS]: http://lesscss.org
+[plist]: http://en.wikipedia.org/wiki/Property_list
+[R]: http://en.wikipedia.org/wiki/R_(programming_language)
+[TextMate]: http://macromates.com
+[TextMateOrg]: https://github.com/textmate/r.tmbundle
diff --git a/docs/converting-a-text-mate-theme.md b/docs/converting-a-text-mate-theme.md
new file mode 100644
index 000000000..3fd454d27
--- /dev/null
+++ b/docs/converting-a-text-mate-theme.md
@@ -0,0 +1,68 @@
+## Converting a TextMate Theme
+
+This guide will show you how to convert a [TextMate][TextMate] theme to an Atom
+theme.
+
+### Differences
+
+TextMate themes use [plist][plist] files while Atom themes use [CSS][CSS] or
+[LESS][LESS] to style the UI and syntax in the editor.
+
+The utility that converts the theme first parses the theme's plist file and
+then creates comparable CSS rules and properties that will style Atom similarly.
+
+### Install apm
+
+The `apm` command line utility that ships with Atom supports converting
+a TextMate theme to an Atom theme.
+
+Check that you have `apm` installed by running the following command in your
+terminal:
+
+```sh
+apm help init
+```
+
+You should see a message print out with details about the `apm init` command.
+
+If you do not, launch Atom and run the _Atom > Install Shell Commmands_ menu
+to install the `apm` and `atom` commands.
+
+You can now run `apm help init` to see all the options for initializing new
+packages and themes.
+
+### Convert the Theme
+
+Download the theme you wish to convert, you can browse existing TextMate themes
+[here][TextMateThemes].
+
+Now, let's say you've downloaded the theme to `~/Downloads/MyTheme.tmTheme`,
+you can convert the theme with the following command:
+
+```sh
+apm init --theme ~/.atom/packages/my-theme --convert ~/Downloads/MyTheme.tmTheme
+```
+
+You can browse to `~/.atom/packages/my-theme` to see the converted theme.
+
+### Activate the Theme
+
+Now that your theme is installed to `~/.atom/packages` you can enable it
+by launching Atom and selecting the _Atom > Preferences..._ menu.
+
+Select the _Themes_ link on the left side and choose _My Theme_ from the
+__Syntax Theme__ dropdown menu to enable your new theme.
+
+:tada: Your theme is now enabled, open an editor to see it in action!
+
+### Further Reading
+
+* Check out [Publishing a Package](publish-a-package.html) for more information
+  on publishing the theme you just created to [atom.io][atomio].
+
+[atomio]: https://atom.io
+[CSS]: http://en.wikipedia.org/wiki/Cascading_Style_Sheets
+[LESS]: http://lesscss.org
+[plist]: http://en.wikipedia.org/wiki/Property_list
+[TextMate]: http://macromates.com
+[TextMateThemes]: http://wiki.macromates.com/Themes/UserSubmittedThemes
diff --git a/docs/customizing-atom.md b/docs/customizing-atom.md
index e6ad89305..49d196e50 100644
--- a/docs/customizing-atom.md
+++ b/docs/customizing-atom.md
@@ -112,14 +112,16 @@ namespaces: `core` and `editor`.
 
 ### Quick Personal Hacks
 
-### user.coffee
+### init.coffee
 
-When Atom finishes loading, it will evaluate _user.coffee_ in your _~/.atom_
+When Atom finishes loading, it will evaluate _init.coffee_ in your _~/.atom_
 directory, giving you a chance to run arbitrary personal CoffeeScript code to
 make customizations. You have full access to Atom's API from code in this file.
 If customizations become extensive, consider [creating a
 package][create-a-package].
 
+This file can also be named _init.js_ and contain JavaScript code.
+
 ### styles.css
 
 If you want to apply quick-and-dirty personal styling changes without creating
diff --git a/docs/proposals/atom-docs.md b/docs/proposals/atom-docs.md
deleted file mode 100644
index f3b6a0ec9..000000000
--- a/docs/proposals/atom-docs.md
+++ /dev/null
@@ -1,63 +0,0 @@
-## Atom Documentation Format
-
-This document describes our documentation format, which is markdown with
-a few rules.
-
-### Philosophy
-
-1. Method and argument names **should** clearly communicate its use.
-1. Use documentation to enhance and not correct method/argument names.
-
-#### Basic
-
-In some cases all that's required is a single line. **Do not** feel
-obligated to write more because we have a format.
-
-```markdown
-# Private: Returns the number of pixels from the top of the screen.
-```
-
-* **Each method should declare whether it's public or private by using `Public:`
-or `Private:`** prefix.
-* Following the colon, there should be a short description (that isn't redundant with the
-method name).
-* Documentation should be hard wrapped to 80 columns.
-
-### Public vs Private
-
-If a method is public it can be used by other classes (and possibly by
-the public API). The appropriate steps should be taken to minimize the impact
-when changing public methods. In some cases that might mean adding an
-appropriate release note. In other cases it might mean doing the legwork to
-ensure all affected packages are updated.
-
-#### Complex
-
-For complex methods it's necessary to explain exactly what arguments
-are required and how different inputs effect the operation of the
-function.
-
-The idea is to communicate things that the API user might not know about,
-so repeating information that can be gleaned from the method or argument names
-is not useful.
-
-```markdown
-# Private: Determine the accelerator for a given command.
-#
-# * command:
-#   The name of the command.
-# * keystrokesByCommand:
-#   An {Object} whose keys are commands and the values are Arrays containing
-#   the keystrokes.
-# * options:
-#     + accelerators:
-#       Boolean to determine whether accelerators should be shown.
-#
-# Returns a String containing the keystroke in a format that can be interpreted
-# by atom shell to provide nice icons where available.
-#
-# Raises an Exception if no window is available.
-```
-
-* Use curly brackets `{}` to provide links to other classes.
-* Use `+` for the options list.
diff --git a/docs/publishing-a-package.md b/docs/publishing-a-package.md
new file mode 100644
index 000000000..62e2a9591
--- /dev/null
+++ b/docs/publishing-a-package.md
@@ -0,0 +1,97 @@
+## Publishing a Package
+
+This guide will show you how to publish a package or theme to the
+[atom.io][atomio] package registry.
+
+Publishing a package allows other people to install it and use it in Atom. It
+is a great way to share what you've made and get feedback and contributions from
+others.
+
+This guide assumes your package's name is `my-package` and but you should pick a
+better name.
+
+### Install apm
+
+The `apm` command line utility that ships with Atom supports publishing packages
+to the atom.io registry.
+
+Check that you have `apm` installed by running the following command in your
+terminal:
+
+```sh
+apm help publish
+```
+
+You should see a message print out with details about the `apm publish` command.
+
+If you do not, launch Atom and run the _Atom > Install Shell Commmands_ menu
+to install the `apm` and `atom` commands.
+
+### Prepare Your Package
+
+If you've followed the steps in the [your first package][your-first-package]
+doc then you should be ready to publish and you can skip to the next step.
+
+If not, there are a few things you should check before publishing:
+
+  * Your *package.json* file has `name`, `description`, and `repository` fields.
+  * Your *package.json* file has a `version` field with a value of  `"0.0.0"`.
+  * Your *package.json* file has an `engines` field that contains an entry
+    for Atom such as: `"engines": {"atom": ">=0.50.0"}`.
+  * Your package has a `README.md` file at the root.
+  * Your package is in a Git repository that has been pushed to
+    [GitHub][github]. Follow [this guide][repo-guide] if your package isn't
+    already on GitHub.
+  
+### Publish Your Package
+
+Before you publish a package it is a good idea to check ahead of time if
+a package with the same name has already been published to atom.io. You can do
+that by visiting `http://atom.io/packages/my-package` to see if the package
+already exists. If it does, update your package's name to something that is
+available before proceeding.
+
+Now let's review what the `apm publish` command does:
+
+  1. Registers the package name on atom.io if it is being published for the
+     first time.
+  2. Updates the `version` field in the *package.json* file and commits it.
+  3. Creates a new [Git tag][git-tag] for the version being published.
+  4. Pushes the tag and current branch up to GitHub.
+  5. Updates atom.io with the new version being published.
+  
+Now run the following commands to publish your package:
+
+```sh
+cd ~/github/my-package
+apm publish minor
+```
+
+If this is the first package you are publishing, the `apm publish` command may
+prompt you for your GitHub username and password. This is required to publish
+and you only need to enter this information the first time you publish. The
+credentials are stored securely in your [keychain][keychain] once you login.
+
+:tada: Your package is now published and available on atom.io. Head on over to
+`http://atom.io/packages/my-package` to see your package's page.
+
+The `minor` option to the publish command tells apm to increment the second
+digit of the version before publishing so the published version will be `0.1.0`
+and the Git tag created will be `v0.1.0`.
+
+In the future you can run `apm publish major` to publish the `1.0.0` version but
+since this was the first version being published it is a good idead to start
+with a minor release.
+
+### Further Reading
+
+* Check out [semantic versioning][semver] to learn more about versioning your
+  package releases.
+
+[atomio]: https://atom.io
+[github]: https://github.com
+[git-tag]: http://git-scm.com/book/en/Git-Basics-Tagging
+[keychain]: http://en.wikipedia.org/wiki/Keychain_(Apple)
+[repo-guide]: http://guides.github.com/overviews/desktop
+[semver]: http://semver.org
+[your-first-package]: your-first-package.html
diff --git a/docs/your-first-package.md b/docs/your-first-package.md
index c1e0b991d..aea24456b 100644
--- a/docs/your-first-package.md
+++ b/docs/your-first-package.md
@@ -5,6 +5,7 @@ selected text with [ascii art](http://en.wikipedia.org/wiki/ASCII_art). When you
 run our new command with the word "cool" selected, it will be replaced with:
 
 ```
+                     ___
                     /\_ \
   ___    ___     ___\//\ \
  /'___\ / __`\  / __`\\ \ \
@@ -25,17 +26,17 @@ Atom will open a new window with the contents of our new _ascii-art_ package
 displayed in the Tree View. Because this window is opened **after** the package
 is created, the ASCII Art package will be loaded and available in our new
 window. To verify this, toggle the Command Palette (`cmd-shift-P`) and type
-"ASCII Art" you'll see a new `ASCII Art: Toggle` command. When triggered, this
+"ASCII Art". You'll see a new `ASCII Art: Toggle` command. When triggered, this
 command displays a default message.
 
-Now let's edit the package files to make our ascii art package do something
+Now let's edit the package files to make our ASCII Art package do something
 interesting. Since this package doesn't need any UI, we can remove all
 view-related code. Start by opening up _lib/ascii-art.coffee_. Remove all view
-code, so the file looks like this:
+code, so the `module.exports` section looks like this:
 
 ```coffeescript
-  module.exports =
-    activate: ->
+module.exports =
+  activate: ->
 ```
 
 ## Create a Command
@@ -69,23 +70,24 @@ command palette or by pressing `ctrl-alt-cmd-l`.
 ## Trigger the Command
 
 Now open the command panel and search for the `ascii-art:convert` command. But
-its not there! To fix this open _package.json_ and find the property called
-`activationEvents`. Activation Events speed up load time by allowing an Atom to
-delay a package's activation until it's needed. So add the `ascii-art:convert`
-to the activationEvents array:
+it's not there! To fix this, open _package.json_ and find the property called
+`activationEvents`. Activation Events speed up load time by allowing Atom to
+delay a package's activation until it's needed. So remove the existing command
+and add `ascii-art:convert` to the `activationEvents` array:
 
 ```json
 "activationEvents": ["ascii-art:convert"],
 ```
 
-First, run reload the window by running the command `window:reload`. Now when
-you run the `ascii-art:convert` command it will output 'Hello, World!'
+First, reload the window by running the command `window:reload`. Now when you
+run the `ascii-art:convert` command it will output 'Hello, World!'
 
-## Add A Key Binding
+## Add a Key Binding
 
 Now let's add a key binding to trigger the `ascii-art:convert` command. Open
 _keymaps/ascii-art.cson_ and add a key binding linking `ctrl-alt-a` to the
-`ascii-art:convert` command. When finished, the file will look like this:
+`ascii-art:convert` command. You can delete the pre-existing key binding since
+you don't need it anymore. When finished, the file will look like this:
 
 ```coffeescript
 '.editor':
@@ -105,25 +107,25 @@ that it **doesn't** work when the Tree View is focused.
 
 ## Add the ASCII Art
 
-Now we need to convert the selected text to ascii art. To do this we will use
+Now we need to convert the selected text to ASCII art. To do this we will use
 the [figlet](https://npmjs.org/package/figlet) [node](http://nodejs.org/) module
 from [npm](https://npmjs.org/). Open _package.json_ and add the latest version of
 figlet to the dependencies:
 
 ```json
-  "dependencies": {
-     "figlet": "1.0.8"
-  }
+"dependencies": {
+   "figlet": "1.0.8"
+}
 ```
 
-After saving the file run the command 'update-package-dependencies:update' from
-the Command Palette. This will install the packages node module dependencies,
+After saving the file, run the command 'update-package-dependencies:update' from
+the Command Palette. This will install the package's node module dependencies,
 only figlet in this case. You will need to run
 'update-package-dependencies:update' whenever you update the dependencies field
 in your _package.json_ file.
 
 Now require the figlet node module in _lib/ascii-art.coffee_ and instead of
-inserting 'Hello, World!' convert the selected text to ascii art!
+inserting 'Hello, World!' convert the selected text to ASCII art.
 
 ```coffeescript
 convert: ->
@@ -139,7 +141,15 @@ convert: ->
       selection.insertText("\n#{asciiArt}\n")
 ```
 
+Select some text in an editor window and hit `cmd-alt-a`. :tada: You're now an
+ASCII art professional!
+
 ## Further reading
 
-For more information on the mechanics of packages, check out [Creating a
-Package](creating-a-package.html)
+* [Getting your project on GitHub guide](http://guides.github.com/overviews/desktop)
+
+* [Creating a package guide](creating-a-package.html) for more information
+  on the mechanics of packages
+
+* [Publishing a package guide](publish-a-package.html) for more information
+  on publishing your package to [atom.io](https://atom.io)
diff --git a/dot-atom/init.coffee b/dot-atom/init.coffee
new file mode 100644
index 000000000..4d10e775b
--- /dev/null
+++ b/dot-atom/init.coffee
@@ -0,0 +1,14 @@
+# Your init script
+#
+# Atom will evaluate this file each time a new window is opened. It is run
+# after packages are loaded/activated and after the previous editor state
+# has been restored.
+#
+# An example hack to make opened Markdown files always be soft wrapped:
+#
+# path = require 'path'
+#
+# atom.workspaceView.eachEditorView (editorView) ->
+#   editor = editorView.getEditor()
+#   if path.extname(editor.getPath()) is '.md'
+#     editor.setSoftWrap(true)
diff --git a/dot-atom/keymap.cson b/dot-atom/keymap.cson
index 872395168..bce80b757 100644
--- a/dot-atom/keymap.cson
+++ b/dot-atom/keymap.cson
@@ -1,9 +1,13 @@
-# User keymap
+# Your keymap
 #
 # Atom keymaps work similarly to stylesheets. Just as stylesheets use selectors
 # to apply styles to elements, Atom keymaps use selectors to associate
-# keystrokes with events in specific contexts. Here's a small example, excerpted
-# from Atom's built-in keymaps:
+# keystrokes with events in specific contexts.
+#
+# You can create a new keybinding in this file by typing "key" and then hitting
+# tab.
+#
+# Here's an example taken from Atom's built-in keymap:
 #
 # '.editor':
 #   'enter': 'editor:newline'
@@ -11,3 +15,4 @@
 # 'body':
 #   'ctrl-P': 'core:move-up'
 #   'ctrl-p': 'core:move-down'
+#
diff --git a/dot-atom/snippets.cson b/dot-atom/snippets.cson
index e9d644de1..957899361 100644
--- a/dot-atom/snippets.cson
+++ b/dot-atom/snippets.cson
@@ -3,7 +3,7 @@
 # Atom snippets allow you to enter a simple prefix in the editor and hit tab to
 # expand the prefix into a larger code block with templated values.
 #
-# You can create a new snippet in this file by typing `snip` and then hitting
+# You can create a new snippet in this file by typing "snip" and then hitting
 # tab.
 #
 # An example CoffeeScript snippet to expand log to console.log:
diff --git a/dot-atom/user.coffee b/dot-atom/user.coffee
deleted file mode 100644
index 60880641d..000000000
--- a/dot-atom/user.coffee
+++ /dev/null
@@ -1 +0,0 @@
-# For more on how to configure atom open `~/github/atom/docs/configuring-and-extending.md`
diff --git a/exports/atom.coffee b/exports/atom.coffee
index f4fd1053a..ca48423f8 100644
--- a/exports/atom.coffee
+++ b/exports/atom.coffee
@@ -4,7 +4,6 @@ module.exports =
   _: require 'underscore-plus'
   BufferedNodeProcess: require '../src/buffered-node-process'
   BufferedProcess: require '../src/buffered-process'
-  ConfigObserver: require '../src/config-observer'
   Directory: require '../src/directory'
   File: require '../src/file'
   fs: require 'fs-plus'
diff --git a/keymaps/darwin.cson b/keymaps/darwin.cson
index a112bfbf7..750a1468f 100644
--- a/keymaps/darwin.cson
+++ b/keymaps/darwin.cson
@@ -68,6 +68,8 @@
   'cmd-=': 'window:increase-font-size'
   'cmd-+': 'window:increase-font-size'
   'cmd--': 'window:decrease-font-size'
+  'cmd-_': 'window:decrease-font-size'
+  'cmd-0': 'window:reset-font-size'
 
   'cmd-k up': 'pane:split-up' # Atom Specific
   'cmd-k down': 'pane:split-down' # Atom Specific
@@ -75,8 +77,12 @@
   'cmd-k right': 'pane:split-right' # Atom Specific
   'cmd-k cmd-w': 'pane:close' # Atom Specific
   'cmd-k alt-cmd-w': 'pane:close-other-items' # Atom Specific
-  'cmd-k cmd-left': 'window:focus-previous-pane'
-  'cmd-k cmd-right': 'window:focus-next-pane'
+  'cmd-k cmd-p': 'window:focus-previous-pane'
+  'cmd-k cmd-n': 'window:focus-next-pane'
+  'cmd-k cmd-up': 'window:focus-pane-above'
+  'cmd-k cmd-down': 'window:focus-pane-below'
+  'cmd-k cmd-left': 'window:focus-pane-on-left'
+  'cmd-k cmd-right': 'window:focus-pane-on-right'
   'cmd-1': 'pane:show-item-1'
   'cmd-2': 'pane:show-item-2'
   'cmd-3': 'pane:show-item-3'
@@ -118,7 +124,6 @@
   'alt-cmd-z': 'editor:checkout-head-revision'
   'cmd-<': 'editor:scroll-to-cursor'
   'alt-cmd-ctrl-f': 'editor:fold-selection'
-  'cmd-=': 'editor:auto-indent'
 
   # Sublime Parity
   'cmd-enter': 'editor:newline-below'
diff --git a/keymaps/win32.cson b/keymaps/win32.cson
index 3b6a230a5..ca306414e 100644
--- a/keymaps/win32.cson
+++ b/keymaps/win32.cson
@@ -40,6 +40,8 @@
   'ctrl-=': 'window:increase-font-size'
   'ctrl-+': 'window:increase-font-size'
   'ctrl--': 'window:decrease-font-size'
+  'ctrl-_': 'window:decrease-font-size'
+  'ctrl-0': 'window:reset-font-size'
 
   'ctrl-k up': 'pane:split-up' # Atom Specific
   'ctrl-k down': 'pane:split-down' # Atom Specific
@@ -47,8 +49,12 @@
   'ctrl-k right': 'pane:split-right' # Atom Specific
   'ctrl-k ctrl-w': 'pane:close' # Atom Specific
   'ctrl-k alt-ctrl-w': 'pane:close-other-items' # Atom Specific
-  'ctrl-k ctrl-left': 'window:focus-previous-pane'
-  'ctrl-k ctrl-right': 'window:focus-next-pane'
+  'ctrl-k ctrl-p': 'window:focus-previous-pane'
+  'ctrl-k ctrl-n': 'window:focus-next-pane'
+  'ctrl-k ctrl-up':    'window:focus-pane-above'
+  'ctrl-k ctrl-down':  'window:focus-pane-below'
+  'ctrl-k ctrl-left':  'window:focus-pane-on-left'
+  'ctrl-k ctrl-right': 'window:focus-pane-on-right'
 
 '.workspace .editor':
   # Windows specific
@@ -65,7 +71,6 @@
   'alt-ctrl-z': 'editor:checkout-head-revision'
   'ctrl-<': 'editor:scroll-to-cursor'
   'alt-ctrl-f': 'editor:fold-selection'
-  'ctrl-=': 'editor:auto-indent'
 
   # Sublime Parity
   'ctrl-enter': 'editor:newline-below'
diff --git a/menus/darwin.cson b/menus/darwin.cson
index 44e88dead..27f4b1a03 100644
--- a/menus/darwin.cson
+++ b/menus/darwin.cson
@@ -4,10 +4,12 @@
     submenu: [
       { label: 'About Atom', command: 'application:about' }
       { label: "VERSION", enabled: false }
-      { label: "Install update", command: 'application:install-update', visible: false }
+      { label: "Restart and Install Update", command: 'application:install-update', visible: false}
+      { label: "Check for Update", command: 'application:check-for-update', visible: false}
       { type: 'separator' }
       { label: 'Preferences...', command: 'application:show-settings' }
       { label: 'Open Your Config', command: 'application:open-your-config' }
+      { label: 'Open Your Init Script', command: 'application:open-your-init-script' }
       { label: 'Open Your Keymap', command: 'application:open-your-keymap' }
       { label: 'Open Your Snippets', command: 'application:open-your-snippets' }
       { label: 'Open Your Stylesheet', command: 'application:open-your-stylesheet' }
diff --git a/package.json b/package.json
index 178f4a20e..5060d8d00 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "0.49.0",
+  "version": "0.51.0",
   "main": "./src/browser/main.js",
   "repository": {
     "type": "git",
@@ -16,7 +16,7 @@
       "url": "http://github.com/atom/atom/raw/master/LICENSE.md"
     }
   ],
-  "atomShellVersion": "0.8.7",
+  "atomShellVersion": "0.9.2",
   "dependencies": {
     "async": "0.2.6",
     "bootstrap": "git://github.com/atom/bootstrap.git#6af81906189f1747fd6c93479e3d998ebe041372",
@@ -25,11 +25,11 @@
     "coffeestack": "0.7.0",
     "delegato": "1.x",
     "emissary": "1.x",
-    "first-mate": ">=1.1 <2.0",
+    "first-mate": ">=1.1.4 <2.0",
     "fs-plus": "1.x",
     "fstream": "0.1.24",
     "fuzzaldrin": "1.x",
-    "git-utils": "0.34.0",
+    "git-utils": "1.x",
     "guid": "0.0.10",
     "jasmine-tagged": "1.x",
     "mkdirp": "0.3.5",
@@ -42,102 +42,103 @@
     "pathwatcher": "0.14.2",
     "pegjs": "0.8.0",
     "property-accessors": "1.x",
-    "q": "0.9.7",
-    "scandal": "0.13.0",
+    "q": "1.0.x",
+    "runas": "0.5.x",
+    "scandal": "0.14.0",
     "season": "1.x",
     "semver": "1.1.4",
     "serializable": "1.x",
     "space-pen": "3.1.1",
     "temp": "0.5.0",
-    "text-buffer": "0.16.0",
+    "text-buffer": "1.x",
     "theorist": "1.x",
     "underscore-plus": "1.x",
     "vm-compatibility-layer": "0.1.0"
   },
   "packageDependencies": {
-    "atom-dark-syntax": "0.12.0",
-    "atom-dark-ui": "0.21.0",
-    "atom-light-syntax": "0.12.0",
-    "atom-light-ui": "0.20.0",
-    "base16-tomorrow-dark-theme": "0.10.0",
-    "solarized-dark-syntax": "0.8.0",
-    "solarized-light-syntax": "0.4.0",
-    "archive-view": "0.21.0",
-    "autocomplete": "0.21.0",
-    "autoflow": "0.12.0",
-    "autosave": "0.10.0",
-    "background-tips": "0.5.0",
-    "bookmarks": "0.18.0",
-    "bracket-matcher": "0.19.0",
-    "command-logger": "0.10.0",
-    "command-palette": "0.15.0",
-    "dev-live-reload": "0.23.0",
-    "editor-stats": "0.12.0",
+    "atom-dark-syntax": "0.13.0",
+    "atom-dark-ui": "0.22.0",
+    "atom-light-syntax": "0.13.0",
+    "atom-light-ui": "0.21.0",
+    "base16-tomorrow-dark-theme": "0.11.0",
+    "solarized-dark-syntax": "0.9.0",
+    "solarized-light-syntax": "0.5.0",
+    "archive-view": "0.22.0",
+    "autocomplete": "0.22.0",
+    "autoflow": "0.14.0",
+    "autosave": "0.11.0",
+    "background-tips": "0.7.0",
+    "bookmarks": "0.19.0",
+    "bracket-matcher": "0.20.0",
+    "command-logger": "0.11.0",
+    "command-palette": "0.16.0",
+    "dev-live-reload": "0.24.0",
+    "editor-stats": "0.13.0",
     "exception-reporting": "0.13.0",
-    "feedback": "0.22.0",
-    "find-and-replace": "0.81.0",
-    "fuzzy-finder": "0.32.0",
-    "gists": "0.15.0",
-    "git-diff": "0.23.0",
-    "github-sign-in": "0.18.0",
+    "feedback": "0.23.0",
+    "find-and-replace": "0.83.0",
+    "fuzzy-finder": "0.34.0",
+    "gists": "0.17.0",
+    "git-diff": "0.24.0",
+    "github-sign-in": "0.19.0",
     "go-to-line": "0.16.0",
-    "grammar-selector": "0.18.0",
-    "image-view": "0.17.0",
-    "keybinding-resolver": "0.9.0",
-    "link": "0.15.0",
-    "markdown-preview": "0.25.1",
-    "metrics": "0.24.0",
-    "package-generator": "0.25.0",
-    "release-notes": "0.17.0",
-    "settings-view": "0.63.0",
-    "snippets": "0.24.0",
-    "spell-check": "0.21.0",
+    "grammar-selector": "0.19.0",
+    "image-view": "0.23.0",
+    "keybinding-resolver": "0.10.0",
+    "link": "0.17.0",
+    "markdown-preview": "0.29.0",
+    "metrics": "0.26.0",
+    "package-generator": "0.26.0",
+    "release-notes": "0.20.0",
+    "settings-view": "0.72.0",
+    "snippets": "0.27.0",
+    "spell-check": "0.24.0",
     "status-bar": "0.32.0",
-    "styleguide": "0.22.0",
-    "symbols-view": "0.30.0",
-    "tabs": "0.18.0",
+    "styleguide": "0.23.0",
+    "symbols-view": "0.33.0",
+    "tabs": "0.19.0",
     "terminal": "0.27.0",
     "timecop": "0.13.0",
-    "to-the-hubs": "0.18.0",
-    "tree-view": "0.65.0",
-    "update-package-dependencies": "0.2.0",
-    "visual-bell": "0.6.0",
+    "to-the-hubs": "0.19.0",
+    "tree-view": "0.69.0",
+    "update-package-dependencies": "0.3.0",
+    "visual-bell": "0.7.0",
     "welcome": "0.4.0",
-    "whitespace": "0.10.0",
-    "wrap-guide": "0.12.0",
-    "language-c": "0.2.0",
+    "whitespace": "0.12.0",
+    "wrap-guide": "0.14.0",
+    "language-c": "0.4.0",
     "language-clojure": "0.1.0",
-    "language-coffee-script": "0.6.0",
-    "language-css": "0.2.0",
-    "language-gfm": "0.12.0",
-    "language-git": "0.3.0",
-    "language-go": "0.2.0",
-    "language-html": "0.2.0",
+    "language-coffee-script": "0.7.0",
+    "language-css": "0.3.0",
+    "language-gfm": "0.16.0",
+    "language-git": "0.4.0",
+    "language-go": "0.3.0",
+    "language-html": "0.3.0",
     "language-hyperlink": "0.3.0",
-    "language-java": "0.2.0",
-    "language-javascript": "0.5.0",
-    "language-json": "0.2.0",
-    "language-less": "0.1.0",
-    "language-make": "0.1.0",
-    "language-mustache": "0.1.0",
-    "language-objective-c": "0.2.0",
-    "language-pegjs": "0.1.0",
-    "language-perl": "0.2.0",
-    "language-php": "0.3.0",
-    "language-property-list": "0.2.0",
-    "language-puppet": "0.2.0",
-    "language-python": "0.2.0",
-    "language-ruby": "0.8.0",
-    "language-ruby-on-rails": "0.4.0",
-    "language-sass": "0.3.0",
-    "language-shellscript": "0.2.0",
-    "language-source": "0.2.0",
-    "language-sql": "0.2.0",
-    "language-text": "0.2.0",
-    "language-todo": "0.2.0",
-    "language-toml": "0.7.0",
-    "language-xml": "0.2.0",
-    "language-yaml": "0.1.0"
+    "language-java": "0.3.0",
+    "language-javascript": "0.6.0",
+    "language-json": "0.3.0",
+    "language-less": "0.2.0",
+    "language-make": "0.2.0",
+    "language-mustache": "0.2.0",
+    "language-objective-c": "0.3.0",
+    "language-pegjs": "0.2.0",
+    "language-perl": "0.3.0",
+    "language-php": "0.4.0",
+    "language-property-list": "0.3.0",
+    "language-puppet": "0.3.0",
+    "language-python": "0.3.0",
+    "language-ruby": "0.9.0",
+    "language-ruby-on-rails": "0.5.0",
+    "language-sass": "0.4.0",
+    "language-shellscript": "0.3.0",
+    "language-source": "0.3.0",
+    "language-sql": "0.3.0",
+    "language-text": "0.3.0",
+    "language-todo": "0.3.0",
+    "language-toml": "0.8.0",
+    "language-xml": "0.3.0",
+    "language-yaml": "0.2.0"
   },
   "private": true,
   "scripts": {
diff --git a/resources/win/atom.ico b/resources/win/atom.ico
index 2cf161e68..446140277 100644
Binary files a/resources/win/atom.ico and b/resources/win/atom.ico differ
diff --git a/script/utils/update-octicons b/script/utils/update-octicons
deleted file mode 100755
index b66402d88..000000000
--- a/script/utils/update-octicons
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env coffee
-
-usage = """
-Usage:
-  update-octicons PATH-TO-OCTICONS
-"""
-
-path = require 'path'
-fs = require 'fs'
-YAML = require 'js-yaml'
-
-scriptPath = process.argv[1]
-pathToOcticons = process.argv[2] ? path.join(process.env.HOME, 'github', 'octicons')
-atomDir = path.resolve(scriptPath, "../../..")
-
-unless fs.existsSync(pathToOcticons)
-  console.error(usage)
-  process.exit(1)
-
-# Copy font-file
-fontSrc = path.join(pathToOcticons, 'octicons', 'octicons.woff')
-fontDest = path.join(atomDir, 'static', 'octicons.woff')
-fs.createReadStream(fontSrc).pipe(fs.createWriteStream(fontDest))
-
-# Update Octicon UTF codes
-glyphsSrc = path.join(pathToOcticons, 'data', 'glyphs.yml')
-octiconUtfDest = path.join atomDir, 'static', 'variables', 'octicon-utf-codes.less'
-output = []
-for {css, code} in YAML.load(fs.readFileSync(glyphsSrc).toString())
-  output.push "@#{css}: \"\\#{code}\";"
-
-fs.writeFileSync octiconUtfDest, "#{output.join('\n')}\n"
diff --git a/spec/atom-reporter.coffee b/spec/atom-reporter.coffee
index c9b5e1bd2..aca1da3ff 100644
--- a/spec/atom-reporter.coffee
+++ b/spec/atom-reporter.coffee
@@ -1,35 +1,49 @@
-{View, $, $$} = require '../src/space-pen-extensions'
+path = require 'path'
 _ = require 'underscore-plus'
 {convertStackTrace} = require 'coffeestack'
+{View, $, $$} = require '../src/space-pen-extensions'
 
 sourceMaps = {}
-formatStackTrace = (stackTrace) ->
+formatStackTrace = (message='', stackTrace) ->
   return stackTrace unless stackTrace
 
-  jasminePath = require.resolve('../vendor/jasmine')
-  jasminePattern = new RegExp("\\(#{_.escapeRegExp(jasminePath)}:\\d+:\\d+\\)\\s*$")
+  jasminePattern = /^\s*at\s+.*\(?.*\/jasmine(-[^\/]*)?\.js:\d+:\d+\)?\s*$/
+  firstJasmineLinePattern = /^\s*at \/.*\/jasmine(-[^\/]*)?\.js:\d+:\d+\)?\s*$/
   convertedLines = []
   for line in stackTrace.split('\n')
     convertedLines.push(line) unless jasminePattern.test(line)
+    break if firstJasmineLinePattern.test(line)
 
-  convertStackTrace(convertedLines.join('\n'), sourceMaps)
+  stackTrace = convertStackTrace(convertedLines.join('\n'), sourceMaps)
+  lines = stackTrace.split('\n')
+
+  # Remove first line of stack when it is the same as the error message
+  errorMatch = lines[0]?.match(/^Error: (.*)/)
+  lines.shift() if message.trim() is errorMatch?[1]?.trim()
+
+  # Remove prefix of lines matching: at [object Object].<anonymous> (path:1:2)
+  for line, index in lines
+    prefixMatch = line.match(/at \[object Object\]\.<anonymous> \(([^\)]+)\)/)
+    lines[index] = "at #{prefixMatch[1]}" if prefixMatch
+
+  lines = lines.map (line) -> line.trim()
+  lines.join('\n')
 
 module.exports =
 class AtomReporter extends View
   @content: ->
-    @div id: 'HTMLReporter', class: 'jasmine_reporter', =>
-      @div outlet: 'specPopup', class: "spec-popup"
+    @div class: 'spec-reporter', =>
       @div outlet: "suites"
-      @div outlet: 'coreArea', =>
-        @div outlet: 'coreHeader', class: 'symbolHeader'
-        @ul outlet: 'coreSummary', class: 'symbolSummary list-unstyled'
-      @div outlet: 'bundledArea', =>
-        @div outlet: 'bundledHeader', class: 'symbolHeader'
-        @ul outlet: 'bundledSummary', class: 'symbolSummary list-unstyled'
-      @div outlet: 'userArea', =>
-        @div outlet: 'userHeader', class: 'symbolHeader'
-        @ul outlet: 'userSummary', class: 'symbolSummary list-unstyled'
-      @div outlet: "status", class: 'status', =>
+      @div outlet: 'coreArea', class: 'symbol-area', =>
+        @div outlet: 'coreHeader', class: 'symbol-header'
+        @ul outlet: 'coreSummary', class: 'symbol-summary list-unstyled'
+      @div outlet: 'bundledArea', class: 'symbol-area', =>
+        @div outlet: 'bundledHeader', class: 'symbol-header'
+        @ul outlet: 'bundledSummary', class: 'symbol-summary list-unstyled'
+      @div outlet: 'userArea', class: 'symbol-area', =>
+        @div outlet: 'userHeader', class: 'symbol-header'
+        @ul outlet: 'userSummary', class: 'symbol-summary list-unstyled'
+      @div outlet: "status", class: 'status alert alert-info', =>
         @div outlet: "time", class: 'time'
         @div outlet: "specCount", class: 'spec-count'
         @div outlet: "message", class: 'message'
@@ -46,7 +60,7 @@ class AtomReporter extends View
 
   reportRunnerStarting: (runner) ->
     @handleEvents()
-    @startedAt = new Date()
+    @startedAt = Date.now()
     specs = runner.specs()
     @totalSpecCount = specs.length
     @addSpecs(specs)
@@ -54,57 +68,29 @@ class AtomReporter extends View
 
   reportRunnerResults: (runner) ->
     @updateSpecCounts()
-    if @failedCount == 0
-      @message.text "Success!"
+    @status.addClass('alert-success').removeClass('alert-info') if @failedCount is 0
+    if @failedCount is 1
+      @message.text "#{@failedCount} failure"
     else
-      @message.text "Game Over"
+      @message.text "#{@failedCount} failures"
 
   reportSuiteResults: (suite) ->
 
   reportSpecResults: (spec) ->
     @completeSpecCount++
-    spec.endedAt = new Date().getTime()
+    spec.endedAt = Date.now()
     @specComplete(spec)
     @updateStatusView(spec)
 
   reportSpecStarting: (spec) ->
     @specStarted(spec)
 
-  specFilter: (spec) ->
-    globalFocusPriority = jasmine.getEnv().focusPriority
-    parent = spec.parentSuite ? spec.suite
-
-    if !globalFocusPriority
-      true
-    else if spec.focusPriority >= globalFocusPriority
-      true
-    else if not parent
-      false
-    else
-      @specFilter(parent)
-
   handleEvents: ->
-    $(document).on "mouseover", ".spec-summary", ({currentTarget}) =>
-      element = $(currentTarget)
-      description = element.data("description")
-      return unless description
-
-      clearTimeout @timeoutId if @timeoutId?
-      @specPopup.show()
-      spec = _.find(window.timedSpecs, ({fullName}) -> description is fullName)
-      description = "#{description} #{spec.time}ms" if spec
-      @specPopup.text description
-      {left, top} = element.offset()
-      left += 20
-      top += 20
-      @specPopup.offset({left, top})
-      @timeoutId = setTimeout((=> @specPopup.hide()), 3000)
-
     $(document).on "click", ".spec-toggle", ({currentTarget}) =>
       element = $(currentTarget)
       specFailures = element.parent().find('.spec-failures')
       specFailures.toggle()
-      if specFailures.is(":visible") then element.text "\uf03d" else element.html "\uf03f"
+      element.toggleClass('folded')
       false
 
   updateSpecCounts: ->
@@ -116,7 +102,7 @@ class AtomReporter extends View
 
   updateStatusView: (spec) ->
     if @failedCount > 0
-      @status.addClass('failed') unless @status.hasClass('failed')
+      @status.addClass('alert-danger').removeClass('alert-info')
 
     @updateSpecCounts()
 
@@ -124,7 +110,7 @@ class AtomReporter extends View
     rootSuite = rootSuite.parentSuite while rootSuite.parentSuite
     @message.text rootSuite.description
 
-    time = "#{Math.round((spec.endedAt - @startedAt.getTime()) / 10)}"
+    time = "#{Math.round((spec.endedAt - @startedAt) / 10)}"
     time = "0#{time}" if time.length < 3
     @time[0].textContent = "#{time[0...-2]}.#{time[-2..]}s"
 
@@ -146,15 +132,22 @@ class AtomReporter extends View
           @userSummary.append symbol
 
     if coreSpecs > 0
-      @coreHeader.text("Core Specs (#{coreSpecs}):")
+      @coreHeader.text("Core Specs (#{coreSpecs})")
     else
       @coreArea.hide()
     if bundledPackageSpecs > 0
-      @bundledHeader.text("Bundled Package Specs (#{bundledPackageSpecs}):")
+      @bundledHeader.text("Bundled Package Specs (#{bundledPackageSpecs})")
     else
       @bundledArea.hide()
     if userPackageSpecs > 0
-      @userHeader.text("User Package Specs (#{userPackageSpecs}):")
+      if coreSpecs is 0 and bundledPackageSpecs is 0
+        # Package specs being run, show a more descriptive label
+        {specDirectory} = specs[0]
+        packageFolderName = path.basename(path.dirname(specDirectory))
+        packageName = _.undasherize(_.uncamelcase(packageFolderName))
+        @userHeader.text("#{packageName} Specs")
+      else
+        @userHeader.text("User Package Specs (#{userPackageSpecs})")
     else
       @userArea.hide()
 
@@ -164,7 +157,7 @@ class AtomReporter extends View
   specComplete: (spec) ->
     specSummaryElement = $("#spec-summary-#{spec.id}")
     specSummaryElement.removeClass('pending')
-    specSummaryElement.data("description", spec.getFullName())
+    specSummaryElement.setTooltip(title: spec.getFullName(), container: '.spec-reporter')
 
     results = spec.results()
     if results.skipped
@@ -185,11 +178,9 @@ class SuiteResultView extends View
     @div class: 'suite', =>
       @div outlet: 'description', class: 'description'
 
-  suite: null
-
   initialize: (@suite) ->
     @attr('id', "suite-view-#{@suite.id}")
-    @description.html @suite.description
+    @description.text(@suite.description)
 
   attach: ->
     (@parentSuiteView() or $('.results')).append this
@@ -206,20 +197,22 @@ class SuiteResultView extends View
 class SpecResultView extends View
   @content: ->
     @div class: 'spec', =>
-      @div "\uf03d", class: 'spec-toggle'
+      @div class: 'spec-toggle'
       @div outlet: 'description', class: 'description'
       @div outlet: 'specFailures', class: 'spec-failures'
-  spec: null
 
   initialize: (@spec) ->
     @addClass("spec-view-#{@spec.id}")
-    @description.html @spec.description
+
+    description = @spec.description
+    description = "it #{description}" if description.indexOf('it ') isnt 0
+    @description.text(description)
 
     for result in @spec.results().getItems() when not result.passed()
-      stackTrace = formatStackTrace(result.trace.stack)
+      stackTrace = formatStackTrace(result.message, result.trace.stack)
       @specFailures.append $$ ->
-        @div result.message, class: 'resultMessage fail'
-        @div stackTrace, class: 'stackTrace' if stackTrace
+        @div result.message, class: 'result-message fail'
+        @pre stackTrace, class: 'stack-trace padded' if stackTrace
 
   attach: ->
     @parentSuiteView().append this
diff --git a/spec/atom-spec.coffee b/spec/atom-spec.coffee
index 24b646b95..038318b07 100644
--- a/spec/atom-spec.coffee
+++ b/spec/atom-spec.coffee
@@ -1,6 +1,7 @@
 {$, $$, fs, WorkspaceView}  = require 'atom'
 Exec = require('child_process').exec
 path = require 'path'
+AtomPackage = require '../src/atom-package'
 ThemeManager = require '../src/theme-manager'
 
 describe "the `atom` global", ->
@@ -9,35 +10,28 @@ describe "the `atom` global", ->
 
   describe "package lifecycle methods", ->
     describe ".loadPackage(name)", ->
-      describe "when the package has deferred deserializers", ->
-        it "requires the package's main module if one of its deferred deserializers is referenced", ->
-          pack = atom.packages.loadPackage('package-with-activation-events')
-          spyOn(pack, 'activateStylesheets').andCallThrough()
-          expect(pack.mainModule).toBeNull()
-          object = atom.deserializers.deserialize({deserializer: 'Foo', data: 5})
-          expect(pack.mainModule).toBeDefined()
-          expect(object.constructor.name).toBe 'Foo'
-          expect(object.data).toBe 5
-          expect(pack.activateStylesheets).toHaveBeenCalled()
+      it "continues if the package has an invalid package.json", ->
+        spyOn(console, 'warn')
+        atom.config.set("core.disabledPackages", [])
+        expect(-> atom.packages.loadPackage("package-with-broken-package-json")).not.toThrow()
 
-        it "continues if the package has an invalid package.json", ->
-          spyOn(console, 'warn')
-          atom.config.set("core.disabledPackages", [])
-          expect(-> atom.packages.loadPackage("package-with-broken-package-json")).not.toThrow()
-
-        it "continues if the package has an invalid keymap", ->
-          atom.config.set("core.disabledPackages", [])
-          expect(-> atom.packages.loadPackage("package-with-broken-keymap")).not.toThrow()
+      it "continues if the package has an invalid keymap", ->
+        atom.config.set("core.disabledPackages", [])
+        expect(-> atom.packages.loadPackage("package-with-broken-keymap")).not.toThrow()
 
     describe ".unloadPackage(name)", ->
       describe "when the package is active", ->
         it "throws an error", ->
-          pack = atom.packages.activatePackage('package-with-main')
-          expect(atom.packages.isPackageLoaded(pack.name)).toBeTruthy()
-          expect(atom.packages.isPackageActive(pack.name)).toBeTruthy()
-          expect( -> atom.packages.unloadPackage(pack.name)).toThrow()
-          expect(atom.packages.isPackageLoaded(pack.name)).toBeTruthy()
-          expect(atom.packages.isPackageActive(pack.name)).toBeTruthy()
+          pack = null
+          waitsForPromise ->
+            atom.packages.activatePackage('package-with-main').then (p) -> pack = p
+
+          runs ->
+            expect(atom.packages.isPackageLoaded(pack.name)).toBeTruthy()
+            expect(atom.packages.isPackageActive(pack.name)).toBeTruthy()
+            expect( -> atom.packages.unloadPackage(pack.name)).toThrow()
+            expect(atom.packages.isPackageLoaded(pack.name)).toBeTruthy()
+            expect(atom.packages.isPackageActive(pack.name)).toBeTruthy()
 
       describe "when the package is not loaded", ->
         it "throws an error", ->
@@ -54,22 +48,42 @@ describe "the `atom` global", ->
 
     describe ".activatePackage(id)", ->
       describe "atom packages", ->
+        describe "when called multiple times", ->
+          it "it only calls activate on the package once", ->
+            spyOn(AtomPackage.prototype, 'activateNow').andCallThrough()
+            atom.packages.activatePackage('package-with-index')
+            atom.packages.activatePackage('package-with-index')
+
+            waitsForPromise ->
+              atom.packages.activatePackage('package-with-index')
+
+            runs ->
+              expect(AtomPackage.prototype.activateNow.callCount).toBe 1
+
         describe "when the package has a main module", ->
           describe "when the metadata specifies a main module path˜", ->
             it "requires the module at the specified path", ->
               mainModule = require('./fixtures/packages/package-with-main/main-module')
               spyOn(mainModule, 'activate')
-              pack = atom.packages.activatePackage('package-with-main')
-              expect(mainModule.activate).toHaveBeenCalled()
-              expect(pack.mainModule).toBe mainModule
+              pack = null
+              waitsForPromise ->
+                atom.packages.activatePackage('package-with-main').then (p) -> pack = p
+
+              runs ->
+                expect(mainModule.activate).toHaveBeenCalled()
+                expect(pack.mainModule).toBe mainModule
 
           describe "when the metadata does not specify a main module", ->
             it "requires index.coffee", ->
               indexModule = require('./fixtures/packages/package-with-index/index')
               spyOn(indexModule, 'activate')
-              pack = atom.packages.activatePackage('package-with-index')
-              expect(indexModule.activate).toHaveBeenCalled()
-              expect(pack.mainModule).toBe indexModule
+              pack = null
+              waitsForPromise ->
+                atom.packages.activatePackage('package-with-index').then (p) -> pack = p
+
+              runs ->
+                expect(indexModule.activate).toHaveBeenCalled()
+                expect(pack.mainModule).toBe indexModule
 
           it "assigns config defaults from the module", ->
             expect(atom.config.get('package-with-config-defaults.numbers.one')).toBeUndefined()
@@ -78,20 +92,22 @@ describe "the `atom` global", ->
             expect(atom.config.get('package-with-config-defaults.numbers.two')).toBe 2
 
           describe "when the package metadata includes activation events", ->
-            [mainModule, pack] = []
+            [mainModule, promise] = []
 
             beforeEach ->
               mainModule = require './fixtures/packages/package-with-activation-events/index'
               spyOn(mainModule, 'activate').andCallThrough()
               AtomPackage = require '../src/atom-package'
               spyOn(AtomPackage.prototype, 'requireMainModule').andCallThrough()
-              pack = atom.packages.activatePackage('package-with-activation-events')
+
+              promise = atom.packages.activatePackage('package-with-activation-events')
 
             it "defers requiring/activating the main module until an activation event bubbles to the root view", ->
-              expect(pack.requireMainModule).not.toHaveBeenCalled()
-              expect(mainModule.activate).not.toHaveBeenCalled()
+              expect(promise.isFulfilled()).not.toBeTruthy()
               atom.workspaceView.trigger 'activation-event'
-              expect(mainModule.activate).toHaveBeenCalled()
+
+              waitsForPromise ->
+                promise
 
             it "triggers the activation event on all handlers registered during activation", ->
               atom.workspaceView.openSync()
@@ -116,13 +132,17 @@ describe "the `atom` global", ->
             expect(console.warn).not.toHaveBeenCalled()
 
         it "passes the activate method the package's previously serialized state if it exists", ->
-          pack = atom.packages.activatePackage("package-with-serialization")
-          expect(pack.mainModule.someNumber).not.toBe 77
-          pack.mainModule.someNumber = 77
-          atom.packages.deactivatePackage("package-with-serialization")
-          spyOn(pack.mainModule, 'activate').andCallThrough()
-          atom.packages.activatePackage("package-with-serialization")
-          expect(pack.mainModule.activate).toHaveBeenCalledWith({someNumber: 77})
+          pack = null
+          waitsForPromise ->
+            atom.packages.activatePackage("package-with-serialization").then (p) -> pack = p
+
+          runs ->
+            expect(pack.mainModule.someNumber).not.toBe 77
+            pack.mainModule.someNumber = 77
+            atom.packages.deactivatePackage("package-with-serialization")
+            spyOn(pack.mainModule, 'activate').andCallThrough()
+            atom.packages.activatePackage("package-with-serialization")
+            expect(pack.mainModule.activate).toHaveBeenCalledWith({someNumber: 77})
 
         it "logs warning instead of throwing an exception if the package fails to load", ->
           atom.config.set("core.disabledPackages", [])
@@ -245,29 +265,38 @@ describe "the `atom` global", ->
 
         describe "scoped-property loading", ->
           it "loads the scoped properties", ->
-            atom.packages.activatePackage("package-with-scoped-properties")
-            expect(atom.syntax.getProperty ['.source.omg'], 'editor.increaseIndentPattern').toBe '^a'
+            waitsForPromise ->
+              atom.packages.activatePackage("package-with-scoped-properties")
+
+            runs ->
+              expect(atom.syntax.getProperty ['.source.omg'], 'editor.increaseIndentPattern').toBe '^a'
 
       describe "textmate packages", ->
         it "loads the package's grammars", ->
           expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
-          atom.packages.activatePackage('language-ruby', sync: true)
-          expect(atom.syntax.selectGrammar("file.rb").name).toBe "Ruby"
+
+          waitsForPromise ->
+            atom.packages.activatePackage('language-ruby')
+
+          runs ->
+            expect(atom.syntax.selectGrammar("file.rb").name).toBe "Ruby"
 
         it "translates the package's scoped properties to Atom terms", ->
           expect(atom.syntax.getProperty(['.source.ruby'], 'editor.commentStart')).toBeUndefined()
-          atom.packages.activatePackage('language-ruby', sync: true)
-          expect(atom.syntax.getProperty(['.source.ruby'], 'editor.commentStart')).toBe '# '
+
+          waitsForPromise ->
+            atom.packages.activatePackage('language-ruby')
+
+          runs ->
+            expect(atom.syntax.getProperty(['.source.ruby'], 'editor.commentStart')).toBe '# '
 
         describe "when the package has no grammars but does have preferences", ->
           it "loads the package's preferences as scoped properties", ->
             jasmine.unspy(window, 'setTimeout')
             spyOn(atom.syntax, 'addProperties').andCallThrough()
 
