Update style guide

Signed-off-by: Max Brunsfeld <maxbrunsfeld@gmail.com>

CONTRIBUTING.md

@@ -87,6 +87,7 @@ For more information on how to work with Atom's official packages, see
     * :white_check_mark: `:white_check_mark:` when adding tests
     * :lock: `:lock:` when dealing with security
     * :arrow_up: `:arrow_up:` when upgrading dependencies
+    * :arrow_down: `:arrow_down:` when downgrading dependencies
 
 ## CoffeeScript Styleguide
 
@@ -98,6 +99,10 @@ For more information on how to work with Atom's official packages, see
 * Avoid spaces inside the curly-braces of hash literals:
     * `{a: 1, b: 2}` instead of `{ a: 1, b: 2 }`
 * Include a single line of whitespace between methods.
+* Capitalize initialisms and acronyms in names, except for the first word, which
+  should be lower-case:
+  * `getURI` instead of `getUri`
+  * `uriToOpen` instead of `URIToOpen`
 
 ## Documentation Styleguide
 

apm/package.json

@@ -6,6 +6,6 @@
     "url": "https://github.com/atom/atom.git"
   },
   "dependencies": {
-    "atom-package-manager": "0.116.0"
+    "atom-package-manager": "0.119.0"
   }
 }

build/package.json

@@ -12,19 +12,19 @@
     "fs-plus": "2.x",
     "github-releases": "~0.2.0",
     "grunt": "~0.4.1",
-    "grunt-atom-shell-installer": "^0.13.0",
+    "grunt-atom-shell-installer": "^0.16.0",
     "grunt-cli": "~0.1.9",
     "grunt-coffeelint": "git+https://github.com/atom/grunt-coffeelint.git#cfb99aa99811d52687969532bd5a98011ed95bfe",
-    "grunt-contrib-coffee": "~0.9.0",
+    "grunt-contrib-coffee": "~0.12.0",
     "grunt-contrib-csslint": "~0.1.2",
     "grunt-contrib-less": "~0.8.0",
-    "grunt-cson": "0.10.0",
+    "grunt-cson": "0.11.0",
     "grunt-download-atom-shell": "~0.10.0",
     "grunt-lesslint": "0.13.0",
     "grunt-peg": "~1.1.0",
     "grunt-shell": "~0.3.1",
     "harmony-collections": "~0.3.8",
-    "legal-eagle": "~0.6.0",
+    "legal-eagle": "~0.8.0",
     "minidump": "~0.8",
     "npm": "~1.4.5",
     "rcedit": "~0.3.0",

build/tasks/build-task.coffee

@@ -71,6 +71,7 @@ module.exports = (grunt) ->
       path.join('build', 'Release', 'obj')
       path.join('build', 'Release', '.deps')
       path.join('vendor', 'apm')
+      path.join('resources', 'linux')
       path.join('resources', 'mac')
       path.join('resources', 'win')
 

build/tasks/install-task.coffee

@@ -1,4 +1,3 @@
-fs = require 'fs'
 path = require 'path'
 _ = require 'underscore-plus'
 fs = require 'fs-plus'

build/tasks/publish-build-task.coffee

@@ -101,7 +101,7 @@ getAssets = ->
 logError = (message, error, details) ->
   grunt.log.error(message)
   grunt.log.error(error.message ? error) if error?
-  grunt.log.error(details) if details
+  grunt.log.error(require('util').inspect(details)) if details
 
 zipAssets = (buildDir, assets, callback) ->
   zip = (directory, sourcePath, assetName, callback) ->
@@ -142,7 +142,30 @@ getAtomDraftRelease = (callback) ->
             firstDraft.assets = assets
             callback(null, firstDraft)
       else
-        callback(new Error('No draft release in atom/atom repo'))
+        createAtomDraftRelease(callback)
+
+createAtomDraftRelease = (callback) ->
+  {version} = require('../../package.json')
+  options =
+    uri: 'https://api.github.com/repos/atom/atom/releases'
+    method: 'POST'
+    headers: defaultHeaders
+    json:
+      tag_name: "v#{version}"
+      name: version
+      draft: true
+      body: """
+        ### Notable Changes
+
+        * Something new
+      """
+
+  request options, (error, response, body='') ->
+    if error? or response.statusCode isnt 201
+      logError("Creating atom/atom draft release failed", error, body)
+      callback(error ? new Error(response.statusCode))
+    else
+      callback(null, body)
 
 deleteRelease = (release) ->
   options =

build/tasks/spec-task.coffee

@@ -12,11 +12,18 @@ module.exports = (grunt) ->
   packageSpecQueue = null
 
   logDeprecations = (label, {stderr}={}) ->
-    if process.env.JANKY_SHA1 and stderr?.indexOf('Calls to deprecated functions') isnt -1
-      grunt.log.error(label)
-      stderr = stderr.replace(/^\[.*\] "/g, '')
-      stderr = stderr.replace(/source: .*$/g, '')
-      grunt.log.error(stderr)
+    return unless process.env.JANKY_SHA1
+    stderr ?= ''
+    deprecatedStart = stderr.indexOf('Calls to deprecated functions')
+    return if deprecatedStart is -1
+
+    grunt.log.error(label)
+    stderr = stderr.substring(deprecatedStart)
+    stderr = stderr.replace(/^\s*\[[^\]]+\]\s+/gm, '')
+    stderr = stderr.replace(/source: .*$/gm, '')
+    stderr = stderr.replace(/^"/gm, '')
+    stderr = stderr.replace(/",\s*$/gm, '')
+    grunt.log.error(stderr)
 
   getAppPath = ->
     contentsDir = grunt.config.get('atom.contentsDir')

build/tasks/update-octicons-task.coffee

@@ -1,22 +0,0 @@
-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

docs/advanced/keymaps.md

@@ -3,7 +3,7 @@
 ## Structure of a Keymap File
 
 Keymap files are encoded as JSON or CSON files containing nested hashes. They
-work much like stylesheets, but instead of applying style properties to elements
+work much like style sheets, but instead of applying style properties to elements
 matching the selector, they specify the meaning of keystrokes on elements
 matching the selector. Here is an example of some bindings that apply when
 keystrokes pass through `atom-text-editor` elements:

docs/apm-rest-api.md

@@ -30,8 +30,8 @@ All requests that take parameters require `application/json`.
 Parameters:
 
 - **page** (optional)
-- **sort** (optional, values: `created_at`, `updated_at`, `downloads`)
-- **direction** (optional, values: `asc`, `desc`)
+- **sort** (optional) - One of `downloads`, `created_at`, `updated_at`, `stars`. Defaults to `downloads`
+- **direction** (optional) - `asc` or `desc`. Defaults to `desc`. `stars` can only be ordered `desc`
 
 Returns a list of all packages in the following format:
 ```json
@@ -61,17 +61,18 @@ Link: <https://www.atom.io/api/packages?page=1>; rel="self",
 
 By default, results are sorted by download count, descending.
 
+### Searching packages
+
 #### GET /api/packages/search
 
 Parameters:
 
-- **q** String query to search
-- **sort** (optional, values: `created_at`, `updated_at`, `downloads`)
-- **direction** (optional, values: `asc`, `desc`)
+- **q** (required) - Search query
+- **page** (optional)
+- **sort** (optional) - One of `downloads`, `created_at`, `updated_at`, `stars`. Defaults to the relevance of the search query.
+- **direction** (optional) - `asc` or `desc`. Defaults to `desc`.
 
-Returns a list of all packages in the same format as `/api/packages`.
-
-By default, results sorted by relevance to search query.
+Returns results in the same format as [listing packages](#listing-packages).
 
 ### Showing package details
 

docs/build-instructions/linux.md

@@ -26,13 +26,17 @@ Ubuntu LTS 12.04 64-bit is the recommended platform.
 
 ### Arch
 
-* `sudo pacman -S base-devel git nodejs libgnome-keyring python2`
+* `sudo pacman -S gconf base-devel git nodejs libgnome-keyring python2`
 * `export PYTHON=/usr/bin/python2` before building Atom.
 
 ### Slackware
 
 * `sbopkg -k -i node -i atom`
 
+### openSUSE
+
+* `sudo zypper install nodejs make gcc gcc-c++ glibc-devel git-core libgnome-keyring-devel rpmdevtools`
+
 ## Instructions
 
 If you have problems with permissions don't forget to prefix with `sudo`

docs/creating-a-package.md

@@ -15,7 +15,7 @@ my-package/
   menus/
   spec/
   snippets/
-  stylesheets/
+  styles/
   index.coffee
   package.json
 ```
@@ -38,10 +38,10 @@ In addition to the regular [npm package.json keys][npm-keys] available, Atom
 package.json files have their own additions.
 