-            atom.packages.activatePackage('package-with-preferences-tmbundle')
-
-            waitsFor ->
-              atom.syntax.addProperties.callCount > 0
+            waitsForPromise ->
+              atom.packages.activatePackage('package-with-preferences-tmbundle')
 
             runs ->
               expect(atom.syntax.getProperty(['.source.pref'], 'editor.increaseIndentPattern')).toBe '^abc$'
@@ -275,80 +304,118 @@ describe "the `atom` global", ->
     describe ".deactivatePackage(id)", ->
       describe "atom packages", ->
         it "calls `deactivate` on the package's main module if activate was successful", ->
-          pack = atom.packages.activatePackage("package-with-deactivate")
-          expect(atom.packages.isPackageActive("package-with-deactivate")).toBeTruthy()
-          spyOn(pack.mainModule, 'deactivate').andCallThrough()
+          pack = null
+          waitsForPromise ->
+            atom.packages.activatePackage("package-with-deactivate").then (p) -> pack = p
 
-          atom.packages.deactivatePackage("package-with-deactivate")
-          expect(pack.mainModule.deactivate).toHaveBeenCalled()
-          expect(atom.packages.isPackageActive("package-with-module")).toBeFalsy()
+          runs ->
+            expect(atom.packages.isPackageActive("package-with-deactivate")).toBeTruthy()
+            spyOn(pack.mainModule, 'deactivate').andCallThrough()
 
-          spyOn(console, 'warn')
-          badPack = atom.packages.activatePackage("package-that-throws-on-activate")
-          expect(atom.packages.isPackageActive("package-that-throws-on-activate")).toBeTruthy()
-          spyOn(badPack.mainModule, 'deactivate').andCallThrough()
+            atom.packages.deactivatePackage("package-with-deactivate")
+            expect(pack.mainModule.deactivate).toHaveBeenCalled()
+            expect(atom.packages.isPackageActive("package-with-module")).toBeFalsy()
 
-          atom.packages.deactivatePackage("package-that-throws-on-activate")
-          expect(badPack.mainModule.deactivate).not.toHaveBeenCalled()
-          expect(atom.packages.isPackageActive("package-that-throws-on-activate")).toBeFalsy()
+            spyOn(console, 'warn')
+
+          badPack = null
+          waitsForPromise ->
+            atom.packages.activatePackage("package-that-throws-on-activate").then (p) -> badPack = p
+
+          runs ->
+            expect(atom.packages.isPackageActive("package-that-throws-on-activate")).toBeTruthy()
+            spyOn(badPack.mainModule, 'deactivate').andCallThrough()
+
+            atom.packages.deactivatePackage("package-that-throws-on-activate")
+            expect(badPack.mainModule.deactivate).not.toHaveBeenCalled()
+            expect(atom.packages.isPackageActive("package-that-throws-on-activate")).toBeFalsy()
 
         it "does not serialize packages that have not been activated called on their main module", ->
           spyOn(console, 'warn')
-          badPack = atom.packages.activatePackage("package-that-throws-on-activate")
-          spyOn(badPack.mainModule, 'serialize').andCallThrough()
+          badPack = null
+          waitsForPromise ->
+            atom.packages.activatePackage("package-that-throws-on-activate").then (p) -> badPack = p
 
-          atom.packages.deactivatePackage("package-that-throws-on-activate")
-          expect(badPack.mainModule.serialize).not.toHaveBeenCalled()
+          runs ->
+            spyOn(badPack.mainModule, 'serialize').andCallThrough()
+
+            atom.packages.deactivatePackage("package-that-throws-on-activate")
+            expect(badPack.mainModule.serialize).not.toHaveBeenCalled()
 
         it "absorbs exceptions that are thrown by the package module's serialize methods", ->
           spyOn(console, 'error')
-          atom.packages.activatePackage('package-with-serialize-error',  immediate: true)
-          atom.packages.activatePackage('package-with-serialization', immediate: true)
-          atom.packages.deactivatePackages()
-          expect(atom.packages.packageStates['package-with-serialize-error']).toBeUndefined()
-          expect(atom.packages.packageStates['package-with-serialization']).toEqual someNumber: 1
-          expect(console.error).toHaveBeenCalled()
+
+          waitsForPromise ->
+            atom.packages.activatePackage('package-with-serialize-error')
+
+          waitsForPromise ->
+            atom.packages.activatePackage('package-with-serialization')
+
+          runs ->
+            atom.packages.deactivatePackages()
+            expect(atom.packages.packageStates['package-with-serialize-error']).toBeUndefined()
+            expect(atom.packages.packageStates['package-with-serialization']).toEqual someNumber: 1
+            expect(console.error).toHaveBeenCalled()
 
         it "removes the package's grammars", ->
-          atom.packages.activatePackage('package-with-grammars')
-          atom.packages.deactivatePackage('package-with-grammars')
-          expect(atom.syntax.selectGrammar('a.alot').name).toBe 'Null Grammar'
-          expect(atom.syntax.selectGrammar('a.alittle').name).toBe 'Null Grammar'
+          waitsForPromise ->
+            atom.packages.activatePackage('package-with-grammars')
+
+          runs ->
+            atom.packages.deactivatePackage('package-with-grammars')
+            expect(atom.syntax.selectGrammar('a.alot').name).toBe 'Null Grammar'
+            expect(atom.syntax.selectGrammar('a.alittle').name).toBe 'Null Grammar'
 
         it "removes the package's keymaps", ->
-          atom.packages.activatePackage('package-with-keymaps')
-          atom.packages.deactivatePackage('package-with-keymaps')
-          expect(atom.keymap.keyBindingsForKeystrokeMatchingElement('ctrl-z', $$ -> @div class: 'test-1')).toHaveLength 0
-          expect(atom.keymap.keyBindingsForKeystrokeMatchingElement('ctrl-z', $$ -> @div class: 'test-2')).toHaveLength 0
+          waitsForPromise ->
+            atom.packages.activatePackage('package-with-keymaps')
+
+          runs ->
+            atom.packages.deactivatePackage('package-with-keymaps')
+            expect(atom.keymap.keyBindingsForKeystrokeMatchingElement('ctrl-z', $$ -> @div class: 'test-1')).toHaveLength 0
+            expect(atom.keymap.keyBindingsForKeystrokeMatchingElement('ctrl-z', $$ -> @div class: 'test-2')).toHaveLength 0
 
         it "removes the package's stylesheets", ->
-          atom.packages.activatePackage('package-with-stylesheets')
-          atom.packages.deactivatePackage('package-with-stylesheets')
-          one = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/1.css")
-          two = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/2.less")
-          three = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/3.css")
-          expect(atom.themes.stylesheetElementForId(one)).not.toExist()
-          expect(atom.themes.stylesheetElementForId(two)).not.toExist()
-          expect(atom.themes.stylesheetElementForId(three)).not.toExist()
+          waitsForPromise ->
+            atom.packages.activatePackage('package-with-stylesheets')
+
+          runs ->
+            atom.packages.deactivatePackage('package-with-stylesheets')
+            one = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/1.css")
+            two = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/2.less")
+            three = require.resolve("./fixtures/packages/package-with-stylesheets-manifest/stylesheets/3.css")
+            expect(atom.themes.stylesheetElementForId(one)).not.toExist()
+            expect(atom.themes.stylesheetElementForId(two)).not.toExist()
+            expect(atom.themes.stylesheetElementForId(three)).not.toExist()
 
         it "removes the package's scoped-properties", ->
-          atom.packages.activatePackage("package-with-scoped-properties")
-          expect(atom.syntax.getProperty ['.source.omg'], 'editor.increaseIndentPattern').toBe '^a'
-          atom.packages.deactivatePackage("package-with-scoped-properties")
-          expect(atom.syntax.getProperty ['.source.omg'], 'editor.increaseIndentPattern').toBeUndefined()
+          waitsForPromise ->
+            atom.packages.activatePackage("package-with-scoped-properties")
+
+          runs ->
+            expect(atom.syntax.getProperty ['.source.omg'], 'editor.increaseIndentPattern').toBe '^a'
+            atom.packages.deactivatePackage("package-with-scoped-properties")
+            expect(atom.syntax.getProperty ['.source.omg'], 'editor.increaseIndentPattern').toBeUndefined()
 
       describe "textmate packages", ->
         it "removes the package's grammars", ->
           expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
-          atom.packages.activatePackage('language-ruby', sync: true)
-          expect(atom.syntax.selectGrammar("file.rb").name).toBe "Ruby"
-          atom.packages.deactivatePackage('language-ruby')
-          expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
+
+          waitsForPromise ->
+            atom.packages.activatePackage('language-ruby')
+
+          runs ->
+            expect(atom.syntax.selectGrammar("file.rb").name).toBe "Ruby"
+            atom.packages.deactivatePackage('language-ruby')
+            expect(atom.syntax.selectGrammar("file.rb").name).toBe "Null Grammar"
 
         it "removes the package's scoped properties", ->
-          atom.packages.activatePackage('language-ruby', sync: true)
-          atom.packages.deactivatePackage('language-ruby')
-          expect(atom.syntax.getProperty(['.source.ruby'], 'editor.commentStart')).toBeUndefined()
+          waitsForPromise ->
+            atom.packages.activatePackage('language-ruby')
+
+          runs ->
+            atom.packages.deactivatePackage('language-ruby')
+            expect(atom.syntax.getProperty(['.source.ruby'], 'editor.commentStart')).toBeUndefined()
 
     describe ".activate()", ->
       packageActivator = null
@@ -382,7 +449,7 @@ describe "the `atom` global", ->
         themes = themeActivator.mostRecentCall.args[0]
         expect(['theme']).toContain(theme.getType()) for theme in themes
 
-    describe ".en/disablePackage()", ->
+    describe ".enablePackage() and disablePackage()", ->
       describe "with packages", ->
         it ".enablePackage() enables a disabled package", ->
           packageName = 'package-with-main'
@@ -391,28 +458,36 @@ describe "the `atom` global", ->
           expect(atom.config.get('core.disabledPackages')).toContain packageName
 
           pack = atom.packages.enablePackage(packageName)
-
           loadedPackages = atom.packages.getLoadedPackages()
-          activatedPackages = atom.packages.getActivePackages()
-          expect(loadedPackages).toContain(pack)
-          expect(activatedPackages).toContain(pack)
-          expect(atom.config.get('core.disabledPackages')).not.toContain packageName
+          activatedPackages = null
+          waitsFor ->
+            activatedPackages = atom.packages.getActivePackages()
+            activatedPackages.length > 0
+
+          runs ->
+            expect(loadedPackages).toContain(pack)
+            expect(activatedPackages).toContain(pack)
+            expect(atom.config.get('core.disabledPackages')).not.toContain packageName
 
         it ".disablePackage() disables an enabled package", ->
           packageName = 'package-with-main'
-          atom.packages.activatePackage(packageName)
-          atom.packages.observeDisabledPackages()
-          expect(atom.config.get('core.disabledPackages')).not.toContain packageName
+          waitsForPromise ->
+            atom.packages.activatePackage(packageName)
 
-          pack = atom.packages.disablePackage(packageName)
+          runs ->
+            atom.packages.observeDisabledPackages()
+            expect(atom.config.get('core.disabledPackages')).not.toContain packageName
 
-          activatedPackages = atom.packages.getActivePackages()
-          expect(activatedPackages).not.toContain(pack)
-          expect(atom.config.get('core.disabledPackages')).toContain packageName
+            pack = atom.packages.disablePackage(packageName)
+
+            activatedPackages = atom.packages.getActivePackages()
+            expect(activatedPackages).not.toContain(pack)
+            expect(atom.config.get('core.disabledPackages')).toContain packageName
 
       describe "with themes", ->
         beforeEach ->
-          atom.themes.activateThemes()
+          waitsForPromise ->
+            atom.themes.activateThemes()
 
         afterEach ->
           atom.themes.deactivateThemes()
@@ -426,18 +501,24 @@ describe "the `atom` global", ->
 
           # enabling of theme
           pack = atom.packages.enablePackage(packageName)
-          activatedPackages = atom.packages.getActivePackages()
-          expect(activatedPackages).toContain(pack)
-          expect(atom.config.get('core.themes')).toContain packageName
-          expect(atom.config.get('core.disabledPackages')).not.toContain packageName
 
-          # disabling of theme
-          pack = atom.packages.disablePackage(packageName)
-          activatedPackages = atom.packages.getActivePackages()
-          expect(activatedPackages).not.toContain(pack)
-          expect(atom.config.get('core.themes')).not.toContain packageName
-          expect(atom.config.get('core.themes')).not.toContain packageName
-          expect(atom.config.get('core.disabledPackages')).not.toContain packageName
+          activatedPackages = null
+          waitsFor ->
+            activatedPackages = atom.packages.getActivePackages()
+            activatedPackages.length > 0
+
+          runs ->
+            expect(activatedPackages).toContain(pack)
+            expect(atom.config.get('core.themes')).toContain packageName
+            expect(atom.config.get('core.disabledPackages')).not.toContain packageName
+
+            # disabling of theme
+            pack = atom.packages.disablePackage(packageName)
+            activatedPackages = atom.packages.getActivePackages()
+            expect(activatedPackages).not.toContain(pack)
+            expect(atom.config.get('core.themes')).not.toContain packageName
+            expect(atom.config.get('core.themes')).not.toContain packageName
+            expect(atom.config.get('core.disabledPackages')).not.toContain packageName
 
   describe ".isReleasedVersion()", ->
     it "returns false if the version is a SHA and true otherwise", ->
diff --git a/spec/clipboard-spec.coffee b/spec/clipboard-spec.coffee
new file mode 100644
index 000000000..0553f0eae
--- /dev/null
+++ b/spec/clipboard-spec.coffee
@@ -0,0 +1,12 @@
+describe "Clipboard", ->
+  describe "write(text, metadata) and read()", ->
+    it "writes and reads text to/from the native clipboard", ->
+      expect(atom.clipboard.read()).toBe 'initial clipboard content'
+      atom.clipboard.write('next')
+      expect(atom.clipboard.read()).toBe 'next'
+
+    it "returns metadata if the item on the native clipboard matches the last written item", ->
+      atom.clipboard.write('next', {meta: 'data'})
+      expect(atom.clipboard.read()).toBe 'next'
+      expect(atom.clipboard.readWithMetadata().text).toBe 'next'
+      expect(atom.clipboard.readWithMetadata().metadata).toEqual {meta: 'data'}
diff --git a/spec/command-installer-spec.coffee b/spec/command-installer-spec.coffee
index 6bd66b4d3..a597f919d 100644
--- a/spec/command-installer-spec.coffee
+++ b/spec/command-installer-spec.coffee
@@ -20,7 +20,7 @@ describe "install(commandPath, callback)", ->
 
       installDone = false
       installError = null
-      installer.install commandFilePath, (error) ->
+      installer.install commandFilePath, false, (error) ->
         installDone = true
         installError = error
 
diff --git a/spec/config-spec.coffee b/spec/config-spec.coffee
index 77455c5c2..02ef6d6d8 100644
--- a/spec/config-spec.coffee
+++ b/spec/config-spec.coffee
@@ -63,6 +63,19 @@ describe "Config", ->
       atom.config.toggle('foo.a')
       expect(atom.config.get('foo.a')).toBe false
 
+  describe ".restoreDefault(keyPath)", ->
+    it "sets the value of the key path to its default", ->
+      atom.config.setDefaults('a', b: 3)
+      atom.config.set('a.b', 4)
+      expect(atom.config.get('a.b')).toBe 4
+      atom.config.restoreDefault('a.b')
+      expect(atom.config.get('a.b')).toBe 3
+
+      atom.config.set('a.c', 5)
+      expect(atom.config.get('a.c')).toBe 5
+      atom.config.restoreDefault('a.c')
+      expect(atom.config.get('a.c')).toBeUndefined()
+
   describe ".pushAtKeyPath(keyPath, value)", ->
     it "pushes the given value to the array at the key path and updates observers", ->
       atom.config.set("foo.bar.baz", ["a"])
@@ -220,6 +233,8 @@ describe "Config", ->
           expect(fs.existsSync(path.join(atom.config.configDirPath, 'packages'))).toBeTruthy()
           expect(fs.isFileSync(path.join(atom.config.configDirPath, 'snippets.cson'))).toBeTruthy()
           expect(fs.isFileSync(path.join(atom.config.configDirPath, 'config.cson'))).toBeTruthy()
+          expect(fs.isFileSync(path.join(atom.config.configDirPath, 'init.coffee'))).toBeTruthy()
+          expect(fs.isFileSync(path.join(atom.config.configDirPath, 'styles.css'))).toBeTruthy()
 
   describe ".loadUserConfig()", ->
     beforeEach ->
diff --git a/spec/display-buffer-spec.coffee b/spec/display-buffer-spec.coffee
index e85a05049..6e13ee8f4 100644
--- a/spec/display-buffer-spec.coffee
+++ b/spec/display-buffer-spec.coffee
@@ -5,12 +5,15 @@ describe "DisplayBuffer", ->
   [displayBuffer, buffer, changeHandler, tabLength] = []
   beforeEach ->
     tabLength = 2
-    atom.packages.activatePackage('language-javascript', sync: true)
+
     buffer = atom.project.bufferForPathSync('sample.js')
     displayBuffer = new DisplayBuffer({buffer, tabLength})
     changeHandler = jasmine.createSpy 'changeHandler'
     displayBuffer.on 'changed', changeHandler
 
+    waitsForPromise ->
+      atom.packages.activatePackage('language-javascript')
+
   afterEach ->
     displayBuffer.destroy()
     buffer.release()
diff --git a/spec/editor-spec.coffee b/spec/editor-spec.coffee
index ecd6e6d7a..821299f8c 100644
--- a/spec/editor-spec.coffee
+++ b/spec/editor-spec.coffee
@@ -16,11 +16,13 @@ describe "Editor", ->
 
   describe "with default options", ->
     beforeEach ->
-      atom.packages.activatePackage('language-javascript', sync: true)
       editor = atom.project.openSync('sample.js', autoIndent: false)
       buffer = editor.buffer
       lineLengths = buffer.getLines().map (line) -> line.length
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-javascript')
+
     describe "when the editor is deserialized", ->
       it "restores selections and folds based on markers in the buffer", ->
         editor.setSelectedBufferRange([[1, 2], [3, 4]])
@@ -1856,12 +1858,12 @@ describe "Editor", ->
             expect(editor.getCursorBufferPosition()).toEqual [0, 2]
             expect(editor.getCursorScreenPosition()).toEqual [0, editor.getTabLength() * 2]
 
-      describe "pasteboard operations", ->
+      describe "clipboard operations", ->
         beforeEach ->
           editor.setSelectedBufferRanges([[[0, 4], [0, 13]], [[1, 6], [1, 10]]])
 
         describe ".cutSelectedText()", ->
-          it "removes the selected text from the buffer and places it on the pasteboard", ->
+          it "removes the selected text from the buffer and places it on the clipboard", ->
             editor.cutSelectedText()
             expect(buffer.lineForRow(0)).toBe "var  = function () {"
             expect(buffer.lineForRow(1)).toBe "  var  = function(items) {"
@@ -1885,7 +1887,7 @@ describe "Editor", ->
                 editor.cutToEndOfLine()
                 expect(buffer.lineForRow(2)).toBe '    if (items.length'
                 expect(buffer.lineForRow(3)).toBe '    var pivot = item'
-                expect(atom.pasteboard.read()[0]).toBe ' <= 1) return items;\ns.shift(), current, left = [], right = [];'
+                expect(atom.clipboard.read()).toBe ' <= 1) return items;\ns.shift(), current, left = [], right = [];'
 
             describe "when text is selected", ->
               it "only cuts the selected text, not to the end of the line", ->
@@ -1895,7 +1897,7 @@ describe "Editor", ->
 
                 expect(buffer.lineForRow(2)).toBe '    if (items.lengthurn items;'
                 expect(buffer.lineForRow(3)).toBe '    var pivot = item'
-                expect(atom.pasteboard.read()[0]).toBe ' <= 1) ret\ns.shift(), current, left = [], right = [];'
+                expect(atom.clipboard.read()).toBe ' <= 1) ret\ns.shift(), current, left = [], right = [];'
 
         describe ".copySelectedText()", ->
           it "copies selected text onto the clipboard", ->
@@ -1906,7 +1908,7 @@ describe "Editor", ->
 
         describe ".pasteText()", ->
           it "pastes text into the buffer", ->
-            atom.pasteboard.write('first')
+            atom.clipboard.write('first')
             editor.pasteText()
             expect(editor.buffer.lineForRow(0)).toBe "var first = function () {"
             expect(buffer.lineForRow(1)).toBe "  var first = function(items) {"
@@ -2733,19 +2735,26 @@ describe "Editor", ->
 
   describe "when the editor's grammar has an injection selector", ->
     beforeEach ->
-      atom.packages.activatePackage('language-text', sync: true)
-      atom.packages.activatePackage('language-javascript', sync: true)
+
+      waitsForPromise ->
+        atom.packages.activatePackage('language-text')
+
+      waitsForPromise ->
+        atom.packages.activatePackage('language-javascript')
 
     it "includes the grammar's patterns when the selector matches the current scope in other grammars", ->
-      atom.packages.activatePackage('language-hyperlink', sync: true)
-      grammar = atom.syntax.selectGrammar("text.js")
-      {tokens} = grammar.tokenizeLine("var i; // http://github.com")
+      waitsForPromise ->
+        atom.packages.activatePackage('language-hyperlink')
 
-      expect(tokens[0].value).toBe "var"
-      expect(tokens[0].scopes).toEqual ["source.js", "storage.modifier.js"]
+      runs ->
+        grammar = atom.syntax.selectGrammar("text.js")
+        {tokens} = grammar.tokenizeLine("var i; // http://github.com")
 
-      expect(tokens[6].value).toBe "http://github.com"
-      expect(tokens[6].scopes).toEqual ["source.js", "comment.line.double-slash.js", "markup.underline.link.http.hyperlink"]
+        expect(tokens[0].value).toBe "var"
+        expect(tokens[0].scopes).toEqual ["source.js", "storage.modifier.js"]
+
+        expect(tokens[6].value).toBe "http://github.com"
+        expect(tokens[6].scopes).toEqual ["source.js", "comment.line.double-slash.js", "markup.underline.link.http.hyperlink"]
 
     describe "when the grammar is added", ->
       it "retokenizes existing buffers that contain tokens that match the injection selector", ->
@@ -2756,11 +2765,13 @@ describe "Editor", ->
         expect(tokens[1].value).toBe " http://github.com"
         expect(tokens[1].scopes).toEqual ["source.js", "comment.line.double-slash.js"]
 
-        atom.packages.activatePackage('language-hyperlink', sync: true)
+        waitsForPromise ->
+          atom.packages.activatePackage('language-hyperlink')
 
-        {tokens} = editor.lineForScreenRow(0)
-        expect(tokens[2].value).toBe "http://github.com"
-        expect(tokens[2].scopes).toEqual ["source.js", "comment.line.double-slash.js", "markup.underline.link.http.hyperlink"]
+        runs ->
+          {tokens} = editor.lineForScreenRow(0)
+          expect(tokens[2].value).toBe "http://github.com"
+          expect(tokens[2].scopes).toEqual ["source.js", "comment.line.double-slash.js", "markup.underline.link.http.hyperlink"]
 
     describe "when the grammar is updated", ->
       it "retokenizes existing buffers that contain tokens that match the injection selector", ->
@@ -2771,14 +2782,17 @@ describe "Editor", ->
         expect(tokens[1].value).toBe " SELECT * FROM OCTOCATS"
         expect(tokens[1].scopes).toEqual ["source.js", "comment.line.double-slash.js"]
 
-        atom.packages.activatePackage('package-with-injection-selector', sync: true)
+
+        atom.packages.activatePackage('package-with-injection-selector')
 
         {tokens} = editor.lineForScreenRow(0)
         expect(tokens[1].value).toBe " SELECT * FROM OCTOCATS"
         expect(tokens[1].scopes).toEqual ["source.js", "comment.line.double-slash.js"]
 
-        atom.packages.activatePackage('language-sql', sync: true)
+        waitsForPromise ->
+          atom.packages.activatePackage('language-sql')
 
-        {tokens} = editor.lineForScreenRow(0)
-        expect(tokens[2].value).toBe "SELECT"
-        expect(tokens[2].scopes).toEqual ["source.js", "comment.line.double-slash.js", "keyword.other.DML.sql"]
+        runs ->
+          {tokens} = editor.lineForScreenRow(0)
+          expect(tokens[2].value).toBe "SELECT"
+          expect(tokens[2].scopes).toEqual ["source.js", "comment.line.double-slash.js", "keyword.other.DML.sql"]
diff --git a/spec/editor-view-spec.coffee b/spec/editor-view-spec.coffee
index 23804de70..33db23b42 100644
--- a/spec/editor-view-spec.coffee
+++ b/spec/editor-view-spec.coffee
@@ -10,8 +10,6 @@ describe "EditorView", ->
   [buffer, editorView, editor, cachedLineHeight, cachedCharWidth] = []
 
   beforeEach ->
-    atom.packages.activatePackage('language-text', sync: true)
-    atom.packages.activatePackage('language-javascript', sync: true)
     editor = atom.project.openSync('sample.js')
     buffer = editor.buffer
     editorView = new EditorView(editor)
@@ -26,6 +24,12 @@ describe "EditorView", ->
       @width(getCharWidth() * widthInChars) if widthInChars
       $('#jasmine-content').append(this)
 
+    waitsForPromise ->
+      atom.packages.activatePackage('language-text', sync: true)
+
+    waitsForPromise ->
+      atom.packages.activatePackage('language-javascript', sync: true)
+
   getLineHeight = ->
     return cachedLineHeight if cachedLineHeight?
     calcDimensions()
@@ -2515,9 +2519,9 @@ describe "EditorView", ->
       expect(edited).toBe false
 
   describe "when editor:copy-path is triggered", ->
-    it "copies the absolute path to the editor view's file to the pasteboard", ->
+    it "copies the absolute path to the editor view's file to the clipboard", ->
       editorView.trigger 'editor:copy-path'
-      expect(atom.pasteboard.read()[0]).toBe editor.getPath()
+      expect(atom.clipboard.read()).toBe editor.getPath()
 
   describe "when editor:move-line-up is triggered", ->
     describe "when there is no selection", ->
@@ -2532,6 +2536,52 @@ describe "EditorView", ->
         editorView.trigger 'editor:move-line-up'
         expect(editor.getCursorBufferPosition()).toEqual [0,2]
 
+      describe "when the line above is folded", ->
+        it "moves the line around the fold", ->
+          editor.foldBufferRow(1)
+          editor.setCursorBufferPosition([10, 0])
+          editorView.trigger 'editor:move-line-up'
+
+          expect(editor.getCursorBufferPosition()).toEqual [1, 0]
+          expect(buffer.lineForRow(1)).toBe ''
+          expect(buffer.lineForRow(2)).toBe '  var sort = function(items) {'
+          expect(editor.isFoldedAtBufferRow(1)).toBe false
+          expect(editor.isFoldedAtBufferRow(2)).toBe true
+
+        describe "when the line being moved is folded", ->
+          it "moves the fold around the fold above it", ->
+            editor.setCursorBufferPosition([0, 0])
+            editor.insertText """
+              var a = function() {
+                b = 3;
+              };
+
+            """
+            editor.foldBufferRow(0)
+            editor.foldBufferRow(3)
+            editor.setCursorBufferPosition([3, 0])
+            editorView.trigger 'editor:move-line-up'
+
+            expect(editor.getCursorBufferPosition()).toEqual [0, 0]
+            expect(buffer.lineForRow(0)).toBe 'var quicksort = function () {'
+            expect(buffer.lineForRow(13)).toBe 'var a = function() {'
+            editor.logScreenLines()
+            expect(editor.isFoldedAtBufferRow(0)).toBe true
+            expect(editor.isFoldedAtBufferRow(13)).toBe true
+
+      describe "when the line above is empty and the line above that is folded", ->
+        it "moves the line to the empty line", ->
+          editor.foldBufferRow(2)
+          editor.setCursorBufferPosition([11, 0])
+          editorView.trigger 'editor:move-line-up'
+
+          expect(editor.getCursorBufferPosition()).toEqual [10, 0]
+          expect(buffer.lineForRow(9)).toBe '  };'
+          expect(buffer.lineForRow(10)).toBe '  return sort(Array.apply(this, arguments));'
+          expect(buffer.lineForRow(11)).toBe ''
+          expect(editor.isFoldedAtBufferRow(2)).toBe true
+          expect(editor.isFoldedAtBufferRow(10)).toBe false
+
     describe "where there is a selection", ->
       describe "when the selection falls inside the line", ->
         it "maintains the selection", ->
@@ -2631,6 +2681,54 @@ describe "EditorView", ->
         editorView.trigger 'editor:move-line-down'
         expect(editor.getCursorBufferPosition()).toEqual [1, 2]
 
+      describe "when the line below is folded", ->
+        it "moves the line around the fold", ->
+          editor.setCursorBufferPosition([0, 0])
+          editor.foldBufferRow(1)
+          editorView.trigger 'editor:move-line-down'
+
+          expect(editor.getCursorBufferPosition()).toEqual [9, 0]
+          expect(buffer.lineForRow(0)).toBe '  var sort = function(items) {'
+          expect(buffer.lineForRow(9)).toBe 'var quicksort = function () {'
+          expect(editor.isFoldedAtBufferRow(0)).toBe true
+          expect(editor.isFoldedAtBufferRow(9)).toBe false
+
+        describe "when the line being moved is folded", ->
+          it "moves the fold around the fold below it", ->
+            editor.setCursorBufferPosition([0, 0])
+            editor.insertText """
+              var a = function() {
+                b = 3;
+              };
+
+            """
+            editor.foldBufferRow(0)
+            editor.foldBufferRow(3)
+            editor.setCursorBufferPosition([0, 0])
+            editorView.trigger 'editor:move-line-down'
+
+            expect(editor.getCursorBufferPosition()).toEqual [13, 0]
+            expect(buffer.lineForRow(0)).toBe 'var quicksort = function () {'
+            expect(buffer.lineForRow(13)).toBe 'var a = function() {'
+            expect(editor.isFoldedAtBufferRow(0)).toBe true
+            expect(editor.isFoldedAtBufferRow(13)).toBe true
+
+      describe "when the line below is empty and the line below that is folded", ->
+        it "moves the line to the empty line", ->
+          editor.setCursorBufferPosition([0, Infinity])
+          editor.insertText('\n')
+          editor.setCursorBufferPosition([0, 0])
+          editor.foldBufferRow(2)
+          editorView.trigger 'editor:move-line-down'
+
+          expect(editor.getCursorBufferPosition()).toEqual [1, 0]
+          expect(buffer.lineForRow(0)).toBe ''
+          expect(buffer.lineForRow(1)).toBe 'var quicksort = function () {'
+          expect(buffer.lineForRow(2)).toBe '  var sort = function(items) {'
+          expect(editor.isFoldedAtBufferRow(0)).toBe false
+          expect(editor.isFoldedAtBufferRow(1)).toBe false
+          expect(editor.isFoldedAtBufferRow(2)).toBe true
+
     describe "when the cursor is on the last line", ->
       it "does not move the line", ->
         editor.moveCursorToBottom()
diff --git a/spec/fixtures/packages/package-with-activation-events/package.cson b/spec/fixtures/packages/package-with-activation-events/package.cson
index 45d8dfea1..dfa55c54d 100644
--- a/spec/fixtures/packages/package-with-activation-events/package.cson
+++ b/spec/fixtures/packages/package-with-activation-events/package.cson
@@ -1,2 +1 @@
 'activationEvents': ['activation-event']
-'deferredDeserializers': ['Foo']
diff --git a/spec/fixtures/packages/package-with-serialize-error/package.cson b/spec/fixtures/packages/package-with-serialize-error/package.cson
index d49a175ed..300ce2fc0 100644
--- a/spec/fixtures/packages/package-with-serialize-error/package.cson
+++ b/spec/fixtures/packages/package-with-serialize-error/package.cson
@@ -1,5 +1 @@
-# This package loads async, otherwise it would log errors when it
-# is automatically serialized when workspaceView is deactivatated
-
 'main': 'index.coffee'
-'activationEvents': ['activation-event']
diff --git a/spec/fixtures/packages/theme-with-index-css/package.json b/spec/fixtures/packages/theme-with-index-css/package.json
index a4dc0188d..16e770b05 100644
--- a/spec/fixtures/packages/theme-with-index-css/package.json
+++ b/spec/fixtures/packages/theme-with-index-css/package.json
@@ -1,3 +1,3 @@
 {
-  "theme": true
+  "theme": "ui"
 }
diff --git a/spec/fixtures/packages/theme-with-index-less/package.json b/spec/fixtures/packages/theme-with-index-less/package.json
index a4dc0188d..16e770b05 100644
--- a/spec/fixtures/packages/theme-with-index-less/package.json
+++ b/spec/fixtures/packages/theme-with-index-less/package.json
@@ -1,3 +1,3 @@
 {
-  "theme": true
+  "theme": "ui"
 }
diff --git a/spec/fixtures/packages/theme-with-multiple-imported-files/package.json b/spec/fixtures/packages/theme-with-multiple-imported-files/package.json
index a4dc0188d..16e770b05 100644
--- a/spec/fixtures/packages/theme-with-multiple-imported-files/package.json
+++ b/spec/fixtures/packages/theme-with-multiple-imported-files/package.json
@@ -1,3 +1,3 @@
 {
-  "theme": true
+  "theme": "ui"
 }
diff --git a/spec/fixtures/packages/theme-with-package-file/package.json b/spec/fixtures/packages/theme-with-package-file/package.json
index b429a1151..a5e06495a 100644
--- a/spec/fixtures/packages/theme-with-package-file/package.json
+++ b/spec/fixtures/packages/theme-with-package-file/package.json
@@ -1,4 +1,4 @@
 {
-  "theme": true,
+  "theme": "ui",
   "stylesheets": ["first.css", "second.less", "last.css"]
 }
diff --git a/spec/fixtures/packages/theme-with-ui-variables/package.json b/spec/fixtures/packages/theme-with-ui-variables/package.json
index fa1446fd6..047ee57c9 100644
--- a/spec/fixtures/packages/theme-with-ui-variables/package.json
+++ b/spec/fixtures/packages/theme-with-ui-variables/package.json
@@ -1,4 +1,4 @@
 {
-  "theme": true,
+  "theme": "ui",
   "stylesheets": ["editor.less"]
 }
diff --git a/spec/jasmine-helper.coffee b/spec/jasmine-helper.coffee
index 5ff4ee868..87765634c 100644
--- a/spec/jasmine-helper.coffee
+++ b/spec/jasmine-helper.coffee
@@ -21,10 +21,6 @@ module.exports.runSpecSuite = (specSuite, logFile, logErrors=true) ->
       print: (str) ->
         log(str)
       onComplete: (runner) ->
-        log('\n')
-        timeReporter.logLongestSuites 10, (line) -> log("#{line}\n")
-        log('\n')
-        timeReporter.logLongestSpecs 10, (line) -> log("#{line}\n")
         fs.closeSync(logStream) if logStream?
         atom.exit(runner.results().failedCount > 0 ? 1 : 0)
   else
diff --git a/spec/language-mode-spec.coffee b/spec/language-mode-spec.coffee
index 2f7b1cc91..a72470704 100644
--- a/spec/language-mode-spec.coffee
+++ b/spec/language-mode-spec.coffee
@@ -6,10 +6,12 @@ describe "LanguageMode", ->
 
   describe "javascript", ->
     beforeEach ->
-      atom.packages.activatePackage('language-javascript', sync: true)
       editor = atom.project.openSync('sample.js', autoIndent: false)
       {buffer, languageMode} = editor
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-javascript')
+
     describe ".minIndentLevelForRowRange(startRow, endRow)", ->
       it "returns the minimum indent level for the given row range", ->
         expect(languageMode.minIndentLevelForRowRange(4, 7)).toBe 2
@@ -100,10 +102,12 @@ describe "LanguageMode", ->
 
   describe "coffeescript", ->
     beforeEach ->
-      atom.packages.activatePackage('language-coffee-script', sync: true)
       editor = atom.project.openSync('coffee.coffee', autoIndent: false)
       {buffer, languageMode} = editor
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-coffee-script')
+
     describe ".toggleLineCommentsForBufferRows(start, end)", ->
       it "comments/uncomments lines in the given range", ->
         languageMode.toggleLineCommentsForBufferRows(4, 6)
@@ -147,10 +151,12 @@ describe "LanguageMode", ->
 
   describe "css", ->
     beforeEach ->
-      atom.packages.activatePackage('language-css', sync: true)
       editor = atom.project.openSync('css.css', autoIndent: false)
       {buffer, languageMode} = editor
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-css')
+
     describe ".toggleLineCommentsForBufferRows(start, end)", ->
       it "comments/uncomments lines in the given range", ->
         languageMode.toggleLineCommentsForBufferRows(0, 1)
@@ -188,11 +194,15 @@ describe "LanguageMode", ->
 
   describe "less", ->
     beforeEach ->
-      atom.packages.activatePackage('language-less', sync: true)
-      atom.packages.activatePackage('language-css', sync: true)
       editor = atom.project.openSync('sample.less', autoIndent: false)
       {buffer, languageMode} = editor
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-less')
+
+      waitsForPromise ->
+        atom.packages.activatePackage('language-css')
+
     describe "when commenting lines", ->
       it "only uses the `commentEnd` pattern if it comes from the same grammar as the `commentStart`", ->
         languageMode.toggleLineCommentsForBufferRows(0, 0)
@@ -200,10 +210,12 @@ describe "LanguageMode", ->
 
   describe "folding", ->
     beforeEach ->
-      atom.packages.activatePackage('language-javascript', sync: true)
       editor = atom.project.openSync('sample.js', autoIndent: false)
       {buffer, languageMode} = editor
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-javascript')
+
     it "maintains cursor buffer position when a folding/unfolding", ->
       editor.setCursorBufferPosition([5,5])
       languageMode.foldAll()
@@ -298,10 +310,12 @@ describe "LanguageMode", ->
 
   describe "folding with comments", ->
     beforeEach ->
-      atom.packages.activatePackage('language-javascript', sync: true)
       editor = atom.project.openSync('sample-with-comments.js', autoIndent: false)
       {buffer, languageMode} = editor
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-javascript')
+
     describe ".unfoldAll()", ->
       it "unfolds every folded line", ->
         initialScreenLineCount = editor.getScreenLineCount()
@@ -362,10 +376,12 @@ describe "LanguageMode", ->
 
   describe "css", ->
     beforeEach ->
-      atom.packages.activatePackage('language-source', sync: true)
-      atom.packages.activatePackage('language-css', sync: true)
       editor = atom.project.openSync('css.css', autoIndent: true)
 
+      waitsForPromise ->
+        atom.packages.activatePackage('language-source')
+        atom.packages.activatePackage('language-css')
+
     describe "suggestedIndentForBufferRow", ->
       it "does not return negative values (regression)", ->
         editor.setText('.test {\npadding: 0;\n}')
diff --git a/spec/pane-container-view-spec.coffee b/spec/pane-container-view-spec.coffee
index 667d3bd6a..28fbd56a6 100644
--- a/spec/pane-container-view-spec.coffee
+++ b/spec/pane-container-view-spec.coffee
@@ -27,32 +27,6 @@ describe "PaneContainerView", ->
   afterEach ->
     atom.deserializers.remove(TestView)
 
-  describe ".focusNextPane()", ->
-    it "focuses the pane following the focused pane or the first pane if no pane has focus", ->
-      container.attachToDom()
-      container.focusNextPane()
-      expect(pane1.activeItem).toMatchSelector ':focus'
-      container.focusNextPane()
-      expect(pane2.activeItem).toMatchSelector ':focus'
-      container.focusNextPane()
-      expect(pane3.activeItem).toMatchSelector ':focus'
-      container.focusNextPane()
-      expect(pane1.activeItem).toMatchSelector ':focus'
-
-  describe ".focusPreviousPane()", ->
-    it "focuses the pane preceding the focused pane or the last pane if no pane has focus", ->
-      container.attachToDom()
-      container.getPanes()[0].focus() # activate first pane
-
-      container.focusPreviousPane()
-      expect(pane3.activeItem).toMatchSelector ':focus'
-      container.focusPreviousPane()
-      expect(pane2.activeItem).toMatchSelector ':focus'
-      container.focusPreviousPane()
-      expect(pane1.activeItem).toMatchSelector ':focus'
-      container.focusPreviousPane()
-      expect(pane3.activeItem).toMatchSelector ':focus'
-
   describe ".getActivePane()", ->
     it "returns the most-recently focused pane", ->
       focusStealer = $$ -> @div tabindex: -1, "focus stealer"
@@ -265,3 +239,115 @@ describe "PaneContainerView", ->
         pane1.remove()
         pane2.remove()
         expect(activeItemChangedHandler).not.toHaveBeenCalled()
+
+  describe ".focusNextPane()", ->
+    it "focuses the pane following the focused pane or the first pane if no pane has focus", ->
+      container.attachToDom()
+      container.focusNextPane()
+      expect(pane1.activeItem).toMatchSelector ':focus'
+      container.focusNextPane()
+      expect(pane2.activeItem).toMatchSelector ':focus'
+      container.focusNextPane()
+      expect(pane3.activeItem).toMatchSelector ':focus'
+      container.focusNextPane()
+      expect(pane1.activeItem).toMatchSelector ':focus'
+
+  describe ".focusPreviousPane()", ->
+    it "focuses the pane preceding the focused pane or the last pane if no pane has focus", ->
+      container.attachToDom()
+      container.getPanes()[0].focus() # activate first pane
+
+      container.focusPreviousPane()
+      expect(pane3.activeItem).toMatchSelector ':focus'
+      container.focusPreviousPane()
+      expect(pane2.activeItem).toMatchSelector ':focus'
+      container.focusPreviousPane()
+      expect(pane1.activeItem).toMatchSelector ':focus'
+      container.focusPreviousPane()
+      expect(pane3.activeItem).toMatchSelector ':focus'
+
+  describe "changing focus directionally between panes", ->
+    [pane1, pane2, pane3, pane4, pane5, pane6, pane7, pane8, pane9] = []
+
+    beforeEach ->
+      # Set up a grid of 9 panes, in the following arrangement, where the
+      # numbers correspond to the variable names below.
+      #
+      # -------
+      # |1|2|3|
+      # -------
+      # |4|5|6|
+      # -------
+      # |7|8|9|
+      # -------
+
+      container = new PaneContainerView
+      pane1 = container.getRoot()
+      pane1.activateItem(new TestView('1'))
+      pane4 = pane1.splitDown(new TestView('4'))
+      pane7 = pane4.splitDown(new TestView('7'))
+
+      pane2 = pane1.splitRight(new TestView('2'))
+      pane3 = pane2.splitRight(new TestView('3'))
+
+      pane5 = pane4.splitRight(new TestView('5'))
+      pane6 = pane5.splitRight(new TestView('6'))
+
+      pane8 = pane7.splitRight(new TestView('8'))
+      pane9 = pane8.splitRight(new TestView('9'))
+
+      container.height(400)
+      container.width(400)
+      container.attachToDom()
+
+    describe ".focusPaneAbove()", ->
+      describe "when there are multiple rows above the focused pane", ->
+        it "focuses up to the adjacent row", ->
+          pane8.focus()
+          container.focusPaneAbove()
+          expect(pane5.activeItem).toMatchSelector ':focus'
+
+      describe "when there are no rows above the focused pane", ->
+        it "keeps the current pane focused", ->
+          pane2.focus()
+          container.focusPaneAbove()
+          expect(pane2.activeItem).toMatchSelector ':focus'
+
+    describe ".focusPaneBelow()", ->
+      describe "when there are multiple rows below the focused pane", ->
+        it "focuses down to the adjacent row", ->
+          pane2.focus()
+          container.focusPaneBelow()
+          expect(pane5.activeItem).toMatchSelector ':focus'
+
+      describe "when there are no rows below the focused pane", ->
+        it "keeps the current pane focused", ->
+          pane8.focus()
+          container.focusPaneBelow()
+          expect(pane8.activeItem).toMatchSelector ':focus'
+
+    describe ".focusPaneOnLeft()", ->
+      describe "when there are multiple columns to the left of the focused pane", ->
+        it "focuses left to the adjacent column", ->
+          pane6.focus()
+          container.focusPaneOnLeft()
+          expect(pane5.activeItem).toMatchSelector ':focus'
+
+      describe "when there are no columns to the left of the focused pane", ->
+        it "keeps the current pane focused", ->
+          pane4.focus()
+          container.focusPaneOnLeft()
+          expect(pane4.activeItem).toMatchSelector ':focus'
+
+    describe ".focusPaneOnRight()", ->
+      describe "when there are multiple columns to the right of the focused pane", ->
+        it "focuses right to the adjacent column", ->
+          pane4.focus()
+          container.focusPaneOnRight()
+          expect(pane5.activeItem).toMatchSelector ':focus'
+
+      describe "when there are no columns to the right of the focused pane", ->
+        it "keeps the current pane focused", ->
+          pane6.focus()
+          container.focusPaneOnRight()
+          expect(pane6.activeItem).toMatchSelector ':focus'
diff --git a/spec/pasteboard-spec.coffee b/spec/pasteboard-spec.coffee
deleted file mode 100644
index 467418204..000000000
--- a/spec/pasteboard-spec.coffee
+++ /dev/null
@@ -1,10 +0,0 @@
-describe "Pasteboard", ->
-  describe "write(text, metadata) and read()", ->
-    it "writes and reads text to/from the native pasteboard", ->
-      expect(atom.pasteboard.read()).toEqual ['initial pasteboard content']
-      atom.pasteboard.write('next')
-      expect(atom.pasteboard.read()[0]).toBe 'next'
-
-    it "returns metadata if the item on the native pasteboard matches the last written item", ->
-      atom.pasteboard.write('next', {meta: 'data'})
-      expect(atom.pasteboard.read()).toEqual ['next', {meta: 'data'}]
diff --git a/spec/project-spec.coffee b/spec/project-spec.coffee
index 1ac76e204..e33413f97 100644
--- a/spec/project-spec.coffee
+++ b/spec/project-spec.coffee
@@ -72,7 +72,7 @@ describe "Project", ->
       expect(atom.project.getEditors()[1]).toBe editor2
 
   describe ".openSync(path)", ->
-    [fooOpener, barOpener, absolutePath, newBufferHandler, newEditorHandler] = []
+    [absolutePath, newBufferHandler, newEditorHandler] = []
     beforeEach ->
       absolutePath = require.resolve('./fixtures/dir/a')
       newBufferHandler = jasmine.createSpy('newBufferHandler')
@@ -80,129 +80,92 @@ describe "Project", ->
       newEditorHandler = jasmine.createSpy('newEditorHandler')
       atom.project.on 'editor-created', newEditorHandler
 
-      fooOpener = (pathToOpen, options) -> { foo: pathToOpen, options } if pathToOpen?.match(/\.foo/)
-      barOpener = (pathToOpen) -> { bar: pathToOpen } if pathToOpen?.match(/^bar:\/\//)
-      atom.project.registerOpener(fooOpener)
-      atom.project.registerOpener(barOpener)
+    describe "when given an absolute path that hasn't been opened previously", ->
+      it "returns a new edit session for the given path and emits 'buffer-created' and 'editor-created' events", ->
+        editor = atom.project.openSync(absolutePath)
+        expect(editor.buffer.getPath()).toBe absolutePath
+        expect(newBufferHandler).toHaveBeenCalledWith editor.buffer
+        expect(newEditorHandler).toHaveBeenCalledWith editor
 
-    afterEach ->
-      atom.project.unregisterOpener(fooOpener)
-      atom.project.unregisterOpener(barOpener)
+    describe "when given a relative path that hasn't been opened previously", ->
+      it "returns a new edit session for the given path (relative to the project root) and emits 'buffer-created' and 'editor-created' events", ->
+        editor = atom.project.openSync('a')
+        expect(editor.buffer.getPath()).toBe absolutePath
+        expect(newBufferHandler).toHaveBeenCalledWith editor.buffer
+        expect(newEditorHandler).toHaveBeenCalledWith editor
 
-    describe "when passed a path that doesn't match a custom opener", ->
-      describe "when given an absolute path that hasn't been opened previously", ->
-        it "returns a new edit session for the given path and emits 'buffer-created' and 'editor-created' events", ->
-          editor = atom.project.openSync(absolutePath)
+    describe "when passed the path to a buffer that has already been opened", ->
+      it "returns a new edit session containing previously opened buffer and emits a 'editor-created' event", ->
+        editor = atom.project.openSync(absolutePath)
+        newBufferHandler.reset()
+        expect(atom.project.openSync(absolutePath).buffer).toBe editor.buffer
+        expect(atom.project.openSync('a').buffer).toBe editor.buffer
+        expect(newBufferHandler).not.toHaveBeenCalled()
+        expect(newEditorHandler).toHaveBeenCalledWith editor
+
+    describe "when not passed a path", ->
+      it "returns a new edit session and emits 'buffer-created' and 'editor-created' events", ->
+        editor = atom.project.openSync()
+        expect(editor.buffer.getPath()).toBeUndefined()
+        expect(newBufferHandler).toHaveBeenCalledWith(editor.buffer)
+        expect(newEditorHandler).toHaveBeenCalledWith editor
+
+  describe ".open(path)", ->
+    [absolutePath, newBufferHandler, newEditorHandler] = []
+
+    beforeEach ->
+      absolutePath = require.resolve('./fixtures/dir/a')
+      newBufferHandler = jasmine.createSpy('newBufferHandler')
+      atom.project.on 'buffer-created', newBufferHandler
+      newEditorHandler = jasmine.createSpy('newEditorHandler')
+      atom.project.on 'editor-created', newEditorHandler
+
+    describe "when given an absolute path that isn't currently open", ->
+      it "returns a new edit session for the given path and emits 'buffer-created' and 'editor-created' events", ->
+        editor = null
+        waitsForPromise ->
+          atom.project.open(absolutePath).then (o) -> editor = o
+
+        runs ->
           expect(editor.buffer.getPath()).toBe absolutePath
           expect(newBufferHandler).toHaveBeenCalledWith editor.buffer
           expect(newEditorHandler).toHaveBeenCalledWith editor
 
-      describe "when given a relative path that hasn't been opened previously", ->
-        it "returns a new edit session for the given path (relative to the project root) and emits 'buffer-created' and 'editor-created' events", ->
-          editor = atom.project.openSync('a')
+    describe "when given a relative path that isn't currently opened", ->
+      it "returns a new edit session for the given path (relative to the project root) and emits 'buffer-created' and 'editor-created' events", ->
+        editor = null
+        waitsForPromise ->
+          atom.project.open(absolutePath).then (o) -> editor = o
+
+        runs ->
           expect(editor.buffer.getPath()).toBe absolutePath
           expect(newBufferHandler).toHaveBeenCalledWith editor.buffer
           expect(newEditorHandler).toHaveBeenCalledWith editor
 
-      describe "when passed the path to a buffer that has already been opened", ->
-        it "returns a new edit session containing previously opened buffer and emits a 'editor-created' event", ->
-          editor = atom.project.openSync(absolutePath)
+    describe "when passed the path to a buffer that is currently opened", ->
+      it "returns a new edit session containing currently opened buffer and emits a 'editor-created' event", ->
+        editor = null
+        waitsForPromise ->
+          atom.project.open(absolutePath).then (o) -> editor = o
+
+        runs ->
           newBufferHandler.reset()
           expect(atom.project.openSync(absolutePath).buffer).toBe editor.buffer
           expect(atom.project.openSync('a').buffer).toBe editor.buffer
           expect(newBufferHandler).not.toHaveBeenCalled()
           expect(newEditorHandler).toHaveBeenCalledWith editor
 
-      describe "when not passed a path", ->
-        it "returns a new edit session and emits 'buffer-created' and 'editor-created' events", ->
-          editor = atom.project.openSync()
+    describe "when not passed a path", ->
+      it "returns a new edit session and emits 'buffer-created' and 'editor-created' events", ->
+        editor = null
+        waitsForPromise ->
+          atom.project.open().then (o) -> editor = o
+
+        runs ->
           expect(editor.buffer.getPath()).toBeUndefined()
           expect(newBufferHandler).toHaveBeenCalledWith(editor.buffer)
           expect(newEditorHandler).toHaveBeenCalledWith editor
 
-    describe "when passed a path that matches a custom opener", ->
-      it "returns the resource returned by the custom opener", ->
-        pathToOpen = atom.project.resolve('a.foo')
-        expect(atom.project.openSync(pathToOpen, hey: "there")).toEqual { foo: pathToOpen, options: {hey: "there"} }
-        expect(atom.project.openSync("bar://baz")).toEqual { bar: "bar://baz" }
-
-  describe ".open(path)", ->
-    [fooOpener, barOpener, absolutePath, newBufferHandler, newEditorHandler] = []
-
-    beforeEach ->
-      absolutePath = require.resolve('./fixtures/dir/a')
-      newBufferHandler = jasmine.createSpy('newBufferHandler')
-      atom.project.on 'buffer-created', newBufferHandler
-      newEditorHandler = jasmine.createSpy('newEditorHandler')
-      atom.project.on 'editor-created', newEditorHandler
-
-      fooOpener = (pathToOpen, options) -> { foo: pathToOpen, options } if pathToOpen?.match(/\.foo/)
-      barOpener = (pathToOpen) -> { bar: pathToOpen } if pathToOpen?.match(/^bar:\/\//)
-      atom.project.registerOpener(fooOpener)
-      atom.project.registerOpener(barOpener)
-
-    afterEach ->
-      atom.project.unregisterOpener(fooOpener)
-      atom.project.unregisterOpener(barOpener)
-
-    describe "when passed a path that doesn't match a custom opener", ->
-      describe "when given an absolute path that isn't currently open", ->
-        it "returns a new edit session for the given path and emits 'buffer-created' and 'editor-created' events", ->
-          editor = null
-          waitsForPromise ->
-            atom.project.open(absolutePath).then (o) -> editor = o
-
-          runs ->
-            expect(editor.buffer.getPath()).toBe absolutePath
-            expect(newBufferHandler).toHaveBeenCalledWith editor.buffer
-            expect(newEditorHandler).toHaveBeenCalledWith editor
-
-      describe "when given a relative path that isn't currently opened", ->
-        it "returns a new edit session for the given path (relative to the project root) and emits 'buffer-created' and 'editor-created' events", ->
-          editor = null
-          waitsForPromise ->
-            atom.project.open(absolutePath).then (o) -> editor = o
-
-          runs ->
-            expect(editor.buffer.getPath()).toBe absolutePath
-            expect(newBufferHandler).toHaveBeenCalledWith editor.buffer
-            expect(newEditorHandler).toHaveBeenCalledWith editor
-
-      describe "when passed the path to a buffer that is currently opened", ->
-        it "returns a new edit session containing currently opened buffer and emits a 'editor-created' event", ->
-          editor = null
-          waitsForPromise ->
-            atom.project.open(absolutePath).then (o) -> editor = o
-
-          runs ->
-            newBufferHandler.reset()
-            expect(atom.project.openSync(absolutePath).buffer).toBe editor.buffer
-            expect(atom.project.openSync('a').buffer).toBe editor.buffer
-            expect(newBufferHandler).not.toHaveBeenCalled()
-            expect(newEditorHandler).toHaveBeenCalledWith editor
-
-      describe "when not passed a path", ->
-        it "returns a new edit session and emits 'buffer-created' and 'editor-created' events", ->
-          editor = null
-          waitsForPromise ->
-            atom.project.open().then (o) -> editor = o
-
-          runs ->
-            expect(editor.buffer.getPath()).toBeUndefined()
-            expect(newBufferHandler).toHaveBeenCalledWith(editor.buffer)
-            expect(newEditorHandler).toHaveBeenCalledWith editor
-
-    describe "when passed a path that matches a custom opener", ->
-      it "returns the resource returned by the custom opener", ->
-        waitsForPromise ->
-          pathToOpen = atom.project.resolve('a.foo')
-          atom.project.open(pathToOpen, hey: "there").then (item) ->
-            expect(item).toEqual { foo: pathToOpen, options: {hey: "there"} }
-
-        waitsForPromise ->
-          atom.project.open("bar://baz").then (item) ->
-            expect(item).toEqual { bar: "bar://baz" }
-
     it "returns number of read bytes as progress indicator", ->
       filePath = atom.project.resolve 'a'
       totalBytes = 0
diff --git a/spec/space-pen-extensions-spec.coffee b/spec/space-pen-extensions-spec.coffee
index 28849c72c..92b95c600 100644
--- a/spec/space-pen-extensions-spec.coffee
+++ b/spec/space-pen-extensions-spec.coffee
@@ -11,35 +11,6 @@ describe "SpacePen extensions", ->
     parent = $$ -> @div()
     parent.append(view)
 
-  describe "View.observeConfig(keyPath, callback)", ->
-    observeHandler = null
-
-    beforeEach ->
-      observeHandler = jasmine.createSpy("observeHandler")
-      view.observeConfig "foo.bar", observeHandler
-      expect(view.hasParent()).toBeTruthy()
-
-    it "observes the keyPath and cancels the subscription when `.unobserveConfig()` is called", ->
-      expect(observeHandler).toHaveBeenCalledWith(undefined)
-      observeHandler.reset()
-
-      atom.config.set("foo.bar", "hello")
-
-      expect(observeHandler).toHaveBeenCalledWith("hello", previous: undefined)
-      observeHandler.reset()
-
-      view.unobserveConfig()
-
-      atom.config.set("foo.bar", "goodbye")
-
-      expect(observeHandler).not.toHaveBeenCalled()
-
-    it "unobserves when the view is removed", ->
-      observeHandler.reset()
-      parent.remove()
-      atom.config.set("foo.bar", "hello")
-      expect(observeHandler).not.toHaveBeenCalled()
-
   describe "View.subscribe(eventEmitter, eventName, callback)", ->
     [emitter, eventHandler] = []
 
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index 8e939d03d..8e9fa939d 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -95,9 +95,9 @@ beforeEach ->
   TokenizedBuffer.prototype.chunkSize = Infinity
   spyOn(TokenizedBuffer.prototype, "tokenizeInBackground").andCallFake -> @tokenizeNextChunk()
 
-  pasteboardContent = 'initial pasteboard content'
-  spyOn(clipboard, 'writeText').andCallFake (text) -> pasteboardContent = text
-  spyOn(clipboard, 'readText').andCallFake -> pasteboardContent
+  clipboardContent = 'initial clipboard content'
+  spyOn(clipboard, 'writeText').andCallFake (text) -> clipboardContent = text
+  spyOn(clipboard, 'readText').andCallFake -> clipboardContent
 
   addCustomMatchers(this)
 
@@ -159,6 +159,16 @@ addCustomMatchers = (spec) ->
       @message = -> return "Expected path '" + @actual + "'" + notText + " to exist."
       fs.existsSync(@actual)
 
+    toHaveFocus: ->
+      notText = this.isNot and " not" or ""
+      if not document.hasFocus()
+        console.error "Specs will fail because the Dev Tools have focus. To fix this close the Dev Tools or click the spec runner."
+
+      @message = -> return "Expected element '" + @actual + "' or its descendants" + notText + " to have focus."
+      element = @actual
+      element = element.get(0) if element.jquery
+      element.webkitMatchesSelector(":focus") or element.querySelector(":focus")
+
 window.keyIdentifierForKey = (key) ->
   if key.length > 1 # named key
     key
diff --git a/spec/syntax-spec.coffee b/spec/syntax-spec.coffee
index 92373c53d..c39d12152 100644
--- a/spec/syntax-spec.coffee
+++ b/spec/syntax-spec.coffee
@@ -4,10 +4,18 @@ temp = require 'temp'
 
 describe "the `syntax` global", ->
   beforeEach ->
-    atom.packages.activatePackage('language-text', sync: true)
-    atom.packages.activatePackage('language-javascript', sync: true)
-    atom.packages.activatePackage('language-coffee-script', sync: true)
-    atom.packages.activatePackage('language-ruby', sync: true)
+
+    waitsForPromise ->
+      atom.packages.activatePackage('language-text')
+
+    waitsForPromise ->
+      atom.packages.activatePackage('language-javascript')
+
+    waitsForPromise ->
+      atom.packages.activatePackage('language-coffee-script')
+
+    waitsForPromise ->
+      atom.packages.activatePackage('language-ruby')
 
   describe "serialization", ->
     it "remembers grammar overrides by path", ->
@@ -20,29 +28,33 @@ describe "the `syntax` global", ->
 
   describe ".selectGrammar(filePath)", ->
     it "can use the filePath to load the correct grammar based on the grammar's filetype", ->
-      atom.packages.activatePackage('language-git', sync: true)
+      waitsForPromise ->
+        atom.packages.activatePackage('language-git')
 
-      expect(atom.syntax.selectGrammar("file.js").name).toBe "JavaScript" # based on extension (.js)
-      expect(atom.syntax.selectGrammar(path.join(temp.dir, '.git', 'config')).name).toBe "Git Config" # based on end of the path (.git/config)
-      expect(atom.syntax.selectGrammar("Rakefile").name).toBe "Ruby" # based on the file's basename (Rakefile)
-      expect(atom.syntax.selectGrammar("curb").name).toBe "Null Grammar"
-      expect(atom.syntax.selectGrammar("/hu.git/config").name).toBe "Null Grammar"
+      runs ->
+        expect(atom.syntax.selectGrammar("file.js").name).toBe "JavaScript" # based on extension (.js)
+        expect(atom.syntax.selectGrammar(path.join(temp.dir, '.git', 'config')).name).toBe "Git Config" # based on end of the path (.git/config)
+        expect(atom.syntax.selectGrammar("Rakefile").name).toBe "Ruby" # based on the file's basename (Rakefile)
+        expect(atom.syntax.selectGrammar("curb").name).toBe "Null Grammar"
+        expect(atom.syntax.selectGrammar("/hu.git/config").name).toBe "Null Grammar"
 
     it "uses the filePath's shebang line if the grammar cannot be determined by the extension or basename", ->
       filePath = require.resolve("./fixtures/shebang")
       expect(atom.syntax.selectGrammar(filePath).name).toBe "Ruby"
 
     it "uses the number of newlines in the first line regex to determine the number of lines to test against", ->
-      atom.packages.activatePackage('language-property-list', sync: true)
+      waitsForPromise ->
+        atom.packages.activatePackage('language-property-list')
 
-      fileContent = "first-line\n<html>"
-      expect(atom.syntax.selectGrammar("dummy.coffee", fileContent).name).toBe "CoffeeScript"
+      runs ->
+        fileContent = "first-line\n<html>"
+        expect(atom.syntax.selectGrammar("dummy.coffee", fileContent).name).toBe "CoffeeScript"
 
-      fileContent = '<?xml version="1.0" encoding="UTF-8"?>'
-      expect(atom.syntax.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Null Grammar"
+        fileContent = '<?xml version="1.0" encoding="UTF-8"?>'
+        expect(atom.syntax.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Null Grammar"
 
-      fileContent += '\n<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">'
-      expect(atom.syntax.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Property List (XML)"
+        fileContent += '\n<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">'
+        expect(atom.syntax.selectGrammar("grammar.tmLanguage", fileContent).name).toBe "Property List (XML)"
 
     it "doesn't read the file when the file contents are specified", ->
       filePath = require.resolve("./fixtures/shebang")
diff --git a/spec/text-buffer-spec.coffee b/spec/text-buffer-spec.coffee
index 7f26c663b..70e1a773f 100644
--- a/spec/text-buffer-spec.coffee
+++ b/spec/text-buffer-spec.coffee
@@ -571,6 +571,23 @@ describe 'TextBuffer', ->
         saveBuffer.reload()
         expect(events).toEqual ['will-reload', 'reloaded']
 
+      it "no longer reports being in conflict", ->
+        saveBuffer.setText('a')
+        saveBuffer.save()
+        saveBuffer.setText('ab')
+
+        fs.writeFileSync(saveBuffer.getPath(), 'c')
+        conflictHandler = jasmine.createSpy('conflictHandler')
+        saveBuffer.on 'contents-conflicted', conflictHandler
+
+        waitsFor ->
+          conflictHandler.callCount > 0
+
+        runs ->
+          expect(saveBuffer.isInConflict()).toBe true
+          saveBuffer.save()
+          expect(saveBuffer.isInConflict()).toBe false
+
     describe "when the buffer has no path", ->
       it "throws an exception", ->
         saveBuffer = atom.project.bufferForPathSync(null)
diff --git a/spec/theme-manager-spec.coffee b/spec/theme-manager-spec.coffee
index c8d257b54..384844e93 100644
--- a/spec/theme-manager-spec.coffee
+++ b/spec/theme-manager-spec.coffee
@@ -26,11 +26,14 @@ describe "ThemeManager", ->
       expect(themes.length).toBeGreaterThan(2)
 
     it 'getActiveThemes get all the active themes', ->
-      themeManager.activateThemes()
-      names = atom.config.get('core.themes')
-      expect(names.length).toBeGreaterThan(0)
-      themes = themeManager.getActiveThemes()
-      expect(themes).toHaveLength(names.length)
+      waitsForPromise ->
+        themeManager.activateThemes()
+
+      runs ->
+        names = atom.config.get('core.themes')
+        expect(names.length).toBeGreaterThan(0)
+        themes = themeManager.getActiveThemes()
+        expect(themes).toHaveLength(names.length)
 
   describe "getImportPaths()", ->
     it "returns the theme directories before the themes are loaded", ->
@@ -51,29 +54,58 @@ describe "ThemeManager", ->
     it "add/removes stylesheets to reflect the new config value", ->
       themeManager.on 'reloaded', reloadHandler = jasmine.createSpy()
       spyOn(themeManager, 'getUserStylesheetPath').andCallFake -> null
-      themeManager.activateThemes()
 
-      atom.config.set('core.themes', [])
-      expect($('style.theme').length).toBe 0
-      expect(reloadHandler).toHaveBeenCalled()
+      waitsForPromise ->
+        themeManager.activateThemes()
 
-      atom.config.set('core.themes', ['atom-dark-syntax'])
-      expect($('style.theme').length).toBe 1
-      expect($('style.theme:eq(0)').attr('id')).toMatch /atom-dark-syntax/
+      runs ->
+        reloadHandler.reset()
+        atom.config.set('core.themes', [])
 
-      atom.config.set('core.themes', ['atom-light-syntax', 'atom-dark-syntax'])
-      expect($('style.theme').length).toBe 2
-      expect($('style.theme:eq(0)').attr('id')).toMatch /atom-dark-syntax/
-      expect($('style.theme:eq(1)').attr('id')).toMatch /atom-light-syntax/
+      waitsFor ->
+        reloadHandler.callCount == 1
 
-      atom.config.set('core.themes', [])
-      expect($('style.theme').length).toBe 0
+      runs ->
+        reloadHandler.reset()
+        expect($('style.theme')).toHaveLength 0
+        atom.config.set('core.themes', ['atom-dark-syntax'])
 
-      # atom-dark-ui has an directory path, the syntax one doesn't
-      atom.config.set('core.themes', ['theme-with-index-less', 'atom-dark-ui'])
-      importPaths = themeManager.getImportPaths()
-      expect(importPaths.length).toBe 1
-      expect(importPaths[0]).toContain 'atom-dark-ui'
+      waitsFor ->
+        reloadHandler.callCount == 1
+
+      runs ->
+        reloadHandler.reset()
+        expect($('style.theme')).toHaveLength 1
+        expect($('style.theme:eq(0)').attr('id')).toMatch /atom-dark-syntax/
+        atom.config.set('core.themes', ['atom-light-syntax', 'atom-dark-syntax'])
+
+      waitsFor ->
+        reloadHandler.callCount == 1
+
+      runs ->
+        reloadHandler.reset()
+        expect($('style.theme')).toHaveLength 2
+        expect($('style.theme:eq(0)').attr('id')).toMatch /atom-dark-syntax/
+        expect($('style.theme:eq(1)').attr('id')).toMatch /atom-light-syntax/
+        atom.config.set('core.themes', [])
+
+      waitsFor ->
+        reloadHandler.callCount == 1
+
+      runs ->
+        reloadHandler.reset()
+        expect($('style.theme')).toHaveLength 0
+        # atom-dark-ui has an directory path, the syntax one doesn't
+        atom.config.set('core.themes', ['theme-with-index-less', 'atom-dark-ui'])
+
+      waitsFor ->
+        reloadHandler.callCount == 1
+
+      runs ->
+        expect($('style.theme')).toHaveLength 2
+        importPaths = themeManager.getImportPaths()
+        expect(importPaths.length).toBe 1
+        expect(importPaths[0]).toContain 'atom-dark-ui'
 
   describe "when a theme fails to load", ->
     it "logs a warning", ->
@@ -145,18 +177,25 @@ describe "ThemeManager", ->
       atom.workspaceView = new WorkspaceView
       atom.workspaceView.append $$ -> @div class: 'editor'
       atom.workspaceView.attachToDom()
-      themeManager.activateThemes()
+
+      waitsForPromise ->
+        themeManager.activateThemes()
 
     it "loads the correct values from the theme's ui-variables file", ->
+      themeManager.on 'reloaded', reloadHandler = jasmine.createSpy()
       atom.config.set('core.themes', ['theme-with-ui-variables'])
 
-      # an override loaded in the base css
-      expect(atom.workspaceView.css("background-color")).toBe "rgb(0, 0, 255)"
+      waitsFor ->
+        reloadHandler.callCount > 0
 
-      # from within the theme itself
-      expect($(".editor").css("padding-top")).toBe "150px"
-      expect($(".editor").css("padding-right")).toBe "150px"
-      expect($(".editor").css("padding-bottom")).toBe "150px"
+      runs ->
+        # an override loaded in the base css
+        expect(atom.workspaceView.css("background-color")).toBe "rgb(0, 0, 255)"
+
+        # from within the theme itself
+        expect($(".editor").css("padding-top")).toBe "150px"
+        expect($(".editor").css("padding-right")).toBe "150px"
+        expect($(".editor").css("padding-bottom")).toBe "150px"
 
   describe "when the user stylesheet changes", ->
     it "reloads it", ->
@@ -164,12 +203,14 @@ describe "ThemeManager", ->
       fs.writeFileSync(userStylesheetPath, 'body {border-style: dotted !important;}')
 
       spyOn(themeManager, 'getUserStylesheetPath').andReturn userStylesheetPath
-      themeManager.activateThemes()
 
-      expect($(document.body).css('border-style')).toBe 'dotted'
-      spyOn(themeManager, 'loadUserStylesheet').andCallThrough()
+      waitsForPromise ->
+        themeManager.activateThemes()
 
-      fs.writeFileSync(userStylesheetPath, 'body {border-style: dashed}')
+      runs ->
+        expect($(document.body).css('border-style')).toBe 'dotted'
+        spyOn(themeManager, 'loadUserStylesheet').andCallThrough()
+        fs.writeFileSync(userStylesheetPath, 'body {border-style: dashed}')
 
       waitsFor ->
         themeManager.loadUserStylesheet.callCount is 1
diff --git a/spec/tokenized-buffer-spec.coffee b/spec/tokenized-buffer-spec.coffee
index a9df78a56..2fad95256 100644
--- a/spec/tokenized-buffer-spec.coffee
+++ b/spec/tokenized-buffer-spec.coffee
@@ -5,11 +5,13 @@ describe "TokenizedBuffer", ->
   [tokenizedBuffer, buffer, changeHandler] = []
 
   beforeEach ->
-    atom.packages.activatePackage('language-javascript', sync: true)
     # enable async tokenization
     TokenizedBuffer.prototype.chunkSize = 5
     jasmine.unspy(TokenizedBuffer.prototype, 'tokenizeInBackground')
 
+    waitsForPromise ->
+      atom.packages.activatePackage('language-javascript')
+
   startTokenizing = (tokenizedBuffer) ->
     tokenizedBuffer.setVisible(true)
 
@@ -311,10 +313,13 @@ describe "TokenizedBuffer", ->
 
   describe "when the buffer contains hard-tabs", ->
     beforeEach ->
-      atom.packages.activatePackage('language-coffee-script', sync: true)
-      buffer = atom.project.bufferForPathSync('sample-with-tabs.coffee')
-      tokenizedBuffer = new TokenizedBuffer({buffer})
-      startTokenizing(tokenizedBuffer)
+      waitsForPromise ->
+        atom.packages.activatePackage('language-coffee-script')
+
+      runs ->
+        buffer = atom.project.bufferForPathSync('sample-with-tabs.coffee')
+        tokenizedBuffer = new TokenizedBuffer({buffer})
+        startTokenizing(tokenizedBuffer)
 
     afterEach ->
       tokenizedBuffer.destroy()
@@ -341,14 +346,17 @@ describe "TokenizedBuffer", ->
 
   describe "when the buffer contains surrogate pairs", ->
     beforeEach ->
-      atom.packages.activatePackage('language-javascript', sync: true)
-      buffer = atom.project.bufferForPathSync 'sample-with-pairs.js'
-      buffer.setText """
-        'abc\uD835\uDF97def'
-        //\uD835\uDF97xyz
-      """
-      tokenizedBuffer = new TokenizedBuffer({buffer})
-      fullyTokenize(tokenizedBuffer)
+      waitsForPromise ->
+        atom.packages.activatePackage('language-javascript')
+
+      runs ->
+        buffer = atom.project.bufferForPathSync 'sample-with-pairs.js'
+        buffer.setText """
+          'abc\uD835\uDF97def'
+          //\uD835\uDF97xyz
+        """
+        tokenizedBuffer = new TokenizedBuffer({buffer})
+        fullyTokenize(tokenizedBuffer)
 
     afterEach ->
       tokenizedBuffer.destroy()
@@ -379,22 +387,30 @@ describe "TokenizedBuffer", ->
 
   describe "when the grammar is updated because a grammar it includes is activated", ->
     it "retokenizes the buffer", ->
-      atom.packages.activatePackage('language-ruby-on-rails', sync: true)
-      atom.packages.activatePackage('language-ruby', sync: true)
 
-      buffer = atom.project.bufferForPathSync()
-      buffer.setText "<div class='name'><%= User.find(2).full_name %></div>"
-      tokenizedBuffer = new TokenizedBuffer({buffer})
-      tokenizedBuffer.setGrammar(atom.syntax.selectGrammar('test.erb'))
-      fullyTokenize(tokenizedBuffer)
+      waitsForPromise ->
+        atom.packages.activatePackage('language-ruby-on-rails')
 
-      {tokens} = tokenizedBuffer.lineForScreenRow(0)
-      expect(tokens[0]).toEqual value: "<div class='name'>", scopes: ["text.html.ruby"]
+      waitsForPromise ->
+        atom.packages.activatePackage('language-ruby')
 
-      atom.packages.activatePackage('language-html', sync: true)
-      fullyTokenize(tokenizedBuffer)
-      {tokens} = tokenizedBuffer.lineForScreenRow(0)
-      expect(tokens[0]).toEqual value: '<', scopes: ["text.html.ruby","meta.tag.block.any.html","punctuation.definition.tag.begin.html"]
+      runs ->
+        buffer = atom.project.bufferForPathSync()
+        buffer.setText "<div class='name'><%= User.find(2).full_name %></div>"
+        tokenizedBuffer = new TokenizedBuffer({buffer})
+        tokenizedBuffer.setGrammar(atom.syntax.selectGrammar('test.erb'))
+        fullyTokenize(tokenizedBuffer)
+
+        {tokens} = tokenizedBuffer.lineForScreenRow(0)
+        expect(tokens[0]).toEqual value: "<div class='name'>", scopes: ["text.html.ruby"]
+
+      waitsForPromise ->
+        atom.packages.activatePackage('language-html')
+
+      runs ->
+        fullyTokenize(tokenizedBuffer)
+        {tokens} = tokenizedBuffer.lineForScreenRow(0)
+        expect(tokens[0]).toEqual value: '<', scopes: ["text.html.ruby","meta.tag.block.any.html","punctuation.definition.tag.begin.html"]
 
   describe ".tokenForPosition(position)", ->
     afterEach ->
diff --git a/spec/workspace-spec.coffee b/spec/workspace-spec.coffee
index 937069482..312e3ea4e 100644
--- a/spec/workspace-spec.coffee
+++ b/spec/workspace-spec.coffee
@@ -7,49 +7,141 @@ describe "Workspace", ->
     atom.project.setPath(atom.project.resolve('dir'))
     workspace = new Workspace
 
-  describe "::open(uri)", ->
+  describe "::open(uri, options)", ->
     beforeEach ->
-      spyOn(workspace.activePane, 'activate')
-
-    describe "when called without a uri", ->
-      it "adds and activates an empty editor on the active pane", ->
-        editor = null
-        waitsForPromise ->
-          workspace.open().then (o) -> editor = o
-
-        runs ->
-          expect(editor.getPath()).toBeUndefined()
-          expect(workspace.activePane.items).toEqual [editor]
-          expect(workspace.activePaneItem).toBe editor
-          expect(workspace.activePane.activate).toHaveBeenCalled()
-
-    describe "when called with a uri", ->
-      describe "when the active pane already has an editor for the given uri", ->
-        it "activates the existing editor on the active pane", ->
-          editor1 = workspace.openSync('a')
-          editor2 = workspace.openSync('b')
+      spyOn(workspace.activePane, 'activate').andCallThrough()
 
+    describe "when the 'searchAllPanes' option is false (default)", ->
+      describe "when called without a uri", ->
+        it "adds and activates an empty editor on the active pane", ->
           editor = null
           waitsForPromise ->
-            workspace.open('a').then (o) -> editor = o
+            workspace.open().then (o) -> editor = o
 
           runs ->
-            expect(editor).toBe editor1
-            expect(workspace.activePaneItem).toBe editor
-            expect(workspace.activePane.activate).toHaveBeenCalled()
-
-      describe "when the active pane does not have an editor for the given uri", ->
-        it "adds and activates a new editor for the given path on the active pane", ->
-          editor = null
-          waitsForPromise ->
-            workspace.open('a').then (o) -> editor = o
-
-          runs ->
-            expect(editor.getUri()).toBe 'a'
-            expect(workspace.activePaneItem).toBe editor
+            expect(editor.getPath()).toBeUndefined()
             expect(workspace.activePane.items).toEqual [editor]
+            expect(workspace.activePaneItem).toBe editor
             expect(workspace.activePane.activate).toHaveBeenCalled()
 
+      describe "when called with a uri", ->
+        describe "when the active pane already has an editor for the given uri", ->
+          it "activates the existing editor on the active pane", ->
+            editor1 = workspace.openSync('a')
+            editor2 = workspace.openSync('b')
+
+            editor = null
+            waitsForPromise ->
+              workspace.open('a').then (o) -> editor = o
+
+            runs ->
+              expect(editor).toBe editor1
+              expect(workspace.activePaneItem).toBe editor
+              expect(workspace.activePane.activate).toHaveBeenCalled()
+
+        describe "when the active pane does not have an editor for the given uri", ->
+          it "adds and activates a new editor for the given path on the active pane", ->
+            editor = null
+            waitsForPromise ->
+              workspace.open('a').then (o) -> editor = o
+
+            runs ->
+              expect(editor.getUri()).toBe 'a'
+              expect(workspace.activePaneItem).toBe editor
+              expect(workspace.activePane.items).toEqual [editor]
+              expect(workspace.activePane.activate).toHaveBeenCalled()
+
+    describe "when the 'searchAllPanes' option is true", ->
+      describe "when an editor for the given uri is already open on an inactive pane", ->
+        it "activates the existing editor on the inactive pane, then activates that pane", ->
+          editor1 = workspace.openSync('a')
+          pane1 = workspace.activePane
+          pane2 = workspace.activePane.splitRight()
+          editor2 = workspace.openSync('b')
+          expect(workspace.activePaneItem).toBe editor2
+
+          waitsForPromise ->
+            workspace.open('a', searchAllPanes: true)
+
+          runs ->
+            expect(workspace.activePane).toBe pane1
+            expect(workspace.activePaneItem).toBe editor1
+
+      describe "when no editor for the given uri is open in any pane", ->
+        it "opens an editor for the given uri in the active pane", ->
+          editor = null
+          waitsForPromise ->
+            workspace.open('a', searchAllPanes: true).then (o) -> editor = o
+
+          runs ->
+            expect(workspace.activePaneItem).toBe editor
+
+    describe "when the 'split' option is set", ->
+      describe "when the 'split' option is 'left'", ->
+        it "opens the editor in the leftmost pane of the current pane axis", ->
+          pane1 = workspace.activePane
+          pane2 = pane1.splitRight()
+          expect(workspace.activePane).toBe pane2
+
+          editor = null
+          waitsForPromise ->
+            workspace.open('a', split: 'left').then (o) -> editor = o
+
+          runs ->
+            expect(workspace.activePane).toBe pane1
+            expect(pane1.items).toEqual [editor]
+            expect(pane2.items).toEqual []
+
+          # Focus right pane and reopen the file on the left
+          waitsForPromise ->
+            pane2.focus()
+            workspace.open('a', split: 'left').then (o) -> editor = o
+
+          runs ->
+            expect(workspace.activePane).toBe pane1
+            expect(pane1.items).toEqual [editor]
+            expect(pane2.items).toEqual []
+
+      describe "when the 'split' option is 'right'", ->
+        it "opens the editor in the rightmost pane of the current pane axis", ->
+          editor = null
+          pane1 = workspace.activePane
+          pane2 = null
+          waitsForPromise ->
+            workspace.open('a', split: 'right').then (o) -> editor = o
+
+          runs ->
+            pane2 = workspace.getPanes().filter((p) -> p != pane1)[0]
+            expect(workspace.activePane).toBe pane2
+            expect(pane1.items).toEqual []
+            expect(pane2.items).toEqual [editor]
+
+          # Focus right pane and reopen the file on the right
+          waitsForPromise ->
+            pane1.focus()
+            workspace.open('a', split: 'right').then (o) -> editor = o
+
+          runs ->
+            expect(workspace.activePane).toBe pane2
+            expect(pane1.items).toEqual []
+            expect(pane2.items).toEqual [editor]
+
+    describe "when passed a path that matches a custom opener", ->
+      it "returns the resource returned by the custom opener", ->
+        fooOpener = (pathToOpen, options) -> { foo: pathToOpen, options } if pathToOpen?.match(/\.foo/)
+        barOpener = (pathToOpen) -> { bar: pathToOpen } if pathToOpen?.match(/^bar:\/\//)
+        workspace.registerOpener(fooOpener)
+        workspace.registerOpener(barOpener)
+
+        waitsForPromise ->
+          pathToOpen = atom.project.resolve('a.foo')
+          workspace.open(pathToOpen, hey: "there").then (item) ->
+            expect(item).toEqual { foo: pathToOpen, options: {hey: "there"} }
+
+        waitsForPromise ->
+          workspace.open("bar://baz").then (item) ->
+            expect(item).toEqual { bar: "bar://baz" }
+
   describe "::openSync(uri, options)", ->
     [activePane, initialItemCount] = []
 
@@ -92,61 +184,6 @@ describe "Workspace", ->
         workspace.openSync('b', activatePane: false)
         expect(activePane.activate).not.toHaveBeenCalled()
 
-  describe "::openSingletonSync(uri, options)", ->
-    describe "when an editor for the given uri is already open on the active pane", ->
-      it "activates the existing editor", ->
-        editor1 = workspace.openSync('a')
-        editor2 = workspace.openSync('b')
-        expect(workspace.activePaneItem).toBe editor2
-        workspace.openSingletonSync('a')
-        expect(workspace.activePaneItem).toBe editor1
-
-    describe "when an editor for the given uri is already open on an inactive pane", ->
-      it "activates the existing editor on the inactive pane, then activates that pane", ->
-        editor1 = workspace.openSync('a')
-        pane1 = workspace.activePane
-        pane2 = workspace.activePane.splitRight()
-        editor2 = workspace.openSync('b')
-        expect(workspace.activePaneItem).toBe editor2
-        workspace.openSingletonSync('a')
-        expect(workspace.activePane).toBe pane1
-        expect(workspace.activePaneItem).toBe editor1
-
-    describe "when no editor for the given uri is open in any pane", ->
-      it "opens an editor for the given uri in the active pane", ->
-        editor1 = workspace.openSingletonSync('a')
-        expect(workspace.activePaneItem).toBe editor1
-
-      describe "when the 'split' option is 'left'", ->
-        it "opens the editor in the leftmost pane of the current pane axis", ->
-          pane1 = workspace.activePane
-          pane2 = pane1.splitRight()
-          expect(workspace.activePane).toBe pane2
-          editor1 = workspace.openSingletonSync('a', split: 'left')
-          expect(workspace.activePane).toBe pane1
-          expect(pane1.items).toEqual [editor1]
-          expect(pane2.items).toEqual []
-
-      describe "when the 'split' option is 'right'", ->
-        describe "when the active pane is in a horizontal pane axis", ->
-          it "activates the editor on the rightmost pane of the current pane axis", ->
-            pane1 = workspace.activePane
-            pane2 = pane1.splitRight()
-            pane1.activate()
-            editor1 = workspace.openSingletonSync('a', split: 'right')
-            expect(workspace.activePane).toBe pane2
-            expect(pane2.items).toEqual [editor1]
-            expect(pane1.items).toEqual []
-
-        describe "when the active pane is not in a horizontal pane axis", ->
-          it "splits the current pane to the right, then activates the editor on the right pane", ->
-            pane1 = workspace.activePane
-            editor1 = workspace.openSingletonSync('a', split: 'right')
-            pane2 = workspace.activePane
-            expect(workspace.paneContainer.root.children).toEqual [pane1, pane2]
-            expect(pane2.items).toEqual [editor1]
-            expect(pane1.items).toEqual []
-
   describe "::reopenItemSync()", ->
     it "opens the uri associated with the last closed pane that isn't currently open", ->
       pane = workspace.activePane
diff --git a/src/atom-package.coffee b/src/atom-package.coffee
index 6546945bb..ea9358670 100644
--- a/src/atom-package.coffee
+++ b/src/atom-package.coffee
@@ -2,12 +2,13 @@ Package = require './package'
 fs = require 'fs-plus'
 path = require 'path'
 _ = require 'underscore-plus'
+Q = require 'q'
 {$} = require './space-pen-extensions'
 CSON = require 'season'
 {Emitter} = require 'emissary'
 
-### Internal: Loads and resolves packages. ###
-
+# Loads and activates a package's main module and resources such as
+# stylesheets, keymaps, grammar, editor properties, and menus.
 module.exports =
 class AtomPackage extends Package
   Emitter.includeInto(this)
@@ -42,11 +43,7 @@ class AtomPackage extends Package
         @loadStylesheets()
         @loadGrammars()
         @loadScopedProperties()
-
-        if @metadata.activationEvents?
-          @registerDeferredDeserializers()
-        else
-          @requireMainModule()
+        @requireMainModule() unless @metadata.activationEvents?
 
       catch e
         console.warn "Failed to load package named '#{@name}'", e.stack ? e
@@ -59,14 +56,19 @@ class AtomPackage extends Package
     @grammars = []
     @scopedProperties = []
 
-  activate: ({immediate}={}) ->
+  activate: ->
+    return @activationDeferred.promise if @activationDeferred?
+
+    @activationDeferred = Q.defer()
     @measure 'activateTime', =>
       @activateResources()
-      if @metadata.activationEvents? and not immediate
+      if @metadata.activationEvents?
         @subscribeToActivationEvents()
       else
         @activateNow()
 
+    @activationDeferred.promise
+
   activateNow: ->
     try
       @activateConfig()
@@ -77,6 +79,8 @@ class AtomPackage extends Package
     catch e
       console.warn "Failed to activate package named '#{@name}'", e.stack
 
+    @activationDeferred.resolve()
+
   activateConfig: ->
     return if @configActivated
 
@@ -162,6 +166,8 @@ class AtomPackage extends Package
         console.error "Error serializing package '#{@name}'", e.stack
 
   deactivate: ->
+    @activationDeferred?.reject()
+    @activationDeferred = null
     @unsubscribeFromActivationEvents()
     @deactivateResources()
     @deactivateConfig()
@@ -203,12 +209,6 @@ class AtomPackage extends Package
         path.join(@path, 'index')
     @mainModulePath = fs.resolveExtension(mainModulePath, ["", _.keys(require.extensions)...])
 