 - `main` (**Required**): the path to the CoffeeScript file that's the entry point
-to your package
-- `stylesheets` (**Optional**): an Array of Strings identifying the order of the
+to your package.
+- `styles` (**Optional**): an Array of Strings identifying the order of the
 style sheets your package needs to load. If not specified, style sheets in the
-_stylesheets_ directory are added alphabetically.
+_styles_ directory are added alphabetically.
 - `keymaps`(**Optional**): an Array of Strings identifying the order of the
 key mappings your package needs to load. If not specified, mappings in the
 _keymaps_ directory are added alphabetically.
@@ -121,10 +121,10 @@ like you.
 
 ## Style Sheets
 
-Style sheets for your package should be placed in the _stylesheets_ directory.
+Style sheets for your package should be placed in the _styles_ directory.
 Any style sheets in this directory will be loaded and attached to the DOM when
-your package is activated. Style sheets can be written as CSS or [LESS] (but
-LESS is recommended).
+your package is activated. Style sheets can be written as CSS or [LESS], but
+LESS is recommended.
 
 Ideally, you won't need much in the way of styling. We've provided a standard
 set of components which define both the colors and UI elements for any package
@@ -138,7 +138,7 @@ taken from the active theme's [ui-variables.less][ui-variables]. For more
 information, see the [theme variables docs][theme-variables]. If you follow this
 guideline, your package will look good out of the box with any theme!
 
-An optional `stylesheets` array in your _package.json_ can list the style sheets
+An optional `styleSheets` array in your _package.json_ can list the style sheets
 by name to specify a loading order; otherwise, style sheets are loaded
 alphabetically.
 
@@ -418,8 +418,8 @@ all the other available commands.
 [underscore]: http://underscorejs.org/
 [jasmine]: http://jasmine.github.io
 [cson]: https://github.com/atom/season
-[less]: http://lesscss.org
-[ui-variables]: https://github.com/atom/atom-dark-ui/blob/master/stylesheets/ui-variables.less
+[LESS]: http://lesscss.org
+[ui-variables]: https://github.com/atom/atom-dark-ui/blob/master/styles/ui-variables.less
 [first-package]: your-first-package.html
 [convert-bundle]: converting-a-text-mate-bundle.html
 [convert-theme]: converting-a-text-mate-theme.html

docs/creating-a-theme.md

@@ -1,8 +1,8 @@
 # Creating a Theme
 
-Atom's interface is rendered using HTML, and it's styled via [LESS] (a superset
-of CSS). Don't worry if you haven't heard of LESS before; it's just like CSS,
-but with a few handy extensions.
+Atom's interface is rendered using HTML, and it's styled via [LESS] which is a
+superset of CSS. Don't worry if you haven't heard of LESS before; it's just like
+CSS, but with a few handy extensions.
 
 Atom supports two types of themes: _UI_ and _syntax_.  UI themes style
 elements such as the tree view, the tabs, drop-down lists, and the status bar.
@@ -42,10 +42,10 @@ _Motif_ theme listed in the _Syntax Theme_ drop-down. Select it from the menu to
 activate it, now when you open an editor you should see that your new
 _motif-syntax_ theme in action.
 
-Open up _stylesheets/colors.less_ to change the various colors variables which
+Open up _styles/colors.less_ to change the various colors variables which
 have been already been defined. For example, turn `@red` into `#f4c2c1`.
 
-Then open _stylesheets/base.less_ and modify the various selectors that have
+Then open _styles/base.less_ and modify the various selectors that have
 been already been defined. These selectors style different parts of code in the
 editor such as comments, strings and the line numbers in the gutter.
 
@@ -131,7 +131,7 @@ _styleguide_, or use the shortcut `cmd-ctrl-shift-g`.
 ![styleguide-img]
 
 [atomio]: http://atom.io/packages
-[less]: http://lesscss.org/
+[LESS]: http://lesscss.org/
 [git]: http://git-scm.com/
 [atom]: https://atom.io/
 [package.json]: ./creating-a-package.html#package-json

docs/customizing-atom.md

@@ -54,7 +54,7 @@ You can also use `apm` to find new packages to install:
 
 ## Customizing Key Bindings
 
-Atom keymaps work similarly to stylesheets. Just as stylesheets use selectors
+Atom keymaps work similarly to style sheets. Just as style sheets 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:

docs/debugging.md

@@ -3,7 +3,8 @@
 Atom provides several tools to help you understand unexpected behavior and debug problems. This guide describes some of those tools and a few approaches to help you debug and provide more helpful information when [submitting issues]:
 
 * [Update to the latest version](#update-to-the-latest-version)
-* [Check Atom and package settings](#check-atom-and-package-settings) 
+* [Check for linked packages](#check-for-linked-packages)
+* [Check Atom and package settings](#check-atom-and-package-settings)
 * [Check the keybindings](#check-the-keybindings)
 * [Check if the problem shows up in safe mode](#check-if-the-problem-shows-up-in-safe-mode)
 * [Check your config files](#check-your-config-files)
@@ -24,6 +25,16 @@ $ atom --version
 
 Head on over to the [list of releases][atom releases] and see if there's a more recent release. You can update to the most recent release by downloading Atom from the releases page, or with the in-app auto-updater. The in-app auto-updater checks for and downloads a new version after you restart Atom, or if you use the Atom > Check for Update menu option.
 
+## Check for linked packages
+
+If you develop or contribute to Atom packages, there may be left-over packages linked to your `~/.atom/packages` or `~/.atom/dev/packages` directories. You can use:
+
+```shell
+$ apm links
+```
+
+to list all linked development packages. You can remove the links using the `apm unlink` command. See `apm unlink --help` for details.
+
 ## Check Atom and package settings
 
 In some cases, unexpected behavior might be caused by misconfigured or unconfigured settings in Atom or in one of the packages.

docs/upgrading/upgrading-your-ui-theme.md

@@ -1,6 +1,6 @@
 # Upgrading Your UI Theme Or Package Selectors
 
-In addition to changes in Atom's scripting API, we'll also be making some breaking changes to Atom's DOM structure, requiring stylesheets and keymaps in both packages and themes to be updated.
+In addition to changes in Atom's scripting API, we'll also be making some breaking changes to Atom's DOM structure, requiring style sheets and keymaps in both packages and themes to be updated.
 
 ## Deprecation Cop
 
@@ -121,12 +121,12 @@ The selector features discussed above allow you to target shadow DOM content wit
 
 ```
 my-ui-theme/
-  stylesheets/
+  styles/
     index.less                   # loaded globally
     index.atom-text-editor.less  # loaded in the text editor shadow DOM
 ```
 
-Check out this [style sheet](https://github.com/atom/decoration-example/blob/master/stylesheets/decoration-example.atom-text-editor.less) from the decoration-example package for an example of context-targeting.
+Check out this [style sheet](https://github.com/atom/decoration-example/blob/master/styles/decoration-example.atom-text-editor.less) from the decoration-example package for an example of context-targeting.
 
 Inside a context-targeted style sheet, there's no need to use the `::shadow` or `/deep/` expressions. If you want to refer to the element containing the shadow root, you can use the `::host` pseudo-element.
 