-  registerDeferredDeserializers: ->
-    for deserializerName in @metadata.deferredDeserializers ? []
-      atom.deserializers.addDeferred deserializerName, =>
-        @activateStylesheets()
-        @requireMainModule()
-
   subscribeToActivationEvents: ->
     return unless @metadata.activationEvents?
     if _.isArray(@metadata.activationEvents)
@@ -226,6 +226,8 @@ class AtomPackage extends Package
     @unsubscribeFromActivationEvents()
 
   unsubscribeFromActivationEvents: ->
+    return unless atom.workspaceView?
+
     if _.isArray(@metadata.activationEvents)
       atom.workspaceView.off(event, @handleActivationEvent) for event in @metadata.activationEvents
     else if _.isString(@metadata.activationEvents)
diff --git a/src/atom.coffee b/src/atom.coffee
index 3cc30c31e..0f951aebc 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -6,8 +6,6 @@ path = require 'path'
 remote = require 'remote'
 screen = require 'screen'
 shell = require 'shell'
-dialog = remote.require 'dialog'
-app = remote.require 'app'
 
 _ = require 'underscore-plus'
 {Model} = require 'theorist'
@@ -22,16 +20,18 @@ WindowEventHandler = require './window-event-handler'
 #
 # ## Useful properties available:
 #
-#  * `atom.config`      - A {Config} instance
-#  * `atom.contextMenu` - A {ContextMenuManager} instance
-#  * `atom.keymap`      - A {Keymap} instance
-#  * `atom.menu`        - A {MenuManager} instance
-#  * `atom.workspaceView`    - A {WorkspaceView} instance
-#  * `atom.packages`    - A {PackageManager} instance
-#  * `atom.pasteboard`  - A {Pasteboard} instance
-#  * `atom.project`     - A {Project} instance
-#  * `atom.syntax`      - A {Syntax} instance
-#  * `atom.themes`      - A {ThemeManager} instance
+#  * `atom.clipboard`     - A {Clipboard} instance
+#  * `atom.config`        - A {Config} instance
+#  * `atom.contextMenu`   - A {ContextMenuManager} instance
+#  * `atom.deserializers` - A {DeserializerManager} instance
+#  * `atom.keymap`        - A {Keymap} instance
+#  * `atom.menu`          - A {MenuManager} instance
+#  * `atom.packages`      - A {PackageManager} instance
+#  * `atom.project`       - A {Project} instance
+#  * `atom.syntax`        - A {Syntax} instance
+#  * `atom.themes`        - A {ThemeManager} instance
+#  * `atom.workspace`     - A {Workspace} instance
+#  * `atom.workspaceView` - A {WorkspaceView} instance
 module.exports =
 class Atom extends Model
   # Public: Load or create the Atom environment in the given mode.
@@ -43,11 +43,11 @@ class Atom extends Model
   @loadOrCreate: (mode) ->
     @deserialize(@loadState(mode)) ? new this({mode, version: @getVersion()})
 
-  # Private: Deserializes the Atom environment from a state object
+  # Deserializes the Atom environment from a state object
   @deserialize: (state) ->
     new this(state) if state?.version is @getVersion()
 
-  # Private: Loads and returns the serialized state corresponding to this window
+  # Loads and returns the serialized state corresponding to this window
   # if it exists; otherwise returns undefined.
   @loadState: (mode) ->
     statePath = @getStatePath(mode)
@@ -65,7 +65,7 @@ class Atom extends Model
     catch error
       console.warn "Error parsing window state: #{statePath} #{error.stack}", error
 
-  # Private: Returns the path where the state for the current window will be
+  # Returns the path where the state for the current window will be
   # located if it exists.
   @getStatePath: (mode) ->
     switch mode
@@ -82,41 +82,47 @@ class Atom extends Model
     else
       null
 
-  # Private: Get the directory path to Atom's configuration area.
+  # Get the directory path to Atom's configuration area.
   #
   # Returns the absolute path to ~/.atom
   @getConfigDirPath: ->
     @configDirPath ?= fs.absolute('~/.atom')
 
-  # Private: Get the path to Atom's storage directory.
+  # Get the path to Atom's storage directory.
   #
   # Returns the absolute path to ~/.atom/storage
   @getStorageDirPath: ->
     @storageDirPath ?= path.join(@getConfigDirPath(), 'storage')
 
-  # Private: Returns the load settings hash associated with the current window.
+  # Returns the load settings hash associated with the current window.
   @getLoadSettings: ->
-    _.deepClone(@loadSettings ?= _.deepClone(@getCurrentWindow().loadSettings))
+    @loadSettings ?= JSON.parse(decodeURIComponent(location.search.substr(14)))
+    cloned = _.deepClone(@loadSettings)
+    # The loadSettings.windowState could be large, request it only when needed.
+    cloned.__defineGetter__ 'windowState', =>
+      @getCurrentWindow().loadSettings.windowState
+    cloned.__defineSetter__ 'windowState', (value) =>
+      @getCurrentWindow().loadSettings.windowState = value
+    cloned
 
-  # Private:
   @getCurrentWindow: ->
     remote.getCurrentWindow()
 
-  # Private: Get the version of the Atom application.
+  # Get the version of the Atom application.
   @getVersion: ->
-    @version ?= app.getVersion()
+    @version ?= @getLoadSettings().appVersion
 
-  # Private: Determine whether the current version is an official release.
+  # Determine whether the current version is an official release.
   @isReleasedVersion: ->
     not /\w{7}/.test(@getVersion()) # Check if the release is a 7-character SHA prefix
 
   workspaceViewParentSelector: 'body'
 
-  # Private: Call .loadOrCreate instead
+  # Call .loadOrCreate instead
   constructor: (@state) ->
     {@mode} = @state
     DeserializerManager = require './deserializer-manager'
-    @deserializers = new DeserializerManager(this)
+    @deserializers = new DeserializerManager()
 
   # Public: Sets up the basic services that should be available in all modes
   # (both spec and application). Call after this instance has been assigned to
@@ -134,7 +140,7 @@ class Atom extends Model
     Config = require './config'
     Keymap = require './keymap'
     PackageManager = require './package-manager'
-    Pasteboard = require './pasteboard'
+    Clipboard = require './clipboard'
     Syntax = require './syntax'
     ThemeManager = require './theme-manager'
     ContextMenuManager = require './context-menu-manager'
@@ -148,7 +154,8 @@ class Atom extends Model
     @themes = new ThemeManager({packageManager: @packages, configDirPath, resourcePath})
     @contextMenu = new ContextMenuManager(devMode)
     @menu = new MenuManager({resourcePath})
-    @pasteboard = new Pasteboard()
+    @clipboard = new Clipboard()
+
     @syntax = @deserializers.deserialize(@state.syntax) ? new Syntax()
 
     @subscribe @packages, 'activated', => @watchThemes()
@@ -167,7 +174,6 @@ class Atom extends Model
   # Deprecated: Callers should be converted to use atom.deserializers
   registerRepresentationClasses: ->
 
-  # Private:
   setBodyPlatformClass: ->
     document.body.classList.add("platform-#{process.platform}")
 
@@ -196,15 +202,13 @@ class Atom extends Model
   #    + width: The new width.
   #    + height: The new height.
   setWindowDimensions: ({x, y, width, height}) ->
-    browserWindow = @getCurrentWindow()
     if width? and height?
-      browserWindow.setSize(width, height)
+      @setSize(width, height)
     if x? and y?
-      browserWindow.setPosition(x, y)
+      @setPosition(x, y)
     else
-      browserWindow.center()
+      @center()
 
-  # Private:
   restoreWindowDimensions: ->
     workAreaSize = screen.getPrimaryDisplay().workAreaSize
     windowDimensions = @state.windowDimensions ? {}
@@ -213,7 +217,6 @@ class Atom extends Model
     windowDimensions.width ?= initialSize?.width ? Math.min(workAreaSize.width, 1024)
     @setWindowDimensions(windowDimensions)
 
-  # Private:
   storeWindowDimensions: ->
     @state.windowDimensions = @getWindowDimensions()
 
@@ -223,12 +226,10 @@ class Atom extends Model
   getLoadSettings: ->
     @constructor.getLoadSettings()
 
-  # Private:
   deserializeProject: ->
     Project = require './project'
     @project ?= @deserializers.deserialize(@project) ? new Project(path: @getLoadSettings().initialPath)
 
-  # Private:
   deserializeWorkspaceView: ->
     Workspace = require './workspace'
     WorkspaceView = require './workspace-view'
@@ -236,24 +237,22 @@ class Atom extends Model
     @workspaceView = new WorkspaceView(@workspace)
     $(@workspaceViewParentSelector).append(@workspaceView)
 
-  # Private:
   deserializePackageStates: ->
     @packages.packageStates = @state.packageStates ? {}
     delete @state.packageStates
 
-  # Private:
   deserializeEditorWindow: ->
     @deserializePackageStates()
     @deserializeProject()
     @deserializeWorkspaceView()
 
-  # Private: Call this method when establishing a real application window.
+  # Call this method when establishing a real application window.
   startEditorWindow: ->
     CommandInstaller = require './command-installer'
     resourcePath = atom.getLoadSettings().resourcePath
-    CommandInstaller.installAtomCommand resourcePath, (error) ->
+    CommandInstaller.installAtomCommand resourcePath, false, (error) ->
       console.warn error.message if error?
-    CommandInstaller.installApmCommand resourcePath, (error) ->
+    CommandInstaller.installApmCommand resourcePath, false, (error) ->
       console.warn error.message if error?
 
     @restoreWindowDimensions()
@@ -276,7 +275,6 @@ class Atom extends Model
 
     @displayWindow()
 
-  # Private:
   unloadEditorWindow: ->
     return if not @project and not @workspaceView
 
@@ -292,11 +290,9 @@ class Atom extends Model
     @keymap.destroy()
     @windowState = null
 
-  # Private:
   loadThemes: ->
     @themes.load()
 
-  # Private:
   watchThemes: ->
     @themes.on 'reloaded', =>
       # Only reload stylesheets from non-theme packages
@@ -309,31 +305,32 @@ class Atom extends Model
   # Calling this method without an options parameter will open a prompt to pick
   # a file/folder to open in the new window.
   #
-  # * options
-  #   * pathsToOpen: A string array of paths to open
+  # options - An {Object} with the following keys:
+  #   :pathsToOpen -  An {Array} of {String} paths to open.
   open: (options) ->
     ipc.sendChannel('open', options)
 
   # Public: Open a confirm dialog.
   #
-  # ## Example:
-  # ```coffeescript
+  # ## Example
+  #
+  # ```coffee
   #   atom.confirm
-  #      message: 'How you feeling?'
-  #      detailedMessage: 'Be honest.'
-  #      buttons:
-  #        Good: -> window.alert('good to hear')
-  #        Bad: ->  window.alert('bummer')
+  #     message: 'How you feeling?'
+  #     detailedMessage: 'Be honest.'
+  #     buttons:
+  #       Good: -> window.alert('good to hear')
+  #       Bad:  -> window.alert('bummer')
   # ```
   #
-  # * options:
-  #    + message: The string message to display.
-  #    + detailedMessage: The string detailed message to display.
-  #    + buttons: Either an array of strings or an object where the values
-  #      are callbacks to invoke when clicked.
+  # options - An {Object} with the following keys:
+  #   :message - The {String} message to display.
+  #   :detailedMessage - The {String} detailed message to display.
+  #   :buttons - Either an array of strings or an object where keys are
+  #              button names and the values are callbacks to invoke when
+  #              clicked.
   #
-  # Returns the chosen index if buttons was an array or the return of the
-  # callback if buttons was an object.
+  # Returns the chosen button index {Number} if the buttons option was an array.
   confirm: ({message, detailedMessage, buttons}={}) ->
     buttons ?= {}
     if _.isArray(buttons)
@@ -341,6 +338,7 @@ class Atom extends Model
     else
       buttonLabels = Object.keys(buttons)
 
+    dialog = remote.require('dialog')
     chosen = dialog.showMessageBox @getCurrentWindow(),
       type: 'info'
       message: message
@@ -353,42 +351,59 @@ class Atom extends Model
       callback = buttons[buttonLabels[chosen]]
       callback?()
 
-  # Private:
   showSaveDialog: (callback) ->
     callback(showSaveDialogSync())
 
-  # Private:
   showSaveDialogSync: (defaultPath) ->
     defaultPath ?= @project?.getPath()
     currentWindow = @getCurrentWindow()
+    dialog = remote.require('dialog')
     dialog.showSaveDialog currentWindow, {title: 'Save File', defaultPath}
 
   # Public: Open the dev tools for the current window.
   openDevTools: ->
-    @getCurrentWindow().openDevTools()
+    ipc.sendChannel('call-window-method', 'openDevTools')
 
   # Public: Toggle the visibility of the dev tools for the current window.
   toggleDevTools: ->
-    @getCurrentWindow().toggleDevTools()
+    ipc.sendChannel('call-window-method', 'toggleDevTools')
 
   # Public: Reload the current window.
   reload: ->
-    @getCurrentWindow().restart()
+    ipc.sendChannel('call-window-method', 'restart')
 
   # Public: Focus the current window.
   focus: ->
-    @getCurrentWindow().focus()
+    ipc.sendChannel('call-window-method', 'focus')
     $(window).focus()
 
   # Public: Show the current window.
   show: ->
-    @getCurrentWindow().show()
+    ipc.sendChannel('call-window-method', 'show')
 
   # Public: Hide the current window.
   hide: ->
-    @getCurrentWindow().hide()
+    ipc.sendChannel('call-window-method', 'hide')
 
-  # Private: Schedule the window to be shown and focused on the next tick.
+  # Public: Set the size of current window.
+  #
+  # width  - The {Number} of pixels.
+  # height - The {Number} of pixels.
+  setSize: (width, height) ->
+    ipc.sendChannel('call-window-method', 'setSize', width, height)
+
+  # Public: Set the position of current window.
+  #
+  # x - The {Number} of pixels.
+  # y - The {Number} of pixels.
+  setPosition: (x, y) ->
+    ipc.sendChannel('call-window-method', 'setPosition', x, y)
+
+  # Public: Move current window to the center of the screen.
+  center: ->
+    ipc.sendChannel('call-window-method', 'center')
+
+  # Schedule the window to be shown and focused on the next tick.
   #
   # This is done in a next tick to prevent a white flicker from occurring
   # if called synchronously.
@@ -402,8 +417,9 @@ class Atom extends Model
   close: ->
     @getCurrentWindow().close()
 
-  # Private:
-  exit: (status) -> app.exit(status)
+  exit: (status) ->
+    app = remote.require('app')
+    app.exit(status)
 
   # Public: Is the current window in development mode?
   inDevMode: ->
@@ -419,7 +435,7 @@ class Atom extends Model
 
   # Public: Set the full screen state of the current window.
   setFullScreen: (fullScreen=false) ->
-    @getCurrentWindow().setFullScreen(fullScreen)
+    ipc.sendChannel('call-window-method', 'setFullScreen', fullScreen)
 
   # Public: Is the current window in full screen mode?
   isFullScreen: ->
@@ -450,7 +466,6 @@ class Atom extends Model
   getConfigDirPath: ->
     @constructor.getConfigDirPath()
 
-  # Private:
   saveSync: ->
     stateString = JSON.stringify(@state)
     if statePath = @constructor.getStatePath(@mode)
@@ -468,11 +483,9 @@ class Atom extends Model
   getWindowLoadTime: ->
     @loadTime
 
-  # Private:
   crashMainProcess: ->
     remote.process.crash()
 
-  # Private:
   crashRenderProcess: ->
     process.crash()
 
@@ -481,9 +494,12 @@ class Atom extends Model
     shell.beep() if @config.get('core.audioBeep')
     @workspaceView.trigger 'beep'
 
-  # Private:
+  getUserInitScriptPath: ->
+    initScriptPath = fs.resolve(@getConfigDirPath(), 'init', ['js', 'coffee'])
+    initScriptPath ? path.join(@getConfigDirPath(), 'init.coffee')
+
   requireUserInitScript: ->
-    if userInitScriptPath = fs.resolve(@getConfigDirPath(), 'user', ['js', 'coffee'])
+    if userInitScriptPath = @getUserInitScriptPath()
       try
         require userInitScriptPath
       catch error
@@ -493,6 +509,9 @@ class Atom extends Model
   #
   # The globals will be set on the `window` object and removed after the
   # require completes.
+  #
+  # id - The {String} module name or path.
+  # globals - An {Object} to set as globals during require (default: {})
   requireWithGlobals: (id, globals={}) ->
     existingGlobals = {}
     for key, value of globals
diff --git a/src/browser/application-menu.coffee b/src/browser/application-menu.coffee
index 7de362838..905655ac8 100644
--- a/src/browser/application-menu.coffee
+++ b/src/browser/application-menu.coffee
@@ -3,7 +3,7 @@ ipc = require 'ipc'
 Menu = require 'menu'
 _ = require 'underscore-plus'
 
-# Private: Used to manage the global application menu.
+# Used to manage the global application menu.
 #
 # It's created by {AtomApplication} upon instantiation and used to add, remove
 # and maintain the state of all menu items.
@@ -29,7 +29,7 @@ class ApplicationMenu
     @menu = Menu.buildFromTemplate(template)
     Menu.setApplicationMenu(@menu)
 
-  # Private: Flattens the given menu and submenu items into an single Array.
+  # Flattens the given menu and submenu items into an single Array.
   #
   # * menu:
   #   A complete menu configuration object for atom-shell's menu API.
@@ -42,7 +42,7 @@ class ApplicationMenu
       items = items.concat(@flattenMenuItems(item.submenu)) if item.submenu
     items
 
-  # Private: Flattens the given menu template into an single Array.
+  # Flattens the given menu template into an single Array.
   #
   # * template:
   #   An object describing the menu item.
@@ -64,26 +64,22 @@ class ApplicationMenu
     for item in @flattenMenuItems(@menu)
       item.enabled = enable if item.metadata?['windowSpecific']
 
-  # Private: Replaces VERSION with the current version.
+  # Replaces VERSION with the current version.
   substituteVersion: (template) ->
     if (item = _.find(@flattenMenuTemplate(template), (i) -> i.label == 'VERSION'))
       item.label = "Version #{@version}"
 
-  # Public: Makes the download menu item visible if available.
-  #
-  # Note: The update menu item's must match 'Install update' exactly otherwise
-  # this function will fail to work.
-  #
-  # * newVersion:
-  #   FIXME: Unused.
-  # * quitAndUpdateCallback:
-  #   Function to call when the install menu item has been clicked.
-  showDownloadUpdateItem: (newVersion, quitAndUpdateCallback) ->
-    if (item = _.find(@flattenMenuItems(@menu), (i) -> i.label == 'Install update'))
-      item.visible = true
-      item.click = quitAndUpdateCallback
+  # Toggles Install Update Item
+  showInstallUpdateItem: (visible=true) ->
+    if (item = _.find(@flattenMenuItems(@menu), (i) -> i.label == 'Restart and Install Update'))
+      item.visible = visible
 
-  # Private: Default list of menu items.
+  # Toggles Check For Update Item
+  showCheckForUpdateItem: (visible=true) ->
+    if (item = _.find(@flattenMenuItems(@menu), (i) -> i.label == 'Check for Update'))
+      item.visible = visible
+
+  # Default list of menu items.
   #
   # Returns an Array of menu item Objects.
   getDefaultTemplate: ->
@@ -97,7 +93,7 @@ class ApplicationMenu
       ]
     ]
 
-  # Private: Combines a menu template with the appropriate keystroke.
+  # Combines a menu template with the appropriate keystroke.
   #
   # * template:
   #   An Object conforming to atom-shell's menu api but lacking accelerator and
@@ -117,7 +113,7 @@ class ApplicationMenu
       @translateTemplate(item.submenu, keystrokesByCommand) if item.submenu
     template
 
-  # Private: Determine the accelerator for a given command.
+  # Determine the accelerator for a given command.
   #
   # * command:
   #   The name of the command.
diff --git a/src/browser/atom-application.coffee b/src/browser/atom-application.coffee
index affabc0ae..68e864862 100644
--- a/src/browser/atom-application.coffee
+++ b/src/browser/atom-application.coffee
@@ -1,6 +1,7 @@
 AtomWindow = require './atom-window'
 ApplicationMenu = require './application-menu'
 AtomProtocolHandler = require './atom-protocol-handler'
+BrowserWindow = require 'browser-window'
 Menu = require 'menu'
 autoUpdater = require 'auto-updater'
 app = require 'app'
@@ -21,7 +22,7 @@ socketPath =
   else
     path.join(os.tmpdir(), 'atom.sock')
 
-# Private: The application's singleton class.
+# The application's singleton class.
 #
 # It's the entry point into the Atom application and maintains the global state
 # of the application.
@@ -72,11 +73,11 @@ class AtomApplication
     @listenForArgumentsFromNewProcess()
     @setupJavaScriptArguments()
     @handleEvents()
-    @checkForUpdates()
+    @setupAutoUpdater()
 
     @openWithOptions(options)
 
-  # Private: Opens a new window based on the options provided.
+  # Opens a new window based on the options provided.
   openWithOptions: ({pathsToOpen, urlsToOpen, test, pidToKillWhenClosed, devMode, newWindow, specDirectory, logFile}) ->
     if test
       @runSpecs({exitWhenDone: true, @resourcePath, specDirectory, logFile})
@@ -97,7 +98,7 @@ class AtomApplication
     @windows.push window
     @applicationMenu?.enableWindowSpecificItems(true)
 
-  # Private: Creates server to listen for additional atom application launches.
+  # Creates server to listen for additional atom application launches.
   #
   # You can run the atom command multiple times, but after the first launch
   # the other launches will just pass their information to this server and then
@@ -112,23 +113,60 @@ class AtomApplication
     server.listen socketPath
     server.on 'error', (error) -> console.error 'Application server failed', error
 
-  # Private: Configures required javascript environment flags.
+  # Configures required javascript environment flags.
   setupJavaScriptArguments: ->
     app.commandLine.appendSwitch 'js-flags', '--harmony_collections --harmony-proxies'
 
-  # Private: Enable updates unless running from a local build of Atom.
-  checkForUpdates: ->
-    versionIsSha = /\w{7}/.test @version
+  # Enable updates unless running from a local build of Atom.
+  setupAutoUpdater: ->
+    autoUpdater.setFeedUrl "https://atom.io/api/updates?version=#{@version}"
 
-    if versionIsSha
-      autoUpdater.setAutomaticallyDownloadsUpdates false
-      autoUpdater.setAutomaticallyChecksForUpdates false
-    else
-      autoUpdater.setAutomaticallyDownloadsUpdates true
-      autoUpdater.setAutomaticallyChecksForUpdates true
-      autoUpdater.checkForUpdatesInBackground()
+    autoUpdater.on 'checking-for-update', =>
+      @applicationMenu.showInstallUpdateItem(false)
+      @applicationMenu.showCheckForUpdateItem(false)
 
-  # Private: Registers basic application commands, non-idempotent.
+    autoUpdater.on 'update-not-available', =>
+      @applicationMenu.showInstallUpdateItem(false)
+      @applicationMenu.showCheckForUpdateItem(true)
+
+    autoUpdater.on 'update-downloaded', (event, releaseNotes, releaseName, releaseDate, releaseURL) =>
+      atomWindow.sendCommand('window:update-available', releaseName) for atomWindow in @windows
+      @applicationMenu.showInstallUpdateItem(true)
+      @applicationMenu.showCheckForUpdateItem(false)
+      @updateVersion = releaseName
+
+    autoUpdater.on 'error', (event, message) =>
+      @applicationMenu.showInstallUpdateItem(false)
+      @applicationMenu.showCheckForUpdateItem(true)
+
+    # Check for update after Atom has fully started and the menus are created
+    setTimeout((-> autoUpdater.checkForUpdates()), 5000)
+
+  checkForUpdate: ->
+    autoUpdater.once 'update-available', ->
+      dialog.showMessageBox
+        type: 'info'
+        buttons: ['OK']
+        message: 'Update available.'
+        detail: 'A new update is being downloading.'
+
+    autoUpdater.once 'update-not-available', =>
+      dialog.showMessageBox
+        type: 'info'
+        buttons: ['OK']
+        message: 'No update available.'
+        detail: "Version #{@version} is the latest version."
+
+    autoUpdater.once 'error', (event, message)->
+      dialog.showMessageBox
+        type: 'warning'
+        buttons: ['OK']
+        message: 'There was an error checking for updates.'
+        detail: message
+
+    autoUpdater.checkForUpdates()
+
+  # Registers basic application commands, non-idempotent.
   handleEvents: ->
     @on 'application:about', -> Menu.sendActionToFirstResponder('orderFrontStandardAboutPanel:')
     @on 'application:run-all-specs', -> @runSpecs(exitWhenDone: false, resourcePath: global.devResourcePath)
@@ -147,9 +185,12 @@ class AtomApplication
     @on 'application:inspect', ({x,y}) -> @focusedWindow().browserWindow.inspectElement(x, y)
     @on 'application:open-documentation', -> shell.openExternal('https://www.atom.io/docs/latest/?app')
     @on 'application:report-issue', -> shell.openExternal('https://github.com/atom/atom/issues/new')
+    @on 'application:install-update', -> autoUpdater.quitAndInstall()
+    @on 'application:check-for-update', => @checkForUpdate()
 
     @openPathOnEvent('application:show-settings', 'atom://config')
     @openPathOnEvent('application:open-your-config', 'atom://.atom/config')
+    @openPathOnEvent('application:open-your-init-script', 'atom://.atom/init-script')
     @openPathOnEvent('application:open-your-keymap', 'atom://.atom/keymap')
     @openPathOnEvent('application:open-your-snippets', 'atom://.atom/snippets')
     @openPathOnEvent('application:open-your-stylesheet', 'atom://.atom/stylesheet')
@@ -170,12 +211,6 @@ class AtomApplication
       event.preventDefault()
       @openUrl({urlToOpen, @devMode})
 
-    autoUpdater.on 'ready-for-update-on-quit', (event, version, quitAndUpdateCallback) =>
-      event.preventDefault()
-      @updateVersion = version
-      @applicationMenu.showDownloadUpdateItem(version, quitAndUpdateCallback)
-      atomWindow.sendCommand('window:update-available', version) for atomWindow in @windows
-
     # A request from the associated render process to open a new render process.
     ipc.on 'open', (processId, routingId, options) =>
       if options?
@@ -195,6 +230,14 @@ class AtomApplication
     ipc.on 'command', (processId, routingId, command) =>
       @emit(command)
 
+    ipc.on 'window-command', (processId, routingId, command, args...) ->
+      win = BrowserWindow.fromProcessIdAndRoutingId(processId, routingId)
+      win.emit(command, args...)
+
+    ipc.on 'call-window-method', (processId, routingId, method, args...) ->
+      win = BrowserWindow.fromProcessIdAndRoutingId(processId, routingId)
+      win[method](args...)
+
   # Public: Executes the given command.
   #
   # If it isn't handled globally, delegate to the currently focused window.
@@ -221,7 +264,7 @@ class AtomApplication
       else
         @openPath({pathToOpen})
 
-  # Private: Returns the {AtomWindow} for the given path.
+  # Returns the {AtomWindow} for the given path.
   windowForPath: (pathToOpen) ->
     for atomWindow in @windows
       return atomWindow if atomWindow.containsPath(pathToOpen)
@@ -309,7 +352,7 @@ class AtomApplication
             console.log("Killing process #{pid} failed: #{error.code}")
         delete @pidsToOpenWindows[pid]
 
-  # Private: Open an atom:// url.
+  # Open an atom:// url.
   #
   # The host of the URL being opened is assumed to be the package name
   # responsible for opening the URL.  A new window will be created with
@@ -341,7 +384,7 @@ class AtomApplication
     else
       console.log "Opening unknown url: #{urlToOpen}"
 
-  # Private: Opens up a new {AtomWindow} to run specs within.
+  # Opens up a new {AtomWindow} to run specs within.
   #
   # * options
   #    + exitWhenDone:
@@ -372,7 +415,7 @@ class AtomApplication
     isSpec = true
     new AtomWindow({bootstrapScript, @resourcePath, isSpec})
 
-  # Private: Opens a native dialog to prompt the user for a path.
+  # Opens a native dialog to prompt the user for a path.
   #
   # Once paths are selected, they're opened in a new or existing {AtomWindow}s.
   #
diff --git a/src/browser/atom-protocol-handler.coffee b/src/browser/atom-protocol-handler.coffee
index 247a67dcc..786d50243 100644
--- a/src/browser/atom-protocol-handler.coffee
+++ b/src/browser/atom-protocol-handler.coffee
@@ -3,7 +3,7 @@ fs = require 'fs-plus'
 path = require 'path'
 protocol = require 'protocol'
 
-# Private: Handles requests with 'atom' protocol.
+# Handles requests with 'atom' protocol.
 #
 # It's created by {AtomApplication} upon instantiation, and is used to create a
 # custom resource loader by adding the 'atom' custom protocol.
@@ -18,7 +18,7 @@ class AtomProtocolHandler
 
     @registerAtomProtocol()
 
-  # Private: Creates the 'atom' custom protocol handler.
+  # Creates the 'atom' custom protocol handler.
   registerAtomProtocol: ->
     protocol.registerProtocol 'atom', (request) =>
       relativePath = path.normalize(request.url.substr(7))
diff --git a/src/browser/atom-window.coffee b/src/browser/atom-window.coffee
index 4ca0ab3ad..156db8f6e 100644
--- a/src/browser/atom-window.coffee
+++ b/src/browser/atom-window.coffee
@@ -1,13 +1,14 @@
 BrowserWindow = require 'browser-window'
 Menu = require 'menu'
 ContextMenu = require './context-menu'
+app = require 'app'
 dialog = require 'dialog'
 ipc = require 'ipc'
 path = require 'path'
 fs = require 'fs'
+url = require 'url'
 _ = require 'underscore-plus'
 
-# Private:
 module.exports =
 class AtomWindow
   @iconPath: path.resolve(__dirname, '..', '..', 'resources', 'atom.png')
@@ -31,6 +32,7 @@ class AtomWindow
 
     loadSettings = _.extend({}, settings)
     loadSettings.windowState ?= '{}'
+    loadSettings.appVersion = app.getVersion()
 
     # Only send to the first non-spec window created
     if @constructor.includeShellLoadTime and not @isSpec
@@ -43,7 +45,7 @@ class AtomWindow
 
     @browserWindow.loadSettings = loadSettings
     @browserWindow.once 'window:loaded', => @loaded = true
-    @browserWindow.loadUrl "file://#{@resourcePath}/static/index.html"
+    @browserWindow.loadUrl @getUrl(loadSettings)
     @browserWindow.focusOnWebView() if @isSpec
 
     @openPath(pathToOpen, initialLine)
@@ -51,6 +53,18 @@ class AtomWindow
   setupNodePath: (resourcePath) ->
     process.env['NODE_PATH'] = path.resolve(resourcePath, 'exports')
 
+  getUrl: (loadSettingsObj) ->
+    # Ignore the windowState when passing loadSettings via URL, since it could
+    # be quite large.
+    loadSettings = _.clone(loadSettingsObj)
+    delete loadSettings['windowState']
+
+    url.format
+      protocol: 'file'
+      pathname: "#{@resourcePath}/static/index.html"
+      slashes: true
+      query: {loadSettings: JSON.stringify(loadSettings)}
+
   getInitialPath: ->
     @browserWindow.loadSettings.initialPath
 
diff --git a/src/browser/context-menu.coffee b/src/browser/context-menu.coffee
index 85d3b0426..e3044b30d 100644
--- a/src/browser/context-menu.coffee
+++ b/src/browser/context-menu.coffee
@@ -1,6 +1,5 @@
 Menu = require 'menu'
 
-# Private:
 module.exports =
 class ContextMenu
   constructor: (template, browserWindow) ->
@@ -8,7 +7,7 @@ class ContextMenu
     menu = Menu.buildFromTemplate(template)
     menu.popup(browserWindow)
 
-  # Private: It's necessary to build the event handlers in this process, otherwise
+  # It's necessary to build the event handlers in this process, otherwise
   # closures are drug across processes and failed to be garbage collected
   # appropriately.
   createClickHandlers: (template) ->
diff --git a/src/browser/main.coffee b/src/browser/main.coffee
index 5d4a66224..c72081cd7 100644
--- a/src/browser/main.coffee
+++ b/src/browser/main.coffee
@@ -1,6 +1,5 @@
 global.shellStartTime = Date.now()
 
-autoUpdater = require 'auto-updater'
 crashReporter = require 'crash-reporter'
 app = require 'app'
 fs = require 'fs'
@@ -42,7 +41,6 @@ start = ->
 
   app.on 'will-finish-launching', ->
     setupCrashReporter()
-    setupAutoUpdater()
 
   app.on 'finish-launching', ->
     app.removeListener 'open-file', addPathToOpen
@@ -66,9 +64,6 @@ global.devResourcePath = path.join(app.getHomeDir(), 'github', 'atom')
 setupCrashReporter = ->
   crashReporter.start(productName: 'Atom', companyName: 'GitHub')
 
-setupAutoUpdater = ->
-  autoUpdater.setFeedUrl 'https://speakeasy.githubapp.com/apps/27/appcast.xml'
-
 parseCommandLine = ->
   version = app.getVersion()
   options = optimist(process.argv[1..])
diff --git a/src/buffered-process.coffee b/src/buffered-process.coffee
index b27c315be..ed0907f3f 100644
--- a/src/buffered-process.coffee
+++ b/src/buffered-process.coffee
@@ -12,30 +12,27 @@ class BufferedProcess
   process: null
   killed: false
 
-  # Executes the given executable.
+  # Public: Executes the given executable.
   #
-  # * options
-  #    + command:
-  #      The path to the executable to execute.
-  #    + args:
-  #      The array of arguments to pass to the script (optional).
-  #    + options:
-  #      The options Object to pass to Node's `ChildProcess.spawn` (optional).
-  #    + stdout:
-  #      The callback that receives a single argument which contains the
-  #      standard output of the script. The callback is called as data is
-  #      received but it's buffered to ensure only complete lines are passed
-  #      until the source stream closes. After the source stream has closed
-  #      all remaining data is sent in a final call (optional).
-  #    + stderr:
-  #      The callback that receives a single argument which contains the
-  #      standard error of the script. The callback is called as data is
-  #      received but it's buffered to ensure only complete lines are passed
-  #      until the source stream closes. After the source stream has closed
-  #      all remaining data is sent in a final call (optional).
-  #    + exit:
-  #      The callback which receives a single argument containing the exit
-  #      status (optional).
+  # options - An {Object} with the following keys:
+  #   :command - The {String} command to execute.
+  #   :args - The {String}} of arguments to pass to the script (optional).
+  #   :options - The options {Object} to pass to Node's `ChildProcess.spawn`
+  #              (optional).
+  #   :stdout - The callback that receives a single argument which contains the
+  #             standard output of the script. The callback is called as data is
+  #             received but it's buffered to ensure only complete lines are
+  #             passed until the source stream closes. After the source stream
+  #             has closed all remaining data is sent in a final call
+  #             (optional).
+  #   :stderr - The callback that receives a single argument which contains the
+  #             standard error of the script. The callback is called as data is
+  #             received but it's buffered to ensure only complete lines are
+  #             passed until the source stream closes. After the source stream
+  #             has closed all remaining data is sent in a final call
+  #             (optional).
+  #   :exit - The callback which receives a single argument containing the exit
+  #           status (optional).
   constructor: ({command, args, options, stdout, stderr, exit}={}) ->
     options ?= {}
     @process = ChildProcess.spawn(command, args, options)
@@ -68,7 +65,7 @@ class BufferedProcess
         processExited = true
         triggerExitCallback()
 
-  # Private: Helper method to pass data line by line.
+  # Helper method to pass data line by line.
   #
   # * stream:
   #   The Stream to read from.
@@ -93,7 +90,7 @@ class BufferedProcess
       onLines(buffered) if buffered.length > 0
       onDone()
 
-  # Public: Terminates the process.
+  # Public: Terminate the process.
   kill: ->
     @killed = true
     @process.kill()
diff --git a/src/clipboard.coffee b/src/clipboard.coffee
new file mode 100644
index 000000000..82d75d2d4
--- /dev/null
+++ b/src/clipboard.coffee
@@ -0,0 +1,49 @@
+clipboard = require 'clipboard'
+crypto = require 'crypto'
+
+# Public: Represents the clipboard used for copying and pasting in Atom.
+#
+# An instance of this class is always available as the `atom.clipboard` global.
+module.exports =
+class Clipboard
+  metadata: null
+  signatureForMetadata: null
+
+  # Creates an `md5` hash of some text.
+  #
+  # text - A {String} to hash.
+  #
+  # Returns a hashed {String}.
+  md5: (text) ->
+    crypto.createHash('md5').update(text, 'utf8').digest('hex')
+
+  # Public: Write the given text to the clipboard.
+  #
+  # The metadata associated with the text is available by calling
+  # {.readWithMetadata}.
+  #
+  # text - The {String} to store.
+  # metadata - The additional info to associate with the text.
+  write: (text, metadata) ->
+    @signatureForMetadata = @md5(text)
+    @metadata = metadata
+    clipboard.writeText(text)
+
+  # Public: Read the text from the clipboard.
+  #
+  # Returns a {String}.
+  read: ->
+    clipboard.readText()
+
+  # Public: Read the text from the clipboard and return both the text and the
+  # associated metadata.
+  #
+  # Returns an {Object} with the following keys:
+  #   :text - The {String} clipboard text.
+  #   :metadata - The metadata stored by an earlier call to {.write}.
+  readWithMetadata: ->
+    text = @read()
+    if @signatureForMetadata is @md5(text)
+      {text, @metadata}
+    else
+      {text}
diff --git a/src/command-installer.coffee b/src/command-installer.coffee
index a0374bf99..e59dbd05c 100644
--- a/src/command-installer.coffee
+++ b/src/command-installer.coffee
@@ -3,52 +3,55 @@ _ = require 'underscore-plus'
 async = require 'async'
 fs = require 'fs-plus'
 mkdirp = require 'mkdirp'
+runas = require 'runas'
 
 symlinkCommand = (sourcePath, destinationPath, callback) ->
-  mkdirp path.dirname(destinationPath), (error) ->
-    if error?
+  fs.unlink destinationPath, (error) ->
+    if error? and error?.code != 'ENOENT'
       callback(error)
     else
-      fs.symlink sourcePath, destinationPath, (error) ->
+      mkdirp path.dirname(destinationPath), (error) ->
         if error?
           callback(error)
         else
-          fs.chmod(destinationPath, 0o755, callback)
+          fs.symlink sourcePath, destinationPath, (error) ->
+            if error?
+              callback(error)
+            else
+              fs.chmod(destinationPath, '755', callback)
 
-unlinkCommand = (destinationPath, callback) ->
-  fs.unlink destinationPath, (error) ->
-    if error? and error.code isnt 'ENOENT'
-      callback(error)
-    else
-      callback()
+symlinkCommandWithPrivilegeSync = (sourcePath, destinationPath) ->
+  if runas('/bin/rm', ['-f', destinationPath], admin: true) != 0
+    throw new Error("Failed to remove '#{destinationPath}'")
+
+  if runas('/bin/mkdir', ['-p', path.dirname(destinationPath)], admin: true) != 0
+    throw new Error("Failed to create directory '#{destinationPath}'")
+
+  if runas('/bin/ln', ['-s', sourcePath, destinationPath], admin: true) != 0
+    throw new Error("Failed to symlink '#{sourcePath}' to '#{destinationPath}'")
 
 module.exports =
   getInstallDirectory: ->
     "/usr/local/bin"
 
-  install: (commandPath, callback) ->
+  install: (commandPath, askForPrivilege, callback) ->
     return unless process.platform is 'darwin'
 
     commandName = path.basename(commandPath, path.extname(commandPath))
-    directory = @getInstallDirectory()
-    if fs.existsSync(directory)
-      destinationPath = path.join(directory, commandName)
-      unlinkCommand destinationPath, (error) =>
-        if error?
-          error = new Error "Could not remove file at #{destinationPath}." if error
-          callback?(error)
-        else
-          symlinkCommand commandPath, destinationPath, (error) =>
-            error = new Error "Failed to symlink #{commandPath} to #{destinationPath}." if error
-            callback?(error)
-    else
-      error = new Error "Directory '#{directory} doesn't exist."
+    destinationPath = path.join(@getInstallDirectory(), commandName)
+    symlinkCommand commandPath, destinationPath, (error) =>
+      if askForPrivilege and error?.code is 'EACCES'
+        try
+          error = null
+          symlinkCommandWithPrivilegeSync(commandPath, destinationPath)
+        catch error
+
       callback?(error)
 
-  installAtomCommand: (resourcePath, callback) ->
+  installAtomCommand: (resourcePath, askForPrivilege, callback) ->
     commandPath = path.join(resourcePath, 'atom.sh')
-    @install commandPath, callback
+    @install commandPath, askForPrivilege, callback
 
-  installApmCommand: (resourcePath, callback) ->
+  installApmCommand: (resourcePath, askForPrivilege, callback) ->
     commandPath = path.join(resourcePath, 'apm', 'node_modules', '.bin', 'apm')
-    @install commandPath, callback
+    @install commandPath, askForPrivilege, callback
diff --git a/src/config-observer.coffee b/src/config-observer.coffee
deleted file mode 100644
index 46d3c44dd..000000000
--- a/src/config-observer.coffee
+++ /dev/null
@@ -1,12 +0,0 @@
-Mixin = require 'mixto'
-
-module.exports =
-class ConfigObserver extends Mixin
-  observeConfig: (keyPath, args...) ->
-    @configSubscriptions ?= {}
-    @configSubscriptions[keyPath] = atom.config.observe(keyPath, args...)
-
-  unobserveConfig: ->
-    if @configSubscriptions?
-      subscription.off() for keyPath, subscription of @configSubscriptions
-      @configSubscriptions = null
diff --git a/src/config.coffee b/src/config.coffee
index 68a7b464f..775d051ee 100644
--- a/src/config.coffee
+++ b/src/config.coffee
@@ -8,15 +8,14 @@ pathWatcher = require 'pathwatcher'
 
 # Public: Used to access all of Atom's configuration details.
 #
-# A global instance of this class is available to all plugins which can be
-# referenced using `atom.config`
+# An instance of this class is always available as the `atom.config` global.
 #
-# ### Best practices
+# ## Best practices
 #
 # * Create your own root keypath using your package's name.
 # * Don't depend on (or write to) configuration keys outside of your keypath.
 #
-# ### Example
+# ## Example
 #
 # ```coffeescript
 # atom.config.set('myplugin.key', 'value')
@@ -27,18 +26,14 @@ module.exports =
 class Config
   Emitter.includeInto(this)
 
-  defaultSettings: null
-  settings: null
-  configFileHasErrors: null
-
-  # Private: Created during initialization, available as `global.config`
+  # Created during initialization, available as `atom.config`
   constructor: ({@configDirPath, @resourcePath}={}) ->
     @defaultSettings = {}
     @settings = {}
+    @configFileHasErrors = false
     @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
     @configFilePath ?= path.join(@configDirPath, 'config.cson')
 
-  # Private:
   initializeConfigDirectory: (done) ->
     return if fs.existsSync(@configDirPath)
 
@@ -55,13 +50,11 @@ class Config
       queue.push({sourcePath, destinationPath})
     fs.traverseTree(templateConfigDirPath, onConfigDirFile, (path) -> true)
 
-  # Private:
   load: ->
     @initializeConfigDirectory()
     @loadUserConfig()
     @observeUserConfig()
 
-  # Private:
   loadUserConfig: ->
     unless fs.existsSync(@configFilePath)
       fs.makeTreeSync(path.dirname(@configFilePath))
@@ -77,17 +70,14 @@ class Config
       console.error "Failed to load user config '#{@configFilePath}'", e.message
       console.error e.stack
 
-  # Private:
   observeUserConfig: ->
     @watchSubscription ?= pathWatcher.watch @configFilePath, (eventType) =>
       @loadUserConfig() if eventType is 'change' and @watchSubscription?
 
-  # Private:
   unobserveUserConfig: ->
     @watchSubscription?.close()
     @watchSubscription = null
 
-  # Private:
   setDefaults: (keyPath, defaults) ->
     keys = keyPath.split('.')
     hash = @defaultSettings
@@ -160,6 +150,14 @@ class Config
   toggle: (keyPath) ->
     @set(keyPath, !@get(keyPath))
 
+  # Public: Restore the key path to its default value.
+  #
+  # keyPath - The {String} name of the key.
+  #
+  # Returns the new value.
+  restoreDefault: (keyPath) ->
+    @set(keyPath, _.valueForKeyPath(@defaultSettings, keyPath))
+
   # Public: Push the value to the array at the key path.
   #
   # keyPath - The {String} key path.
@@ -205,6 +203,9 @@ class Config
   # options - An optional {Object} containing the `callNow` key.
   # callback - The {Function} that fires when the. It is given a single argument, `value`,
   #            which is the new value of `keyPath`.
+  #
+  # Returns an {Object} with the following keys:
+  #  :off - A {Function} that unobserves the `keyPath` with called.
   observe: (keyPath, options={}, callback) ->
     if _.isFunction(options)
       callback = options
@@ -230,12 +231,10 @@ class Config
   unobserve: (keyPath) ->
     @off("updated.#{keyPath.replace(/\./, '-')}")
 
-  # Private:
   update: ->
     return if @configFileHasErrors
     @save()
     @emit 'updated'
 
-  # Private:
   save: ->
     CSON.writeFileSync(@configFilePath, @settings)
diff --git a/src/context-menu-manager.coffee b/src/context-menu-manager.coffee
index 2cbfe0364..40228156b 100644
--- a/src/context-menu-manager.coffee
+++ b/src/context-menu-manager.coffee
@@ -5,10 +5,10 @@ remote = require 'remote'
 # Public: Provides a registry for commands that you'd like to appear in the
 # context menu.
 #
-# Should be accessed via `atom.contextMenu`.
+# An instance of this class is always available as the `atom.contextMenu`
+# global.
 module.exports =
 class ContextMenuManager
-  # Private:
   constructor: (@devMode=false) ->
     @definitions = {}
     @devModeDefinitions = {}
@@ -24,11 +24,11 @@ class ContextMenuManager
   # Public: Creates menu definitions from the object specified by the menu
   # cson API.
   #
-  # * name: The path of the file that contains the menu definitions.
-  # * object: The 'context-menu' object specified in the menu cson API.
-  # * options:
-  #    + devMode - Determines whether the entries should only be shown when
-  #      the window is in dev mode.
+  # name - The path of the file that contains the menu definitions.
+  # object - The 'context-menu' object specified in the menu cson API.
+  # options - An {Object} with the following keys:
+  #   :devMode - Determines whether the entries should only be shown when
+  #              the window is in dev mode.
   #
   # Returns nothing.
   add: (name, object, {devMode}={}) ->
@@ -36,20 +36,20 @@ class ContextMenuManager
       for label, command of items
         @addBySelector(selector, {label, command}, {devMode})
 
-  # Private: Registers a command to be displayed when the relevant item is right
+  # Registers a command to be displayed when the relevant item is right
   # clicked.
   #
-  # * selector: The css selector for the active element which should include
-  #   the given command in its context menu.
-  # * definition: The object containing keys which match the menu template API.
-  # * options:
-  #    + devMode: Indicates whether this command should only appear while the
-  #      editor is in dev mode.
+  # selector - The css selector for the active element which should include
+  #            the given command in its context menu.
+  # definition - The object containing keys which match the menu template API.
+  # options - An {Object} with the following keys:
+  #   :devMode - Indicates whether this command should only appear while the
+  #              editor is in dev mode.
   addBySelector: (selector, definition, {devMode}={}) ->
     definitions = if devMode then @devModeDefinitions else @definitions
     (definitions[selector] ?= []).push(definition)
 
-  # Private: Returns definitions which match the element and devMode.
+  # Returns definitions which match the element and devMode.
   definitionsForElement: (element, {devMode}={}) ->
     definitions = if devMode then @devModeDefinitions else @definitions
     matchedDefinitions = []
@@ -58,14 +58,14 @@ class ContextMenuManager
 
     matchedDefinitions
 
-  # Private: Used to generate the context menu for a specific element and it's
+  # Used to generate the context menu for a specific element and it's
   # parents.
   #
   # The menu items are sorted such that menu items that match closest to the
   # active element are listed first. The further down the list you go, the higher
   # up the ancestor hierarchy they match.
   #
-  # * element: The DOM element to generate the menu template for.
+  # element - The DOM element to generate the menu template for.
   menuTemplateForMostSpecificElement: (element, {devMode}={}) ->
     menuTemplate = @definitionsForElement(element, {devMode})
     if element.parentElement
@@ -73,7 +73,7 @@ class ContextMenuManager
     else
       menuTemplate
 
-  # Private: Returns a menu template for both normal entries as well as
+  # Returns a menu template for both normal entries as well as
   # development mode entries.
   combinedMenuTemplateForElement: (element) ->
     normalItems = @menuTemplateForMostSpecificElement(element)
@@ -83,7 +83,7 @@ class ContextMenuManager
     menuTemplate.push({ type: 'separator' }) if normalItems.length > 0 and devItems.length > 0
     menuTemplate.concat(devItems)
 
-  # Private: Executes `executeAtBuild` if defined for each menu item with
+  # Executes `executeAtBuild` if defined for each menu item with
   # the provided event and then removes the `executeAtBuild` property from
   # the menu item.
   #
diff --git a/src/cursor-view.coffee b/src/cursor-view.coffee
index f76de9436..857e5e137 100644
--- a/src/cursor-view.coffee
+++ b/src/cursor-view.coffee
@@ -1,38 +1,49 @@
 {View} = require './space-pen-extensions'
-{Point, Range} = require 'text-buffer'
 _ = require 'underscore-plus'
 
-### Internal ###
 module.exports =
 class CursorView extends View
   @content: ->
     @div class: 'cursor idle', => @raw '&nbsp;'
 
-  blinkPeriod: 800
-  editorView: null
-  visible: true
+  @blinkPeriod: 800
 
+  @blinkCursors: ->
+    element.classList.toggle('blink-off') for [element] in @cursorViews
+
+  @startBlinking: (cursorView) ->
+    @cursorViews ?= []
+    @cursorViews.push(cursorView)
+    if @cursorViews.length is 1
+      @blinkInterval = setInterval(@blinkCursors.bind(this), @blinkPeriod / 2)
+
+  @stopBlinking: (cursorView) ->
+    cursorView[0].classList.remove('blink-off')
+    _.remove(@cursorViews, cursorView)
+    clearInterval(@blinkInterval) if @cursorViews.length is 0
+
+  blinking: false
+  visible: true
   needsUpdate: true
   needsRemoval: false
   shouldPauseBlinking: false
 
   initialize: (@cursor, @editorView) ->
-    @cursor.on 'moved.cursor-view', =>
+    @subscribe @cursor, 'moved', =>
       @needsUpdate = true
       @shouldPauseBlinking = true
 
-    @cursor.on 'visibility-changed.cursor-view', (visible) =>
+    @subscribe @cursor, 'visibility-changed', =>
       @needsUpdate = true
 
-    @cursor.on 'autoscrolled.cursor-view', =>
+    @subscribe @cursor, 'autoscrolled', =>
       @editorView.requestDisplayUpdate()
 
-    @cursor.on 'destroyed.cursor-view', =>
+    @subscribe @cursor, 'destroyed', =>
       @needsRemoval = true
 
   beforeRemove: ->
     @editorView.removeCursorView(this)
-    @cursor.off('.cursor-view')
     @stopBlinking()
 
   updateDisplay: ->
@@ -53,11 +64,7 @@ class CursorView extends View
 
   # Override for speed. The base function checks the computedStyle
   isHidden: ->
-    style = this[0].style
-    if style.display == 'none' or not @isOnDom()
-      true
-    else
-      false
+    this[0].style.display is 'none' or not @isOnDom()
 
   needsAutoscroll: ->
     @cursor.needsAutoscroll
@@ -69,19 +76,17 @@ class CursorView extends View
     @editorView.pixelPositionForScreenPosition(@getScreenPosition())
 
   setVisible: (visible) ->
-    unless @visible == visible
+    unless @visible is visible
       @visible = visible
       @toggle(@visible)
 
   stopBlinking: ->
-    clearInterval(@blinkInterval) if @blinkInterval
-    @blinkInterval = null
-    this[0].classList.remove('blink-off')
+    @constructor.stopBlinking(this) if @blinking
+    @blinking = false
 
   startBlinking: ->
-    return if @blinkInterval?
-    blink = => @toggleClass('blink-off')
-    @blinkInterval = setInterval(blink, @blinkPeriod / 2)
+    @constructor.startBlinking(this) unless @blinking
+    @blinking = true
 
   resetBlinking: ->
     @stopBlinking()
diff --git a/src/cursor.coffee b/src/cursor.coffee
index daf91e4dc..6b3747479 100644
--- a/src/cursor.coffee
+++ b/src/cursor.coffee
@@ -17,7 +17,7 @@ class Cursor
   visible: true
   needsAutoscroll: null
 
-  # Private: Instantiated by an {Editor}
+  # Instantiated by an {Editor}
   constructor: ({@editor, @marker}) ->
     @updateVisibility()
     @marker.on 'changed', (e) =>
@@ -45,11 +45,9 @@ class Cursor
       @emit 'destroyed'
     @needsAutoscroll = true
 
-  # Private:
   destroy: ->
     @marker.destroy()
 
-  # Private:
   changePosition: (options, fn) ->
     @clearSelection()
     @needsAutoscroll = options.autoscroll ? @isLastCursor()
@@ -58,12 +56,11 @@ class Cursor
 
   # Public: Moves a cursor to a given screen position.
   #
-  # * screenPosition:
-  #   An {Array} of two numbers: the screen row, and the screen column.
-  # * options:
-  #    + autoscroll:
-  #      A Boolean which, if `true`, scrolls the {Editor} to wherever the
-  #      cursor moves to.
+  # screenPosition - An {Array} of two numbers: the screen row, and the screen
+  #                  column.
+  # options - An {Object} with the following keys:
+  #   :autoscroll - A Boolean which, if `true`, scrolls the {Editor} to wherever
+  #                 the cursor moves to.
   setScreenPosition: (screenPosition, options={}) ->
     @changePosition options, =>
       @marker.setHeadScreenPosition(screenPosition, options)
@@ -74,12 +71,11 @@ class Cursor
 
   # Public: Moves a cursor to a given buffer position.
   #
-  # * bufferPosition:
-  #   An {Array} of two numbers: the buffer row, and the buffer column.
-  # * options:
-  #    + autoscroll:
-  #      A Boolean which, if `true`, scrolls the {Editor} to wherever the
-  #      cursor moves to.
+  # bufferPosition - An {Array} of two numbers: the buffer row, and the buffer
+  #                  column.
+  # options - An {Object} with the following keys:
+  #   :autoscroll - A Boolean which, if `true`, scrolls the {Editor} to wherever
+  #                 the cursor moves to.
   setBufferPosition: (bufferPosition, options={}) ->
     @changePosition options, =>
       @marker.setHeadBufferPosition(bufferPosition, options)
@@ -104,11 +100,11 @@ class Cursor
 
   # Public: Get the RegExp used by the cursor to determine what a "word" is.
   #
-  # * options:
-  #    + includeNonWordCharacters:
-  #      A Boolean indicating whether to include non-word characters in the regex.
+  # options: An {Object} with the following keys:
+  #   :includeNonWordCharacters - A {Boolean} indicating whether to include
+  #                               non-word characters in the regex.
   #
-  # Returns a RegExp.
+  # Returns a {RegExp}.
   wordRegExp: ({includeNonWordCharacters}={})->
     includeNonWordCharacters ?= true
     nonWordCharacters = atom.config.get('editor.nonWordCharacters')
@@ -122,7 +118,7 @@ class Cursor
   #
   # "Last" is defined as the most recently added cursor.
   #
-  # Returns a Boolean.
+  # Returns a {Boolean}.
   isLastCursor: ->
     this == @editor.getCursor()
 
@@ -131,7 +127,7 @@ class Cursor
   # "Surrounded" here means that all characters before and after the cursor is
   # whitespace.
   #
-  # Returns a Boolean.
+  # Returns a {Boolean}.
   isSurroundedByWhitespace: ->
     {row, column} = @getBufferPosition()
     range = [[row, Math.min(0, column - 1)], [row, Math.max(0, column + 1)]]
@@ -217,9 +213,9 @@ class Cursor
 
   # Public: Moves the cursor left one screen column.
   #
-  # * options:
-  #    + moveToEndOfSelection:
-  #      if true, move to the left of the selection if a selection exists.
+  # options - An {Object} with the following keys:
+  #   :moveToEndOfSelection - if true, move to the left of the selection if a
+  #                           selection exists.
   moveLeft: ({moveToEndOfSelection}={}) ->
     range = @marker.getScreenRange()
     if moveToEndOfSelection and not range.isEmpty()
@@ -231,9 +227,9 @@ class Cursor
 
   # Public: Moves the cursor right one screen column.
   #
-  # * options:
-  #    + moveToEndOfSelection:
-  #      if true, move to the right of the selection if a selection exists.
+  # options - An {Object} with the following keys:
+  #   :moveToEndOfSelection - if true, move to the right of the selection if a
+  #                           selection exists.
   moveRight: ({moveToEndOfSelection}={}) ->
     range = @marker.getScreenRange()
     if moveToEndOfSelection and not range.isEmpty()
@@ -313,12 +309,12 @@ class Cursor
 
   # Public: Retrieves the buffer position of where the current word starts.
   #
-  # * options:
-  #    + wordRegex:
-  #      A RegExp indicating what constitutes a "word" (default: {.wordRegExp})
-  #    + includeNonWordCharacters:
-  #      A Boolean indicating whether to include non-word characters in the
-  #      default word regex. Has no effect if wordRegex is set.
+  # options - An {Object} with the following keys:
+  #   :wordRegex - A {RegExp} indicating what constitutes a "word"
+  #                (default: {.wordRegExp}).
+  #   :includeNonWordCharacters - A {Boolean} indicating whether to include
+  #                               non-word characters in the default word regex.
+  #                               Has no effect if wordRegex is set.
   #
   # Returns a {Range}.
   getBeginningOfCurrentWordBufferPosition: (options = {}) ->
@@ -381,12 +377,12 @@ class Cursor
 
   # Public: Retrieves the buffer position of where the current word ends.
   #
-  # * options:
-  #    + wordRegex:
-  #      A RegExp indicating what constitutes a "word" (default: {.wordRegExp})
-  #    + includeNonWordCharacters:
-  #      A Boolean indicating whether to include non-word characters in the
-  #      default word regex. Has no effect if wordRegex is set.
+  # options - An {Object} with the following keys:
+  #   :wordRegex - A {RegExp} indicating what constitutes a "word"
+  #                (default: {.wordRegExp})
+  #   :includeNonWordCharacters - A Boolean indicating whether to include
+  #                               non-word characters in the default word regex.
+  #                               Has no effect if wordRegex is set.
   #
   # Returns a {Range}.
   getEndOfCurrentWordBufferPosition: (options = {}) ->
@@ -405,9 +401,9 @@ class Cursor
 
   # Public: Retrieves the buffer position of where the next word starts.
   #
-  # * options:
-  #    + wordRegex:
-  #      A RegExp indicating what constitutes a "word" (default: {.wordRegExp})
+  # options -
+  #   :wordRegex - A {RegExp} indicating what constitutes a "word"
+  #                (default: {.wordRegExp}).
   #
   # Returns a {Range}.
   getBeginningOfNextWordBufferPosition: (options = {}) ->
@@ -424,9 +420,9 @@ class Cursor
 
   # Public: Returns the buffer Range occupied by the word located under the cursor.
   #
-  # * options:
-  #    + wordRegex:
-  #      A RegExp indicating what constitutes a "word" (default: {.wordRegExp})
+  # options -
+  #   :wordRegex - A {RegExp} indicating what constitutes a "word"
+  #                (default: {.wordRegExp}).
   getCurrentWordBufferRange: (options={}) ->
     startOptions = _.extend(_.clone(options), allowPrevious: false)
     endOptions = _.extend(_.clone(options), allowNext: false)
@@ -434,9 +430,9 @@ class Cursor
 
   # Public: Returns the buffer Range for the current line.
   #
-  # * options:
-  #    + includeNewline:
-  #      A boolean which controls whether the Range should include the newline.
+  # options -
+  #   :includeNewline: - A {Boolean} which controls whether the Range should
+  #                      include the newline.
   getCurrentLineBufferRange: (options) ->
     @editor.bufferRangeForBufferRow(@getBufferRow(), options)
 
diff --git a/src/deserializer-manager.coffee b/src/deserializer-manager.coffee
index 60df24b0a..3c7cc2f5e 100644
--- a/src/deserializer-manager.coffee
+++ b/src/deserializer-manager.coffee
@@ -1,25 +1,39 @@
 # Public: Manages the deserializers used for serialized state
 #
-# Should be accessed via `atom.deserializers`
+# An instance of this class is always available as the `atom.deserializers`
+# global.
+#
+# ### Registering a deserializer
+#
+# ```coffee
+# class MyPackageView extends View
+#   atom.deserializers.add(this)
+#
+#   @deserialize: (state) ->
+#     new MyPackageView(state)
+# ```
 module.exports =
 class DeserializerManager
-  constructor: (@environment) ->
+  constructor: ->
     @deserializers = {}
-    @deferredDeserializers = {}
 
   # Public: Register the given class(es) as deserializers.
-  add: (klasses...) ->
-    @deserializers[klass.name] = klass for klass in klasses
-
-  # Public: Add a deferred deserializer for the given class name.
-  addDeferred: (name, fn) ->
-    @deferredDeserializers[name] = fn
+  #
+  # classes - One or more classes to register.
+  add: (classes...) ->
+    @deserializers[klass.name] = klass for klass in classes
 
   # Public: Remove the given class(es) as deserializers.
-  remove: (klasses...) ->
-    delete @deserializers[klass.name] for klass in klasses
+  #
+  # classes - One or more classes to remove.
+  remove: (classes...) ->
+    delete @deserializers[name] for {name} in classes
 
   # Public: Deserialize the state and params.
+  #
+  # state  - The state {Object} to deserialize.
+  # params - The params {Object} to pass as the second arguments to the
+  #          deserialize method of the deserializer.
   deserialize: (state, params) ->
     return unless state?
 
@@ -30,13 +44,11 @@ class DeserializerManager
     else
       console.warn "No deserializer found for", state
 
-  # Private: Get the deserializer for the state.
+  # Get the deserializer for the state.
+  #
+  # state - The state {Object} being deserialized.
   get: (state) ->
     return unless state?
 
     name = state.get?('deserializer') ? state.deserializer
-    if @deferredDeserializers[name]
-      @deferredDeserializers[name]()
-      delete @deferredDeserializers[name]
-
     @deserializers[name]
diff --git a/src/directory.coffee b/src/directory.coffee
index 6404dc5ba..790de62f6 100644
--- a/src/directory.coffee
+++ b/src/directory.coffee
@@ -7,7 +7,7 @@ pathWatcher = require 'pathwatcher'
 
 File = require './file'
 
-# Public: Represents a directory using {File}s.
+# Public: Represents a directory on disk.
 #
 # ## Requiring in packages
 #
@@ -18,15 +18,12 @@ module.exports =
 class Directory
   Emitter.includeInto(this)
 
-  path: null
   realPath: null
 
   # Public: Configures a new Directory instance, no files are accessed.
   #
-  # * path:
-  #   A String containing the absolute path to the directory.
-  # + symlink:
-  #   A Boolean indicating if the path is a symlink (defaults to false).
+  # path - A {String} containing the absolute path to the directory.
+  # symlink - A {Boolean} indicating if the path is a symlink (default: false).
   constructor: (@path, @symlink=false) ->
     @on 'first-contents-changed-subscription-will-be-added', =>
       # Triggered by emissary, when a new contents-changed listener attaches
@@ -36,7 +33,7 @@ class Directory
       # Triggered by emissary, when the last contents-changed listener detaches
       @unsubscribeFromNativeChangeEvents()
 
-  # Public: Returns the basename of the directory.
+  # Public: Returns the {String} basename of the directory.
   getBaseName: ->
     path.basename(@path)
 
@@ -108,8 +105,8 @@ class Directory
 
   # Public: Reads file entries in this directory from disk asynchronously.
   #
-  # * callback: A function to call with an Error as the first argument and
-  #   an {Array} of {File} and {Directory} objects as the second argument.
+  # callback - A {Function} to call with an {Error} as the 1st argument and
+  #            an {Array} of {File} and {Directory} objects as the 2nd argument.
   getEntries: (callback) ->
     fs.list @path, (error, entries) ->
       return callback(error) if error?
@@ -134,18 +131,16 @@ class Directory
       async.eachLimit entries, 1, statEntry, ->
         callback(null, directories.concat(files))
 
-  # Private:
   subscribeToNativeChangeEvents: ->
     unless @watchSubscription?
       @watchSubscription = pathWatcher.watch @path, (eventType) =>
         @emit "contents-changed" if eventType is "change"
 
-  # Private:
   unsubscribeFromNativeChangeEvents: ->
     if @watchSubscription?
       @watchSubscription.close()
       @watchSubscription = null
 
-  # Private: Does given full path start with the given prefix?
+  # Does given full path start with the given prefix?
   isPathPrefixOf: (prefix, fullPath) ->
     fullPath.indexOf(prefix) is 0 and fullPath[prefix.length] is path.sep
diff --git a/src/display-buffer-marker.coffee b/src/display-buffer-marker.coffee
index 8c08b3c9e..184162622 100644
--- a/src/display-buffer-marker.coffee
+++ b/src/display-buffer-marker.coffee
@@ -2,7 +2,6 @@
 _ = require 'underscore-plus'
 {Emitter, Subscriber} = require 'emissary'
 
-# Private:
 module.exports =
 class DisplayBufferMarker
   Emitter.includeInto(this)
@@ -15,8 +14,6 @@ class DisplayBufferMarker
   oldTailScreenPosition: null
   wasValid: true
 
-  ### Internal ###
-
   constructor: ({@bufferMarker, @displayBuffer}) ->
     @id = @bufferMarker.id
     @oldHeadBufferPosition = @getHeadBufferPosition()
@@ -28,8 +25,6 @@ class DisplayBufferMarker
     @subscribe @bufferMarker, 'destroyed', => @destroyed()
     @subscribe @bufferMarker, 'changed', (event) => @notifyObservers(event)
 
-  ### Public ###
-
   copy: (attributes) ->
     @displayBuffer.getMarker(@bufferMarker.copy(attributes).id)
 
@@ -170,8 +165,6 @@ class DisplayBufferMarker
   inspect: ->
     "DisplayBufferMarker(id: #{@id}, bufferRange: #{@getBufferRange()})"
 
-  ### Internal ###
-
   destroyed: ->
     delete @displayBuffer.markers[@id]
     @emit 'destroyed'
diff --git a/src/display-buffer.coffee b/src/display-buffer.coffee
index 2891cba99..b5063a280 100644
--- a/src/display-buffer.coffee
+++ b/src/display-buffer.coffee
@@ -1,5 +1,5 @@
 _ = require 'underscore-plus'
-{Emitter, Subscriber} = require 'emissary'
+{Emitter} = require 'emissary'
 guid = require 'guid'
 Serializable = require 'serializable'
 {Model} = require 'theorist'
@@ -9,13 +9,10 @@ RowMap = require './row-map'
 Fold = require './fold'
 Token = require './token'
 DisplayBufferMarker = require './display-buffer-marker'
-ConfigObserver = require './config-observer'
 
-# Private:
 module.exports =
 class DisplayBuffer extends Model
   Serializable.includeInto(this)
-  ConfigObserver.includeInto(this)
 
   @properties
     softWrap: null
@@ -39,10 +36,10 @@ class DisplayBuffer extends Model
       @emit 'soft-wrap-changed', softWrap
       @updateWrappedScreenLines()
 
-    @observeConfig 'editor.preferredLineLength', callNow: false, =>
+    @subscribe atom.config.observe 'editor.preferredLineLength', callNow: false, =>
       @updateWrappedScreenLines() if @softWrap and atom.config.get('editor.softWrapAtPreferredLineLength')
 
-    @observeConfig 'editor.softWrapAtPreferredLineLength', callNow: false, =>
+    @subscribe atom.config.observe 'editor.softWrapAtPreferredLineLength', callNow: false, =>
       @updateWrappedScreenLines() if @softWrap
 
   serializeParams: ->
@@ -82,8 +79,6 @@ class DisplayBuffer extends Model
     bufferDelta = 0
     @emitChanged({ start, end, screenDelta, bufferDelta })
 
-  ### Public ###
-
   # Sets the visibility of the tokenized buffer.
   #
   # visible - A {Boolean} indicating of the tokenized buffer is shown
@@ -419,8 +414,6 @@ class DisplayBuffer extends Model
       column = screenLine.clipScreenColumn(column, options)
     new Point(row, column)
 
-  ### Public ###
-
   # Given a line, finds the point where it would wrap.
   #
   # line - The {String} to check
@@ -470,7 +463,7 @@ class DisplayBuffer extends Model
   getMarkerCount: ->
     @buffer.getMarkerCount()
 
-  # Constructs a new marker at the given screen range.
+  # Public: Constructs a new marker at the given screen range.
   #
   # range - The marker {Range} (representing the distance between the head and tail)
   # options - Options to pass to the {Marker} constructor
@@ -480,7 +473,7 @@ class DisplayBuffer extends Model
     bufferRange = @bufferRangeForScreenRange(args.shift())
     @markBufferRange(bufferRange, args...)
 
-  # Constructs a new marker at the given buffer range.
+  # Public: Constructs a new marker at the given buffer range.
   #
   # range - The marker {Range} (representing the distance between the head and tail)
   # options - Options to pass to the {Marker} constructor
@@ -489,7 +482,7 @@ class DisplayBuffer extends Model
   markBufferRange: (args...) ->
     @getMarker(@buffer.markRange(args...).id)
 
-  # Constructs a new marker at the given screen position.
+  # Public: Constructs a new marker at the given screen position.
   #
   # range - The marker {Range} (representing the distance between the head and tail)
   # options - Options to pass to the {Marker} constructor
@@ -498,7 +491,7 @@ class DisplayBuffer extends Model
   markScreenPosition: (screenPosition, options) ->
     @markBufferPosition(@bufferPositionForScreenPosition(screenPosition), options)
 
-  # Constructs a new marker at the given buffer position.
+  # Public: Constructs a new marker at the given buffer position.
   #
   # range - The marker {Range} (representing the distance between the head and tail)
   # options - Options to pass to the {Marker} constructor
@@ -507,7 +500,7 @@ class DisplayBuffer extends Model
   markBufferPosition: (bufferPosition, options) ->
     @getMarker(@buffer.markPosition(bufferPosition, options).id)
 
-  # Removes the marker with the given id.
+  # Public: Removes the marker with the given id.
   #
   # id - The {Number} of the ID to remove
   destroyMarker: (id) ->
@@ -573,15 +566,12 @@ class DisplayBuffer extends Model
     marker.unsubscribe() for marker in @getMarkers()
     @tokenizedBuffer.destroy()
     @unsubscribe()
-    @unobserveConfig()
 
   logLines: (start=0, end=@getLastRow())->
     for row in [start..end]
       line = @lineForRow(row).text
       console.log row, @bufferRowForScreenRow(row), line, line.length
 
-  ### Internal ###
-
   handleTokenizedBufferChange: (tokenizedBufferChange) =>
     {start, end, delta, bufferChange} = tokenizedBufferChange
     @updateScreenLines(start, end + 1, delta, delayChangeEvent: bufferChange?)
diff --git a/src/editor-view.coffee b/src/editor-view.coffee
index c3754070b..b64f41379 100644
--- a/src/editor-view.coffee
+++ b/src/editor-view.coffee
@@ -26,6 +26,7 @@ module.exports =
 class EditorView extends View
   @characterWidthCache: {}
   @configDefaults:
+    fontFamily: ''
     fontSize: 20
     showInvisibles: false
     showIndentGuide: false
@@ -41,8 +42,6 @@ class EditorView extends View
 
   @nextEditorId: 1
 
-  ### Internal ###
-
   @content: (params) ->
     attributes = { class: @classes(params), tabindex: -1 }
     _.extend(attributes, params.attributes) if params.attributes
@@ -79,14 +78,12 @@ class EditorView extends View
   redrawOnReattach: false
   bottomPaddingInLines: 10
 
-  ### Public ###
-
   # The constructor for setting up an `EditorView` instance.
   #
   # editorOrOptions - Either an {Editor}, or an object with one property, `mini`.
-  #                        If `mini` is `true`, a "miniature" `Editor` is constructed.
-  #                        Typically, this is ideal for scenarios where you need an Atom editor,
-  #                        but without all the chrome, like scrollbars, gutter, _e.t.c._.
+  #                   If `mini` is `true`, a "miniature" `Editor` is constructed.
+  #                   Typically, this is ideal for scenarios where you need an Atom editor,
+  #                   but without all the chrome, like scrollbars, gutter, _e.t.c._.
   #
   initialize: (editorOrOptions) ->
     if editorOrOptions instanceof Editor
@@ -120,7 +117,7 @@ class EditorView extends View
     else
       throw new Error("Must supply an Editor or mini: true")
 
-  # Internal: Sets up the core Atom commands.
+  # Sets up the core Atom commands.
   #
   # Some commands are excluded from mini-editors.
   bindKeys: ->
@@ -209,7 +206,7 @@ class EditorView extends View
         'editor:toggle-line-comments': => @toggleLineCommentsInSelection()
         'editor:log-cursor-scope': => @logCursorScope()
         'editor:checkout-head-revision': => @checkoutHead()
-        'editor:copy-path': => @copyPathToPasteboard()
+        'editor:copy-path': => @copyPathToClipboard()
         'editor:move-line-up': => @editor.moveLineUp()
         'editor:move-line-down': => @editor.moveLineDown()
         'editor:duplicate-line': => @editor.duplicateLine()
@@ -223,6 +220,9 @@ class EditorView extends View
       do (name, method) =>
         @command name, (e) -> method(e); false
 
+  # Public: Get the underlying editor model for this view.
+  #
+  # Returns an {Editor}.
   getEditor: ->
     @editor
 
@@ -238,7 +238,6 @@ class EditorView extends View
   insertText: (text, options) ->
     @editor.insertText(text, options)
 
-  # Private:
   setHeightInLines: (heightInLines)->
     heightInLines ?= @calculateHeightInLines()
     @heightInLines = heightInLines if heightInLines
@@ -248,39 +247,41 @@ class EditorView extends View
     widthInChars ?= @calculateWidthInChars()
     @editor.setEditorWidthInChars(widthInChars) if widthInChars
 
-  # Public: Emulates the "page down" key, where the last row of a buffer scrolls to become the first.
+  # Public: Emulates the "page down" key, where the last row of a buffer scrolls
+  # to become the first.
   pageDown: ->
     newScrollTop = @scrollTop() + @scrollView[0].clientHeight
     @editor.moveCursorDown(@getPageRows())
     @scrollTop(newScrollTop,  adjustVerticalScrollbar: true)
 
-  # Public: Emulates the "page up" key, where the frst row of a buffer scrolls to become the last.
+  # Public: Emulates the "page up" key, where the frst row of a buffer scrolls
+  # to become the last.
   pageUp: ->
     newScrollTop = @scrollTop() - @scrollView[0].clientHeight
     @editor.moveCursorUp(@getPageRows())
     @scrollTop(newScrollTop,  adjustVerticalScrollbar: true)
 
-  # Gets the number of actual page rows existing in an editor.
+  # Public: Gets the number of actual page rows existing in an editor.
   #
   # Returns a {Number}.
   getPageRows: ->
     Math.max(1, Math.ceil(@scrollView[0].clientHeight / @lineHeight))
 
-  # Set whether invisible characters are shown.
+  # Public: Set whether invisible characters are shown.
   #
-  # showInvisibles - A {Boolean} which, if `true`, show invisible characters
+  # showInvisibles - A {Boolean} which, if `true`, show invisible characters.
   setShowInvisibles: (showInvisibles) ->
     return if showInvisibles == @showInvisibles
     @showInvisibles = showInvisibles
     @resetDisplay()
 
-  # Defines which characters are invisible.
+  # Public: Defines which characters are invisible.
   #
-  # invisibles - A hash defining the invisible characters: The defaults are:
-  #              eol: `\u00ac`
-  #              space: `\u00b7`
-  #              tab: `\u00bb`
-  #              cr: `\u00a4`
+  # invisibles - An {Object} defining the invisible characters:
+  #   :eol   - The end of line invisible {String} (default: `\u00ac`).
+  #   :space - The space invisible {String} (default: `\u00b7`).
+  #   :tab   - The tab invisible {String} (default: `\u00bb`).
+  #   :cr    - The carriage return invisible {String} (default: `\u00a4`).
   setInvisibles: (@invisibles={}) ->
     _.defaults @invisibles,
       eol: '\u00ac'
@@ -289,14 +290,20 @@ class EditorView extends View
       cr: '\u00a4'
     @resetDisplay()
 
-  # Sets whether you want to show the indentation guides.
+  # Public: Sets whether you want to show the indentation guides.
   #
-  # showIndentGuide - A {Boolean} you can set to `true` if you want to see the indentation guides.
+  # showIndentGuide - A {Boolean} you can set to `true` if you want to see the
+  #                   indentation guides.
   setShowIndentGuide: (showIndentGuide) ->
     return if showIndentGuide == @showIndentGuide
     @showIndentGuide = showIndentGuide
     @resetDisplay()
 
+  # Public: Set the text to appear in the editor when it is empty.
+  #
+  # This only affects mini editors.
+  #
+  # placeholderText - A {String} of text to display when empty.
   setPlaceholderText: (placeholderText) ->
     return unless @mini
     @placeholderText = placeholderText
@@ -310,15 +317,13 @@ class EditorView extends View
     if path = @editor.getPath()
       atom.project.getRepo()?.checkoutHead(path)
 
-  ### Internal ###
-
   configure: ->
-    @observeConfig 'editor.showLineNumbers', (showLineNumbers) => @gutter.setShowLineNumbers(showLineNumbers)
-    @observeConfig 'editor.showInvisibles', (showInvisibles) => @setShowInvisibles(showInvisibles)
-    @observeConfig 'editor.showIndentGuide', (showIndentGuide) => @setShowIndentGuide(showIndentGuide)
-    @observeConfig 'editor.invisibles', (invisibles) => @setInvisibles(invisibles)
-    @observeConfig 'editor.fontSize', (fontSize) => @setFontSize(fontSize)
-    @observeConfig 'editor.fontFamily', (fontFamily) => @setFontFamily(fontFamily)
+    @subscribe atom.config.observe 'editor.showLineNumbers', (showLineNumbers) => @gutter.setShowLineNumbers(showLineNumbers)
+    @subscribe atom.config.observe 'editor.showInvisibles', (showInvisibles) => @setShowInvisibles(showInvisibles)
+    @subscribe atom.config.observe 'editor.showIndentGuide', (showIndentGuide) => @setShowIndentGuide(showIndentGuide)
+    @subscribe atom.config.observe 'editor.invisibles', (invisibles) => @setInvisibles(invisibles)
+    @subscribe atom.config.observe 'editor.fontSize', (fontSize) => @setFontSize(fontSize)
+    @subscribe atom.config.observe 'editor.fontFamily', (fontFamily) => @setFontFamily(fontFamily)
 
   handleEvents: ->
     @on 'focus', =>
@@ -488,12 +493,11 @@ class EditorView extends View
 
     @trigger 'editor:attached', [this]
 
-  # TODO: This should be private and only called from the constructor
   edit: (editor) ->
     return if editor is @editor
 
     if @editor
-      @saveScrollPositionForeditor()
+      @saveScrollPositionForEditor()
       @editor.off(".editor")
 
     @editor = editor
@@ -590,19 +594,18 @@ class EditorView extends View
     else
       @scrollView.scrollRight()
 
-  ### Public ###
-
-  # Scrolls the editor to the bottom.
+  # Public: Scrolls the editor to the bottom.
   scrollToBottom: ->
     @scrollBottom(@editor.getScreenLineCount() * @lineHeight)
 
-  # Scrolls the editor to the position of the most recently added cursor.
+  # Public: Scrolls the editor to the position of the most recently added
+  # cursor.
   #
   # The editor is also centered.
   scrollToCursorPosition: ->
     @scrollToBufferPosition(@editor.getCursorBufferPosition(), center: true)
 
-  # Scrolls the editor to the given buffer position.
+  # Public: Scrolls the editor to the given buffer position.
   #
   # bufferPosition - An object that represents a buffer position. It can be either
   #                  an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
@@ -610,7 +613,7 @@ class EditorView extends View
   scrollToBufferPosition: (bufferPosition, options) ->
     @scrollToPixelPosition(@pixelPositionForBufferPosition(bufferPosition), options)
 
-  # Scrolls the editor to the given screen position.
+  # Public: Scrolls the editor to the given screen position.
   #
   # screenPosition - An object that represents a buffer position. It can be either
   #                  an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
@@ -618,18 +621,20 @@ class EditorView extends View
   scrollToScreenPosition: (screenPosition, options) ->
     @scrollToPixelPosition(@pixelPositionForScreenPosition(screenPosition), options)
 
-  # Scrolls the editor to the given pixel position.
+  # Public: Scrolls the editor to the given pixel position.
   #
   # pixelPosition - An object that represents a pixel position. It can be either
-  #                  an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
+  #                 an {Object} (`{row, column}`), {Array} (`[row, column]`), or
+  #                 {Point}.
   # options - A hash with the following keys:
-  #          center: if `true`, the position is scrolled such that it's in the center of the editor
+  #   :center - if `true`, the position is scrolled such that it's in
+  #             the center of the editor
   scrollToPixelPosition: (pixelPosition, options) ->
     return unless @attached
     @scrollVertically(pixelPosition, options)
     @scrollHorizontally(pixelPosition)
 
-  # Highlight all the folds within the given buffer range.
+  # Public: Highlight all the folds within the given buffer range.
   #
   # "Highlighting" essentially just adds the `fold-selected` class to the line's
   # DOM element.
@@ -647,29 +652,27 @@ class EditorView extends View
         else
           element.removeClass('fold-selected')
 
-  saveScrollPositionForeditor: ->
+  saveScrollPositionForEditor: ->
     if @attached
       @editor.setScrollTop(@scrollTop())
       @editor.setScrollLeft(@scrollLeft())
 
-  # Toggle soft tabs on the edit session.
+  # Public: Toggle soft tabs on the edit session.
   toggleSoftTabs: ->
     @editor.setSoftTabs(not @editor.getSoftTabs())
 
-  # Toggle soft wrap on the edit session.
+  # Public: Toggle soft wrap on the edit session.
   toggleSoftWrap: ->
     @setWidthInChars()
     @editor.setSoftWrap(not @editor.getSoftWrap())
 
-  # Private:
   calculateWidthInChars: ->
     Math.floor(@scrollView.width() / @charWidth)
 
-  # Private:
   calculateHeightInLines: ->
     Math.ceil($(window).height() / @lineHeight)
 
-  # Enables/disables soft wrap on the editor.
+  # Public: Enables/disables soft wrap on the editor.
   #
   # softWrap - A {Boolean} which, if `true`, enables soft wrap
   setSoftWrap: (softWrap) ->
@@ -679,7 +682,7 @@ class EditorView extends View
     else
       @removeClass 'soft-wrap'
 
-  # Sets the font size for the editor.
+  # Public: Sets the font size for the editor.
   #
   # fontSize - A {Number} indicating the font size in pixels.
   setFontSize: (fontSize) ->
@@ -692,15 +695,15 @@ class EditorView extends View
     else
       @redrawOnReattach = @attached
 
-  # Retrieves the font size for the editor.
+  # Public: Retrieves the font size for the editor.
   #
   # Returns a {Number} indicating the font size in pixels.
   getFontSize: ->
     parseInt(@css("font-size"))
 
-  # Sets the font family for the editor.
+  # Public: Sets the font family for the editor.
   #
-  # fontFamily - A {String} identifying the CSS `font-family`,
+  # fontFamily - A {String} identifying the CSS `font-family`.
   setFontFamily: (fontFamily='') ->
     @css('font-family', fontFamily)
 
@@ -708,12 +711,12 @@ class EditorView extends View
 
     @redraw()
 
-  # Gets the font family for the editor.
+  # Public: Gets the font family for the editor.
   #
-  # Returns a {String} identifying the CSS `font-family`,
+  # Returns a {String} identifying the CSS `font-family`.
   getFontFamily: -> @css("font-family")
 
-  # Redraw the editor
+  # Public: Redraw the editor
   redraw: ->
     return unless @hasParent()
     return unless @attached
@@ -723,23 +726,27 @@ class EditorView extends View
     @updateLayerDimensions()
     @requestDisplayUpdate()
 
+  # Public: Split the editor view left.
   splitLeft: ->
     pane = @getPane()
     pane?.splitLeft(pane?.copyActiveItem()).activeView
 
+  # Public: Split the editor view right.
   splitRight: ->
     pane = @getPane()
     pane?.splitRight(pane?.copyActiveItem()).activeView
 
+  # Public: Split the editor view up.
   splitUp: ->
     pane = @getPane()
     pane?.splitUp(pane?.copyActiveItem()).activeView
 
+  # Public: Split the editor view down.
   splitDown: ->
     pane = @getPane()
     pane?.splitDown(pane?.copyActiveItem()).activeView
 
-  # Retrieve's the `EditorView`'s pane.
+  # Public: Get this view's pane.
   #
   # Returns a {Pane}.
   getPane: ->
@@ -750,7 +757,6 @@ class EditorView extends View
     super
     atom.workspaceView?.focus()
 
-  # Private:
   beforeRemove: ->
     @trigger 'editor:will-be-removed'
     @removed = true
@@ -797,8 +803,6 @@ class EditorView extends View
   appendToLinesView: (view) ->
     @overlayer.append(view)
 
-  ### Internal ###
-
   # Scrolls the editor vertically to a given position.
   scrollVertically: (pixelPosition, {center}={}) ->
     scrollViewHeight = @scrollView.height()
@@ -835,7 +839,7 @@ class EditorView extends View
       @scrollRight(desiredRight)
     else if desiredLeft < @scrollLeft()
       @scrollLeft(desiredLeft)
-    @saveScrollPositionForeditor()
+    @saveScrollPositionForEditor()
 
   calculateDimensions: ->
     fragment = $('<div class="line" style="position: absolute; visibility: hidden;"><span>x</span></div>')
@@ -1135,9 +1139,8 @@ class EditorView extends View
     @renderedLines.css('padding-bottom', paddingBottom)
     @gutter.lineNumbers.css('padding-bottom', paddingBottom)
 
-  ### Public ###
-
-  # Retrieves the number of the row that is visible and currently at the top of the editor.
+  # Public: Retrieves the number of the row that is visible and currently at the
+  # top of the editor.
   #
   # Returns a {Number}.
   getFirstVisibleScreenRow: ->
@@ -1145,7 +1148,8 @@ class EditorView extends View
     screenRow = 0 if isNaN(screenRow)
     screenRow
 
-  # Retrieves the number of the row that is visible and currently at the bottom of the editor.
+  # Public: Retrieves the number of the row that is visible and currently at the
+  # bottom of the editor.
   #
   # Returns a {Number}.
   getLastVisibleScreenRow: ->
@@ -1154,7 +1158,7 @@ class EditorView extends View
     screenRow = 0 if isNaN(screenRow)
     screenRow
 
-  # Given a row number, identifies if it is currently visible.
+  # Public: Given a row number, identifies if it is currently visible.
   #
   # row - A row {Number} to check
   #
@@ -1162,8 +1166,6 @@ class EditorView extends View
   isScreenRowVisible: (row) ->
     @getFirstVisibleScreenRow() <= row <= @getLastVisibleScreenRow()
 
-  ### Internal ###
-
   handleScreenLinesChange: (change) ->
     @pendingChanges.push(change)
     @requestDisplayUpdate()
@@ -1246,21 +1248,19 @@ class EditorView extends View
   toggleLineCommentsInSelection: ->
     @editor.toggleLineCommentsInSelection()
 
-  ### Public ###
-
-  # Converts a buffer position to a pixel position.
+  # Public: Converts a buffer position to a pixel position.
   #
   # position - An object that represents a buffer position. It can be either
-  #                  an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
+  #            an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
   #
   # Returns an object with two values: `top` and `left`, representing the pixel positions.
   pixelPositionForBufferPosition: (position) ->
     @pixelPositionForScreenPosition(@editor.screenPositionForBufferPosition(position))
 
-  # Converts a screen position to a pixel position.
+  # Public: Converts a screen position to a pixel position.
   #
   # position - An object that represents a screen position. It can be either
-  #                  an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
+  #            an {Object} (`{row, column}`), {Array} (`[row, column]`), or {Point}
   #
   # Returns an object with two values: `top` and `left`, representing the pixel positions.
   pixelPositionForScreenPosition: (position) ->
@@ -1297,7 +1297,6 @@ class EditorView extends View
         index++
     left
 
-  # Private:
   measureToColumn: (lineElement, tokenizedLine, screenColumn) ->
     left = oldLeft = index = 0
     iterator = document.createNodeIterator(lineElement, NodeFilter.SHOW_TEXT, TextNodeFilter)
@@ -1343,7 +1342,6 @@ class EditorView extends View
 
     returnLeft ? left
 
-  # Private:
   getCharacterWidthCache: (scopes, char) ->
     scopes ?= NoScope
     obj = @constructor.characterWidthCache
@@ -1352,7 +1350,6 @@ class EditorView extends View
       return null unless obj?
     obj[char]
 
-  # Private:
   setCharacterWidthCache: (scopes, char, val) ->
     scopes ?= NoScope
     obj = @constructor.characterWidthCache
@@ -1361,7 +1358,6 @@ class EditorView extends View
       obj = obj[scope]
     obj[char] = val
 
-  # Private:
   clearCharacterWidthCache: ->
     @constructor.characterWidthCache = {}
 
@@ -1411,11 +1407,9 @@ class EditorView extends View
       @highlightedLine = null
 
   # Copies the current file path to the native clipboard.
-  copyPathToPasteboard: ->
+  copyPathToClipboard: ->
     path = @editor.getPath()
-    atom.pasteboard.write(path) if path?
-
-  ### Internal ###
+    atom.clipboard.write(path) if path?
 
   @buildLineHtml: ({tokens, text, lineEnding, fold, isSoftWrapped, invisibles, eolInvisibles, htmlEolInvisibles, attributes, showIndentGuide, indentation, editor, mini}) ->
     scopeStack = []
@@ -1426,7 +1420,7 @@ class EditorView extends View
     line.push("<div #{attributePairs}>")
 
     if text == ''
-      html = EditorView.buildEmptyLineHtml(showIndentGuide, eolInvisibles, htmlEolInvisibles, indentation, editor, mini)
+      html = @buildEmptyLineHtml(showIndentGuide, eolInvisibles, htmlEolInvisibles, indentation, editor, mini)
       line.push(html) if html
     else
       firstNonWhitespacePosition = text.search(/\S/)
diff --git a/src/editor.coffee b/src/editor.coffee
index 74d1b1505..633604e54 100644
--- a/src/editor.coffee
+++ b/src/editor.coffee
@@ -78,7 +78,7 @@ class Editor extends Model
         position = [0, 0]
       @addCursorAtBufferPosition(position)
 
-    @languageMode = new LanguageMode(this, @buffer.getExtension())
+    @languageMode = new LanguageMode(this)
 
     @subscribe @$scrollTop, (scrollTop) => @emit 'scroll-top-changed', scrollTop
     @subscribe @$scrollLeft, (scrollLeft) => @emit 'scroll-left-changed', scrollLeft
@@ -97,7 +97,6 @@ class Editor extends Model
     params.registerEditor = true
     params
 
-  # Private:
   subscribeToBuffer: ->
     @buffer.retain()
     @subscribe @buffer, "path-changed", =>
@@ -111,7 +110,6 @@ class Editor extends Model
     @subscribe @buffer, "destroyed", => @destroy()
     @preserveCursorPositionOnBufferReload()
 
-  # Private:
   subscribeToDisplayBuffer: ->
     @subscribe @displayBuffer, 'marker-created', @handleMarkerCreated
     @subscribe @displayBuffer, "changed", (e) => @emit 'screen-lines-changed', e
@@ -119,11 +117,9 @@ class Editor extends Model
     @subscribe @displayBuffer, 'grammar-changed', => @handleGrammarChange()
     @subscribe @displayBuffer, 'soft-wrap-changed', (args...) => @emit 'soft-wrap-changed', args...
 
-  # Private:
   getViewClass: ->
     require './editor-view'
 
-  # Private:
   destroyed: ->
     @unsubscribe()
     selection.destroy() for selection in @getSelections()
@@ -132,7 +128,7 @@ class Editor extends Model
     @languageMode.destroy()
     atom.project?.removeEditor(this)
 
-  # Private: Creates an {Editor} with the same initial state
+  # Creates an {Editor} with the same initial state
   copy: ->
     tabLength = @getTabLength()
     displayBuffer = @displayBuffer.copy()
@@ -238,15 +234,14 @@ class Editor extends Model
 
   # Public: Given a position, this clips it to a real position.
   #
-  # For example, if `position`'s row exceeds the row count of the buffer,
+  # For example, if `bufferPosition`'s row exceeds the row count of the buffer,
   # or if its column goes beyond a line's length, this "sanitizes" the value
   # to a real position.
   #
-  # * position:
-  #   The {Point} to clip
+  # bufferPosition - The {Point} to clip.
   #
   # Returns the new, clipped {Point}. Note that this could be the same as
-  #   `position` if no clipping was performed.
+  #   `bufferPosition` if no clipping was performed.
   clipBufferPosition: (bufferPosition) -> @buffer.clipPosition(bufferPosition)
 
   # Public: Given a range, this clips it to a real range.
@@ -255,8 +250,7 @@ class Editor extends Model
   # or if its column goes beyond a line's length, this "sanitizes" the value
   # to a real range.
   #
-  # * range:
-  #   The {Range} to clip
+  # range - The {Range} to clip.
   #
   # Returns the new, clipped {Range}. Note that this could be the same as
   #   `range` if no clipping was performed.
@@ -264,17 +258,14 @@ class Editor extends Model
 
   # Public: Returns the indentation level of the given a buffer row
   #
-  # * bufferRow:
-  #   A Number indicating the buffer row.
+  # bufferRow - A {Number} indicating the buffer row.
   indentationForBufferRow: (bufferRow) ->
     @indentLevelForLine(@lineForBufferRow(bufferRow))
 
   # Public: Sets the indentation level for the given buffer row.
   #
-  # * bufferRow:
-  #   A {Number} indicating the buffer row.
-  # * newLevel:
-  #   A {Number} indicating the new indentation level.
+  # bufferRow - A {Number} indicating the buffer row.
+  # newLevel - A {Number} indicating the new indentation level.
   setIndentationForBufferRow: (bufferRow, newLevel) ->
     currentIndentLength = @lineForBufferRow(bufferRow).match(/^\s*/)[0].length
     newIndentString = @buildIndentString(newLevel)
@@ -282,8 +273,7 @@ class Editor extends Model
 
   # Public: Returns the indentation level of the given line of text.
   #
-  # * line:
-  #   A {String} in the current buffer.
+  # line - A {String} in the current buffer.
   #
   # Returns a {Number} or 0 if the text isn't found within the buffer.
   indentLevelForLine: (line) ->
@@ -295,7 +285,7 @@ class Editor extends Model
     else
       0
 
-  # Private: Constructs the string used for tabs.
+  # Constructs the string used for tabs.
   buildIndentString: (number) ->
     if @getSoftTabs()
       _.multiplyString(" ", number * @getTabLength())
@@ -308,9 +298,6 @@ class Editor extends Model
   # {Delegates to: TextBuffer.saveAs}
   saveAs: (path) -> @buffer.saveAs(path)
 
-  # {Delegates to: TextBuffer.getExtension}
-  getFileExtension: -> @buffer.getExtension()
-
   # {Delegates to: TextBuffer.getPath}
   getPath: -> @buffer.getPath()
 
@@ -326,7 +313,7 @@ class Editor extends Model
   # Public: Returns a {Number} representing the number of lines in the editor.
   getLineCount: -> @buffer.getLineCount()
 
-  # Private: Retrieves the current {TextBuffer}.
+  # Retrieves the current {TextBuffer}.
   getBuffer: -> @buffer
 
   # Public: Retrieves the current buffer's URI.
@@ -353,8 +340,8 @@ class Editor extends Model
 
   # Public: Returns the range for the given buffer row.
   #
-  # * row: A row {Number}.
-  # * options: An options hash with an `includeNewline` key.
+  # row - A row {Number}.
+  # options - An options hash with an `includeNewline` key.
   #
   # Returns a {Range}.
   bufferRangeForBufferRow: (row, options) -> @buffer.rangeForRow(row, options)
@@ -362,7 +349,7 @@ class Editor extends Model
   # Public: Returns a {String} representing the contents of the line at the
   # given buffer row.
   #
-  # * row - A {Number} representing a zero-indexed buffer row.
+  # row - A {Number} representing a zero-indexed buffer row.
   lineForBufferRow: (row) -> @buffer.lineForRow(row)
 
   # Public: Returns a {Number} representing the line length for the given
@@ -439,10 +426,8 @@ class Editor extends Model
 
   # Public: Inserts text at the current cursor positions
   #
-  # * text:
-  #   A String representing the text to insert.
-  # * options:
-  #   + A set of options equivalent to {Selection.insertText}
+  # text - A {String} representing the text to insert.
+  # options - A set of options equivalent to {Selection.insertText}.
   insertText: (text, options={}) ->
     options.autoIndentNewline ?= @shouldAutoIndent()
     options.autoDecreaseIndent ?= @shouldAutoIndent()
@@ -469,8 +454,7 @@ class Editor extends Model
 
   # Public: Indents the current line.
   #
-  # * options
-  #    + A set of options equivalent to {Selection.indent}.
+  # options - A set of options equivalent to {Selection.indent}.
   indent: (options={})->
     options.autoIndent ?= @shouldAutoIndent()
     @mutateSelectedText (selection) -> selection.indent(options)
@@ -521,7 +505,7 @@ class Editor extends Model
   #
   # If the language doesn't have comments, nothing happens.
   #
-  # Returns an {Array} of the commented {Ranges}.
+  # Returns an {Array} of the commented {Range}s.
   toggleLineCommentsInSelection: ->
     @mutateSelectedText (selection) -> selection.toggleLineComments()
 
@@ -537,31 +521,30 @@ class Editor extends Model
   # Public: Copies and removes all characters from cursor to the end of the
   # line.
   cutToEndOfLine: ->
-    maintainPasteboard = false
+    maintainClipboard = false
     @mutateSelectedText (selection) ->
-      selection.cutToEndOfLine(maintainPasteboard)
-      maintainPasteboard = true
+      selection.cutToEndOfLine(maintainClipboard)
+      maintainClipboard = true
 
   # Public: Cuts the selected text.
   cutSelectedText: ->
-    maintainPasteboard = false
+    maintainClipboard = false
     @mutateSelectedText (selection) ->
-      selection.cut(maintainPasteboard)
-      maintainPasteboard = true
+      selection.cut(maintainClipboard)
+      maintainClipboard = true
 
   # Public: Copies the selected text.
   copySelectedText: ->
-    maintainPasteboard = false
+    maintainClipboard = false
     for selection in @getSelections()
-      selection.copy(maintainPasteboard)
-      maintainPasteboard = true
+      selection.copy(maintainClipboard)
+      maintainClipboard = true
 
   # Public: Pastes the text in the clipboard.
   #
-  # * options:
-  #    + A set of options equivalent to {Selection.insertText}.
+  # options - A set of options equivalent to {Selection.insertText}.
   pasteText: (options={}) ->
-    [text, metadata] = atom.pasteboard.read()
+    {text, metadata} = atom.clipboard.readWithMetadata()
 
     containsNewlines = text.indexOf('\n') isnt -1
 
@@ -640,7 +623,7 @@ class Editor extends Model
   largestFoldStartingAtScreenRow: (screenRow) ->
     @displayBuffer.largestFoldStartingAtScreenRow(screenRow)
 
-  # Public: Moves the selected line up one row.
+  # Public: Moves the selected lines up one screen row.
   moveLineUp: ->
     selection = @getSelectedBufferRange()
     return if selection.start.row is 0
@@ -652,29 +635,47 @@ class Editor extends Model
       rows = [selection.start.row..selection.end.row]
       if selection.start.row isnt selection.end.row and selection.end.column is 0
         rows.pop() unless @isFoldedAtBufferRow(selection.end.row)
+
+      # Move line around the fold that is directly above the selection
+      precedingScreenRow = @screenPositionForBufferPosition([selection.start.row]).translate([-1])
+      precedingBufferRow = @bufferPositionForScreenPosition(precedingScreenRow).row
+      if fold = @largestFoldContainingBufferRow(precedingBufferRow)
+        insertDelta = fold.getBufferRange().getRowCount()
+      else
+        insertDelta = 1
+
       for row in rows
-        screenRow = @screenPositionForBufferPosition([row]).row
-        if @isFoldedAtScreenRow(screenRow)
-          bufferRange = @bufferRangeForScreenRange([[screenRow], [screenRow + 1]])
+        if fold = @displayBuffer.largestFoldStartingAtBufferRow(row)
+          bufferRange = fold.getBufferRange()
           startRow = bufferRange.start.row
-          endRow = bufferRange.end.row - 1
-          foldedRows.push(endRow - 1)
+          endRow = bufferRange.end.row
+          foldedRows.push(startRow - insertDelta)
         else
           startRow = row
           endRow = row
 
+        insertPosition = Point.fromObject([startRow - insertDelta])
         endPosition = Point.min([endRow + 1], @buffer.getEofPosition())
         lines = @buffer.getTextInRange([[startRow], endPosition])
         if endPosition.row is lastRow and endPosition.column > 0 and not @buffer.lineEndingForRow(endPosition.row)
           lines = "#{lines}\n"
+
         @buffer.deleteRows(startRow, endRow)
-        @buffer.insert([startRow - 1], lines)
 
-      @foldBufferRow(foldedRow) for foldedRow in foldedRows
+        # Make sure the inserted text doesn't go into an existing fold
+        if fold = @displayBuffer.largestFoldStartingAtBufferRow(insertPosition.row)
+          @destroyFoldsContainingBufferRow(insertPosition.row)
+          foldedRows.push(insertPosition.row + endRow - startRow + fold.getBufferRange().getRowCount())
 
-      @setSelectedBufferRange(selection.translate([-1]), preserveFolds: true)
+        @buffer.insert(insertPosition, lines)
 
-  # Public: Moves the selected line down one row.
+      # Restore folds that existed before the lines were moved
+      for foldedRow in foldedRows when 0 <= foldedRow <= @getLastBufferRow()
+        @foldBufferRow(foldedRow)
+
+      @setSelectedBufferRange(selection.translate([-insertDelta]), preserveFolds: true)
+
+  # Public: Moves the selected lines down one screen row.
   moveLineDown: ->
     selection = @getSelectedBufferRange()
     lastRow = @buffer.getLastRow()
@@ -686,13 +687,21 @@ class Editor extends Model
       rows = [selection.end.row..selection.start.row]
       if selection.start.row isnt selection.end.row and selection.end.column is 0
         rows.shift() unless @isFoldedAtBufferRow(selection.end.row)
+
+      # Move line around the fold that is directly below the selection
+      followingScreenRow = @screenPositionForBufferPosition([selection.end.row]).translate([1])
+      followingBufferRow = @bufferPositionForScreenPosition(followingScreenRow).row
+      if fold = @largestFoldContainingBufferRow(followingBufferRow)
+        insertDelta = fold.getBufferRange().getRowCount()
+      else
+        insertDelta = 1
+
       for row in rows
-        screenRow = @screenPositionForBufferPosition([row]).row
-        if @isFoldedAtScreenRow(screenRow)
-          bufferRange = @bufferRangeForScreenRange([[screenRow], [screenRow + 1]])
+        if fold = @displayBuffer.largestFoldStartingAtBufferRow(row)
+          bufferRange = fold.getBufferRange()
           startRow = bufferRange.start.row
-          endRow = bufferRange.end.row - 1
-          foldedRows.push(endRow + 1)
+          endRow = bufferRange.end.row
+          foldedRows.push(endRow + insertDelta)
         else
           startRow = row
           endRow = row
@@ -703,14 +712,23 @@ class Editor extends Model
           endPosition = [endRow + 1]
         lines = @buffer.getTextInRange([[startRow], endPosition])
         @buffer.deleteRows(startRow, endRow)
-        insertPosition = Point.min([startRow + 1], @buffer.getEofPosition())
+
+        insertPosition = Point.min([startRow + insertDelta], @buffer.getEofPosition())
         if insertPosition.row is @buffer.getLastRow() and insertPosition.column > 0
           lines = "\n#{lines}"
+
+        # Make sure the inserted text doesn't go into an existing fold
+        if fold = @displayBuffer.largestFoldStartingAtBufferRow(insertPosition.row)
+          @destroyFoldsContainingBufferRow(insertPosition.row)
+          foldedRows.push(insertPosition.row + fold.getBufferRange().getRowCount())
+
         @buffer.insert(insertPosition, lines)
 
-      @foldBufferRow(foldedRow) for foldedRow in foldedRows
+      # Restore folds that existed before the lines were moved
+      for foldedRow in foldedRows when 0 <= foldedRow <= @getLastBufferRow()
+        @foldBufferRow(foldedRow)
 
-      @setSelectedBufferRange(selection.translate([1]), preserveFolds: true)
+      @setSelectedBufferRange(selection.translate([insertDelta]), preserveFolds: true)
 
   # Public: Duplicates the current line.
   #
@@ -739,11 +757,9 @@ class Editor extends Model
       @setCursorScreenPosition(@getCursorScreenPosition().translate([1]))
       @foldCurrentRow() if cursorRowFolded
 
-  # Private:
   mutateSelectedText: (fn) ->
     @transact => fn(selection) for selection in @getSelections()
 
-  # Private:
   replaceSelectedText: (options={}, fn) ->
     {selectWordIfEmpty} = options
     @mutateSelectedText (selection) ->
@@ -787,7 +803,9 @@ class Editor extends Model
   destroyMarker: (args...) ->
     @displayBuffer.destroyMarker(args...)
 