@@ -134,4 +134,4 @@ During the transition phase, style sheets targeting the `atom-text-editor` conte
 
 [shadow-dom-101]: http://www.html5rocks.com/en/tutorials/webcomponents/shadowdom
 [shadow-dom-201]: http://www.html5rocks.com/en/tutorials/webcomponents/shadowdom-201#toc-style-cat-hat
-[find-and-replace]: https://github.com/atom/find-and-replace/blob/95351f261bc384960a69b66bf12eae8002da63f9/stylesheets/find-and-replace.less#L10
+[find-and-replace]: https://github.com/atom/find-and-replace/blob/95351f261bc384960a69b66bf12eae8002da63f9/styles/find-and-replace.less#L10

docs/writing-specs.md

@@ -127,3 +127,10 @@ describe "when a test is written", ->
     expect("apples").toEqual("apples")
     expect("oranges").not.toEqual("apples")
 ```
+
+### Running on CI
+
+It is now easy to run the specs in a CI environment like Travis and AppVeyor. See the
+[Travis CI For Your Packages](http://blog.atom.io/2014/04/25/ci-for-your-packages.html)
+and [AppVeyor CI For Your Packages](http://blog.atom.io/2014/07/28/windows-ci-for-your-packages.html)
+posts for more details.

dot-atom/keymap.cson

@@ -1,7 +1,7 @@
 # Your keymap
 #
-# Atom keymaps work similarly to stylesheets. Just as stylesheets use selectors
-# to apply styles to elements, Atom keymaps use selectors to associate
+# Atom keymaps work similarly to style sheets. Just as style sheets use
+# selectors to apply styles to elements, Atom keymaps use selectors to associate
 # keystrokes with events in specific contexts.
 #
 # You can create a new keybinding in this file by typing "key" and then hitting

exports/atom.coffee

@@ -40,11 +40,11 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
   Object.defineProperty module.exports, '$', get: ->
     deprecate """
       Requiring `$` from `atom` is no longer supported.
-      If you are using `space-pen`, please require `$` from `space-pen`. Otherwise require `jquery` instead:
-        `{$} = require 'space-pen'`
+      If you are using `space-pen`, please require `$` from `atom-space-pen-views`. Otherwise require `jquery` instead:
+        `{$} = require 'atom-space-pen-views'`
         or
         `$ = require 'jquery'`
-      Add `"space-pen": "^4"` to your package dependencies.
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
       Or add `"jquery": "^2"` to your package dependencies.
     """
     $
@@ -52,27 +52,27 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
   Object.defineProperty module.exports, '$$', get: ->
     deprecate """
       Requiring `$$` from `atom` is no longer supported.
-      Please require `space-pen` instead:
-        `{$$} = require 'space-pen'`
-      Add `"space-pen": "^4"` to your package dependencies.
+      Please require `atom-space-pen-views` instead:
+        `{$$} = require 'atom-space-pen-views'`
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     $$
 
   Object.defineProperty module.exports, '$$$', get: ->
     deprecate """
       Requiring `$$$` from `atom` is no longer supported.
-      Please require `space-pen` instead:
-        `{$$$} = require 'space-pen'`
-      Add `"space-pen": "^4"` to your package dependencies.
+      Please require `atom-space-pen-views` instead:
+        `{$$$} = require 'atom-space-pen-views'`
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     $$$
 
   Object.defineProperty module.exports, 'View', get: ->
     deprecate """
       Requiring `View` from `atom` is no longer supported.
-      Please require `space-pen` instead:
-        `{View} = require 'space-pen'`
-      Add `"space-pen": "^4"` to your package dependencies.
+      Please require `atom-space-pen-views` instead:
+        `{View} = require 'atom-space-pen-views'`
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     View
 
@@ -81,7 +81,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Requiring `EditorView` from `atom` is no longer supported.
       Please require `TextEditorView` from `atom-space-pen-view` instead:
         `{TextEditorView} = require 'atom-space-pen-views'`
-      Add `"atom-space-pen-views": "^0"` to your package dependencies.
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     require '../src/text-editor-view'
 
@@ -90,7 +90,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Requiring `TextEditorView` from `atom` is no longer supported.
       Please require `TextEditorView` from `atom-space-pen-view` instead:
         `{TextEditorView} = require 'atom-space-pen-views'`
-      Add `"atom-space-pen-views": "^0"` to your package dependencies.
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     require '../src/text-editor-view'
 
@@ -100,7 +100,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Please require `ScrollView` from `atom-space-pen-view` instead:
         `{ScrollView} = require 'atom-space-pen-views'`
       Note that the API has changed slightly! Please read the docs at https://github.com/atom/atom-space-pen-views
-      Add `"atom-space-pen-views": "^0"` to your package dependencies.
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     require '../src/scroll-view'
 
@@ -110,7 +110,7 @@ unless process.env.ATOM_SHELL_INTERNAL_RUN_AS_NODE
       Please require `SelectListView` from `atom-space-pen-view` instead:
         `{SelectListView} = require 'atom-space-pen-views'`
       Note that the API has changed slightly! Please read the docs at https://github.com/atom/atom-space-pen-views
-      Add `"atom-space-pen-views": "^0"` to your package dependencies.
+      Add `"atom-space-pen-views": "^2.0.3"` to your package dependencies.
     """
     require '../src/select-list-view'
 

package.json

@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "0.165.0",
+  "version": "0.171.0",
   "description": "A hackable text editor for the 21st Century.",
   "main": "./src/browser/main.js",
   "repository": {
@@ -17,23 +17,24 @@
       "url": "http://github.com/atom/atom/raw/master/LICENSE.md"
     }
   ],
-  "atomShellVersion": "0.19.4",
+  "atomShellVersion": "0.20.5",
   "dependencies": {
     "async": "0.2.6",
-    "atom-keymap": "^2.3.0",
+    "atom-keymap": "^2.5.1",
     "bootstrap": "git+https://github.com/atom/bootstrap.git#6af81906189f1747fd6c93479e3d998ebe041372",
     "clear-cut": "0.4.0",
-    "coffee-script": "1.7.0",
-    "coffeestack": "0.7.0",
+    "coffee-script": "1.8.0",
+    "coffeestack": "0.8.0",
+    "color": "^0.7.3",
     "delegato": "^1",
     "emissary": "^1.3.1",
-    "event-kit": "0.8.1",
-    "first-mate": "^2.2.0",
+    "event-kit": "^1.0.1",
+    "first-mate": "^2.2.4",
     "fs-plus": "^2.3.2",
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
     "git-utils": "^2.2",
-    "grim": "0.12.0",
+    "grim": "1.1.0",
     "guid": "0.0.10",
     "jasmine-json": "~0.0",
     "jasmine-tagged": "^1.1.2",
@@ -45,7 +46,7 @@
     "nslog": "^1.0.1",
     "oniguruma": "^3.0.4",
     "optimist": "0.4.0",
-    "pathwatcher": "^2.3.5",
+    "pathwatcher": "^2.5.0",
     "property-accessors": "^1",
     "q": "^1.0.1",
     "random-words": "0.0.1",
@@ -53,99 +54,99 @@
     "reactionary-atom-fork": "^1.0.0",
     "runas": "1.0.1",
     "scandal": "1.0.3",
-    "scoped-property-store": "^0.15.4",
+    "scoped-property-store": "^0.16.2",
     "scrollbar-style": "^1.0.2",
-    "season": "^1.0.2",
+    "season": "^5.0.2",
     "semver": "2.2.1",
     "serializable": "^1",
     "service-hub": "^0.1.0",
     "space-pen": "3.8.2",
     "temp": "0.7.0",
-    "text-buffer": "^3.8.2",
+    "text-buffer": "^3.8.4",
     "theorist": "^1.0.2",
     "underscore-plus": "^1.6.6",
     "vm-compatibility-layer": "0.1.0"
   },
   "packageDependencies": {
     "atom-dark-syntax": "0.23.0",
-    "atom-dark-ui": "0.42.0",
-    "atom-light-syntax": "0.22.0",
-    "atom-light-ui": "0.36.0",
-    "base16-tomorrow-dark-theme": "0.22.0",
-    "base16-tomorrow-light-theme": "0.5.0",
-    "solarized-dark-syntax": "0.29.0",
-    "solarized-light-syntax": "0.13.0",
-    "archive-view": "0.40.0",
-    "autocomplete": "0.34.0",
+    "atom-dark-ui": "0.43.0",
+    "atom-light-syntax": "0.24.0",
+    "atom-light-ui": "0.37.0",