-  # Public: {Delegates to: DisplayBuffer.getMarkerCount}
+  # Public: Get the number of markers in this editor's buffer.
+  #
+  # Returns a {Number}.
   getMarkerCount: ->
     @buffer.getMarkerCount()
 
@@ -826,10 +844,8 @@ class Editor extends Model
 
   # Public: Creates a new selection at the given marker.
   #
-  # * marker:
-  #   The {DisplayBufferMarker} to highlight
-  # * options:
-  #   + A hash of options that pertain to the {Selection} constructor.
+  # marker  - The {DisplayBufferMarker} to highlight
+  # options - An {Object} that pertains to the {Selection} constructor.
   #
   # Returns the new {Selection}.
   addSelection: (marker, options={}) ->
@@ -850,10 +866,8 @@ class Editor extends Model
 
   # Public: Given a buffer range, this adds a new selection for it.
   #
-  # * bufferRange:
-  #   A {Range} in the buffer
-  # * options:
-  #    + A hash of options for {.markBufferRange}
+  # bufferRange - A {Range} in the buffer.
+  # options - An options {Object} for {.markBufferRange}.
   #
   # Returns the new {Selection}.
   addSelectionForBufferRange: (bufferRange, options={}) ->
@@ -863,20 +877,16 @@ class Editor extends Model
   # Public: Given a buffer range, this removes all previous selections and
   # creates a new selection for it.
   #
-  # * bufferRange:
-  #   A {Range} in the buffer
-  # * options:
-  #    + A hash of options for {.setSelectedBufferRanges}
+  # bufferRange - A {Range} in the buffer.
+  # options - An options {Object} for {.setSelectedBufferRanges}.
   setSelectedBufferRange: (bufferRange, options) ->
     @setSelectedBufferRanges([bufferRange], options)
 
   # Public: Given an array of buffer ranges, this removes all previous
   # selections and creates new selections for them.
   #
-  # * bufferRange:
-  #   A {Range} in the buffer
-  # * options:
-  #    + A hash of options for {.setSelectedBufferRanges}
+  # bufferRange - A {Range} in the buffer.
+  # options - An options {Object} for {.setSelectedBufferRanges}.
   setSelectedBufferRanges: (bufferRanges, options={}) ->
     throw new Error("Passed an empty array to setSelectedBufferRanges") unless bufferRanges.length
 
@@ -893,7 +903,7 @@ class Editor extends Model
 
   # Public: Unselects a given selection.
   #
-  # * selection - The {Selection} to remove.
+  # selection - The {Selection} to remove.
   removeSelection: (selection) ->
     _.remove(@selections, selection)
 
@@ -904,9 +914,7 @@ class Editor extends Model
     @consolidateSelections()
     @getSelection().clear()
 
-  # Public:
-  #
-  # Removes all but one cursor (if there are multiple cursors)
+  # Removes all but one cursor (if there are multiple cursors).
   consolidateSelections: ->
     selections = @getSelections()
     if selections.length > 1
@@ -943,8 +951,7 @@ class Editor extends Model
 
   # Public: Determines if a given buffer range is included in a {Selection}.
   #
-  # * bufferRange:
-  #   The {Range} you're checking against
+  # bufferRange - The {Range} you're checking against.
   #
   # Returns a {Boolean}.
   selectionIntersectsBufferRange: (bufferRange) ->
@@ -953,10 +960,8 @@ class Editor extends Model
 
   # Public: Moves every local cursor to a given screen position.
   #
-  # * position:
-  #   An {Array} of two numbers: the screen row, and the screen column.
-  # * options:
-  #   An object with properties based on {Cursor.setScreenPosition}
+  # position - An {Array} of two numbers: the screen row, and the screen column.
+  # options  - An {Object} with properties based on {Cursor.setScreenPosition}.
   setCursorScreenPosition: (position, options) ->
     @moveCursors (cursor) -> cursor.setScreenPosition(position, options)
 
@@ -975,10 +980,8 @@ class Editor extends Model
 
   # Public: Moves every cursor to a given buffer position.
   #
-  # * position:
-  #   An {Array} of two numbers: the buffer row, and the buffer column.
-  # * options:
-  #    + An object with properties based on {Cursor.setBufferPosition}
+  # position - An {Array} of two numbers: the buffer row, and the buffer column.
+  # options - An object with properties based on {Cursor.setBufferPosition}.
   setCursorBufferPosition: (position, options) ->
     @moveCursors (cursor) -> cursor.setBufferPosition(position, options)
 
@@ -1021,9 +1024,8 @@ class Editor extends Model
 
   # Public: Returns the word under the most recently added local {Cursor}.
   #
-  # * options:
-  #    + An object with properties based on
-  #      {Cursor.getBeginningOfCurrentWordBufferPosition}.
+  # options - An object with properties based on
+  #           {Cursor.getBeginningOfCurrentWordBufferPosition}.
   getWordUnderCursor: (options) ->
     @getTextInBufferRange(@getCursor().getCurrentWordBufferRange(options))
 
@@ -1091,7 +1093,6 @@ class Editor extends Model
   moveCursorToNextWordBoundary: ->
     @moveCursors (cursor) -> cursor.moveToNextWordBoundary()
 
-  # Internal: Executes given function on all local cursors.
   moveCursors: (fn) ->
     fn(cursor) for cursor in @getCursors()
     @mergeCursors()
@@ -1099,8 +1100,7 @@ class Editor extends Model
   # Public: Selects the text from the current cursor position to a given screen
   # position.
   #
-  # * position:
-  #   An instance of {Point}, with a given `row` and `column`.
+  # position - An instance of {Point}, with a given `row` and `column`.
   selectToScreenPosition: (position) ->
     lastSelection = @getLastSelection()
     lastSelection.selectToScreenPosition(position)
@@ -1259,8 +1259,6 @@ class Editor extends Model
       @setSelectedBufferRange(range)
       range
 
-  # Public:
-  #
   # FIXME: Not sure how to describe what this does.
   mergeCursors: ->
     positions = []
@@ -1271,27 +1269,21 @@ class Editor extends Model
       else
         positions.push(position)
 
-  # Public:
-  #
   # FIXME: Not sure how to describe what this does.
   expandSelectionsForward: (fn) ->
     @mergeIntersectingSelections =>
       fn(selection) for selection in @getSelections()
 
-  # Public:
-  #
   # FIXME: Not sure how to describe what this does.
   expandSelectionsBackward: (fn) ->
     @mergeIntersectingSelections isReversed: true, =>
       fn(selection) for selection in @getSelections()
 
-  # Public:
-  #
   # FIXME: No idea what this does.
   finalizeSelections: ->
     selection.finalize() for selection in @getSelections()
 
-  # Private: Merges intersecting selections. If passed a function, it executes
+  # Merges intersecting selections. If passed a function, it executes
   # the function with merging suppressed, then merges intersecting selections
   # afterward.
   mergeIntersectingSelections: (args...) ->
@@ -1315,7 +1307,6 @@ class Editor extends Model
 
     _.reduce(@getSelections(), reducer, [])
 
-  # Private:
   preserveCursorPositionOnBufferReload: ->
     cursorPosition = null
     @subscribe @buffer, "will-reload", =>
@@ -1336,7 +1327,6 @@ class Editor extends Model
   reloadGrammar: ->
     @displayBuffer.reloadGrammar()
 
-  # Private:
   shouldAutoIndent: ->
     atom.config.get("editor.autoIndent")
 
@@ -1347,32 +1337,24 @@ class Editor extends Model
   # undo stack remains relevant.
   transact: (fn) -> @buffer.transact(fn)
 
-  # Private:
   beginTransaction: -> @buffer.beginTransaction()
 
-  # Private:
   commitTransaction: -> @buffer.commitTransaction()
 
-  # Private:
   abortTransaction: -> @buffer.abortTransaction()
 
-  # Private:
   inspect: ->
     "<Editor #{@id}>"
 
-  # Private:
   logScreenLines: (start, end) -> @displayBuffer.logLines(start, end)
 
-  # Private:
   handleGrammarChange: ->
     @unfoldAll()
     @emit 'grammar-changed'
 
-  # Private:
   handleMarkerCreated: (marker) =>
     if marker.matchesAttributes(@getSelectionMarkerAttributes())
       @addSelection(marker)
 
-  # Private:
   getSelectionMarkerAttributes: ->
     type: 'selection', editorId: @id, invalidate: 'never'
diff --git a/src/file.coffee b/src/file.coffee
index bb09cc4f2..b4fffe060 100644
--- a/src/file.coffee
+++ b/src/file.coffee
@@ -5,6 +5,7 @@ Q = require 'q'
 {Emitter} = require 'emissary'
 _ = require 'underscore-plus'
 fs = require 'fs-plus'
+runas = require 'runas'
 
 # Public: Represents an individual file.
 #
@@ -25,16 +26,14 @@ class File
 
   # Public: Creates a new file.
   #
-  # * path:
-  #   A String containing the absolute path to the file
-  # * symlink:
-  #   A Boolean indicating if the path is a symlink (default: false)
+  # path - A {String} containing the absolute path to the file
+  # symlink - A {Boolean} indicating if the path is a symlink (default: false).
   constructor: (@path, @symlink=false) ->
     throw new Error("#{@path} is a directory") if fs.isDirectorySync(@path)
 
     @handleEventSubscriptions()
 
-  # Private: Subscribes to file system notifications when necessary.
+  # Subscribes to file system notifications when necessary.
   handleEventSubscriptions: ->
     eventNames = ['contents-changed', 'moved', 'removed']
 
@@ -49,24 +48,24 @@ class File
       subscriptionsEmpty = _.every eventNames, (eventName) => @getSubscriptionCount(eventName) is 0
       @unsubscribeFromNativeChangeEvents() if subscriptionsEmpty
 
-  # Private: Sets the path for the file.
+  # Sets the path for the file.
   setPath: (@path) ->
 
-  # Public: Returns the path for the file.
+  # Public: Returns the {String} path for the file.
   getPath: -> @path
 
-  # Public: Return the filename without any directory information.
+  # Public: Return the {String} filename without any directory information.
   getBaseName: ->
     path.basename(@path)
 
   # Public: Overwrites the file with the given String.
   write: (text) ->
     previouslyExisted = @exists()
+    @writeFileWithPrivilegeEscalationSync(@getPath(), text)
     @cachedContents = text
-    fs.writeFileSync(@getPath(), text)
     @subscribeToNativeChangeEvents() if not previouslyExisted and @hasSubscriptions()
 
-  # Private: Deprecated
+  # Deprecated
   readSync: (flushCache) ->
     if not @exists()
       @cachedContents = null
@@ -80,9 +79,8 @@ class File
 
   # Public: Reads the contents of the file.
   #
-  # * flushCache:
-  #   A Boolean indicating whether to require a direct read or if a cached
-  #   copy is acceptable.
+  # flushCache - A {Boolean} indicating whether to require a direct read or if
+  #              a cached copy is acceptable.
   #
   # Returns a promise that resovles to a String.
   read: (flushCache) ->
@@ -118,7 +116,6 @@ class File
   exists: ->
     fs.existsSync(@getPath())
 
-  # Private:
   setDigest: (contents) ->
     @digest = crypto.createHash('sha1').update(contents ? '').digest('hex')
 
@@ -126,7 +123,21 @@ class File
   getDigest: ->
     @digest ? @setDigest(@readSync())
 
-  # Private:
+  # Writes the text to specified path.
+  #
+  # Privilege escalation would be asked when current user doesn't have
+  # permission to the path.
+  writeFileWithPrivilegeEscalationSync: (path, text) ->
+    try
+      fs.writeFileSync(path, text)
+    catch error
+      if error.code is 'EACCES' and process.platform is 'darwin'
+        authopen = '/usr/libexec/authopen'  # man 1 authopen
+        unless runas(authopen, ['-w', '-c', path], stdin: text) is 0
+          throw error
+      else
+        throw error
+
   handleNativeChangeEvent: (eventType, path) ->
     if eventType is "delete"
       @unsubscribeFromNativeChangeEvents()
@@ -139,11 +150,9 @@ class File
       @read(true).done (newContents) =>
         @emit 'contents-changed' unless oldContents == newContents
 
-  # Private:
   detectResurrectionAfterDelay: ->
     _.delay (=> @detectResurrection()), 50
 
-  # Private:
   detectResurrection: ->
     if @exists()
       @subscribeToNativeChangeEvents()
@@ -152,13 +161,11 @@ class File
       @cachedContents = null
       @emit "removed"
 
-  # Private:
   subscribeToNativeChangeEvents: ->
     unless @watchSubscription?
       @watchSubscription = pathWatcher.watch @path, (eventType, path) =>
         @handleNativeChangeEvent(eventType, path)
 
-  # Private:
   unsubscribeFromNativeChangeEvents: ->
     if @watchSubscription?
       @watchSubscription.close()
diff --git a/src/fold.coffee b/src/fold.coffee
index 32de3f988..e2d113fc2 100644
--- a/src/fold.coffee
+++ b/src/fold.coffee
@@ -1,6 +1,6 @@
 {Point, Range} = require 'text-buffer'
 
-# Private: Represents a fold that collapses multiple buffer lines into a single
+# Represents a fold that collapses multiple buffer lines into a single
 # line on the screen.
 #
 # Their creation is managed by the {DisplayBuffer}.
@@ -10,8 +10,6 @@ class Fold
   displayBuffer: null
   marker: null
 
-  ### Internal ###
-
   constructor: (@displayBuffer, @marker) ->
     @id = @marker.id
     @displayBuffer.foldsByMarkerId[@marker.id] = this
diff --git a/src/git.coffee b/src/git.coffee
index b22466461..7143b4e69 100644
--- a/src/git.coffee
+++ b/src/git.coffee
@@ -27,17 +27,19 @@ class Git
   Emitter.includeInto(this)
   Subscriber.includeInto(this)
 
-  # Private: Creates a new `Git` instance.
+  # Public: Creates a new Git instance.
   #
-  # * path: The path to the git repository to open
-  # * options:
-  #    + refreshOnWindowFocus:
-  #      A Boolean that identifies if the windows should refresh
+  # path - The path to the Git repository to open.
+  # options - An object with the following keys (default: {}):
+  #   :refreshOnWindowFocus - `true` to refresh the index and statuses when the
+  #                           window is focused.
+  #
+  # Returns a Git instance or null if the repository could not be opened.
   @open: (path, options) ->
     return null unless path
     try
       new Git(path, options)
-    catch e
+    catch
       null
 
   @exists: (path) ->
@@ -47,20 +49,6 @@ class Git
     else
       false
 
-  path: null
-  statuses: null
-  upstream: null
-  branch: null
-  statusTask: null
-
-  # Private: Creates a new `Git` object.
-  #
-  # * path: The {String} representing the path to your git working directory
-  # * options:
-  #    + refreshOnWindowFocus: If `true`, {#refreshIndex} and {#refreshStatus}
-  #      are called on focus
-  #    + project: A project that supplies buffers that will be monitored for
-  #      save and reload events to trigger status refreshes.
   constructor: (path, options={}) ->
     @repo = GitUtils.open(path)
     unless @repo?
@@ -80,7 +68,7 @@ class Git
     if @project?
       @subscribe @project.eachBuffer (buffer) => @subscribeToBuffer(buffer)
 
-  # Private: Subscribes to buffer events.
+  # Subscribes to buffer events.
   subscribeToBuffer: (buffer) ->
     @subscribe buffer, 'saved reloaded path-changed', =>
       if path = buffer.getPath()
@@ -100,29 +88,29 @@ class Git
 
     @unsubscribe()
 
-  # Private: Returns the corresponding {Repository}
+  # Returns the corresponding {Repository}
   getRepo: ->
     unless @repo?
       throw new Error("Repository has been destroyed")
     @repo
 
-  # Public: Reread the index to update any values that have changed since the
+  # Reread the index to update any values that have changed since the
   # last time the index was read.
   refreshIndex: -> @getRepo().refreshIndex()
 
-  # Public: Returns the path of the repository.
+  # Public: Returns the {String} path of the repository.
   getPath: ->
     @path ?= fs.absolute(@getRepo().getPath())
 
-  # Public: Returns the working directory of the repository.
+  # Public: Returns the {String} working directory path of the repository.
   getWorkingDirectory: -> @getRepo().getWorkingDirectory()
 
-  # Public: Returns the status of a single path in the repository.
+  # Public: Get the status of a single path in the repository.
   #
-  # * path:
-  #   A String defining a relative path
+  # path - A {String} repository-relative path.
   #
-  # Returns a {Number}, FIXME representing what?
+  # Returns a {Number} representing the status. This value can be passed to
+  # {.isStatusModified} or {.isStatusNew} to get more information.
   getPathStatus: (path) ->
     currentPathStatus = @statuses[path] ? 0
     pathStatus = @getRepo().getStatus(@relativize(path)) ? 0
@@ -134,7 +122,9 @@ class Git
       @emit 'status-changed', path, pathStatus
     pathStatus
 
-  # Public: Returns true if the given path is ignored.
+  # Public: Is the given path ignored?
+  #
+  # Returns a {Boolean}.
   isPathIgnored: (path) -> @getRepo().isIgnored(@relativize(path))
 
   # Public: Returns true if the given status indicates modification.
@@ -163,22 +153,22 @@ class Git
   # `refs/remotes`.  It also shortens the SHA-1 of a detached `HEAD` to 7
   # characters.
   #
-  # Returns a String.
+  # Returns a {String}.
   getShortHead: -> @getRepo().getShortHead()
 
   # Public: Restore the contents of a path in the working directory and index
   # to the version at `HEAD`.
   #
   # This is essentially the same as running:
+  #
   # ```
   # git reset HEAD -- <path>
   # git checkout HEAD -- <path>
   # ```
   #
-  # * path:
-  #   The String path to checkout
+  # path - The {String} path to checkout.
   #
-  # Returns a Boolean that's true if the method was successful.
+  # Returns a {Boolean} that's true if the method was successful.
   checkoutHead: (path) ->
     headCheckedOut = @getRepo().checkoutHead(@relativize(path))
     @getPathStatus(path) if headCheckedOut
@@ -186,10 +176,9 @@ class Git
 
   # Public: Checks out a branch in your repository.
   #
-  # * reference:
-  #   The String reference to checkout
-  # * create:
-  #   A Boolean value which, if true creates the new reference if it doesn't exist.
+  # reference - The String reference to checkout
+  # create -  A Boolean value which, if true creates the new reference if it
+  #           doesn't exist.
   #
   # Returns a Boolean that's true if the method was successful.
   checkoutReference: (reference, create) ->
@@ -200,27 +189,26 @@ class Git
   # This compares the working directory contents of the path to the `HEAD`
   # version.
   #
-  # * path:
-  #   The String path to check
+  # path - The {String} path to check.
   #
-  # Returns an object with two keys, `added` and `deleted`. These will always
-  # be greater than 0.
+  # Returns an {Object} with the following keys:
+  #   :added - The {Number} of added lines.
+  #   :deleted - The {Number} of deleted lines.
   getDiffStats: (path) -> @getRepo().getDiffStats(@relativize(path))
 
-  # Public: Identifies if a path is a submodule.
+  # Public: Is the given path a submodule in the repository?
   #
-  # * path:
-  #   The String path to check
+  # path - The {String} path to check.
   #
-  # Returns a Boolean.
+  # Returns a {Boolean}.
   isSubmodule: (path) -> @getRepo().isSubmodule(@relativize(path))
 
-  # Public: Retrieves the status of a directory.
+  # Public: Get the status of a directory in the repository's working directory.
   #
-  # * path:
-  #   The String path to check
+  # path - The {String} path to check.
   #
-  # Returns a Number representing the status.
+  # Returns a {Number} representing the status. This value can be passed to
+  # {.isStatusModified} or {.isStatusNew} to get more information.
   getDirectoryStatus: (directoryPath)  ->
     {sep} = require 'path'
     directoryPath = "#{directoryPath}#{sep}"
@@ -232,16 +220,14 @@ class Git
   # Public: Retrieves the line diffs comparing the `HEAD` version of the given
   # path and the given text.
   #
-  # This is similar to the commit numbers reported by `git status` when a
-  # remote tracking branch exists.
+  # path - The {String} path relative to the repository.
+  # text - The {String} to compare against the `HEAD` contents
   #
-  # * path:
-  #   The String path (relative to the repository)
-  # * text:
-  #   The String to compare against the `HEAD` contents
-  #
-  # Returns an object with two keys, `ahead` and `behind`. These will always be
-  # greater than zero.
+  # Returns an {Array} of hunk {Object}s with the following keys:
+  #   :oldStart - The line {Number} of the old hunk.
+  #   :newStart - The line {Number} of the new hunk.
+  #   :oldLines - The {Number} of lines in the old hunk.
+  #   :newLines - The {Number} of lines in the new hunk
   getLineDiffs: (path, text) ->
     # Ignore eol of line differences on windows so that files checked in as
     # LF don't report every line modified when the text contains CRLF endings.
@@ -257,7 +243,7 @@ class Git
   # Public: Returns the upstream branch for the current HEAD, or null if there
   # is no upstream branch for the current HEAD.
   #
-  # Returns a String branch name such as `refs/remotes/origin/master`
+  # Returns a {String} branch name such as `refs/remotes/origin/master`.
   getUpstreamBranch: -> @getRepo().getUpstreamBranch()
 
   # Public: Returns the current SHA for the given reference.
@@ -265,19 +251,21 @@ class Git
 
   # Public: Gets all the local and remote references.
   #
-  # Returns an object with three keys: `heads`, `remotes`, and `tags`. Each key
-  # can be an array of strings containing the reference names.
+  # Returns an {Object} with the following keys:
+  #  :heads - An {Array} of head reference names.
+  #  :remotes - An {Array} of remote reference names.
+  #  :tags - An {Array} of tag reference names.
   getReferences: -> @getRepo().getReferences()
 
   # Public: Returns the number of commits behind the current branch is from the
-  # default remote branch.
+  # its upstream remote branch.
   getAheadBehindCount: (reference) -> @getRepo().getAheadBehindCount(reference)
 
   # Public: Returns true if the given branch exists.
   hasBranch: (branch) -> @getReferenceTarget("refs/heads/#{branch}")?
 
-  # Private: Refreshes the current git status in an outside process and
-  # asynchronously updates the relevant properties.
+  # Refreshes the current git status in an outside process and asynchronously
+  # updates the relevant properties.
   refreshStatus: ->
     @statusTask = Task.once require.resolve('./repository-status-handler'), @getPath(), ({statuses, upstream, branch}) =>
       statusesUnchanged = _.isEqual(statuses, @statuses) and _.isEqual(upstream, @upstream) and _.isEqual(branch, @branch)
diff --git a/src/gutter-view.coffee b/src/gutter-view.coffee
index cae0d51c0..aabc515fc 100644
--- a/src/gutter-view.coffee
+++ b/src/gutter-view.coffee
@@ -2,14 +2,11 @@
 {Range} = require 'text-buffer'
 _ = require 'underscore-plus'
 
-# Private: Represents the portion of the {EditorView} containing row numbers.
+# Represents the portion of the {EditorView} containing row numbers.
 #
 # The gutter also indicates if rows are folded.
 module.exports =
 class GutterView extends View
-
-  ### Internal ###
-
   @content: ->
     @div class: 'gutter', =>
       @div outlet: 'lineNumbers', class: 'line-numbers'
@@ -51,8 +48,6 @@ class GutterView extends View
     $(document).on "mousemove.gutter-#{editorView.id}", moveHandler
     $(document).one "mouseup.gutter-#{editorView.id}", => $(document).off 'mousemove', moveHandler
 
-  ### Public ###
-
   # Retrieves the containing {EditorView}.
   #
   # Returns an {EditorView}.
@@ -138,8 +133,6 @@ class GutterView extends View
       el.classList.remove(klass) if hasClass
     classesRemoved
 
-  ### Internal ###
-
   updateLineNumbers: (changes, startScreenRow, endScreenRow) ->
     # Check if we have something already rendered that overlaps the requested range
     updateAllLines = not (startScreenRow? and endScreenRow?)
@@ -223,7 +216,7 @@ class GutterView extends View
 
     html
 
-  # Private: Called to update the 'foldable' class of line numbers when there's
+  # Called to update the 'foldable' class of line numbers when there's
   # a change to the display buffer that doesn't regenerate all the line numbers
   # anyway.
   updateFoldableClasses: (changes) ->
diff --git a/src/key-binding.coffee b/src/key-binding.coffee
index 1f3ad1d65..46b359858 100644
--- a/src/key-binding.coffee
+++ b/src/key-binding.coffee
@@ -2,8 +2,6 @@ _ = require 'underscore-plus'
 fs = require 'fs-plus'
 {specificity} = require 'clear-cut'
 
-### Internal ###
-
 module.exports =
 class KeyBinding
   @parser: null
diff --git a/src/keymap.coffee b/src/keymap.coffee
index 3c3a8ec44..8fccf060d 100644
--- a/src/keymap.coffee
+++ b/src/keymap.coffee
@@ -9,19 +9,23 @@ File = require './file'
 
 Modifiers = ['alt', 'control', 'ctrl', 'shift', 'cmd']
 
-# Internal: Associates keymaps with actions.
+# Public: Associates keybindings with commands.
 #
-# Keymaps are defined in a CSON format. A typical keymap looks something like this:
+# An instance of this class is always available as the `atom.keymap` global.
+#
+# Keymaps are defined in a CSON/JSON format. A typical keymap looks something
+# like this:
 #
 # ```cson
 # 'body':
-#  'ctrl-l': 'package:do-something'
-#'.someClass':
-#  'enter': 'package:confirm'
+#   'ctrl-l': 'package:do-something'
+# '.someClass':
+#   'enter': 'package:confirm'
 # ```
 #
-# As a key, you define the DOM element you want to work on, using CSS notation. For that
-# key, you define one or more key:value pairs, associating keystrokes with a command to execute.
+# As a key, you define the DOM element you want to work on, using CSS notation.
+# For that key, you define one or more key:value pairs, associating keystrokes
+# with a command to execute.
 module.exports =
 class Keymap
   Emitter.includeInto(this)
@@ -39,10 +43,8 @@ class Keymap
   # Public: Returns a array of {KeyBinding}s (sorted by selector specificity)
   # that match a keystroke and element.
   #
-  # * keystroke:
-  #   The string representing the keys pressed (e.g. ctrl-P).
-  # * element:
-  #   The DOM node that will match a {KeyBinding}'s selector.
+  # keystroke - The {String} representing the keys pressed (e.g. ctrl-P).
+  # element - The DOM node that will match a {KeyBinding}'s selector.
   keyBindingsForKeystrokeMatchingElement: (keystroke, element) ->
     keyBindings = @keyBindingsForKeystroke(keystroke)
     @keyBindingsMatchingElement(element, keyBindings)
@@ -50,41 +52,37 @@ class Keymap
   # Public: Returns a array of {KeyBinding}s (sorted by selector specificity)
   # that match a command.
   #
-  # * command:
-  #   The string representing the command (tree-view:toggle)
-  # * element:
-  #   The DOM node that will match a {KeyBinding}'s selector.
+  # command - The {String} representing the command (tree-view:toggle).
+  # element - The DOM node that will match a {KeyBinding}'s selector.
   keyBindingsForCommandMatchingElement: (command, element) ->
     keyBindings = @keyBindingsForCommand(command)
     @keyBindingsMatchingElement(element, keyBindings)
 
   # Public: Returns an array of {KeyBinding}s that match a keystroke
-  # * keystroke:
-  #   The string representing the keys pressed (e.g. ctrl-P)
+  #
+  # keystroke: The {String} representing the keys pressed (e.g. ctrl-P)
   keyBindingsForKeystroke: (keystroke) ->
     keystroke = KeyBinding.normalizeKeystroke(keystroke)
     @keyBindings.filter (keyBinding) -> keyBinding.matches(keystroke)
 
   # Public: Returns an array of {KeyBinding}s that match a command
-  # * keystroke:
-  #   The string representing the keys pressed (e.g. ctrl-P)
+  #
+  # keystroke - The {String} representing the keys pressed (e.g. ctrl-P)
   keyBindingsForCommand: (command) ->
     @keyBindings.filter (keyBinding) -> keyBinding.command == command
 
   # Public: Returns a array of {KeyBinding}s (sorted by selector specificity)
   # whos selector matches the element.
   #
-  # * element:
-  #   The DOM node that will match a {KeyBinding}'s selector.
+  # element - The DOM node that will match a {KeyBinding}'s selector.
   keyBindingsMatchingElement: (element, keyBindings=@keyBindings) ->
     keyBindings = keyBindings.filter ({selector}) -> $(element).closest(selector).length > 0
     keyBindings.sort (a, b) -> a.compare(b)
 
   # Public: Returns a keystroke string derived from an event.
-  # * event:
-  #   A DOM or jQuery event
-  # * previousKeystroke:
-  #   An optional string used for multiKeystrokes
+  #
+  # event - A DOM or jQuery event.
+  # previousKeystroke - An optional string used for multiKeystrokes.
   keystrokeStringForEvent: (event, previousKeystroke) ->
     if event.originalEvent.keyIdentifier.indexOf('U+') == 0
       hexCharCode = event.originalEvent.keyIdentifier[2..]
diff --git a/src/language-mode.coffee b/src/language-mode.coffee
index da539e08e..c5dae9e0c 100644
--- a/src/language-mode.coffee
+++ b/src/language-mode.coffee
@@ -3,30 +3,19 @@ _ = require 'underscore-plus'
 {OnigRegExp} = require 'oniguruma'
 {Emitter, Subscriber} = require 'emissary'
 
-### Internal ###
-
 module.exports =
 class LanguageMode
   Emitter.includeInto(this)
   Subscriber.includeInto(this)
 
-  buffer: null
-  grammar: null
-  editor: null
-  currentGrammarScore: null
-
-  ### Internal ###
-
-  destroy: ->
-    @unsubscribe()
-
-  ### Public ###
-
   # Sets up a `LanguageMode` for the given {Editor}.
   #
   # editor - The {Editor} to associate with
   constructor: (@editor) ->
-    @buffer = @editor.buffer
+    {@buffer} = @editor
+
+  destroy: ->
+    @unsubscribe()
 
   toggleLineCommentForBufferRow: (row) ->
     @toggleLineCommentsForBufferRows(row, row)
@@ -187,7 +176,7 @@ class LanguageMode
   isFoldableAtBufferRow: (bufferRow) ->
     @isFoldableCodeAtBufferRow(bufferRow) or @isFoldableCommentAtBufferRow(bufferRow)
 
-  # Private: Returns a {Boolean} indicating whether the given buffer row starts
+  # Returns a {Boolean} indicating whether the given buffer row starts
   # a a foldable row range due to the code's indentation patterns.
   isFoldableCodeAtBufferRow: (bufferRow) ->
     return false if @editor.isBufferRowBlank(bufferRow) or @isLineCommentedAtBufferRow(bufferRow)
@@ -195,14 +184,14 @@ class LanguageMode
     return false unless nextNonEmptyRow?
     @editor.indentationForBufferRow(nextNonEmptyRow) > @editor.indentationForBufferRow(bufferRow)
 
-  # Private: Returns a {Boolean} indicating whether the given buffer row starts
+  # Returns a {Boolean} indicating whether the given buffer row starts
   # a foldable row range due to being the start of a multi-line comment.
   isFoldableCommentAtBufferRow: (bufferRow) ->
     @isLineCommentedAtBufferRow(bufferRow) and
       @isLineCommentedAtBufferRow(bufferRow + 1) and
         not @isLineCommentedAtBufferRow(bufferRow - 1)
 
-  # Private: Returns a {Boolean} indicating whether the line at the given buffer
+  # Returns a {Boolean} indicating whether the line at the given buffer
   # row is a comment.
   isLineCommentedAtBufferRow: (bufferRow) ->
     return false unless 0 <= bufferRow <= @editor.getLastBufferRow()
diff --git a/src/less-compile-cache.coffee b/src/less-compile-cache.coffee
index ad9024faa..feccbac4a 100644
--- a/src/less-compile-cache.coffee
+++ b/src/less-compile-cache.coffee
@@ -5,7 +5,7 @@ LessCache = require 'less-cache'
 
 tmpDir = if process.platform is 'win32' then os.tmpdir() else '/tmp'
 
-# Private: {LessCache} wrapper used by {ThemeManager} to read stylesheets.
+# {LessCache} wrapper used by {ThemeManager} to read stylesheets.
 module.exports =
 class LessCompileCache
   Subscriber.includeInto(this)
diff --git a/src/menu-manager.coffee b/src/menu-manager.coffee
index aaf55bf1e..82e8512a7 100644
--- a/src/menu-manager.coffee
+++ b/src/menu-manager.coffee
@@ -8,61 +8,81 @@ fs = require 'fs-plus'
 # Public: Provides a registry for menu items that you'd like to appear in the
 # application menu.
 #
-# Should be accessed via `atom.menu`.
+# An instance of this class is always available as the `atom.menu` global.
 module.exports =
 class MenuManager
-  # Private:
   constructor: ({@resourcePath}) ->
+    @pendingUpdateOperation = null
     @template = []
     atom.keymap.on 'bundled-keymaps-loaded', => @loadPlatformItems()
 
   # Public: Adds the given item definition to the existing template.
   #
-  # * item:
-  #   An object which describes a menu item as defined by
-  #   https://github.com/atom/atom-shell/blob/master/docs/api/browser/menu.md
+  # ## Example
+  # ```coffee
+  #   atom.menu.add [
+  #     {
+  #       label: 'Hello'
+  #       submenu : [{label: 'World!', command: 'hello:world'}]
+  #     }
+  #   ]
+  # ```
+  #
+  # items - An {Array} of menu item {Object}s containing the keys:
+  #   :label   - The {String} menu label.
+  #   :submenu - An optional {Array} of sub menu items.
+  #   :command - An optional {String} command to trigger when the item is
+  #              clicked.
   #
   # Returns nothing.
   add: (items) ->
     @merge(@template, item) for item in items
     @update()
 
-  # Private: Should the binding for the given selector be included in the menu
+  # Should the binding for the given selector be included in the menu
   # commands.
   #
-  # * selector: A String selector to check.
+  # selector - A {String} selector to check.
   #
   # Returns true to include the selector, false otherwise.
   includeSelector: (selector) ->
     return true if document.body.webkitMatchesSelector(selector)
 
-    # Simulate an .editor element attached to a body element that has the same
-    # classes as the current body element.
+    # Simulate an .editor element attached to a .workspace element attached to
+    # a body element that has the same classes as the current body element.
     unless @testEditor?
+      testBody = document.createElement('body')
+      testBody.classList.add(@classesForElement(document.body)...)
+
+      testWorkspace = document.createElement('body')
+      workspaceClasses = @classesForElement(document.body.querySelector('.workspace')) ? ['.workspace']
+      testWorkspace.classList.add(workspaceClasses...)
+
+      testBody.appendChild(testWorkspace)
+
       @testEditor = document.createElement('div')
       @testEditor.classList.add('editor')
-      testBody = document.createElement('body')
-      testBody.classList.add(document.body.classList.toString().split(' ')...)
-      testBody.appendChild(@testEditor)
+      testWorkspace.appendChild(@testEditor)
 
     @testEditor.webkitMatchesSelector(selector)
 
   # Public: Refreshes the currently visible menu.
   update: ->
-    keystrokesByCommand = {}
-    for binding in atom.keymap.getKeyBindings() when @includeSelector(binding.selector)
-      keystrokesByCommand[binding.command] ?= []
-      keystrokesByCommand[binding.command].push binding.keystroke
-    @sendToBrowserProcess(@template, keystrokesByCommand)
+    clearImmediate(@pendingUpdateOperation) if @pendingUpdateOperation?
+    @pendingUpdateOperation = setImmediate =>
+      keystrokesByCommand = {}
+      for binding in atom.keymap.getKeyBindings() when @includeSelector(binding.selector)
+        keystrokesByCommand[binding.command] ?= []
+        keystrokesByCommand[binding.command].push binding.keystroke
+      @sendToBrowserProcess(@template, keystrokesByCommand)
 
-  # Private:
   loadPlatformItems: ->
     menusDirPath = path.join(@resourcePath, 'menus')
     platformMenuPath = fs.resolve(menusDirPath, process.platform, ['cson', 'json'])
     {menu} = CSON.readFileSync(platformMenuPath)
     @add(menu)
 
-  # Private: Merges an item in a submenu aware way such that new items are always
+  # Merges an item in a submenu aware way such that new items are always
   # appended to the bottom of existing menus where possible.
   merge: (menu, item) ->
     item = _.deepClone(item)
@@ -72,7 +92,7 @@ class MenuManager
     else
       menu.push(item) unless _.find(menu, (i) => @normalizeLabel(i.label) == @normalizeLabel(item.label))
 
-  # Private: OSX can't handle displaying accelerators for multiple keystrokes.
+  # OSX can't handle displaying accelerators for multiple keystrokes.
   # If they are sent across, it will stop processing accelerators for the rest
   # of the menu items.
   filterMultipleKeystroke: (keystrokesByCommand) ->
@@ -85,12 +105,10 @@ class MenuManager
         filtered[key].push(binding)
     filtered
 
-  # Private:
   sendToBrowserProcess: (template, keystrokesByCommand) ->
     keystrokesByCommand = @filterMultipleKeystroke(keystrokesByCommand)
     ipc.sendChannel 'update-application-menu', template, keystrokesByCommand
 
-  # Private:
   normalizeLabel: (label) ->
     return undefined unless label?
 
@@ -98,3 +116,7 @@ class MenuManager
       label.replace(/\&/g, '')
     else
       label
+
+  # Get an {Array} of {String} classes for the given element.
+  classesForElement: (element) ->
+    element?.classList.toString().split(' ') ? []
diff --git a/src/package-manager.coffee b/src/package-manager.coffee
index e94a69785..52ea5fedc 100644
--- a/src/package-manager.coffee
+++ b/src/package-manager.coffee
@@ -1,11 +1,14 @@
 {Emitter} = require 'emissary'
 fs = require 'fs-plus'
 _ = require 'underscore-plus'
+Q = require 'q'
 Package = require './package'
 path = require 'path'
 
 # Public: Package manager for coordinating the lifecycle of Atom packages.
 #
+# An instance of this class is always available as the `atom.packages` global.
+#
 # Packages can be loaded, activated, and deactivated, and unloaded:
 #  * Loading a package reads and parses the package's metadata and resources
 #    such as keymaps, menus, stylesheets, etc.
@@ -17,13 +20,10 @@ path = require 'path'
 #
 # Packages can also be enabled/disabled via the `core.disabledPackages` config
 # settings and also by calling `enablePackage()/disablePackage()`.
-#
-# An instance of this class is globally available via `atom.packages`.
 module.exports =
 class PackageManager
   Emitter.includeInto(this)
 
-  # Private:
   constructor: ({configDirPath, devMode, @resourcePath}) ->
     @packageDirPaths = [path.join(configDirPath, "packages")]
     if devMode
@@ -32,7 +32,6 @@ class PackageManager
     @loadedPackages = {}
     @activePackages = {}
     @packageStates = {}
-    @observingDisabledPackages = false
 
     @packageActivators = []
     @registerPackageActivator(this, ['atom', 'textmate'])
@@ -47,11 +46,9 @@ class PackageManager
   getPackageDirPaths: ->
     _.clone(@packageDirPaths)
 
-  # Private:
   getPackageState: (name) ->
     @packageStates[name]
 
-  # Private:
   setPackageState: (name, state) ->
     @packageStates[name] = state
 
@@ -67,44 +64,44 @@ class PackageManager
     pack?.disable()
     pack
 
-  # Private: Activate all the packages that should be activated.
+  # Activate all the packages that should be activated.
   activate: ->
     for [activator, types] in @packageActivators
       packages = @getLoadedPackagesForTypes(types)
       activator.activatePackages(packages)
     @emit 'activated'
 
-  # Private: another type of package manager can handle other package types.
+  # another type of package manager can handle other package types.
   # See ThemeManager
   registerPackageActivator: (activator, types) ->
     @packageActivators.push([activator, types])
 
-  # Private:
   activatePackages: (packages) ->
     @activatePackage(pack.name) for pack in packages
     @observeDisabledPackages()
 
-  # Private: Activate a single package by name
-  activatePackage: (name, options) ->
-    return pack if pack = @getActivePackage(name)
-    if pack = @loadPackage(name, options)
-      @activePackages[pack.name] = pack
-      pack.activate(options)
-      pack
+  # Activate a single package by name
+  activatePackage: (name) ->
+    if pack = @getActivePackage(name)
+      Q(pack)
+    else
+      pack = @loadPackage(name)
+      pack.activate().then =>
+        @activePackages[pack.name] = pack
+        pack
 
-  # Private: Deactivate all packages
+  # Deactivate all packages
   deactivatePackages: ->
-    @deactivatePackage(pack.name) for pack in @getActivePackages()
+    @deactivatePackage(pack.name) for pack in @getLoadedPackages()
     @unobserveDisabledPackages()
 
-  # Private: Deactivate the package with the given name
+  # Deactivate the package with the given name
   deactivatePackage: (name) ->
-    if pack = @getActivePackage(name)
+    pack = @getLoadedPackage(name)
+    if @isPackageActive(name)
       @setPackageState(pack.name, state) if state = pack.serialize?()
-      pack.deactivate()
-      delete @activePackages[pack.name]
-    else
-      throw new Error("No active package for name '#{name}'")
+    pack.deactivate()
+    delete @activePackages[pack.name]
 
   # Public: Get an array of all the active packages
   getActivePackages: ->
@@ -118,17 +115,12 @@ class PackageManager
   isPackageActive: (name) ->
     @getActivePackage(name)?
 
-  # Private:
   unobserveDisabledPackages: ->
-    return unless @observingDisabledPackages
-    atom.config.unobserve('core.disabledPackages')
-    @observingDisabledPackages = false
+    @disabledPackagesSubscription?.off()
+    @disabledPackagesSubscription = null
 
-  # Private:
   observeDisabledPackages: ->
-    return if @observingDisabledPackages
-
-    atom.config.observe 'core.disabledPackages', callNow: false, (disabledPackages, {previous}) =>
+    @disabledPackagesSubscription ?= atom.config.observe 'core.disabledPackages', callNow: false, (disabledPackages, {previous}) =>
       packagesToEnable = _.difference(previous, disabledPackages)
       packagesToDisable = _.difference(disabledPackages, previous)
 
@@ -136,10 +128,7 @@ class PackageManager
       @activatePackage(packageName) for packageName in packagesToEnable
       null
 
-    @observingDisabledPackages = true
-
-  # Private:
-  loadPackages: (options) ->
+  loadPackages: ->
     # Ensure atom exports is already in the require cache so the load time
     # of the first package isn't skewed by being the first to require atom
     require '../exports/atom'
@@ -147,27 +136,24 @@ class PackageManager
     packagePaths = @getAvailablePackagePaths()
     packagePaths = packagePaths.filter (packagePath) => not @isPackageDisabled(path.basename(packagePath))
     packagePaths = _.uniq packagePaths, (packagePath) -> path.basename(packagePath)
-    @loadPackage(packagePath, options) for packagePath in packagePaths
+    @loadPackage(packagePath) for packagePath in packagePaths
     @emit 'loaded'
 
-  # Private:
-  loadPackage: (nameOrPath, options) ->
+  loadPackage: (nameOrPath) ->
     if packagePath = @resolvePackagePath(nameOrPath)
       name = path.basename(nameOrPath)
       return pack if pack = @getLoadedPackage(name)
 
-      pack = Package.load(packagePath, options)
+      pack = Package.load(packagePath)
       @loadedPackages[pack.name] = pack if pack?
       pack
     else
       throw new Error("Could not resolve '#{nameOrPath}' to a package path")
 
-  # Private:
   unloadPackages: ->
     @unloadPackage(name) for name in _.keys(@loadedPackages)
     null
 
-  # Private:
   unloadPackage: (name) ->
     if @isPackageActive(name)
       throw new Error("Tried to unload active package '#{name}'")
@@ -189,9 +175,9 @@ class PackageManager
   getLoadedPackages: ->
     _.values(@loadedPackages)
 
-  # Private: Get packages for a certain package type
+  # Get packages for a certain package type
   #
-  # * types: an {Array} of {String}s like ['atom', 'textmate']
+  # types - an {Array} of {String}s like ['atom', 'textmate'].
   getLoadedPackagesForTypes: (types) ->
     pack for pack in @getLoadedPackages() when pack.getType() in types
 
@@ -209,7 +195,6 @@ class PackageManager
   isPackageDisabled: (name) ->
     _.include(atom.config.get('core.disabledPackages') ? [], name)
 
-  # Private:
   hasAtomEngine: (packagePath) ->
     metadata = Package.loadMetadata(packagePath, true)
     metadata?.engines?.atom?
@@ -218,7 +203,6 @@ class PackageManager
   isBundledPackage: (name) ->
     @getPackageDependencies().hasOwnProperty(name)
 
-  # Private:
   getPackageDependencies: ->
     unless @packageDependencies?
       try
diff --git a/src/package.coffee b/src/package.coffee
index ca4450bc6..7618e80c5 100644
--- a/src/package.coffee
+++ b/src/package.coffee
@@ -1,7 +1,6 @@
 CSON = require 'season'
 {basename, join} = require 'path'
 
-### Internal ###
 module.exports =
 class Package
   @build: (path) ->
@@ -23,9 +22,9 @@ class Package
 
     pack
 
-  @load: (path, options) ->
+  @load: (path) ->
     pack = @build(path)
-    pack?.load(options)
+    pack?.load()
     pack
 
   @loadMetadata: (path, ignoreErrors=false) ->
@@ -44,9 +43,6 @@ class Package
   constructor: (@path) ->
     @name = basename(@path)
 
-  isActive: ->
-    atom.packages.isPackageActive(@name)
-
   enable: ->
     atom.config.removeAtKeyPath('core.disabledPackages', @metadata.name)
 
@@ -54,9 +50,8 @@ class Package
     atom.config.pushAtKeyPath('core.disabledPackages', @metadata.name)
 
   isTheme: ->
-    !!@metadata?.theme
+    @metadata?.theme?
 
-  # Private:
   measure: (key, fn) ->
     startTime = Date.now()
     value = fn()
diff --git a/src/pane-axis-view.coffee b/src/pane-axis-view.coffee
index f478691f6..3039600c0 100644
--- a/src/pane-axis-view.coffee
+++ b/src/pane-axis-view.coffee
@@ -1,7 +1,6 @@
 {View} = require './space-pen-extensions'
 PaneView = null
 
-### Internal ###
 module.exports =
 class PaneAxisView extends View
   initialize: (@model) ->
diff --git a/src/pane-column-view.coffee b/src/pane-column-view.coffee
index ac9d1df6e..fca1938e2 100644
--- a/src/pane-column-view.coffee
+++ b/src/pane-column-view.coffee
@@ -2,7 +2,6 @@
 _ = require 'underscore-plus'
 PaneAxisView = require './pane-axis-view'
 
-# Internal:
 module.exports =
 class PaneColumnView extends PaneAxisView
 
diff --git a/src/pane-container-view.coffee b/src/pane-container-view.coffee
index 8d0d1b0e8..093c3e29d 100644
--- a/src/pane-container-view.coffee
+++ b/src/pane-container-view.coffee
@@ -3,7 +3,7 @@ Delegator = require 'delegato'
 PaneView = require './pane-view'
 PaneContainer = require './pane-container'
 
-# Private: Manages the list of panes within a {WorkspaceView}
+# Manages the list of panes within a {WorkspaceView}
 module.exports =
 class PaneContainerView extends View
   Delegator.includeInto(this)
@@ -27,8 +27,6 @@ class PaneContainerView extends View
       viewClass = model.getViewClass()
       model._view ?= new viewClass(model)
 
-  ### Public ###
-
   getRoot: ->
     @children().first().view()
 
@@ -98,3 +96,50 @@ class PaneContainerView extends View
 
   focusPreviousPane: ->
     @model.activatePreviousPane()
+
+  focusPaneAbove: ->
+    @nearestPaneInDirection('above')?.focus()
+
+  focusPaneBelow: ->
+    @nearestPaneInDirection('below')?.focus()
+
+  focusPaneOnLeft: ->
+    @nearestPaneInDirection('left')?.focus()
+
+  focusPaneOnRight: ->
+    @nearestPaneInDirection('right')?.focus()
+
+  nearestPaneInDirection: (direction) ->
+    distance = (pointA, pointB) ->
+      x = pointB.x - pointA.x
+      y = pointB.y - pointA.y
+      Math.sqrt(Math.pow(x, 2) + Math.pow(y, 2))
+
+    pane = @getActivePane()
+    box = @boundingBoxForPane(pane)
+    panes = @getPanes()
+      .filter (otherPane) =>
+        otherBox = @boundingBoxForPane(otherPane)
+        switch direction
+          when 'left' then otherBox.right.x <= box.left.x
+          when 'right' then otherBox.left.x >= box.right.x
+          when 'above' then otherBox.bottom.y <= box.top.y
+          when 'below' then otherBox.top.y >= box.bottom.y
+      .sort (paneA, paneB) =>
+        boxA = @boundingBoxForPane(paneA)
+        boxB = @boundingBoxForPane(paneB)
+        switch direction
+          when 'left' then distance(box.left, boxA.right) - distance(box.left, boxB.right)
+          when 'right' then distance(box.right, boxA.left) - distance(box.right, boxB.left)
+          when 'above' then distance(box.top, boxA.bottom) - distance(box.top, boxB.bottom)
+          when 'below' then distance(box.bottom, boxA.top) - distance(box.bottom, boxB.top)
+
+    panes[0]
+
+  boundingBoxForPane: (pane) ->
+    boundingBox = pane[0].getBoundingClientRect()
+
+    left: {x: boundingBox.left, y: boundingBox.top}
+    right: {x: boundingBox.right, y: boundingBox.top}
+    top: {x: boundingBox.left, y: boundingBox.top}
+    bottom: {x: boundingBox.left, y: boundingBox.bottom}
diff --git a/src/pane-container.coffee b/src/pane-container.coffee
index de339c8a9..a02afed9e 100644
--- a/src/pane-container.coffee
+++ b/src/pane-container.coffee
@@ -86,6 +86,6 @@ class PaneContainer extends Model
   itemDestroyed: (item) ->
     @emit 'item-destroyed', item
 
-  # Private: Called by Model superclass when destroyed
+  # Called by Model superclass when destroyed
   destroyed: ->
     pane.destroy() for pane in @getPanes()
diff --git a/src/pane-row-view.coffee b/src/pane-row-view.coffee
index 8808ce36c..1ad73d318 100644
--- a/src/pane-row-view.coffee
+++ b/src/pane-row-view.coffee
@@ -2,8 +2,6 @@
 _ = require 'underscore-plus'
 PaneAxisView = require './pane-axis-view'
 
-### Internal ###
-
 module.exports =
 class PaneRowView extends PaneAxisView
   @content: ->
diff --git a/src/pane-view.coffee b/src/pane-view.coffee
index bf1835cb0..09cc2a62b 100644
--- a/src/pane-view.coffee
+++ b/src/pane-view.coffee
@@ -27,11 +27,10 @@ class PaneView extends View
     'destroyItem', 'destroyItems', 'destroyActiveItem', 'destroyInactiveItems',
     'saveActiveItem', 'saveActiveItemAs', 'saveItem', 'saveItemAs', 'saveItems',
     'itemForUri', 'activateItemForUri', 'promptToSaveItem', 'copyActiveItem', 'isActive',
-    'activate', toProperty: 'model'
+    'activate', 'getActiveItem', toProperty: 'model'
 
   previousActiveItem: null
 
-  # Private:
   initialize: (args...) ->
     if args[0] instanceof Pane
       @model = args[0]
@@ -97,7 +96,6 @@ class PaneView extends View
   # Deprecated: Use ::activatePreviousItem
   showPreviousItem: -> @activatePreviousItem()
 
-  # Private:
   afterAttach: (onDom) ->
     @focus() if @model.focused and onDom
 
@@ -167,11 +165,9 @@ class PaneView extends View
     @unsubscribe(item) if typeof item.off is 'function'
     @trigger 'pane:before-item-destroyed', [item]
 
-  # Private:
   activeItemTitleChanged: =>
     @trigger 'pane:active-item-title-changed'
 
-  # Private:
   viewForItem: (item) ->
     return unless item?
     if item instanceof $
@@ -184,7 +180,6 @@ class PaneView extends View
       @viewsByItem.set(item, view)
       view
 
-  # Private:
   @::accessor 'activeView', -> @viewForItem(@activeItem)
 
   splitLeft: (items...) -> @model.splitLeft({items})._view
@@ -195,14 +190,15 @@ class PaneView extends View
 
   splitDown: (items...) -> @model.splitDown({items})._view
 
-  # Public:
+  # Public: Get the container view housing this pane.
+  #
+  # Returns a {View}.
   getContainer: ->
     @closest('.panes').view()
 
   beforeRemove: ->
     @model.destroy() unless @model.isDestroyed()
 
-  # Private:
   remove: (selector, keepData) ->
     return super if keepData
     @unsubscribe()
diff --git a/src/pane.coffee b/src/pane.coffee
index 4375ce588..2e320a3c6 100644
--- a/src/pane.coffee
+++ b/src/pane.coffee
@@ -3,6 +3,7 @@
 {Model, Sequence} = require 'theorist'
 Serializable = require 'serializable'
 PaneAxis = require './pane-axis'
+Editor = require './editor'
 PaneView = null
 
 # Public: A container for multiple items, one of which is *active* at a given
@@ -27,7 +28,6 @@ class Pane extends Model
       .map((activePane) => activePane is this)
       .distinctUntilChanged()
 
-  # Private:
   constructor: (params) ->
     super
 
@@ -43,31 +43,31 @@ class Pane extends Model
 
     @activate() if params?.active
 
-  # Private: Called by the Serializable mixin during serialization.
+  # Called by the Serializable mixin during serialization.
   serializeParams: ->
     items: compact(@items.map((item) -> item.serialize?()))
     activeItemUri: @activeItem?.getUri?()
     focused: @focused
     active: @active
 
-  # Private: Called by the Serializable mixin during deserialization.
+  # Called by the Serializable mixin during deserialization.
   deserializeParams: (params) ->
     {items, activeItemUri} = params
     params.items = compact(items.map (itemState) -> atom.deserializers.deserialize(itemState))
     params.activeItem = find params.items, (item) -> item.getUri?() is activeItemUri
     params
 
-  # Private: Called by the view layer to construct a view for this model.
+  # Called by the view layer to construct a view for this model.
   getViewClass: -> PaneView ?= require './pane-view'
 
   isActive: -> @active
 
-  # Private: Called by the view layer to indicate that the pane has gained focus.
+  # Called by the view layer to indicate that the pane has gained focus.
   focus: ->
     @focused = true
     @activate() unless @isActive()
 
-  # Private: Called by the view layer to indicate that the pane has lost focus.
+  # Called by the view layer to indicate that the pane has lost focus.
   blur: ->
     @focused = false
     true # if this is called from an event handler, don't cancel it
@@ -78,13 +78,25 @@ class Pane extends Model
     @container?.activePane = this
     @emit 'activated'
 
-  # Private:
   getPanes: -> [this]
 
-  # Public:
+  # Public: Get the items in this pane.
+  #
+  # Returns an {Array} of items.
   getItems: ->
     @items.slice()
 
+  # Public: Get the active pane item in this pane.
+  #
+  # Returns a pane item.
+  getActiveItem: ->
+    @activeItem
+
+  # Public: Returns an {Editor} if the pane item is an {Editor}, or null
+  # otherwise.
+  getActiveEditor: ->
+    @activeItem if @activeItem instanceof Editor
+
   # Public: Returns the item at the specified index.
   itemAtIndex: (index) ->
     @items[index]
@@ -105,15 +117,15 @@ class Pane extends Model
     else
       @activateItemAtIndex(@items.length - 1)
 
-  # Public: Returns the index of the current active item.
+  # Returns the index of the current active item.
   getActiveItemIndex: ->
     @items.indexOf(@activeItem)
 
-  # Public: Makes the item at the given index active.
+  # Makes the item at the given index active.
   activateItemAtIndex: (index) ->
     @activateItem(@itemAtIndex(index))
 
-  # Public: Makes the given item active, adding the item if necessary.
+  # Makes the given item active, adding the item if necessary.
   activateItem: (item) ->
     if item?
       @addItem(item)
@@ -121,11 +133,9 @@ class Pane extends Model
 
   # Public: Adds the item to the pane.
   #
-  # * item:
-  #     The item to add. It can be a model with an associated view or a view.
-  # * index:
-  #     An optional index at which to add the item. If omitted, the item is
-  #     added after the current active item.
+  # item - The item to add. It can be a model with an associated view or a view.
+  # index - An optional index at which to add the item. If omitted, the item is
+  #         added after the current active item.
   #
   # Returns the added item
   addItem: (item, index=@getActiveItemIndex() + 1) ->
@@ -138,12 +148,11 @@ class Pane extends Model
 
   # Public: Adds the given items to the pane.
   #
-  # * items:
-  #     An {Array} of items to add. Items can be models with associated views
-  #     or views. Any items that are already present in items will not be added.
-  # * index:
-  #     An optional index at which to add the item. If omitted, the item is
-  #     added after the current active item.
+  # items - An {Array} of items to add. Items can be models with associated
+  #         views or views. Any items that are already present in items will
+  #         not be added.
+  # index - An optional index at which to add the item. If omitted, the item is
+  #         added after the current active item.
   #
   # Returns an {Array} of the added items
   addItems: (items, index=@getActiveItemIndex() + 1) ->
@@ -151,7 +160,6 @@ class Pane extends Model
     @addItem(item, index + i) for item, i in items
     items
 
-  # Private:
   removeItem: (item, destroying) ->
     index = @items.indexOf(item)
     return if index is -1
@@ -207,7 +215,7 @@ class Pane extends Model
   destroy: ->
     super unless @container?.isAlive() and @container?.getPanes().length is 1
 
-  # Private: Called by model superclass.
+  # Called by model superclass.
   destroyed: ->
     @container.activateNextPane() if @isActive()
     item.destroy?() for item in @items.slice()
@@ -238,8 +246,9 @@ class Pane extends Model
 
   # Public: Saves the specified item.
   #
-  # * item: The item to save.
-  # * nextAction: An optional function which will be called after the item is saved.
+  # item - The item to save.
+  # nextAction - An optional function which will be called after the item is
+  #              saved.
   saveItem: (item, nextAction) ->
     if item?.getUri?()
       item.save?()
@@ -249,8 +258,9 @@ class Pane extends Model
 
   # Public: Saves the given item at a prompted-for location.
   #
-  # * item: The item to save.
-  # * nextAction: An optional function which will be called after the item is saved.
+  # item - The item to save.
+  # nextAction - An optional function which will be called after the item is
+  #              saved.
   saveItemAs: (item, nextAction) ->
     return unless item?.saveAs?
 
@@ -279,15 +289,14 @@ class Pane extends Model
     else
       false
 
-  # Private:
   copyActiveItem: ->
     if @activeItem?
       @activeItem.copy?() ? atom.deserializers.deserialize(@activeItem.serialize())
 
   # Public: Creates a new pane to the left of the receiver.
   #
-  # * params:
-  #   + items: An optional array of items with which to construct the new pane.
+  # params - An object with keys:
+  #   :items - An optional array of items with which to construct the new pane.
   #
   # Returns the new {Pane}.
   splitLeft: (params) ->
@@ -295,8 +304,8 @@ class Pane extends Model
 
   # Public: Creates a new pane to the right of the receiver.
   #
-  # * params:
-  #   + items: An optional array of items with which to construct the new pane.
+  # params - An object with keys:
+  #   :items - An optional array of items with which to construct the new pane.
   #
   # Returns the new {Pane}.
   splitRight: (params) ->
@@ -304,8 +313,8 @@ class Pane extends Model
 
   # Public: Creates a new pane above the receiver.
   #
-  # * params:
-  #   + items: An optional array of items with which to construct the new pane.
+  # params - An object with keys:
+  #   :items - An optional array of items with which to construct the new pane.
   #
   # Returns the new {Pane}.
   splitUp: (params) ->
@@ -313,14 +322,13 @@ class Pane extends Model
 
   # Public: Creates a new pane below the receiver.
   #
-  # * params:
-  #   + items: An optional array of items with which to construct the new pane.
+  # params - An object with keys:
+  #   :items - An optional array of items with which to construct the new pane.
   #
   # Returns the new {Pane}.
   splitDown: (params) ->
     @split('vertical', 'after', params)
 
-  # Private:
   split: (orientation, side, params) ->
     if @parent.orientation isnt orientation
       @parent.replaceChild(this, new PaneAxis({@container, orientation, children: [this]}))
@@ -333,7 +341,7 @@ class Pane extends Model
     newPane.activate()
     newPane
 
-  # Private: If the parent is a horizontal axis, returns its first child;
+  # If the parent is a horizontal axis, returns its first child;
   # otherwise this pane.
   findLeftmostSibling: ->
     if @parent.orientation is 'horizontal'
@@ -341,7 +349,7 @@ class Pane extends Model
     else
       this
 
-  # Private: If the parent is a horizontal axis, returns its last child;
+  # If the parent is a horizontal axis, returns its last child;
   # otherwise returns a new pane created by splitting this pane rightward.
   findOrCreateRightmostSibling: ->
     if @parent.orientation is 'horizontal'
diff --git a/src/pasteboard.coffee b/src/pasteboard.coffee
deleted file mode 100644
index 2f97333d8..000000000
--- a/src/pasteboard.coffee
+++ /dev/null
@@ -1,36 +0,0 @@
-clipboard = require 'clipboard'
-crypto = require 'crypto'
-
-# Public: Represents the clipboard used for copying and pasting in Atom.
-#
-# A pasteboard instance is always available under the `atom.pasteboard` global.
-module.exports =
-class Pasteboard
-  signatureForMetadata: null
-
-  # Creates an `md5` hash of some text.
-  #
-  # text - A {String} to encrypt.
-  #
-  # Returns an encrypted {String}.
-  md5: (text) ->
-    crypto.createHash('md5').update(text, 'utf8').digest('hex')
-
-  # Public: Write the given text to the clipboard.
-  #
-  # text - A {String} to store.
-  # metadata - An {Object} of additional info to associate with the text.
-  write: (text, metadata) ->
-    @signatureForMetadata = @md5(text)
-    @metadata = metadata
-    clipboard.writeText(text)
-
-  # Public: Read the text from the clipboard.
-  #
-  # Returns an {Array}. The first element is the saved text and the second is
-  # any metadata associated with the text.
-  read: ->
-    text = clipboard.readText()
-    value = [text]
-    value.push(@metadata) if @signatureForMetadata == @md5(text)
-    value
diff --git a/src/project.coffee b/src/project.coffee
index 62f5f0dbe..d93ef4e4c 100644
--- a/src/project.coffee
+++ b/src/project.coffee
@@ -16,7 +16,7 @@ Git = require './git'
 
 # Public: Represents a project that's opened in Atom.
 #
-# There is always a project available under the `atom.project` global.
+# An instance of this class is always available as the `atom.project` global.
 module.exports =
 class Project extends Model
   atom.deserializers.add(this)
@@ -30,11 +30,12 @@ class Project extends Model
 
   constructor: ({path, @buffers}={}) ->
     @buffers ?= []
+    @openers = []
+
     for buffer in @buffers
       do (buffer) =>
         buffer.once 'destroyed', => @removeBuffer(buffer)
 
-    @openers = []
     @editors = []
     @setPath(path)
 
@@ -46,36 +47,16 @@ class Project extends Model
     params.buffers = params.buffers.map (bufferState) -> atom.deserializers.deserialize(bufferState)
     params
 
-  # Public: Register an opener for project files.
-  #
-  # An {Editor} will be used if no openers return a value.
-  #
-  # ## Example:
-  # ```coffeescript
-  #   atom.project.registerOpener (filePath) ->
-  #     if path.extname(filePath) is '.toml'
-  #       return new TomlEditor(filePath)
-  # ```
-  #
-  # * opener: A function to be called when a path is being opened.
-  registerOpener: (opener) -> @openers.push(opener)
-
-  # Public: Remove a previously registered opener.
-  unregisterOpener: (opener) -> _.remove(@openers, opener)
-
-  # Private:
   destroyed: ->
     editor.destroy() for editor in @getEditors()
     buffer.destroy() for buffer in @getBuffers()
     @destroyRepo()
 
-  # Private:
   destroyRepo: ->
     if @repo?
       @repo.destroy()
       @repo = null
 
-  # Private:
   destroyUnretainedBuffers: ->
     buffer.destroy() for buffer in @getBuffers() when not buffer.isRetained()
 
@@ -111,8 +92,7 @@ class Project extends Model
   # the path is already absolute or if it is prefixed with a scheme, it is
   # returned unchanged.
   #
-  # * uri:
-  #   The String name of the path to convert
+  # uri - The {String} name of the path to convert.
   #
   # Returns a String.
   resolve: (uri) ->
@@ -133,71 +113,53 @@ class Project extends Model
   contains: (pathToCheck) ->
     @rootDirectory?.contains(pathToCheck) ? false
 
-  # Public: Given a path to a file, this constructs and associates a new
+  # Given a path to a file, this constructs and associates a new
   # {Editor}, showing the file.
   #
-  # * filePath:
-  #   The {String} path of the file to associate with
-  # * options:
-  #   Options that you can pass to the {Editor} constructor
+  # filePath - The {String} path of the file to associate with.
+  # options  - Options that you can pass to the {Editor} constructor.
   #
   # Returns a promise that resolves to an {Editor}.
   open: (filePath, options={}) ->
     filePath = @resolve(filePath)
-    resource = null
-    _.find @openers, (opener) -> resource = opener(filePath, options)
+    @bufferForPath(filePath).then (buffer) =>
+      @buildEditorForBuffer(buffer, options)
 
-    if resource
-      Q(resource)
-    else
-      @bufferForPath(filePath).then (buffer) =>
-        @buildEditorForBuffer(buffer, options)
-
-  # Private: Only be used in specs
+  # Deprecated
   openSync: (filePath, options={}) ->
     filePath = @resolve(filePath)
-    for opener in @openers
-      return resource if resource = opener(filePath, options)
-
     @buildEditorForBuffer(@bufferForPathSync(filePath), options)
 
-  # Public: Retrieves all {Editor}s for all open files.
-  #
-  # Returns an {Array} of {Editor}s.
-  getEditors: ->
-    new Array(@editors...)
-
-  # Public: Add the given {Editor}.
+  # Add the given {Editor}.
   addEditor: (editor) ->
     @editors.push editor
     @emit 'editor-created', editor
 
-  # Public: Return and removes the given {Editor}.
+  # Return and removes the given {Editor}.
   removeEditor: (editor) ->
     _.remove(@editors, editor)
 
-  # Private: Retrieves all the {TextBuffer}s in the project; that is, the
+  # Retrieves all the {TextBuffer}s in the project; that is, the
   # buffers for all open files.
   #
   # Returns an {Array} of {TextBuffer}s.
   getBuffers: ->
     @buffers.slice()
 
-  # Private: Is the buffer for the given path modified?
+  # Is the buffer for the given path modified?
   isPathModified: (filePath) ->
     @findBufferForPath(@resolve(filePath))?.isModified()
 
-  # Private:
   findBufferForPath: (filePath) ->
    _.find @buffers, (buffer) -> buffer.getPath() == filePath
 
-  # Private: Only to be used in specs
+  # Only to be used in specs
   bufferForPathSync: (filePath) ->
     absoluteFilePath = @resolve(filePath)
     existingBuffer = @findBufferForPath(absoluteFilePath) if filePath
     existingBuffer ? @buildBufferSync(absoluteFilePath)
 
-  # Private: Given a file path, this retrieves or creates a new {TextBuffer}.
+  # Given a file path, this retrieves or creates a new {TextBuffer}.
   #
   # If the `filePath` already has a `buffer`, that value is used instead. Otherwise,
   # `text` is used as the contents of the new buffer.
@@ -210,21 +172,20 @@ class Project extends Model
     existingBuffer = @findBufferForPath(absoluteFilePath) if absoluteFilePath
     Q(existingBuffer ? @buildBuffer(absoluteFilePath))
 
-  # Private:
   bufferForId: (id) ->
     _.find @buffers, (buffer) -> buffer.id is id
 
-  # Private: DEPRECATED
+  # DEPRECATED
   buildBufferSync: (absoluteFilePath) ->
     buffer = new TextBuffer({filePath: absoluteFilePath})
     @addBuffer(buffer)
     buffer.loadSync()
     buffer
 
-  # Private: Given a file path, this sets its {TextBuffer}.
+  # Given a file path, this sets its {TextBuffer}.
   #
-  # absoluteFilePath - A {String} representing a path
-  # text - The {String} text to use as a buffer
+  # absoluteFilePath - A {String} representing a path.
+  # text - The {String} text to use as a buffer.
   #
   # Returns a promise that resolves to the {TextBuffer}.
   buildBuffer: (absoluteFilePath) ->
@@ -234,38 +195,33 @@ class Project extends Model
       .then((buffer) -> buffer)
       .catch(=> @removeBuffer(buffer))
 
-  # Private:
   addBuffer: (buffer, options={}) ->
     @addBufferAtIndex(buffer, @buffers.length, options)
     buffer.once 'destroyed', => @removeBuffer(buffer)
 
-  # Private:
   addBufferAtIndex: (buffer, index, options={}) ->
     @buffers.splice(index, 0, buffer)
     buffer.once 'destroyed', => @removeBuffer(buffer)
     @emit 'buffer-created', buffer
     buffer
 
-  # Private: Removes a {TextBuffer} association from the project.
+  # Removes a {TextBuffer} association from the project.
   #
   # Returns the removed {TextBuffer}.
   removeBuffer: (buffer) ->
     index = @buffers.indexOf(buffer)
     @removeBufferAtIndex(index) unless index is -1
 
-  # Private:
   removeBufferAtIndex: (index, options={}) ->
     [buffer] = @buffers.splice(index, 1)
     buffer?.destroy()
 
   # Public: Performs a search across all the files in the project.
   #
-  # * regex:
-  #   A RegExp to search with
-  # * options:
-  #   - paths: an {Array} of glob patterns to search within
-  # * iterator:
-  #   A Function callback on each file found
+  # regex - A {RegExp} to search with.
+  # options - An optional options {Object} (default: {}):
+  #   :paths - An {Array} of glob patterns to search within
+  # iterator - A {Function} callback on each file found
   scan: (regex, options={}, iterator) ->
     if _.isFunction(options)
       iterator = options
@@ -304,10 +260,11 @@ class Project extends Model
 
   # Public: Performs a replace across all the specified files in the project.
   #
-  # * regex: A RegExp to search with
-  # * replacementText: Text to replace all matches of regex with
-  # * filePaths: List of file path strings to run the replace on.
-  # * iterator: A Function callback on each file with replacements. `({filePath, replacements}) ->`
+  # regex - A {RegExp} to search with.
+  # replacementText - Text to replace all matches of regex with
+  # filePaths - List of file path strings to run the replace on.
+  # iterator - A {Function} callback on each file with replacements:
+  #            `({filePath, replacements}) ->`.
   replace: (regex, replacementText, filePaths, iterator) ->
     deferred = Q.defer()
 
@@ -339,18 +296,11 @@ class Project extends Model
 
     deferred.promise
 
-  # Private:
   buildEditorForBuffer: (buffer, editorOptions) ->
     editor = new Editor(_.extend({buffer}, editorOptions))
     @addEditor(editor)
     editor
 
-  # Private:
-  eachEditor: (callback) ->
-    callback(editor) for editor in @getEditors()
-    @on 'editor-created', (editor) -> callback(editor)
-
-  # Private:
   eachBuffer: (args...) ->
     subscriber = args.shift() if args.length > 1
     callback = args.shift()
@@ -360,3 +310,20 @@ class Project extends Model
       subscriber.subscribe this, 'buffer-created', (buffer) -> callback(buffer)
     else
       @on 'buffer-created', (buffer) -> callback(buffer)
+
+  # Deprecated: delegate
+  registerOpener: (opener) ->
+    @openers.push(opener)
+
+  # Deprecated: delegate
+  unregisterOpener: (opener) ->
+    _.remove(@openers, opener)
+
+  # Deprecated: delegate
+  eachEditor: (callback) ->
+    callback(editor) for editor in @getEditors()
+    @on 'editor-created', (editor) -> callback(editor)
+
+  # Deprecated: delegate
+  getEditors: ->
+    new Array(@editors...)
diff --git a/src/scroll-view.coffee b/src/scroll-view.coffee
index 7f09cf73d..c2e1aa7b1 100644
--- a/src/scroll-view.coffee
+++ b/src/scroll-view.coffee
@@ -2,8 +2,14 @@
 
 # Public: Represents a view that scrolls.
 #
-# This `View` subclass listens to events such as `page-up`, `page-down`,
-# `move-to-top`, and `move-to-bottom`.
+# Subclasses must call `super` if overriding the `initialize` method or else
+# the following events won't be handled by the ScrollView.
+#
+# ## Events
+#   * `core:page-up`
+#   * `core:page-down`
+#   * `core:move-to-top`
+#   * `core:move-to-bottom`
 #
 # ## Requiring in packages
 #
@@ -12,8 +18,6 @@
 # ```
 module.exports =
 class ScrollView extends View
-
-  # Internal: The constructor.
   initialize: ->
     @on 'core:page-up', => @pageUp()
     @on 'core:page-down', => @pageDown()
diff --git a/src/select-list-view.coffee b/src/select-list-view.coffee
index fc2c52db5..9cf1885ae 100644
--- a/src/select-list-view.coffee
+++ b/src/select-list-view.coffee
@@ -12,8 +12,6 @@ fuzzyFilter = require('fuzzaldrin').filter
 # ```
 module.exports =
 class SelectListView extends View
-
-  # Private:
   @content: ->
     @div class: @viewClass(), =>
       @subview 'miniEditor', new EditorView(mini: true)
@@ -23,7 +21,6 @@ class SelectListView extends View
         @span class: 'badge', outlet: 'loadingBadge'
       @ol class: 'list-group', outlet: 'list'
 
-  # Private:
   @viewClass: -> 'select-list'
 
   maxItems: Infinity
@@ -59,7 +56,6 @@ class SelectListView extends View
       @confirmSelection() if $(e.target).closest('li').hasClass('selected')
       e.preventDefault()
 
-  # Private:
   schedulePopulateList: ->
     clearTimeout(@scheduleTimeout)
     populateCallback = =>
@@ -68,14 +64,14 @@ class SelectListView extends View
 
   # Public: Set the array of items to display in the list.
   #
-  # * array: The array of model elements to display in the list.
+  # array - The {Array} of model elements to display in the list.
   setArray: (@array=[]) ->
     @populateList()
     @setLoading()
 
   # Public: Set the error message to display.
   #
-  # * message: The error message.
+  # message - The {String} error message (default: '').
   setError: (message='') ->
     if message.length is 0
       @error.text('').hide()
@@ -85,7 +81,7 @@ class SelectListView extends View
 
   # Public: Set the loading message to display.
   #
-  # * message: The loading message.
+  # message - The {String} loading message (default: '').
   setLoading: (message='') ->
     if message.length is 0
       @loading.text("")
@@ -135,30 +131,26 @@ class SelectListView extends View
   #
   # Subclasses may override this method to customize the message.
   #
-  # * itemCount: The number of items in the array specified to {.setArray}
-  # * filteredItemCount: The number of items that pass the fuzzy filter test.
+  # itemCount - The {Number} of items in the array specified to {.setArray}
+  # filteredItemCount - The {Number} of items that pass the fuzzy filter test.
   getEmptyMessage: (itemCount, filteredItemCount) -> 'No matches found'
 
-  # Private:
   selectPreviousItem: ->
     item = @getSelectedItem().prev()
     item = @list.find('li:last') unless item.length
     @selectItem(item)
 
-  # Private:
   selectNextItem: ->
     item = @getSelectedItem().next()
     item = @list.find('li:first') unless item.length
     @selectItem(item)
 
-  # Private:
   selectItem: (item) ->
     return unless item.length
     @list.find('.selected').removeClass('selected')
     item.addClass 'selected'
     @scrollToItem(item)
 
-  # Private:
   scrollToItem: (item) ->
     scrollTop = @list.scrollTop()
     desiredTop = item.position().top + scrollTop
@@ -181,7 +173,6 @@ class SelectListView extends View
   getSelectedElement: ->
     @getSelectedItem().data('select-list-element')
 
-  # Private:
   confirmSelection: ->
     element = @getSelectedElement()
     if element?
@@ -193,25 +184,21 @@ class SelectListView extends View
   #
   # This method should be overridden by subclasses.
   #
-  # * element: The selected model element.
+  # element - The selected model element.
   confirmed: (element) ->
 
-  # Private:
   attach: ->
     @storeFocusedElement()
 
-  # Private:
   storeFocusedElement: ->
     @previouslyFocusedElement = $(':focus')
 
-  # Private:
   restoreFocus: ->
     if @previouslyFocusedElement?.isOnDom()
       @previouslyFocusedElement.focus()
     else
       atom.workspaceView.focus()
 
-  # Private:
   cancelled: ->
     @miniEditor.getEditor().setText('')
     @miniEditor.updateDisplay()
diff --git a/src/selection-view.coffee b/src/selection-view.coffee
index beea12f47..e0413b30c 100644
--- a/src/selection-view.coffee
+++ b/src/selection-view.coffee
@@ -1,7 +1,6 @@
 {Point, Range} = require 'text-buffer'
 {View, $$} = require './space-pen-extensions'
 
-# Internal:
 module.exports =
 class SelectionView extends View
 
diff --git a/src/selection.coffee b/src/selection.coffee
index 915f3fb0b..6f5e50788 100644
--- a/src/selection.coffee
+++ b/src/selection.coffee
@@ -14,7 +14,6 @@ class Selection
   wordwise: false
   needsAutoscroll: null
 
-  # Private:
   constructor: ({@cursor, @marker, @editor}) ->
     @cursor.selection = this
     @marker.on 'changed', => @screenRangeChanged()
@@ -23,18 +22,15 @@ class Selection
       @editor.removeSelection(this)
       @emit 'destroyed' unless @editor.isDestroyed()
 
-  # Private:
   destroy: ->
     @marker.destroy()
 
-  # Private:
   finalize: ->
     @initialScreenRange = null unless @initialScreenRange?.isEqual(@getScreenRange())
     if @isEmpty()
       @wordwise = false
       @linewise = false
 
-  # Private:
   clearAutoscroll: ->
     @needsAutoscroll = null
 
@@ -59,10 +55,8 @@ class Selection
 
   # Public: Modifies the screen range for the selection.
   #
-  # * screenRange:
-  #   The new {Range} to use
-  # * options:
-  #   + A hash of options matching those found in {.setBufferRange}
+  # screenRange - The new {Range} to use.
+  # options - A hash of options matching those found in {.setBufferRange}.
   setScreenRange: (screenRange, options) ->
     @setBufferRange(@editor.bufferRangeForScreenRange(screenRange), options)
 
@@ -72,13 +66,11 @@ class Selection
 
   # Public: Modifies the buffer {Range} for the selection.
   #
-  # * screenRange:
-  #   The new {Range} to select
-  # * options
-  #    + preserveFolds:
-  #      if `true`, the fold settings are preserved after the selection moves
-  #    + autoscroll:
-  #      if `true`, the {Editor} scrolls to the new selection
+  # screenRange - The new {Range} to select.
+  # options - An {Object} with the keys:
+  #   :preserveFolds - if `true`, the fold settings are preserved after the
+  #                    selection moves.
+  #   :autoscroll - if `true`, the {Editor} scrolls to the new selection.
   setBufferRange: (bufferRange, options={}) ->
     bufferRange = Range.fromObject(bufferRange)
     @needsAutoscroll = options.autoscroll
@@ -128,8 +120,7 @@ class Selection
 
   # Public: Selects an entire line in the buffer.
   #
-  # * row:
-  #   The line Number to select (default: the row of the cursor)
+  # row - The line {Number} to select (default: the row of the cursor).
   selectLine: (row=@cursor.getBufferPosition().row) ->
     range = @editor.bufferRangeForBufferRow(row, includeNewline: true)
     @setBufferRange(@getBufferRange().union(range))
@@ -148,8 +139,7 @@ class Selection
   # Public: Selects the text from the current cursor position to a given screen
   # position.
   #
-  # * position:
-  #   An instance of {Point}, with a given `row` and `column`.
+  # position - An instance of {Point}, with a given `row` and `column`.
   selectToScreenPosition: (position) ->
     @modifySelection =>
       if @initialScreenRange
@@ -168,8 +158,7 @@ class Selection
   # Public: Selects the text from the current cursor position to a given buffer
   # position.
   #
-  # * position:
-  #   An instance of {Point}, with a given `row` and `column`.
+  # position - An instance of {Point}, with a given `row` and `column`.
   selectToBufferPosition: (position) ->
     @modifySelection => @cursor.setBufferPosition(position)
 
@@ -259,8 +248,6 @@ class Selection
       @editor.addSelectionForBufferRange(range, goalBufferRange: range)
       break
 
-  # Public:
-  #
   # FIXME: I have no idea what this does.
   getGoalBufferRange: ->
     @marker.getAttributes().goalBufferRange
@@ -285,20 +272,14 @@ class Selection
 
   # Public: Replaces text at the current selection.
   #
-  # * text:
-  #   A {String} representing the text to add
-  # * options
-  #    + select:
-  #      if `true`, selects the newly added text
-  #    + autoIndent:
-  #      if `true`, indents all inserted text appropriately
-  #    + autoIndentNewline:
-  #      if `true`, indent newline appropriately
-  #    + autoDecreaseIndent:
-  #      if `true`, decreases indent level appropriately (for example, when a
-  #      closing bracket is inserted)
-  #    + undo:
-  #      if `skip`, skips the undo stack for this operation.
+  # text - A {String} representing the text to add
+  # options - An {Object} with keys:
+  #   :select - if `true`, selects the newly added text.
+  #   :autoIndent - if `true`, indents all inserted text appropriately.
+  #   :autoIndentNewline - if `true`, indent newline appropriately.
+  #   :autoDecreaseIndent - if `true`, decreases indent level appropriately
+  #                         (for example, when a closing bracket is inserted).
+  #   :undo - if `skip`, skips the undo stack for this operation.
   insertText: (text, options={}) ->
     oldBufferRange = @getBufferRange()
     @editor.destroyFoldsContainingBufferRow(oldBufferRange.end.row)
@@ -326,10 +307,8 @@ class Selection
 
   # Public: Indents the given text to the suggested level based on the grammar.
   #
-  # * text:
-  #   The string to indent within the selection.
-  # * indentBasis:
-  #   The beginning indent level.
+  # text - The {String} to indent within the selection.
+  # indentBasis - The beginning indent level.
   normalizeIndents: (text, indentBasis) ->
     textPrecedingCursor = @cursor.getCurrentBufferLine()[0...@cursor.getBufferColumn()]
     isCursorInsideExistingLine = /\S/.test(textPrecedingCursor)
@@ -357,10 +336,9 @@ class Selection
 
   # Public: Indents the selection.
   #
-  # * options - A hash with one key,
-  #    + autoIndent:
-  #      If `true`, the indentation is performed appropriately. Otherwise,
-  #      {Editor.getTabText} is used
+  # options - A {Object} with the keys:
+  #   :autoIndent - If `true`, the indentation is performed appropriately.
+  #                 Otherwise, {Editor.getTabText} is used.
   indent: ({ autoIndent }={})->
     { row, column } = @cursor.getBufferPosition()
 
@@ -505,35 +483,25 @@ class Selection
     @editor.toggleLineCommentsForBufferRows(@getBufferRowRange()...)
 
   # Public: Cuts the selection until the end of the line.
-  #
-  # * maintainPasteboard:
-  #   ?
-  cutToEndOfLine: (maintainPasteboard) ->
+  cutToEndOfLine: (maintainClipboard) ->
     @selectToEndOfLine() if @isEmpty()
-    @cut(maintainPasteboard)
+    @cut(maintainClipboard)
 
-  # Public: Copies the selection to the pasteboard and then deletes it.
-  #
-  # * maintainPasteboard:
-  #   ?
-  cut: (maintainPasteboard=false) ->
-    @copy(maintainPasteboard)
+  # Public: Copies the selection to the clipboard and then deletes it.
+  cut: (maintainClipboard=false) ->
+    @copy(maintainClipboard)
     @delete()
 
-  # Public: Copies the current selection to the pasteboard.
-  #
-  # * maintainPasteboard:
-  #   ?
-  copy: (maintainPasteboard=false) ->
+  # Public: Copies the current selection to the clipboard.
+  copy: (maintainClipboard=false) ->
     return if @isEmpty()
     text = @editor.buffer.getTextInRange(@getBufferRange())
-    if maintainPasteboard
-      [currentText, metadata] = atom.pasteboard.read()
-      text = currentText + '\n' + text
+    if maintainClipboard
+      text = "#{atom.clipboard.read()}\n#{text}"
     else
       metadata = { indentBasis: @editor.indentationForBufferRow(@getBufferRange().start.row) }
 
-    atom.pasteboard.write(text, metadata)
+    atom.clipboard.write(text, metadata)
 
   # Public: Creates a fold containing the current selection.
   fold: ->
@@ -541,14 +509,13 @@ class Selection
     @editor.createFold(range.start.row, range.end.row)
     @cursor.setBufferPosition([range.end.row + 1, 0])
 
-  # Public: ?
   modifySelection: (fn) ->
     @retainSelection = true
     @plantTail()
     fn()
     @retainSelection = false
 
-  # Private: Sets the marker's tail to the same position as the marker's head.
+  # Sets the marker's tail to the same position as the marker's head.
   #
   # This only works if there isn't already a tail position.
   #
@@ -558,8 +525,7 @@ class Selection
 
   # Public: Identifies if a selection intersects with a given buffer range.
   #
-  # * bufferRange:
-  #   A {Range} to check against
+  # bufferRange - A {Range} to check against.
   #
   # Returns a Boolean.
   intersectsBufferRange: (bufferRange) ->
@@ -567,8 +533,7 @@ class Selection
 
   # Public: Identifies if a selection intersects with another selection.
   #
-  # * otherSelection:
-  #   A {Selection} to check against
+  # otherSelection - A {Selection} to check against.
   #
   # Returns a Boolean.
   intersectsWith: (otherSelection) ->
@@ -577,10 +542,8 @@ class Selection
   # Public: Combines the given selection into this selection and then destroys
   # the given selection.
   #
-  # * otherSelection:
-  #   A {Selection} to merge with
-  # * options
-  #    + A hash of options matching those found in {.setBufferRange}
+  # otherSelection - A {Selection} to merge with.
+  # options - A hash of options matching those found in {.setBufferRange}.
   merge: (otherSelection, options) ->
     myGoalBufferRange = @getGoalBufferRange()
     otherGoalBufferRange = otherSelection.getGoalBufferRange()
@@ -596,12 +559,10 @@ class Selection
   #
   # See {Range.compare} for more details.
   #
-  # * otherSelection:
-  #   A {Selection} to compare with.
+  # otherSelection - A {Selection} to compare against.
   compare: (otherSelection) ->
     @getBufferRange().compare(otherSelection.getBufferRange())
 
-  # Private:
   screenRangeChanged: ->
     screenRange = @getScreenRange()
     @emit 'screen-range-changed', screenRange
diff --git a/src/space-pen-extensions.coffee b/src/space-pen-extensions.coffee
index abaa242cb..04e411114 100644
--- a/src/space-pen-extensions.coffee
+++ b/src/space-pen-extensions.coffee
@@ -1,18 +1,13 @@
 _ = require 'underscore-plus'
 spacePen = require 'space-pen'
 {Subscriber} = require 'emissary'
-ConfigObserver = require './config-observer'
 
-ConfigObserver.includeInto(spacePen.View)
 Subscriber.includeInto(spacePen.View)
 
 jQuery = spacePen.jQuery
 originalCleanData = jQuery.cleanData
 jQuery.cleanData = (elements) ->
-  for element in elements
-    if view = jQuery(element).view()
-      view.unobserveConfig()
-      view.unsubscribe()
+  jQuery(element).view()?.unsubscribe() for element in elements
   originalCleanData(elements)
 
 tooltipDefaults =
diff --git a/src/syntax.coffee b/src/syntax.coffee
index af1a6278a..881d5fa2a 100644
--- a/src/syntax.coffee
+++ b/src/syntax.coffee
@@ -8,14 +8,13 @@ Token = require './token'
 
 # Public: Syntax class holding the grammars used for tokenizing.
 #
+# An instance of this class is always available as the `atom.syntax` global.
+#
 # The Syntax class also contains properties for things such as the
 # language-specific comment regexes.
-#
-# There is always a syntax object available under the `atom.syntax` global.
 module.exports =
 class Syntax extends GrammarRegistry
   Subscriber.includeInto(this)
-
   atom.deserializers.add(this)
 
   @deserialize: ({grammarOverridesByPath}) ->
@@ -62,8 +61,8 @@ class Syntax extends GrammarRegistry
   # console.log(comment) # '# '
   # ```
   #
-  # * scope: An {Array} of {String} scopes.
-  # * keyPath: A {String} key path.
+  # scope - An {Array} of {String} scopes.
+  # keyPath - A {String} key path.
   #
   # Returns a {String} property value or undefined.
   getProperty: (scope, keyPath) ->
diff --git a/src/task.coffee b/src/task.coffee
index 538bb9f98..8e2b57277 100644
--- a/src/task.coffee
+++ b/src/task.coffee
@@ -24,18 +24,16 @@ class Task
 
   # Public: A helper method to easily launch and run a task once.
   #
-  # * taskPath:
-  #   The path to the Coffeescript/Javascript file which exports a single
-  #   function to execute.
-  # * args:
-  #   The Array of arguments to pass to the exported function.
+  # taskPath - The {String} path to the CoffeeScript/JavaScript file which
+  #            exports a single {Function} to execute.
+  # args     - The arguments to pass to the exported function.
   @once: (taskPath, args...) ->
     task = new Task(taskPath)
     task.once 'task:completed', -> task.terminate()
     task.start(args...)
     task
 
-  # Public: Called upon task completion.
+  # Called upon task completion.
   #
   # It receives the same arguments that were passed to the task.
   #
@@ -45,9 +43,8 @@ class Task
 
   # Public: Creates a task.
   #
-  # * taskPath:
-  #   The path to the Coffeescript/Javascript file that exports a single
-  #   function to execute.
+  # taskPath - The {String} path to the CoffeeScript/JavaScript file that
+  #            exports a single {Function} to execute.
   constructor: (taskPath) ->
     coffeeCacheRequire = "require('#{require.resolve('./coffee-cache')}').register();"
     coffeeScriptRequire = "require('#{require.resolve('coffee-script')}').register();"
@@ -73,7 +70,7 @@ class Task
 
     @handleEvents()
 
-  # Private: Routes messages from the child to the appropriate event.
+  # Routes messages from the child to the appropriate event.
   handleEvents: ->
     @childProcess.removeAllListeners()
     @childProcess.on 'message', ({event, args}) =>
@@ -81,21 +78,21 @@ class Task
 
   # Public: Starts the task.
   #
-  # * args:
-  #   The Array of arguments to pass to the function exported by the script. If
-  #   the last argument is a function, its removed from the array and called
-  #   upon completion (and replaces the complete function on the task instance).
-  start: (args...) ->
+  # args - The arguments to pass to the function exported by this task's script.
+  # callback - An optional {Function} to call when the task completes.
+  start: (args..., callback) ->
     throw new Error("Cannot start terminated process") unless @childProcess?
 