+    "base16-tomorrow-dark-theme": "0.23.0",
+    "base16-tomorrow-light-theme": "0.6.0",
+    "solarized-dark-syntax": "0.30.0",
+    "solarized-light-syntax": "0.17.0",
+    "archive-view": "0.43.0",
+    "autocomplete": "0.41.0",
     "autoflow": "0.20.0",
     "autosave": "0.19.0",
-    "background-tips": "0.18.0",
-    "bookmarks": "0.31.0",
-    "bracket-matcher": "0.64.0",
-    "command-palette": "0.30.0",
-    "deprecation-cop": "0.20.0",
+    "background-tips": "0.20.0",
+    "bookmarks": "0.33.0",
+    "bracket-matcher": "0.67.0",
+    "command-palette": "0.32.0",
+    "deprecation-cop": "0.25.0",
     "dev-live-reload": "0.36.0",
-    "encoding-selector": "0.12.0",
+    "encoding-selector": "0.14.0",
     "exception-reporting": "0.21.0",
-    "find-and-replace": "0.152.0",
-    "fuzzy-finder": "0.62.0",
-    "git-diff": "0.45.0",
-    "go-to-line": "0.27.0",
-    "grammar-selector": "0.40.0",
-    "image-view": "0.44.0",
-    "incompatible-packages": "0.16.0",
-    "keybinding-resolver": "0.24.0",
-    "link": "0.28.0",
-    "markdown-preview": "0.112.0",
+    "find-and-replace": "0.155.0",
+    "fuzzy-finder": "0.64.0",
+    "git-diff": "0.47.0",
+    "go-to-line": "0.30.0",
+    "grammar-selector": "0.42.0",
+    "image-view": "0.46.0",
+    "incompatible-packages": "0.19.0",
+    "keybinding-resolver": "0.25.0",
+    "link": "0.29.0",
+    "markdown-preview": "0.117.0",
     "metrics": "0.40.0",
-    "notifications": "0.21.0",
-    "open-on-github": "0.31.0",
-    "package-generator": "0.34.0",
-    "release-notes": "0.43.0",
-    "settings-view": "0.161.0",
-    "snippets": "0.60.0",
-    "spell-check": "0.45.0",
-    "status-bar": "0.54.0",
-    "styleguide": "0.36.0",
-    "symbols-view": "0.70.0",
-    "tabs": "0.58.0",
-    "timecop": "0.24.0",
-    "tree-view": "0.139.0",
+    "notifications": "0.23.0",
+    "open-on-github": "0.32.0",
+    "package-generator": "0.36.0",
+    "release-notes": "0.45.0",
+    "settings-view": "0.169.0",
+    "snippets": "0.67.0",
+    "spell-check": "0.49.0",
+    "status-bar": "0.56.0",
+    "styleguide": "0.41.0",
+    "symbols-view": "0.77.0",
+    "tabs": "0.61.0",
+    "timecop": "0.26.0",
+    "tree-view": "0.147.0",
     "update-package-dependencies": "0.7.0",
     "welcome": "0.21.0",
-    "whitespace": "0.27.0",
-    "wrap-guide": "0.27.0",
-    "language-c": "0.33.0",
-    "language-clojure": "0.9.0",
-    "language-coffee-script": "0.38.1",
-    "language-css": "0.24.0",
-    "language-gfm": "0.55.0",
-    "language-git": "0.9.0",
-    "language-go": "0.19.1",
-    "language-html": "0.27.0",
+    "whitespace": "0.28.0",
+    "wrap-guide": "0.29.0",
+    "language-c": "0.37.0",
+    "language-clojure": "0.10.0",
+    "language-coffee-script": "0.39.0",
+    "language-css": "0.26.0",
+    "language-gfm": "0.62.0",
+    "language-git": "0.10.0",
+    "language-go": "0.20.0",
+    "language-html": "0.28.0",
     "language-hyperlink": "0.12.2",
-    "language-java": "0.13.0",
-    "language-javascript": "0.51.0",
-    "language-json": "0.10.0",
-    "language-less": "0.21.0",
-    "language-make": "0.12.0",
+    "language-java": "0.14.0",
+    "language-javascript": "0.54.0",
+    "language-json": "0.11.0",
+    "language-less": "0.24.0",
+    "language-make": "0.13.0",
     "language-mustache": "0.11.0",
-    "language-objective-c": "0.12.0",
-    "language-perl": "0.9.0",
-    "language-php": "0.18.0",
-    "language-property-list": "0.7.0",
-    "language-python": "0.26.0",
-    "language-ruby": "0.45.0",
+    "language-objective-c": "0.15.0",
+    "language-perl": "0.10.0",
+    "language-php": "0.20.0",
+    "language-property-list": "0.8.0",
+    "language-python": "0.30.0",
+    "language-ruby": "0.47.0",
     "language-ruby-on-rails": "0.18.0",
-    "language-sass": "0.29.0",
-    "language-shellscript": "0.10.1",
-    "language-source": "0.8.0",
-    "language-sql": "0.11.0",
+    "language-sass": "0.31.0",
+    "language-shellscript": "0.12.0",
+    "language-source": "0.9.0",
+    "language-sql": "0.13.0",
     "language-text": "0.6.0",
     "language-todo": "0.15.0",
-    "language-toml": "0.14.1",
-    "language-xml": "0.25.0",
-    "language-yaml": "0.21.0"
+    "language-toml": "0.15.0",
+    "language-xml": "0.27.0",
+    "language-yaml": "0.22.0"
   },
   "private": true,
   "scripts": {

spec/atom-reporter.coffee

@@ -117,7 +117,7 @@ class AtomReporter extends View
           @div class: 'result-message fail deprecation-message', =>
             @raw marked(deprecation.message)
 
-          for stack in deprecation.stacks
+          for stack in deprecation.getStacks()
             fullStack = stack.map ({functionName, location}) ->
               if functionName is '<unknown>'
                 "  at #{location}"

spec/fixtures/packages/package-with-empty-keymap/package.json

@@ -0,0 +1,4 @@
+{
+  "name": "package-with-empty-keymap",
+  "version": "1.0.0"
+}

spec/fixtures/packages/package-with-empty-menu/package.json

@@ -0,0 +1,4 @@
+{
+  "name": "package-with-empty-menu",
+  "version": "1.0.0"
+}

spec/fixtures/packages/package-with-style-sheets-manifest/package.cson

@@ -0,0 +1 @@
+styleSheets: ['2', '1']

spec/fixtures/packages/package-with-stylesheets-manifest/package.cson

@@ -1 +1 @@
-stylesheets: ['2', '1']
+styleSheets: ['2', '1']

spec/fixtures/packages/theme-with-package-file/package.json

@@ -1,4 +1,4 @@
 {
   "theme": "ui",
-  "stylesheets": ["first.css", "second.less", "last.css"]
+  "styleSheets": ["first.css", "second.less", "last.css"]
 }

spec/fixtures/task-spec-handler.coffee

@@ -1,2 +1,3 @@
 module.exports = ->
+  emit("some-event", 1, 2, 3)
   'hello'

spec/language-mode-spec.coffee

@@ -381,6 +381,23 @@ describe "LanguageMode", ->
         expect(languageMode.isFoldableAtBufferRow(3)).toBe false
         expect(languageMode.isFoldableAtBufferRow(4)).toBe true
 
+    describe ".foldAllAtIndentLevel(indentLevel)", ->
+      it "folds blocks of text at the given indentation level", ->
+        languageMode.foldAllAtIndentLevel(0)
+        expect(editor.lineTextForScreenRow(0)).toBe "var quicksort = function () {"
+        expect(editor.getLastScreenRow()).toBe 0
+
+        languageMode.foldAllAtIndentLevel(1)
+        expect(editor.lineTextForScreenRow(0)).toBe "var quicksort = function () {"
+        expect(editor.lineTextForScreenRow(1)).toBe "  var sort = function(items) {"
+        expect(editor.getLastScreenRow()).toBe 4
+
+        languageMode.foldAllAtIndentLevel(2)
+        expect(editor.lineTextForScreenRow(0)).toBe "var quicksort = function () {"
+        expect(editor.lineTextForScreenRow(1)).toBe "  var sort = function(items) {"
+        expect(editor.lineTextForScreenRow(2)).toBe "    if (items.length <= 1) return items;"
+        expect(editor.getLastScreenRow()).toBe 9
+
   describe "folding with comments", ->
     beforeEach ->
       waitsForPromise ->

spec/package-spec.coffee

@@ -9,14 +9,14 @@ describe "Package", ->
       spyOn(atom, 'inDevMode').andReturn(false)
 
     it "does not activate it", ->
-      packagePath = atom.project.resolve('packages/package-with-incompatible-native-module')
+      packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-incompatible-native-module')
       pack = new Package(packagePath)
       expect(pack.isCompatible()).toBe false
       expect(pack.incompatibleModules[0].name).toBe 'native-module'
       expect(pack.incompatibleModules[0].path).toBe path.join(packagePath, 'node_modules', 'native-module')
 
     it "caches the incompatible native modules in local storage", ->
-      packagePath = atom.project.resolve('packages/package-with-incompatible-native-module')
+      packagePath = atom.project.getDirectories()[0]?.resolve('packages/package-with-incompatible-native-module')
       cacheKey = null
       cacheItem = null
 
@@ -46,14 +46,14 @@ describe "Package", ->
     describe "when the theme contains a single style file", ->
       it "loads and applies css", ->
         expect($("atom-text-editor").css("padding-bottom")).not.toBe "1234px"
-        themePath = atom.project.resolve('packages/theme-with-index-css')
+        themePath = atom.project.getDirectories()[0]?.resolve('packages/theme-with-index-css')
         theme = new ThemePackage(themePath)
         theme.activate()
         expect($("atom-text-editor").css("padding-top")).toBe "1234px"
 
       it "parses, loads and applies less", ->
         expect($("atom-text-editor").css("padding-bottom")).not.toBe "1234px"
-        themePath = atom.project.resolve('packages/theme-with-index-less')
+        themePath = atom.project.getDirectories()[0]?.resolve('packages/theme-with-index-less')
         theme = new ThemePackage(themePath)
         theme.activate()
         expect($("atom-text-editor").css("padding-top")).toBe "4321px"
@@ -64,7 +64,7 @@ describe "Package", ->
         expect($("atom-text-editor").css("padding-right")).not.toBe("102px")
         expect($("atom-text-editor").css("padding-bottom")).not.toBe("103px")
 
-        themePath = atom.project.resolve('packages/theme-with-package-file')
+        themePath = atom.project.getDirectories()[0]?.resolve('packages/theme-with-package-file')
         theme = new ThemePackage(themePath)
         theme.activate()
         expect($("atom-text-editor").css("padding-top")).toBe("101px")
@@ -77,7 +77,7 @@ describe "Package", ->
         expect($("atom-text-editor").css("padding-right")).not.toBe "20px"
         expect($("atom-text-editor").css("padding-bottom")).not.toBe "30px"
 
-        themePath = atom.project.resolve('packages/theme-without-package-file')
+        themePath = atom.project.getDirectories()[0]?.resolve('packages/theme-without-package-file')
         theme = new ThemePackage(themePath)
         theme.activate()
         expect($("atom-text-editor").css("padding-top")).toBe "10px"
@@ -86,7 +86,7 @@ describe "Package", ->
 
     describe "reloading a theme", ->
       beforeEach ->
-        themePath = atom.project.resolve('packages/theme-with-package-file')
+        themePath = atom.project.getDirectories()[0]?.resolve('packages/theme-with-package-file')
         theme = new ThemePackage(themePath)
         theme.activate()
 
@@ -97,7 +97,7 @@ describe "Package", ->
 
     describe "events", ->
       beforeEach ->
-        themePath = atom.project.resolve('packages/theme-with-package-file')
+        themePath = atom.project.getDirectories()[0]?.resolve('packages/theme-with-package-file')
         theme = new ThemePackage(themePath)
         theme.activate()
 

spec/pane-container-spec.coffee

@@ -129,7 +129,7 @@ describe "PaneContainer", ->
     beforeEach ->
       class TestItem
         shouldPromptToSave: -> true
-        getUri: -> 'test'
+        getURI: -> 'test'
 
       container = new PaneContainer
       container.getRoot().splitRight()

spec/pane-container-view-spec.coffee

@@ -16,7 +16,7 @@ describe "PaneContainerView", ->
       @content: -> @div tabindex: -1
       initialize: (@name) -> @text(@name)
       serialize: -> { deserializer: 'TestView', @name }
-      getUri: -> path.join(temp.dir, @name)
+      getURI: -> path.join(temp.dir, @name)
       save: -> @saved = true
       isEqual: (other) -> @name is other?.name
       onDidChangeTitle: -> new Disposable(->)

spec/pane-spec.coffee

@@ -9,7 +9,7 @@ describe "Pane", ->
   class Item extends Model
     @deserialize: ({name, uri}) -> new this(name, uri)
     constructor: (@name, @uri) ->
-    getUri: -> @uri
+    getURI: -> @uri
     getPath: -> @path
     serialize: -> {deserializer: 'Item', @name, @uri}
     isEqual: (other) -> @name is other?.name
@@ -231,18 +231,18 @@ describe "Pane", ->
         expect(pane.getActiveItem()).toBe item1
 
     describe "if the item is modified", ->
-      itemUri = null
+      itemURI = null
 
       beforeEach ->
         item1.shouldPromptToSave = -> true
         item1.save = jasmine.createSpy("save")
         item1.saveAs = jasmine.createSpy("saveAs")
-        item1.getUri = -> itemUri
+        item1.getURI = -> itemURI
 
       describe "if the [Save] option is selected", ->
         describe "when the item has a uri", ->
           it "saves the item before destroying it", ->
-            itemUri = "test"
+            itemURI = "test"
             spyOn(atom, 'confirm').andReturn(0)
             pane.destroyItem(item1)
 
@@ -252,7 +252,7 @@ describe "Pane", ->
 
         describe "when the item has no uri", ->
           it "presents a save-as dialog, then saves the item with the given uri before removing and destroying it", ->
-            itemUri = null
+            itemURI = null
 
             spyOn(atom, 'showSaveDialogSync').andReturn("/selected/path")
             spyOn(atom, 'confirm').andReturn(0)
@@ -404,15 +404,15 @@ describe "Pane", ->
         pane.saveActiveItemAs()
         expect(atom.showSaveDialogSync).not.toHaveBeenCalled()
 
-  describe "::itemForUri(uri)", ->
-    it "returns the item for which a call to .getUri() returns the given uri", ->
+  describe "::itemForURI(uri)", ->
+    it "returns the item for which a call to .getURI() returns the given uri", ->
       pane = new Pane(items: [new Item("A"), new Item("B"), new Item("C"), new Item("D")])
       [item1, item2, item3] = pane.getItems()
       item1.uri = "a"
       item2.uri = "b"
-      expect(pane.itemForUri("a")).toBe item1
-      expect(pane.itemForUri("b")).toBe item2
-      expect(pane.itemForUri("bogus")).toBeUndefined()
+      expect(pane.itemForURI("a")).toBe item1
+      expect(pane.itemForURI("b")).toBe item2
+      expect(pane.itemForURI("bogus")).toBeUndefined()
 
   describe "::moveItem(item, index)", ->
     [pane, item1, item2, item3, item4] = []
@@ -589,7 +589,7 @@ describe "Pane", ->
       [item1, item2] = pane.getItems()
 
       item1.shouldPromptToSave = -> true
-      item1.getUri = -> "/test/path"
+      item1.getURI = -> "/test/path"
       item1.save = jasmine.createSpy("save")
 
       spyOn(atom, 'confirm').andReturn(0)
@@ -604,7 +604,7 @@ describe "Pane", ->
       [item1, item2] = pane.getItems()
 
       item1.shouldPromptToSave = -> true
-      item1.getUri = -> "/test/path"
+      item1.getURI = -> "/test/path"
       item1.save = jasmine.createSpy("save")
 
       spyOn(atom, 'confirm').andReturn(1)

spec/pane-view-spec.coffee

@@ -15,7 +15,7 @@ describe "PaneView", ->
     initialize: ({@id, @text}) ->
       @emitter = new Emitter
     serialize: -> { deserializer: 'TestView', @id, @text }
-    getUri: -> @id
+    getURI: -> @id
     isEqual: (other) -> other? and @id == other.id and @text == other.text
     changeTitle: ->
       @emitter.emit 'did-change-title', 'title'

spec/project-spec.coffee

@@ -4,12 +4,11 @@ Project = require '../src/project'
 _ = require 'underscore-plus'
 fs = require 'fs-plus'
 path = require 'path'
-platform = require './spec-helper-platform'
 BufferedProcess = require '../src/buffered-process'
 
 describe "Project", ->
   beforeEach ->
-    atom.project.setPaths([atom.project.resolve('dir')])
+    atom.project.setPaths([atom.project.getDirectories()[0]?.resolve('dir')])
 
   describe "serialization", ->
     deserializedProject = null
@@ -110,7 +109,7 @@ describe "Project", ->
           expect(newBufferHandler).toHaveBeenCalledWith(editor.buffer)
 
     it "returns number of read bytes as progress indicator", ->
-      filePath = atom.project.resolve 'a'
+      filePath = atom.project.getDirectories()[0]?.resolve 'a'
       totalBytes = 0
       promise = atom.project.open(filePath)
       promise.progress (bytesRead) -> totalBytes = bytesRead
@@ -149,27 +148,6 @@ describe "Project", ->
           atom.project.bufferForPath("b").then (anotherBuffer) ->
             expect(anotherBuffer).not.toBe buffer
 
-  describe ".resolve(uri)", ->
-    describe "when passed an absolute or relative path", ->
-      it "returns an absolute path based on the atom.project's root", ->
-        absolutePath = require.resolve('./fixtures/dir/a')
-        expect(atom.project.resolve('a')).toBe absolutePath
-        expect(atom.project.resolve(absolutePath + '/../a')).toBe absolutePath