     @handleEvents()
-    @callback = args.pop() if _.isFunction(args[args.length - 1])
+    if _.isFunction(callback)
+      @callback = callback
+    else
+      args = arguments
     @send({event: 'start', args})
 
   # Public: Send message to the task.
   #
-  # * message:
-  #   The message to send
+  # message - The message to send to the task.
   send: (message) ->
     throw new Error("Cannot send message to terminated process") unless @childProcess?
     @childProcess.send(message)
diff --git a/src/text-buffer.coffee b/src/text-buffer.coffee
index 19ea180b9..c884e7e0e 100644
--- a/src/text-buffer.coffee
+++ b/src/text-buffer.coffee
@@ -8,7 +8,7 @@ TextBufferCore = require 'text-buffer'
 
 File = require './file'
 
-# Private: Represents the contents of a file.
+# Represents the contents of a file.
 #
 # The `TextBuffer` is often associated with a {File}. However, this is not always
 # the case, as a `TextBuffer` could be an unsaved chunk of text.
@@ -40,7 +40,6 @@ class TextBuffer extends TextBufferCore
 
     @load() if loadWhenAttached
 
-  # Private:
   serializeParams: ->
     params = super
     _.extend params,
@@ -48,7 +47,6 @@ class TextBuffer extends TextBufferCore
       modifiedWhenLastPersisted: @isModified()
       digestWhenLastPersisted: @file?.getDigest()
 
-  # Private:
   deserializeParams: (params) ->
     params = super(params)
     params.loadWhenAttached = true
@@ -71,8 +69,6 @@ class TextBuffer extends TextBufferCore
       @clearUndoStack()
     this
 
-  ### Internal ###
-
   handleTextChange: (event) =>
     @conflict = false if @conflict and !@isModified()
     @scheduleModifiedEvents()
@@ -127,8 +123,6 @@ class TextBuffer extends TextBufferCore
     @file.on "moved", =>
       @emit "path-changed", this
 
-  ### Public ###
-
   # Identifies if the buffer belongs to multiple editors.
   #
   # For example, if the {EditorView} was split.
@@ -145,11 +139,11 @@ class TextBuffer extends TextBufferCore
     @emitModifiedStatusChanged(false)
     @emit 'reloaded'
 
-  # Private: Rereads the contents of the file, and stores them in the cache.
+  # Rereads the contents of the file, and stores them in the cache.
   updateCachedDiskContentsSync: ->
     @cachedDiskContents = @file?.readSync() ? ""
 
-  # Private: Rereads the contents of the file, and stores them in the cache.
+  # Rereads the contents of the file, and stores them in the cache.
   updateCachedDiskContents: ->
     Q(@file?.read() ? "").then (contents) =>
       @cachedDiskContents = contents
@@ -171,29 +165,20 @@ class TextBuffer extends TextBufferCore
 
   # Sets the path for the file.
   #
-  # path - A {String} representing the new file path
-  setPath: (path) ->
-    return if path == @getPath()
+  # filePath - A {String} representing the new file path
+  setPath: (filePath) ->
+    return if filePath == @getPath()
 
     @file?.off()
 
-    if path
-      @file = new File(path)
+    if filePath
+      @file = new File(filePath)
       @subscribeToFile()
     else
       @file = null
 
     @emit "path-changed", this
 
-  # Retrieves the current buffer's file extension.
-  #
-  # Returns a {String}.
-  getExtension: ->
-    if @getPath()
-      @getPath().split('/').pop().split('.').pop()
-    else
-      null
-
   # Deprecated: Use ::getEndPosition instead
   getEofPosition: -> @getEndPosition()
 
@@ -203,14 +188,15 @@ class TextBuffer extends TextBufferCore
 
   # Saves the buffer at a specific path.
   #
-  # path - The path to save at.
-  saveAs: (path) ->
-    unless path then throw new Error("Can't save buffer with no file path")
+  # filePath - The path to save at.
+  saveAs: (filePath) ->
+    unless filePath then throw new Error("Can't save buffer with no file path")
 
     @emit 'will-be-saved', this
-    @setPath(path)
-    @cachedDiskContents = @getText()
+    @setPath(filePath)
     @file.write(@getText())
+    @cachedDiskContents = @getText()
+    @conflict = false
     @emitModifiedStatusChanged(false)
     @emit 'saved', this
 
@@ -227,7 +213,10 @@ class TextBuffer extends TextBufferCore
     else
       not @isEmpty()
 
-  # Identifies if a buffer is in a git conflict with `HEAD`.
+  # Is the buffer's text in conflict with the text on disk?
+  #
+  # This occurs when the buffer's file changes on disk while the buffer has
+  # unsaved changes.
   #
   # Returns a {Boolean}.
   isInConflict: -> @conflict
@@ -390,8 +379,6 @@ class TextBuffer extends TextBufferCore
         return match[0][0] != '\t'
     undefined
 
-  ### Internal ###
-
   change: (oldRange, newText, options={}) ->
     @setTextInRange(oldRange, newText, options.normalizeLineEndings)
 
diff --git a/src/text-mate-package.coffee b/src/text-mate-package.coffee
index 3daf8d353..5e39ab53b 100644
--- a/src/text-mate-package.coffee
+++ b/src/text-mate-package.coffee
@@ -2,9 +2,7 @@ Package = require './package'
 path = require 'path'
 _ = require 'underscore-plus'
 fs = require 'fs-plus'
-async = require 'async'
-
-### Internal ###
+Q = require 'q'
 
 module.exports =
 class TextMatePackage extends Package
@@ -12,13 +10,12 @@ class TextMatePackage extends Package
     packageName = path.basename(packageName)
     /(^language-.+)|((\.|_|-)tmbundle$)/.test(packageName)
 
-  @getLoadQueue: ->
-    return @loadQueue if @loadQueue
-    @loadQueue = async.queue (pack, done) ->
-      pack.loadGrammars ->
-        pack.loadScopedProperties(done)
-
-    @loadQueue
+  @addToActivationPromise = (pack) ->
+    @activationPromise ?= Q()
+    @activationPromise = @activationPromise.then =>
+      pack.loadGrammars()
+        .then -> pack.loadScopedProperties()
+        .fail (error) -> console.log pack.name, error
 
   constructor: ->
     super
@@ -28,21 +25,16 @@ class TextMatePackage extends Package
 
   getType: -> 'textmate'
 
-  load: ({sync}={}) ->
+  load: ->
     @measure 'loadTime', =>
       @metadata = Package.loadMetadata(@path, true)
 
-      if sync
-        @loadGrammarsSync()
-        @loadScopedPropertiesSync()
-      else
-        TextMatePackage.getLoadQueue().push(this)
+  activate: ({sync, immediate}={})->
+    TextMatePackage.addToActivationPromise(this)
 
-  activate: ->
-    @measure 'activateTime', =>
-      grammar.activate() for grammar in @grammars
-      for { selector, properties } in @scopedProperties
-        atom.syntax.addProperties(@path, selector, properties)
+  activateSync: ->
+    @loadGrammarsSync()
+    @loadScopedPropertiesSync()
 
   activateConfig: -> # noop
 
@@ -52,33 +44,35 @@ class TextMatePackage extends Package
 
   legalGrammarExtensions: ['plist', 'tmLanguage', 'tmlanguage', 'json', 'cson']
 
-  loadGrammars: (done) ->
+  loadGrammars: ->
+    deferred = Q.defer()
     fs.isDirectory @getSyntaxesPath(), (isDirectory) =>
-      if isDirectory
-        fs.list @getSyntaxesPath(), @legalGrammarExtensions, (error, paths) =>
-          if error?
-            console.log("Error loading grammars of TextMate package '#{@path}':", error.stack, error)
-            done()
-          else
-            async.eachSeries(paths, @loadGrammarAtPath, done)
-      else
-        done()
+      return deferred.resolve() unless isDirectory
 
-  loadGrammarAtPath: (grammarPath, done) =>
+      fs.list @getSyntaxesPath(), @legalGrammarExtensions, (error, paths) =>
+        if error?
+          console.log("Error loading grammars of TextMate package '#{@path}':", error.stack, error)
+          deferred.resolve()
+        else
+          promises = paths.map (path) => @loadGrammarAtPath(path)
+          Q.all(promises).then -> deferred.resolve()
+
+    deferred.promise
+
+  loadGrammarAtPath: (grammarPath) ->
+    deferred = Q.defer()
     atom.syntax.readGrammar grammarPath, (error, grammar) =>
       if error?
         console.log("Error loading grammar at path '#{grammarPath}':", error.stack ? error)
       else
         @addGrammar(grammar)
-        done?()
+      deferred.resolve()
 
-  loadGrammarsSync: ->
-    for grammarPath in fs.listSync(@getSyntaxesPath(), @legalGrammarExtensions)
-      @addGrammar(atom.syntax.readGrammarSync(grammarPath))
+    deferred.promise
 
   addGrammar: (grammar) ->
     @grammars.push(grammar)
-    grammar.activate() if @isActive()
+    grammar.activate()
 
   getGrammars: -> @grammars
 
@@ -96,23 +90,7 @@ class TextMatePackage extends Package
     else
       path.join(@path, "Preferences")
 
-  loadScopedPropertiesSync: ->
-    for grammar in @getGrammars()
-      if properties = @propertiesFromTextMateSettings(grammar)
-        selector = atom.syntax.cssSelectorFromScopeSelector(grammar.scopeName)
-        @scopedProperties.push({selector, properties})
-
-    for preferencePath in fs.listSync(@getPreferencesPath())
-      {scope, settings} = fs.readObjectSync(preferencePath)
-      if properties = @propertiesFromTextMateSettings(settings)
-        selector = atom.syntax.cssSelectorFromScopeSelector(scope) if scope?
-        @scopedProperties.push({selector, properties})
-
-    if @isActive()
-      for {selector, properties} in @scopedProperties
-        atom.syntax.addProperties(@path, selector, properties)
-
-  loadScopedProperties: (callback) ->
+  loadScopedProperties: ->
     scopedProperties = []
 
     for grammar in @getGrammars()
@@ -120,38 +98,37 @@ class TextMatePackage extends Package
         selector = atom.syntax.cssSelectorFromScopeSelector(grammar.scopeName)
         scopedProperties.push({selector, properties})
 
-    preferenceObjects = []
-    done = =>
+    @loadTextMatePreferenceObjects().then (preferenceObjects=[]) =>
       for {scope, settings} in preferenceObjects
         if properties = @propertiesFromTextMateSettings(settings)
           selector = atom.syntax.cssSelectorFromScopeSelector(scope) if scope?
           scopedProperties.push({selector, properties})
 
       @scopedProperties = scopedProperties
-      if @isActive()
-        for {selector, properties} in @scopedProperties
-          atom.syntax.addProperties(@path, selector, properties)
-      callback?()
-    @loadTextMatePreferenceObjects(preferenceObjects, done)
+      for {selector, properties} in @scopedProperties
+        atom.syntax.addProperties(@path, selector, properties)
 
-  loadTextMatePreferenceObjects: (preferenceObjects, done) ->
+  loadTextMatePreferenceObjects: ->
+    deferred = Q.defer()
     fs.isDirectory @getPreferencesPath(), (isDirectory) =>
-      return done() unless isDirectory
-
+      return deferred.resolve() unless isDirectory
       fs.list @getPreferencesPath(), (error, paths) =>
         if error?
           console.log("Error loading preferences of TextMate package '#{@path}':", error.stack, error)
-          done()
-          return
+          deferred.resolve()
+        else
+          promises = paths.map (path) => @loadPreferencesAtPath(path)
+          Q.all(promises).then (preferenceObjects) -> deferred.resolve(preferenceObjects)
 
-        loadPreferencesAtPath = (preferencePath, done) ->
-          fs.readObject preferencePath, (error, preferences) =>
-            if error?
-              console.warn("Failed to parse preference at path '#{preferencePath}'", error.stack, error)
-            else
-              preferenceObjects.push(preferences)
-            done()
-        async.eachSeries paths, loadPreferencesAtPath, done
+    deferred.promise
+
+  loadPreferencesAtPath: (preferencePath) ->
+    deferred = Q.defer()
+    fs.readObject preferencePath, (error, preference) ->
+      if error?
+        console.warn("Failed to parse preference at path '#{preferencePath}'", error.stack, error)
+      deferred.resolve(preference)
+    deferred.promise
 
   propertiesFromTextMateSettings: (textMateSettings) ->
     if textMateSettings.shellVariables
@@ -169,3 +146,24 @@ class TextMatePackage extends Package
       completions: textMateSettings.completions
     )
     { editor: editorProperties } if _.size(editorProperties) > 0
+
+  # Deprecated
+  loadGrammarsSync: ->
+    for grammarPath in fs.listSync(@getSyntaxesPath(), @legalGrammarExtensions)
+      @addGrammar(atom.syntax.readGrammarSync(grammarPath))
+
+  # Deprecated
+  loadScopedPropertiesSync: ->
+    for grammar in @getGrammars()
+      if properties = @propertiesFromTextMateSettings(grammar)
+        selector = atom.syntax.cssSelectorFromScopeSelector(grammar.scopeName)
+        @scopedProperties.push({selector, properties})
+
+    for preferencePath in fs.listSync(@getPreferencesPath())
+      {scope, settings} = fs.readObjectSync(preferencePath)
+      if properties = @propertiesFromTextMateSettings(settings)
+        selector = atom.syntax.cssSelectorFromScopeSelector(scope) if scope?
+        @scopedProperties.push({selector, properties})
+
+    for {selector, properties} in @scopedProperties
+      atom.syntax.addProperties(@path, selector, properties)
diff --git a/src/theme-manager.coffee b/src/theme-manager.coffee
index b26d366bf..08ecc0d47 100644
--- a/src/theme-manager.coffee
+++ b/src/theme-manager.coffee
@@ -3,6 +3,7 @@ path = require 'path'
 _ = require 'underscore-plus'
 {Emitter} = require 'emissary'
 fs = require 'fs-plus'
+Q = require 'q'
 
 {$} = require './space-pen-extensions'
 AtomPackage = require './atom-package'
@@ -10,7 +11,7 @@ File = require './file'
 
 # Public: Handles loading and activating available themes.
 #
-# A ThemeManager instance is always available under the `atom.themes` global.
+# An instance of this class is always available as the `atom.themes` global.
 module.exports =
 class ThemeManager
   Emitter.includeInto(this)
@@ -41,7 +42,7 @@ class ThemeManager
 
   activatePackages: (themePackages) -> @activateThemes()
 
-  # Private: Get the enabled theme names from the config.
+  # Get the enabled theme names from the config.
   #
   # Returns an array of theme names in the order that they should be activated.
   getEnabledThemeNames: ->
@@ -53,19 +54,22 @@ class ThemeManager
     themeNames.reverse()
 
   activateThemes: ->
+    deferred = Q.defer()
+
     # atom.config.observe runs the callback once, then on subsequent changes.
     atom.config.observe 'core.themes', =>
       @deactivateThemes()
 
       @refreshLessCache() # Update cache for packages in core.themes config
-      for themeName in @getEnabledThemeNames()
-        @packageManager.activatePackage(themeName)
+      promises = @getEnabledThemeNames().map (themeName) => @packageManager.activatePackage(themeName)
+      Q.all(promises).then =>
+        @refreshLessCache() # Update cache again now that @getActiveThemes() is populated
+        @loadUserStylesheet()
+        @reloadBaseStylesheets()
+        @emit('reloaded')
+        deferred.resolve()
 
-      @refreshLessCache() # Update cache again now that @getActiveThemes() is populated
-      @loadUserStylesheet()
-      @reloadBaseStylesheets()
-
-      @emit('reloaded')
+    deferred.promise
 
   deactivateThemes: ->
     @unwatchUserStylesheet()
@@ -77,7 +81,7 @@ class ThemeManager
 
   # Public: Set the list of enabled themes.
   #
-  # * enabledThemeNames: An {Array} of {String} theme names.
+  # enabledThemeNames - An {Array} of {String} theme names.
   setEnabledThemes: (enabledThemeNames) ->
     atom.config.set('core.themes', enabledThemeNames)
 
@@ -91,7 +95,7 @@ class ThemeManager
         if themePath = @packageManager.resolvePackagePath(themeName)
           themePaths.push(path.join(themePath, AtomPackage.stylesheetsDir))
 
-    themePath for themePath in themePaths when fs.isDirectorySync(themePath)
+    themePaths.filter (themePath) -> fs.isDirectorySync(themePath)
 
   # Public: Returns the {String} path to the user's stylesheet under ~/.atom
   getUserStylesheetPath: ->
@@ -140,8 +144,9 @@ class ThemeManager
   #
   # This supports both CSS and LESS stylsheets.
   #
-  # * stylesheetPath: A {String} path to the stylesheet that can be an absolute
-  #   path or a relative path that will be resolved against the load path.
+  # stylesheetPath - A {String} path to the stylesheet that can be an absolute
+  #                  path or a relative path that will be resolved against the
+  #                  load path.
   #
   # Returns the absolute path to the required stylesheet.
   requireStylesheet: (stylesheetPath, ttype = 'bundled', htmlElement) ->
diff --git a/src/theme-package.coffee b/src/theme-package.coffee
index 2115276fd..2d4f611a6 100644
--- a/src/theme-package.coffee
+++ b/src/theme-package.coffee
@@ -1,11 +1,8 @@
+Q = require 'q'
 AtomPackage = require './atom-package'
-Package = require './package'
-
-### Internal: Loads and resolves packages. ###
 
 module.exports =
 class ThemePackage extends AtomPackage
-
   getType: -> 'theme'
 
   getStylesheetType: -> 'theme'
@@ -25,6 +22,11 @@ class ThemePackage extends AtomPackage
     this
 
   activate: ->
+    return @activationDeferred.promise if @activationDeferred?
+
+    @activationDeferred = Q.defer()
     @measure 'activateTime', =>
       @loadStylesheets()
       @activateNow()
+
+    @activationDeferred.promise
diff --git a/src/token.coffee b/src/token.coffee
index 058f73fb5..366c6a394 100644
--- a/src/token.coffee
+++ b/src/token.coffee
@@ -12,7 +12,7 @@ WhitespaceRegex = /\S/
 
 MaxTokenLength = 20000
 
-# Private: Represents a single unit of text as selected by a grammar.
+# Represents a single unit of text as selected by a grammar.
 module.exports =
 class Token
   value: null
@@ -21,15 +21,11 @@ class Token
   isAtomic: null
   isHardTab: null
 
-  ### Internal ###
-
   constructor: ({@value, @scopes, @isAtomic, @bufferDelta, @isHardTab}) ->
     @screenDelta = @value.length
     @bufferDelta ?= @screenDelta
     @hasSurrogatePair = textUtils.hasSurrogatePair(@value)
 
-  ### Public ###
-
   isEqual: (other) ->
     @value == other.value and _.isEqual(@scopes, other.scopes) and !!@isAtomic == !!other.isAtomic
 
diff --git a/src/tokenized-buffer.coffee b/src/tokenized-buffer.coffee
index f6a4c3681..7ee7d1682 100644
--- a/src/tokenized-buffer.coffee
+++ b/src/tokenized-buffer.coffee
@@ -5,8 +5,6 @@ Serializable = require 'serializable'
 TokenizedLine = require './tokenized-line'
 Token = require './token'
 
-### Internal ###
-
 module.exports =
 class TokenizedBuffer extends Model
   Serializable.includeInto(this)
diff --git a/src/tokenized-line.coffee b/src/tokenized-line.coffee
index 826fdfd5c..75a09497c 100644
--- a/src/tokenized-line.coffee
+++ b/src/tokenized-line.coffee
@@ -1,7 +1,5 @@
 _ = require 'underscore-plus'
 
-### Internal ###
-
 module.exports =
 class TokenizedLine
   constructor: ({tokens, @lineEnding, @ruleStack, @startBufferColumn, @fold, tabLength}) ->
diff --git a/src/window-bootstrap.coffee b/src/window-bootstrap.coffee
index dc8c46c42..42ec7cd91 100644
--- a/src/window-bootstrap.coffee
+++ b/src/window-bootstrap.coffee
@@ -1,9 +1,6 @@
 # Like sands through the hourglass, so are the days of our lives.
 startTime = Date.now()
 
-# Start the crash reporter before anything else.
-require('crash-reporter').start(productName: 'Atom', companyName: 'GitHub')
-
 require './window'
 
 Atom = require './atom'
diff --git a/src/window-event-handler.coffee b/src/window-event-handler.coffee
index 751c7ca19..8cf637cc6 100644
--- a/src/window-event-handler.coffee
+++ b/src/window-event-handler.coffee
@@ -5,7 +5,7 @@ shell = require 'shell'
 {Subscriber} = require 'emissary'
 fs = require 'fs-plus'
 
-# Private: Handles low-level events related to the window.
+# Handles low-level events related to the window.
 module.exports =
 class WindowEventHandler
   Subscriber.includeInto(this)
@@ -75,7 +75,7 @@ class WindowEventHandler
 
     @handleNativeKeybindings()
 
-  # Private: Wire commands that should be handled by the native menu
+  # Wire commands that should be handled by the native menu
   # for elements with the `.native-key-bindings` class.
   handleNativeKeybindings: ->
     menu = null
diff --git a/src/window.coffee b/src/window.coffee
index 891515ed9..9554218ca 100644
--- a/src/window.coffee
+++ b/src/window.coffee
@@ -1,9 +1,8 @@
 # Public: Measure how long a function takes to run.
 #
-# * description:
-#   A {String} description that will be logged to the console.
-# * fn:
-#   A {Function} to measure the duration of.
+# description - A {String} description that will be logged to the console when
+#               the function completes.
+# fn - A {Function} to measure the duration of.
 #
 # Returns the value returned by the given function.
 window.measure = (description, fn) ->
@@ -15,13 +14,11 @@ window.measure = (description, fn) ->
 
 # Public: Create a dev tools profile for a function.
 #
-# * description:
-#   A {String} descrption that will be available in the Profiles tab of the dev
-#   tools.
-# * fn:
-#   A {Function} to profile.
+# description - A {String} description that will be available in the Profiles
+#               tab of the dev tools.
+# fn - A {Function} to profile.
 #
-# Return the value returned by the given function.
+# Returns the value returned by the given function.
 window.profile = (description, fn) ->
   measure description, ->
     console.profile(description)
diff --git a/src/workspace-view.coffee b/src/workspace-view.coffee
index a45b86b04..a83253a89 100644
--- a/src/workspace-view.coffee
+++ b/src/workspace-view.coffee
@@ -16,6 +16,9 @@ Editor = require './editor'
 
 # Public: The container for the entire Atom application.
 #
+# An instance of this class is always available as the `atom.workspaceView`
+# global.
+#
 # ## Commands
 #
 #  * `application:about` - Opens the about dialog.
@@ -48,7 +51,7 @@ class WorkspaceView extends View
   Delegator.includeInto(this)
 
   @delegatesProperty 'fullScreen', 'destroyedItemUris', toProperty: 'model'
-  @delegatesMethods 'open', 'openSync', 'openSingletonSync', 'reopenItemSync',
+  @delegatesMethods 'open', 'openSync', 'reopenItemSync',
     'saveActivePaneItem', 'saveActivePaneItemAs', 'saveAll', 'destroyActivePaneItem',
     'destroyActivePane', 'increaseFontSize', 'decreaseFontSize', toProperty: 'model'
 
@@ -63,14 +66,12 @@ class WorkspaceView extends View
     audioBeep: true
     destroyEmptyPanes: false
 
-  # Private:
   @content: ->
     @div class: 'workspace', tabindex: -1, =>
       @div class: 'horizontal', outlet: 'horizontal', =>
         @div class: 'vertical', outlet: 'vertical', =>
           @div class: 'panes', outlet: 'panes'
 
-  # Private:
   initialize: (@model) ->
     @model ?= new Workspace
 
@@ -106,6 +107,7 @@ class WorkspaceView extends View
     @command 'application:zoom', -> ipc.sendChannel('command', 'application:zoom')
     @command 'application:bring-all-windows-to-front', -> ipc.sendChannel('command', 'application:bring-all-windows-to-front')
     @command 'application:open-your-config', -> ipc.sendChannel('command', 'application:open-your-config')
+    @command 'application:open-your-init-script', -> ipc.sendChannel('command', 'application:open-your-init-script')
     @command 'application:open-your-keymap', -> ipc.sendChannel('command', 'application:open-your-keymap')
     @command 'application:open-your-snippets', -> ipc.sendChannel('command', 'application:open-your-snippets')
     @command 'application:open-your-stylesheet', -> ipc.sendChannel('command', 'application:open-your-stylesheet')
@@ -115,9 +117,14 @@ class WorkspaceView extends View
     @command 'window:run-package-specs', => ipc.sendChannel('run-package-specs', path.join(atom.project.getPath(), 'spec'))
     @command 'window:increase-font-size', => @increaseFontSize()
     @command 'window:decrease-font-size', => @decreaseFontSize()
+    @command 'window:reset-font-size', => @model.resetFontSize()
 
     @command 'window:focus-next-pane', => @focusNextPane()
     @command 'window:focus-previous-pane', => @focusPreviousPane()
+    @command 'window:focus-pane-above', => @focusPaneAbove()
+    @command 'window:focus-pane-below', => @focusPaneBelow()
+    @command 'window:focus-pane-on-left', => @focusPaneOnLeft()
+    @command 'window:focus-pane-on-right', => @focusPaneOnRight()
     @command 'window:save-all', => @saveAll()
     @command 'window:toggle-invisibles', =>
       atom.config.toggle("editor.showInvisibles")
@@ -135,23 +142,22 @@ class WorkspaceView extends View
     showErrorDialog = (error) ->
       installDirectory = CommandInstaller.getInstallDirectory()
       atom.confirm
-        message: error.message
-        detailedMessage: "Make sure #{installDirectory} exists and is writable. Run 'sudo mkdir -p #{installDirectory} && sudo chown $USER #{installDirectory}' to fix this problem."
+        message: "Failed to install shell commands"
+        detailedMessage: error.message
 
     resourcePath = atom.getLoadSettings().resourcePath
-    CommandInstaller.installAtomCommand resourcePath, (error) =>
+    CommandInstaller.installAtomCommand resourcePath, true, (error) =>
       if error?
-        showDialog(error)
+        showErrorDialog(error)
       else
-        CommandInstaller.installApmCommand resourcePath, (error) =>
+        CommandInstaller.installApmCommand resourcePath, true, (error) =>
           if error?
-            showDialog(error)
+            showErrorDialog(error)
           else
             atom.confirm
               message: "Commands installed."
               detailedMessage: "The shell commands `atom` and `apm` are installed."
 
-  # Private:
   handleFocus: (e) ->
     if @getActivePane()
       @getActivePane().focus()
@@ -166,7 +172,6 @@ class WorkspaceView extends View
         $(document.body).focus()
         true
 
-  # Private:
   afterAttach: (onDom) ->
     @focus() if onDom
 
@@ -188,7 +193,7 @@ class WorkspaceView extends View
   setTitle: (title) ->
     document.title = title
 
-  # Private: Returns an Array of  all of the application's {EditorView}s.
+  # Returns an Array of  all of the application's {EditorView}s.
   getEditorViews: ->
     @panes.find('.pane > .item-views > .editor').map(-> $(this).view()).toArray()
 
@@ -225,9 +230,13 @@ class WorkspaceView extends View
     @horizontal.append(element)
 
   # Public: Returns the currently focused {PaneView}.
-  getActivePane: ->
+  getActivePaneView: ->
     @panes.getActivePane()
 
+  # Deprecated: Returns the currently focused {PaneView}.
+  getActivePane: ->
+    @getActivePaneView()
+
   # Public: Returns the currently focused item from within the focused {PaneView}
   getActivePaneItem: ->
     @model.activePaneItem
@@ -242,6 +251,18 @@ class WorkspaceView extends View
   # Public: Focuses the next pane by id.
   focusNextPane: -> @model.activateNextPane()
 
+  # Public: Focuses the pane directly above the active pane.
+  focusPaneAbove: -> @panes.focusPaneAbove()
+
+  # Public: Focuses the pane directly below the active pane.
+  focusPaneBelow: -> @panes.focusPaneBelow()
+
+  # Public: Focuses the pane directly to the left of the active pane.
+  focusPaneOnLeft: -> @panes.focusPaneOnLeft()
+
+  # Public: Focuses the pane directly to the right of the active pane.
+  focusPaneOnRight: -> @panes.focusPaneOnRight()
+
   # Public:
   #
   # FIXME: Difference between active and focused pane?
@@ -266,11 +287,11 @@ class WorkspaceView extends View
     @on('editor:attached', attachedCallback)
     off: => @off('editor:attached', attachedCallback)
 
-  # Private: Called by SpacePen
+  # Called by SpacePen
   beforeRemove: ->
     @model.destroy()
 
-  # Private: Destroys everything.
+  # Destroys everything.
   remove: ->
     editorView.remove() for editorView in @getEditorViews()
     super
diff --git a/src/workspace.coffee b/src/workspace.coffee
index 21663bb59..8b8138b67 100644
--- a/src/workspace.coffee
+++ b/src/workspace.coffee
@@ -7,8 +7,9 @@ PaneContainer = require './pane-container'
 Pane = require './pane'
 
 # Public: Represents the view state of the entire window, including the panes at
-# the center and panels around the periphery. You can access the singleton
-# instance via `atom.workspace`.
+# the center and panels around the periphery.
+#
+# An instance of this class is always available as the `atom.workspace` global.
 module.exports =
 class Workspace extends Model
   atom.deserializers.add(this)
@@ -23,11 +24,10 @@ class Workspace extends Model
     fullScreen: false
     destroyedItemUris: -> []
 
-  # Private:
   constructor: ->
     super
     @subscribe @paneContainer, 'item-destroyed', @onPaneItemDestroyed
-    atom.project.registerOpener (filePath) =>
+    @registerOpener (filePath) =>
       switch filePath
         when 'atom://.atom/stylesheet'
           @open(atom.themes.getUserStylesheetPath())
@@ -35,93 +35,126 @@ class Workspace extends Model
           @open(atom.keymap.getUserKeymapPath())
         when 'atom://.atom/config'
           @open(atom.config.getUserConfigPath())
+        when 'atom://.atom/init-script'
+          @open(atom.getUserInitScriptPath())
 
-  # Private: Called by the Serializable mixin during deserialization
+  # Called by the Serializable mixin during deserialization
   deserializeParams: (params) ->
     params.paneContainer = PaneContainer.deserialize(params.paneContainer)
     params
 
-  # Private: Called by the Serializable mixin during serialization.
+  # Called by the Serializable mixin during serialization.
   serializeParams: ->
     paneContainer: @paneContainer.serialize()
     fullScreen: atom.isFullScreen()
 
+  # Public: Calls callback for every existing {Editor} and for all new {Editors}
+  # that are created.
+  #
+  # callback - A {Function} with an {Editor} as its only argument
+  eachEditor: (callback) ->
+    atom.project.eachEditor(callback)
+
+  # Public: Returns an {Array} of all open {Editor}s.
+  getEditors: ->
+    atom.project.getEditors()
+
   # Public: Asynchronously opens a given a filepath in Atom.
   #
-  # * filePath: A file path
-  # * options
-  #   + initialLine: The buffer line number to open to.
+  # uri - A {String} uri.
+  # options  - An options {Object} (default: {}).
+  #   :initialLine - A {Number} indicating which line number to open to.
+  #   :split - A {String} ('left' or 'right') that opens the filePath in a new
+  #            pane or an existing one if it exists.
+  #   :changeFocus - A {Boolean} that allows the filePath to be opened without
+  #                  changing focus.
+  #   :searchAllPanes - A {Boolean} that will open existing editors from any pane
+  #                     if the uri is already open (default: false)
   #
   # Returns a promise that resolves to the {Editor} for the file URI.
-  open: (filePath, options={}) ->
-    changeFocus = options.changeFocus ? true
-    filePath = atom.project.resolve(filePath)
-    initialLine = options.initialLine
-    activePane = @activePane
+  open: (uri, options={}) ->
+    searchAllPanes = options.searchAllPanes
+    split = options.split
+    uri = atom.project.relativize(uri) ? ''
 
-    editor = activePane.itemForUri(atom.project.relativize(filePath)) if activePane and filePath
-    promise = atom.project.open(filePath, {initialLine}) if not editor
+    pane = switch split
+      when 'left'
+        @activePane.findLeftmostSibling()
+      when 'right'
+        @activePane.findOrCreateRightmostSibling()
+      else
+        if searchAllPanes
+          @paneContainer.paneForUri(uri) ? @activePane
+        else
+          @activePane
 
-    Q(editor ? promise)
-      .then (editor) =>
-        if not activePane
-          activePane = new Pane(items: [editor])
-          @paneContainer.root = activePane
+    @openUriInPane(uri, pane, options)
 
-        @itemOpened(editor)
-        activePane.activateItem(editor)
-        activePane.activate() if changeFocus
-        @emit "uri-opened"
-        editor
-      .catch (error) ->
-        console.error(error.stack ? error)
-
-  # Private: Only used in specs
+  # Only used in specs
   openSync: (uri, options={}) ->
     {initialLine} = options
     # TODO: Remove deprecated changeFocus option
     activatePane = options.activatePane ? options.changeFocus ? true
-    uri = atom.project.relativize(uri)
+    uri = atom.project.relativize(uri) ? ''
 
-    if uri?
-      editor = @activePane.itemForUri(uri) ? atom.project.openSync(uri, {initialLine})
-    else
-      editor = atom.project.openSync()
+    item = @activePane.itemForUri(uri)
+    if uri
+      item ?= opener(atom.project.resolve(uri), options) for opener in @getOpeners() when !item
+    item ?= atom.project.openSync(uri, {initialLine})
 
-    @activePane.activateItem(editor)
-    @itemOpened(editor)
+    @activePane.activateItem(item)
+    @itemOpened(item)
     @activePane.activate() if activatePane
-    editor
+    item
 
-  # Public: Synchronously open an editor for the given URI or activate an existing
-  # editor in any pane if one already exists.
-  openSingletonSync: (uri, options={}) ->
-    {initialLine, split} = options
-    # TODO: Remove deprecated changeFocus option
-    activatePane = options.activatePane ? options.changeFocus ? true
-    uri = atom.project.relativize(uri)
+  openUriInPane: (uri, pane, options={}) ->
+    changeFocus = options.changeFocus ? true
 
-    if pane = @paneContainer.paneForUri(uri)
-      editor = pane.itemForUri(uri)
-    else
-      pane = switch split
-        when 'left'
-          @activePane.findLeftmostSibling()
-        when 'right'
-          @activePane.findOrCreateRightmostSibling()
-        else
-          @activePane
-      editor = atom.project.openSync(uri, {initialLine})
+    item = pane.itemForUri(uri)
+    if uri
+      item ?= opener(atom.project.resolve(uri), options) for opener in @getOpeners() when !item
+    item ?= atom.project.open(uri, options)
 
-    pane.activateItem(editor)
-    pane.activate() if activatePane
-    editor
+    Q(item)
+      .then (item) =>
+        if not pane
+          pane = new Pane(items: [item])
+          @paneContainer.root = pane
+        @itemOpened(item)
+        pane.activateItem(item)
+        pane.activate() if changeFocus
+        @emit "uri-opened"
+        item
+      .catch (error) ->
+        console.error(error.stack ? error)
 
   # Public: Reopens the last-closed item uri if it hasn't already been reopened.
   reopenItemSync: ->
     if uri = @destroyedItemUris.pop()
       @openSync(uri)
 
+  # Public: Register an opener for a uri.
+  #
+  # An {Editor} will be used if no openers return a value.
+  #
+  # ## Example
+  # ```coffeescript
+  #   atom.project.registerOpener (uri) ->
+  #     if path.extname(uri) is '.toml'
+  #       return new TomlEditor(uri)
+  # ```
+  #
+  # opener - A {Function} to be called when a path is being opened.
+  registerOpener: (opener) ->
+    atom.project.registerOpener(opener)
+
+  # Public: Remove a registered opener.
+  unregisterOpener: (opener) ->
+    atom.project.unregisterOpener(opener)
+
+  getOpeners: ->
+    atom.project.openers
+
   # Public: save the active item.
   saveActivePaneItem: ->
     @activePane?.saveActiveItem()
@@ -138,6 +171,11 @@ class Workspace extends Model
   destroyActivePane: ->
     @activePane?.destroy()
 
+  # Public: Returns an {Editor} if the active pane item is an {Editor},
+  # or null otherwise.
+  getActiveEditor: ->
+    @activePane?.getActiveEditor()
+
   increaseFontSize: ->
     atom.config.set("editor.fontSize", atom.config.get("editor.fontSize") + 1)
 
@@ -145,16 +183,19 @@ class Workspace extends Model
     fontSize = atom.config.get("editor.fontSize")
     atom.config.set("editor.fontSize", fontSize - 1) if fontSize > 1
 
-  # Private: Removes the item's uri from the list of potential items to reopen.
+  resetFontSize: ->
+    atom.config.restoreDefault("editor.fontSize")
+
+  # Removes the item's uri from the list of potential items to reopen.
   itemOpened: (item) ->
     if uri = item.getUri?()
       remove(@destroyedItemUris, uri)
 
-  # Private: Adds the destroyed item's uri to the list of items to reopen.
+  # Adds the destroyed item's uri to the list of items to reopen.
   onPaneItemDestroyed: (item) =>
     if uri = item.getUri?()
       @destroyedItemUris.push(uri)
 
-  # Private: Called by Model superclass when destroyed
+  # Called by Model superclass when destroyed
   destroyed: ->
     @paneContainer.destroy()
diff --git a/static/index.html b/static/index.html
index ebc054082..990e08915 100644
--- a/static/index.html
+++ b/static/index.html
@@ -6,15 +6,28 @@
   <script>
     window.onload = function() {
       var path = require('path');
-      var currentWindow = require('remote').getCurrentWindow();
+      var ipc = require('ipc');
       try {
+        // Skip "?loadSettings=".
+        var loadSettings = JSON.parse(decodeURIComponent(location.search.substr(14)));
+
+        // Start the crash reporter before anything else.
+        require('crash-reporter').start({
+          productName: 'Atom',
+          companyName: 'GitHub',
+          // By explicitly passing the app version here, we could save the call
+          // of "require('remote').require('app').getVersion()".
+          extra: {_version: loadSettings.appVersion}
+        });
+
         require('vm-compatibility-layer');
         require('coffee-script').register();
         require(path.resolve(__dirname, '..', 'src', 'coffee-cache')).register();
-        require(currentWindow.loadSettings.bootstrapScript);
-        currentWindow.emit('window:loaded');
+        require(loadSettings.bootstrapScript);
+        ipc.sendChannel('window-command', 'window:loaded')
       }
       catch (error) {
+        var currentWindow = require('remote').getCurrentWindow();
         currentWindow.setSize(800, 600);
         currentWindow.center();
         currentWindow.show();
diff --git a/static/jasmine.less b/static/jasmine.less
index 7c2084807..432f44c0f 100644
--- a/static/jasmine.less
+++ b/static/jasmine.less
@@ -1,171 +1,164 @@
-@import "octicon-mixins.less";
+@import "octicon-mixins";
 
-@font-face { .octicon-font(); }
+#jasmine_content {
+  position: fixed;
+  right: 100%;
+}
 
 body {
-  background-color: #ddd;
+  background-color: #fff;
   padding: 0;
 }
 
-.spec-popup {
-  position: absolute;
-  background-color: #ddd;
-  border: 2px solid black;
-  padding: 5px;
-  font-size: 13px;
-  display: none;
-}
-
-.list-unstyled {
-  list-style: none;
-}
-
-#HTMLReporter { font-size: 11px; font-family: Monaco, Consolas, monospace; line-height: 1.6em; color: #333333; }
-#HTMLReporter #jasmine_content { position: fixed; right: 100%; }
-
-#HTMLReporter .symbolHeader {
-  background-color: #222;
-  color: #c2c2c2;
-  font-size: 12px;
-  margin: 0;
-  padding: 5px 2px 2px 2px;
-}
-
-#HTMLReporter .symbolSummary {
-  background-color: #222;
-  overflow: hidden;
-  margin: 0;
-}
-
-#HTMLReporter .symbolSummary li {
-  float: left;
-  line-height: 10px;
-  height: 10px;
-  width: 10px;
-  font-size: 10px;
-}
-
-#HTMLReporter .symbolSummary li.passed { color: #63AD75 }
-#HTMLReporter .symbolSummary li.failed { color: #FF3F05 }
-#HTMLReporter .symbolSummary li.skipped { color: #444 }
-#HTMLReporter .symbolSummary li.pending { color: #111 }
-
-#HTMLReporter .symbolSummary li:before { content: "\02022"; }
-
-#HTMLReporter .symbolSummary li:hover {
-  color: white;
-}
-
-#HTMLReporter .status {
-  font-size: 20px;
-  color: #222;
-  background-color: #E5FFC0;
-  line-height: 2em;
-  padding: 2px;
-  border: 2px solid #222;
-  border-left: 0;
-  border-right: 0;
-  text-align: center;
-}
-
-#HTMLReporter .status.failed {
-  color: white;
-  background-color: rgba(204,51,63,1.0);
-}
-
-#HTMLReporter .status .spec-count {
-  float: left;
-}
-
-#HTMLReporter .status .message {
-}
-
-#HTMLReporter .status .time {
-  float: right;
-}
-
-#HTMLReporter .results .suite + .suite, #HTMLReporter .results .spec + .spec {
-  border-radius: 0;
-}
-
-#HTMLReporter .results .suite, #HTMLReporter .results .spec {
-  border: 2px solid #222;
-  border-radius: 7px 0 0 0;
-  border-right: none;
-  border-bottom: none;
-  padding: 5px;
-  padding-right: 0;
-  padding-bottom: 0;
-}
-
-#HTMLReporter .results .suite:first-child {
-  border-radius: 0;
-  border: 2px solid #6A4A3C;
-  border-top: 0;
-  border-left: 0;
-  border-right: 0;
-}
-
-#HTMLReporter .results .suite {
-  border: 2px solid #6A4A3C;
-  border-radius: 7px 0 0 0;
-  border-right: none;
-  border-bottom: none;
-  padding: 5px;
-  padding-right: 0;
-  padding-bottom: 0;
-  background-color:rgba(204,51,63,0.33);
-}
-
-#HTMLReporter .results .spec {
-  padding: 10px;
-  background-color:rgba(204,51,63,1.0);
-}
-
-#HTMLReporter .results .suite > .suite, #HTMLReporter .results .suite > .spec {
-  margin-left: 5px
-}
-
-#HTMLReporter .results .description {
-  color: white;
-  font-size: 15px;
-  padding-bottom: 10px
-}
-
-#HTMLReporter .results .spec .spec-toggle {
-  font-family: Octicons Regular;
-  color: white;
-  font-size: 20px;
-  float: right;
-  cursor: pointer;
-  text-shadow: 3px 3px #222;
-  opacity: 0;
-}
-
-#HTMLReporter .results .spec .spec-toggle:hover {
-  text-shadow: none;
-  padding-top: 3px;
-}
-
-#HTMLReporter .results .spec:hover .spec-toggle {
-  opacity: 1;
-}
-
-#HTMLReporter .resultMessage {
-  padding-top: 5px;
-  color: #fff;
-  font-size: 15px
-}
-
-#HTMLReporter .stackTrace {
-  font-size: 12px;
-  padding: 5px;
-  margin: 5px 0 0 0;
-  border-radius: 2px;
-  line-height: 18px;
-  color: #666666;
-  border: 1px solid #ddd;
-  background: white;
-  white-space: pre;
-  overflow: auto;
+.spec-reporter {
+  font-size: 11px;
+  line-height: 1.6em;
+  color: #333;
+
+  .list-unstyled {
+    list-style: none;
+  }
+
+  .symbol-header {
+    font-size: 18px;
+    font-weight: bold;
+    padding-bottom: 10px;
+  }
+
+  .symbol-area {
+    padding: 10px;
+  }
+
+  .symbol-summary {
+    overflow: hidden;
+    margin: 0;
+
+    li {
+      font-family: Monaco, Consolas, monospace;
+      float: left;
+      line-height: 10px;
+      height: 10px;
+      width: 10px;
+      font-size: 10px;
+
+      &.passed {
+        color: #5cb85c;
+      }
+
+      &.failed {
+        color: #d9534f;
+      }
+
+      &.skipped {
+        color: #f0ad4e;
+      }
+
+      &.pending {
+        color: #eee;
+      }
+
+      &:before {
+        content: "\02022";
+      }
+    }
+  }
+
+  .status {
+    font-size: 20px;
+    line-height: 2em;
+    padding: 5px;
+    border-radius: 0;
+    text-align: center;
+
+    .spec-count {
+      float: left;
+    }
+
+    .time {
+      float: right;
+    }
+  }
+
+  .results {
+    padding: 10px;
+
+    .description {
+      font-size: 16px;
+      padding: 5px 0 5px 0;
+    }
+
+    > .suite {
+      > .description {
+        font-size: 18px;
+        font-weight: bold;
+      }
+
+      margin-bottom: 20px;
+    }
+
+    .spec {
+      margin-top: 5px;
+      padding: 0 10px 10px 10px;
+      border-left: 3px solid #d9534f;
+
+      .spec-toggle {
+        .octicon(fold);
+        float: right;
+        cursor: pointer;
+        opacity: 0;
+        color: #999;
+
+        &.folded {
+          .octicon(unfold);
+        }
+      }
+
+      .spec-toggle:hover {
+        color: #333;
+      }
+
+      &:hover .spec-toggle {
+        opacity: 1;
+      }
+    }
+
+    .suite > .suite,
+    .suite > .spec {
+      margin-left: 10px;
+    }
+  }
+
+  .result-message {
+    font-size: 16px;
+    font-weight: bold;
+    color: #d9534f;
+    padding: 5px 0 5px 0;
+  }
+
+  .stack-trace {
+    font-size: 12px;
+    margin: 5px 0 0 0;
+    border-radius: 2px;
+    line-height: 18px;
+    color: #666;
+    border: 1px solid #ddd;
+    overflow: auto;
+  }
+
+  .tooltip {
+    .tooltip-inner {
+      border: 1px solid #ccc;
+      background: #fff;
+      color: #666;
+      max-width: 400px;
+    }
+
+    &.in {
+      opacity: 1;
+    }
+
+    .tooltip-arrow {
+      visibility: hidden;
+    }
+  }
 }
diff --git a/vendor/apm b/vendor/apm
index 739a3ec59..af40a0ed5 160000
--- a/vendor/apm
+++ b/vendor/apm
@@ -1 +1 @@
-Subproject commit 739a3ec593ff32dab65e4e1b4682994cb8300324
+Subproject commit af40a0ed55a5df3e8f7a7707e17ab2493edb94a3