-        expect(atom.project.resolve('a/../a')).toBe absolutePath
-        expect(atom.project.resolve()).toBeUndefined()
-
-    describe "when passed a uri with a scheme", ->
-      it "does not modify uris that begin with a scheme", ->
-        expect(atom.project.resolve('http://zombo.com')).toBe 'http://zombo.com'
-
-    describe "when the project has no path", ->
-      it "returns undefined for relative URIs", ->
-        atom.project.setPaths([])
-        expect(atom.project.resolve('test.txt')).toBeUndefined()
-        expect(atom.project.resolve('http://github.com')).toBe 'http://github.com'
-        absolutePath = fs.absolute(__dirname)
-        expect(atom.project.resolve(absolutePath)).toBe absolutePath
-
   describe ".setPaths(path)", ->
     describe "when path is a file", ->
       it "sets its path to the files parent directory and updates the root directory", ->
@@ -195,290 +173,6 @@ describe "Project", ->
       expect(atom.project.getPaths()[0]).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
       expect(atom.project.getDirectories()[0].path).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
 
-  describe ".replace()", ->
-    [filePath, commentFilePath, sampleContent, sampleCommentContent] = []
-
-    beforeEach ->
-      atom.project.setPaths([atom.project.resolve('../')])
-
-      filePath = atom.project.resolve('sample.js')
-      commentFilePath = atom.project.resolve('sample-with-comments.js')
-      sampleContent = fs.readFileSync(filePath).toString()
-      sampleCommentContent = fs.readFileSync(commentFilePath).toString()
-
-    afterEach ->
-      fs.writeFileSync(filePath, sampleContent)
-      fs.writeFileSync(commentFilePath, sampleCommentContent)
-
-    describe "when a file doesn't exist", ->
-      it "calls back with an error", ->
-        errors = []
-        missingPath = path.resolve('/not-a-file.js')
-        expect(fs.existsSync(missingPath)).toBeFalsy()
-
-        waitsForPromise ->
-          atom.project.replace /items/gi, 'items', [missingPath], (result, error) ->
-            errors.push(error)
-
-        runs ->
-          expect(errors).toHaveLength 1
-          expect(errors[0].path).toBe missingPath
-
-    describe "when called with unopened files", ->
-      it "replaces properly", ->
-        results = []
-        waitsForPromise ->
-          atom.project.replace /items/gi, 'items', [filePath], (result) ->
-            results.push(result)
-
-        runs ->
-          expect(results).toHaveLength 1
-          expect(results[0].filePath).toBe filePath
-          expect(results[0].replacements).toBe 6
-
-    describe "when a buffer is already open", ->
-      it "replaces properly and saves when not modified", ->
-        editor = null
-        results = []
-
-        waitsForPromise ->
-          atom.project.open('sample.js').then (o) -> editor = o
-
-        runs ->
-          expect(editor.isModified()).toBeFalsy()
-
-        waitsForPromise ->
-          atom.project.replace /items/gi, 'items', [filePath], (result) ->
-            results.push(result)
-
-        runs ->
-          expect(results).toHaveLength 1
-          expect(results[0].filePath).toBe filePath
-          expect(results[0].replacements).toBe 6
-
-          expect(editor.isModified()).toBeFalsy()
-
-      it "does not replace when the path is not specified", ->
-        editor = null
-        results = []
-
-        waitsForPromise ->
-          atom.project.open('sample-with-comments.js').then (o) -> editor = o
-
-        waitsForPromise ->
-          atom.project.replace /items/gi, 'items', [commentFilePath], (result) ->
-            results.push(result)
-
-        runs ->
-          expect(results).toHaveLength 1
-          expect(results[0].filePath).toBe commentFilePath
-
-      it "does NOT save when modified", ->
-        editor = null
-        results = []
-
-        waitsForPromise ->
-          atom.project.open('sample.js').then (o) -> editor = o
-
-        runs ->
-          editor.buffer.setTextInRange([[0,0],[0,0]], 'omg')
-          expect(editor.isModified()).toBeTruthy()
-
-        waitsForPromise ->
-          atom.project.replace /items/gi, 'okthen', [filePath], (result) ->
-            results.push(result)
-
-        runs ->
-          expect(results).toHaveLength 1
-          expect(results[0].filePath).toBe filePath
-          expect(results[0].replacements).toBe 6
-
-          expect(editor.isModified()).toBeTruthy()
-
-  describe ".scan(options, callback)", ->
-    describe "when called with a regex", ->
-      it "calls the callback with all regex results in all files in the project", ->
-        results = []
-        waitsForPromise ->
-          atom.project.scan /(a)+/, (result) ->
-            results.push(result)
-
-        runs ->
-          expect(results).toHaveLength(3)
-          expect(results[0].filePath).toBe atom.project.resolve('a')
-          expect(results[0].matches).toHaveLength(3)
-          expect(results[0].matches[0]).toEqual
-            matchText: 'aaa'
-            lineText: 'aaa bbb'
-            lineTextOffset: 0
-            range: [[0, 0], [0, 3]]
-
-      it "works with with escaped literals (like $ and ^)", ->
-        results = []
-        waitsForPromise ->
-          atom.project.scan /\$\w+/, (result) -> results.push(result)
-
-        runs ->
-          expect(results.length).toBe 1
-
-          {filePath, matches} = results[0]
-          expect(filePath).toBe atom.project.resolve('a')
-          expect(matches).toHaveLength 1
-          expect(matches[0]).toEqual
-            matchText: '$bill'
-            lineText: 'dollar$bill'
-            lineTextOffset: 0
-            range: [[2, 6], [2, 11]]
-
-      it "works on evil filenames", ->
-        platform.generateEvilFiles()
-        atom.project.setPaths([path.join(__dirname, 'fixtures', 'evil-files')])
-        paths = []
-        matches = []
-        waitsForPromise ->
-          atom.project.scan /evil/, (result) ->
-            paths.push(result.filePath)
-            matches = matches.concat(result.matches)
-
-        runs ->
-          _.each(matches, (m) -> expect(m.matchText).toEqual 'evil')
-
-          if platform.isWindows()
-            expect(paths.length).toBe 3
-            expect(paths[0]).toMatch /a_file_with_utf8.txt$/
-            expect(paths[1]).toMatch /file with spaces.txt$/
-            expect(path.basename(paths[2])).toBe "utfa\u0306.md"
-          else
-            expect(paths.length).toBe 5
-            expect(paths[0]).toMatch /a_file_with_utf8.txt$/
-            expect(paths[1]).toMatch /file with spaces.txt$/
-            expect(paths[2]).toMatch /goddam\nnewlines$/m
-            expect(paths[3]).toMatch /quote".txt$/m
-            expect(path.basename(paths[4])).toBe "utfa\u0306.md"
-
-      it "ignores case if the regex includes the `i` flag", ->
-        results = []
-        waitsForPromise ->
-          atom.project.scan /DOLLAR/i, (result) -> results.push(result)
-
-        runs ->
-          expect(results).toHaveLength 1
-
-      describe "when the core.excludeVcsIgnoredPaths config is truthy", ->
-        [projectPath, ignoredPath] = []
-
-        beforeEach ->
-          sourceProjectPath = path.join(__dirname, 'fixtures', 'git', 'working-dir')
-          projectPath = path.join(temp.mkdirSync("atom"))
-
-          writerStream = fstream.Writer(projectPath)
-          fstream.Reader(sourceProjectPath).pipe(writerStream)
-
-          waitsFor (done) ->
-            writerStream.on 'close', done
-            writerStream.on 'error', done
-
-          runs ->
-            fs.rename(path.join(projectPath, 'git.git'), path.join(projectPath, '.git'))
-            ignoredPath = path.join(projectPath, 'ignored.txt')
-            fs.writeFileSync(ignoredPath, 'this match should not be included')
-
-        afterEach ->
-          fs.removeSync(projectPath) if fs.existsSync(projectPath)
-
-        it "excludes ignored files", ->
-          atom.project.setPaths([projectPath])
-          atom.config.set('core.excludeVcsIgnoredPaths', true)
-          resultHandler = jasmine.createSpy("result found")
-          waitsForPromise ->
-            atom.project.scan /match/, (results) ->
-              resultHandler()
-
-          runs ->
-            expect(resultHandler).not.toHaveBeenCalled()
-
-      it "includes only files when a directory filter is specified", ->
-        projectPath = path.join(path.join(__dirname, 'fixtures', 'dir'))
-        atom.project.setPaths([projectPath])
-
-        filePath = path.join(projectPath, 'a-dir', 'oh-git')
-
-        paths = []
-        matches = []
-        waitsForPromise ->
-          atom.project.scan /aaa/, paths: ["a-dir#{path.sep}"], (result) ->
-            paths.push(result.filePath)
-            matches = matches.concat(result.matches)
-
-        runs ->
-          expect(paths.length).toBe 1
-          expect(paths[0]).toBe filePath
-          expect(matches.length).toBe 1
-
-      it "includes files and folders that begin with a '.'", ->
-        projectPath = temp.mkdirSync()
-        filePath = path.join(projectPath, '.text')
-        fs.writeFileSync(filePath, 'match this')
-        atom.project.setPaths([projectPath])
-        paths = []
-        matches = []
-        waitsForPromise ->
-          atom.project.scan /match this/, (result) ->
-            paths.push(result.filePath)
-            matches = matches.concat(result.matches)
-
-        runs ->
-          expect(paths.length).toBe 1
-          expect(paths[0]).toBe filePath
-          expect(matches.length).toBe 1
-
-      it "excludes values in core.ignoredNames", ->
-        projectPath = path.join(__dirname, 'fixtures', 'git', 'working-dir')
-        ignoredNames = atom.config.get("core.ignoredNames")
-        ignoredNames.push("a")
-        atom.config.set("core.ignoredNames", ignoredNames)
-
-        resultHandler = jasmine.createSpy("result found")
-        waitsForPromise ->
-          atom.project.scan /dollar/, (results) ->
-            resultHandler()
-
-        runs ->
-          expect(resultHandler).not.toHaveBeenCalled()
-
-      it "scans buffer contents if the buffer is modified", ->
-        editor = null
-        results = []
-
-        waitsForPromise ->
-          atom.project.open('a').then (o) ->
-            editor = o
-            editor.setText("Elephant")
-
-        waitsForPromise ->
-          atom.project.scan /a|Elephant/, (result) -> results.push result
-
-        runs ->
-          expect(results).toHaveLength 3
-          resultForA = _.find results, ({filePath}) -> path.basename(filePath) == 'a'
-          expect(resultForA.matches).toHaveLength 1
-          expect(resultForA.matches[0].matchText).toBe 'Elephant'
-
-      it "ignores buffers outside the project", ->
-        editor = null
-        results = []
-
-        waitsForPromise ->
-          atom.project.open(temp.openSync().path).then (o) ->
-            editor = o
-            editor.setText("Elephant")
-
-        waitsForPromise ->
-          atom.project.scan /Elephant/, (result) -> results.push result
-
-        runs ->
-          expect(results).toHaveLength 0
-
   describe ".eachBuffer(callback)", ->
     beforeEach ->
       atom.project.bufferForPathSync('a')

spec/spec-helper.coffee

@@ -84,6 +84,10 @@ beforeEach ->
   atom.workspaceViewParentSelector = '#jasmine-content'
 
   window.resetTimeouts()
+  spyOn(_._, "now").andCallFake -> window.now
+  spyOn(window, "setTimeout").andCallFake window.fakeSetTimeout
+  spyOn(window, "clearTimeout").andCallFake window.fakeClearTimeout
+
   atom.packages.packageStates = {}
 
   serializedWindowState = null
@@ -102,9 +106,9 @@ beforeEach ->
   spyOn(atom.menu, 'sendToBrowserProcess')
 
   # reset config before each spec; don't load or save from/to `config.json`
+  spyOn(Config::, 'load')
+  spyOn(Config::, 'save')
   config = new Config({resourcePath, configDirPath: atom.getConfigDirPath()})
-  spyOn(config, 'load')
-  spyOn(config, 'save')
   atom.config = config
   atom.loadConfig()
   config.set "core.destroyEmptyPanes", false
@@ -114,6 +118,7 @@ beforeEach ->
   config.set "core.disabledPackages", ["package-that-throws-an-exception",
     "package-with-broken-package-json", "package-with-broken-keymap"]
   config.set "editor.useShadowDOM", true
+  advanceClock(1000)
   config.load.reset()
   config.save.reset()
 
@@ -121,8 +126,6 @@ beforeEach ->
   TextEditorElement::setUpdatedSynchronously(true)
 
   spyOn(atom, "setRepresentedFilename")
-  spyOn(window, "setTimeout").andCallFake window.fakeSetTimeout
-  spyOn(window, "clearTimeout").andCallFake window.fakeClearTimeout
   spyOn(pathwatcher.File.prototype, "detectResurrectionAfterDelay").andCallFake -> @detectResurrection()
   spyOn(TextEditor.prototype, "shouldPromptToSave").andReturn false
 
@@ -204,10 +207,10 @@ jasmine.attachToDOM = (element) ->
 
 deprecationsSnapshot = null
 jasmine.snapshotDeprecations = ->
-  deprecationsSnapshot = Grim.getDeprecations() # suppress deprecations!!
+  deprecationsSnapshot = _.clone(Grim.deprecations)
 
 jasmine.restoreDeprecationsSnapshot = ->
-  Grim.grimDeprecations = deprecationsSnapshot
+  Grim.deprecations = deprecationsSnapshot
 
 addCustomMatchers = (spec) ->
   spec.addMatchers

spec/squirrel-update-spec.coffee

@@ -25,6 +25,16 @@ describe "Windows squirrel updates", ->
       else
         originalSpawn('ls')
 
+  it "ignores errors spawning Squirrel", ->
+    jasmine.unspy(ChildProcess, 'spawn')
+    spyOn(ChildProcess, 'spawn').andCallFake -> throw new Error("EBUSY")
+
+    app = quit: jasmine.createSpy('quit')
+    expect(SquirrelUpdate.handleStartupEvent(app, '--squirrel-install')).toBe true
+
+    waitsFor ->
+      app.quit.callCount is 1
+
   it "quits the app on all squirrel events", ->
     app = quit: jasmine.createSpy('quit')
 

spec/style-manager-spec.coffee

@@ -53,14 +53,16 @@ describe "StyleManager", ->
         expect(addEvents[0].getAttribute('source-path')).toBe '/foo/bar'
         expect(addEvents[0].textContent).toBe "a {color: yellow;}"
 
-    describe "when a group parameter is specified", ->
-      it "inserts the stylesheet at the end of any existing stylesheets for the same group", ->
-        manager.addStyleSheet("a {color: red}", group: 'a')
-        manager.addStyleSheet("a {color: blue}", group: 'b')
-        manager.addStyleSheet("a {color: green}", group: 'a')
+    describe "when a priority parameter is specified", ->
+      it "inserts the style sheet based on the priority", ->
+        manager.addStyleSheet("a {color: red}", priority: 1)
+        manager.addStyleSheet("a {color: blue}", priority: 0)
+        manager.addStyleSheet("a {color: green}", priority: 2)
+        manager.addStyleSheet("a {color: yellow}", priority: 1)
 
         expect(manager.getStyleElements().map (elt) -> elt.textContent).toEqual [
-          "a {color: red}"
-          "a {color: green}"
           "a {color: blue}"
+          "a {color: red}"
+          "a {color: yellow}"
+          "a {color: green}"
         ]

spec/styles-element-spec.coffee

@@ -32,16 +32,18 @@ describe "StylesElement", ->
     expect(element.children[initialChildCount].textContent).toBe "a {color: blue;}"
     expect(removedStyleElements).toEqual [addedStyleElements[0]]
 
-  it "orders style elements by group", ->
+  it "orders style elements by priority", ->
     initialChildCount = element.children.length
 
-    atom.styles.addStyleSheet("a {color: red}", group: 'a')
-    atom.styles.addStyleSheet("a {color: blue}", group: 'b')
-    atom.styles.addStyleSheet("a {color: green}", group: 'a')
+    atom.styles.addStyleSheet("a {color: red}", priority: 1)
+    atom.styles.addStyleSheet("a {color: blue}", priority: 0)
+    atom.styles.addStyleSheet("a {color: green}", priority: 2)
+    atom.styles.addStyleSheet("a {color: yellow}", priority: 1)
 
-    expect(element.children[initialChildCount].textContent).toBe "a {color: red}"
-    expect(element.children[initialChildCount + 1].textContent).toBe "a {color: green}"
-    expect(element.children[initialChildCount + 2].textContent).toBe "a {color: blue}"
+    expect(element.children[initialChildCount].textContent).toBe "a {color: blue}"
+    expect(element.children[initialChildCount + 1].textContent).toBe "a {color: red}"
+    expect(element.children[initialChildCount + 2].textContent).toBe "a {color: yellow}"
+    expect(element.children[initialChildCount + 3].textContent).toBe "a {color: green}"
 
   it "updates existing style nodes when style elements are updated", ->
     initialChildCount = element.children.length

spec/task-spec.coffee

@@ -20,3 +20,26 @@ describe "Task", ->
         expect(handlerResult).toBe 'hello'
         expect(childProcess.kill).toHaveBeenCalled()
         expect(processErrored).toBe false
+
+  it "calls listeners registered with ::on when events are emitted in the task", ->
+    task = new Task(require.resolve('./fixtures/task-spec-handler'))
+
+    eventSpy = jasmine.createSpy('eventSpy')
+    task.on("some-event", eventSpy)
+
+    waitsFor (done) -> task.start(done)
+
+    runs ->
+      expect(eventSpy).toHaveBeenCalledWith(1, 2, 3)
+
+  it "unregisters listeners when the Disposable returned by ::on is disposed", ->
+    task = new Task(require.resolve('./fixtures/task-spec-handler'))
+
+    eventSpy = jasmine.createSpy('eventSpy')
+    disposable = task.on("some-event", eventSpy)
+    disposable.dispose()
+
+    waitsFor (done) -> task.start(done)
+
+    runs ->
+      expect(eventSpy).not.toHaveBeenCalled()

spec/text-editor-component-spec.coffee

@@ -429,7 +429,7 @@ describe "TextEditorComponent", ->
       it "excludes the null byte from character measurement", ->
         editor.setText("a\0b")
         nextAnimationFrame()
-        expect(editor.pixelPositionForScreenPosition([0, Infinity]).left).toEqual 2 * charWidth
+        expect(wrapperNode.pixelPositionForScreenPosition([0, Infinity]).left).toEqual 2 * charWidth
 
     describe "when there is a fold", ->
       it "renders a fold marker on the folded line", ->
@@ -552,14 +552,29 @@ describe "TextEditorComponent", ->
       nextAnimationFrame()
       expect(lineNumbersNode.style.backgroundColor).toBe 'rgb(255, 0, 0)'
 
-    describe "when the editor.showLineNumbers config is false", ->
-      it "doesn't render any line numbers", ->
-        expect(component.refs.gutter).toBeDefined()
-        atom.config.set("editor.showLineNumbers", false)
-        expect(component.refs.gutter).not.toBeDefined()
-        atom.config.set("editor.showLineNumbers", true)
-        expect(component.refs.gutter).toBeDefined()
-        expect(component.lineNumberNodeForScreenRow(3)).toBeDefined()
+    it "hides or shows the gutter based on the '::isGutterVisible' property on the model and the global 'editor.showLineNumbers' config setting", ->
+      expect(component.refs.gutter?).toBe true
+
+      editor.setGutterVisible(false)
+      nextAnimationFrame()
+
+      expect(component.refs.gutter?).toBe false
+
+      atom.config.set("editor.showLineNumbers", false)
+      expect(nextAnimationFrame).toBe noAnimationFrame
+
+      expect(component.refs.gutter?).toBe false
+
+      editor.setGutterVisible(true)
+      expect(nextAnimationFrame).toBe noAnimationFrame
+
+      expect(component.refs.gutter?).toBe false
+
+      atom.config.set("editor.showLineNumbers", true)
+      nextAnimationFrame()
+
+      expect(component.refs.gutter?).toBe true
+      expect(component.lineNumberNodeForScreenRow(3)?).toBe true
 
     describe "fold decorations", ->
       describe "rendering fold decorations", ->
@@ -755,7 +770,6 @@ describe "TextEditorComponent", ->
       expect(cursorNode.offsetWidth).toBe charWidth
 
     it "blinks cursors when they aren't moving", ->
-      spyOn(_._, 'now').andCallFake -> window.now # Ensure _.debounce is based on our fake spec timeline
       cursorsNode = componentNode.querySelector('.cursors')
 
       expect(cursorsNode.classList.contains('blink-off')).toBe false
@@ -802,7 +816,7 @@ describe "TextEditorComponent", ->
       nextAnimationFrame()
       cursorNode = componentNode.querySelector('.cursor')
 
-      {left} = editor.pixelPositionForScreenPosition([1, 10])
+      {left} = wrapperNode.pixelPositionForScreenPosition([1, 10])
       expect(cursorNode.style['-webkit-transform']).toBe "translate(#{left}px, #{editor.getLineHeightInPixels()}px)"
 
   describe "selection rendering", ->
@@ -896,7 +910,7 @@ describe "TextEditorComponent", ->
       nextAnimationFrame()
       selectionNode = componentNode.querySelector('.region')
       expect(selectionNode.offsetTop).toBe editor.getLineHeightInPixels()
-      expect(selectionNode.offsetLeft).toBe editor.pixelPositionForScreenPosition([1, 6]).left
+      expect(selectionNode.offsetLeft).toBe wrapperNode.pixelPositionForScreenPosition([1, 6]).left
 
     it "will flash the selection when flash:true is passed to editor::setSelectedBufferRange", ->
       editor.setSelectedBufferRange([[1, 6], [1, 10]], flash: true)
@@ -1231,7 +1245,7 @@ describe "TextEditorComponent", ->
         decoration = editor.decorateMarker(marker, {type: 'overlay', item})
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([2, 5])
+        position = wrapperNode.pixelPositionForBufferPosition([2, 5])
 
         overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
         expect(overlay.style.left).toBe position.left + 'px'
@@ -1241,7 +1255,7 @@ describe "TextEditorComponent", ->
         editor.moveRight()
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([2, 7])
+        position = wrapperNode.pixelPositionForBufferPosition([2, 7])
 
         expect(overlay.style.left).toBe position.left + 'px'
         expect(overlay.style.top).toBe position.top + editor.getLineHeightInPixels() + 'px'
@@ -1252,7 +1266,7 @@ describe "TextEditorComponent", ->
         decoration = editor.decorateMarker(marker, {type: 'overlay', item})
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([2, 10])
+        position = wrapperNode.pixelPositionForBufferPosition([2, 10])
 
         overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
         expect(overlay.style.left).toBe position.left + 'px'
@@ -1263,7 +1277,7 @@ describe "TextEditorComponent", ->
         decoration = editor.decorateMarker(marker, {type: 'overlay', item})
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([2, 5])
+        position = wrapperNode.pixelPositionForBufferPosition([2, 5])
 
         overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
         expect(overlay.style.left).toBe position.left + 'px'
@@ -1274,7 +1288,7 @@ describe "TextEditorComponent", ->
         decoration = editor.decorateMarker(marker, {type: 'overlay', position: 'tail', item})
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([2, 5])
+        position = wrapperNode.pixelPositionForBufferPosition([2, 5])
 
         overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
         expect(overlay.style.left).toBe position.left + 'px'
@@ -1304,7 +1318,7 @@ describe "TextEditorComponent", ->
         decoration = editor.decorateMarker(marker, {type: 'overlay', item})
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([0, 26])
+        position = wrapperNode.pixelPositionForBufferPosition([0, 26])
 
         overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
         expect(overlay.style.left).toBe position.left + 'px'
@@ -1313,7 +1327,7 @@ describe "TextEditorComponent", ->
         editor.insertText('a')
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([0, 27])
+        position = wrapperNode.pixelPositionForBufferPosition([0, 27])
 
         expect(overlay.style.left).toBe position.left - itemWidth + 'px'
         expect(overlay.style.top).toBe position.top + editor.getLineHeightInPixels() + 'px'
@@ -1323,7 +1337,7 @@ describe "TextEditorComponent", ->
         decoration = editor.decorateMarker(marker, {type: 'overlay', item})
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([4, 0])
+        position = wrapperNode.pixelPositionForBufferPosition([4, 0])
 
         overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
         expect(overlay.style.left).toBe position.left + 'px'
@@ -1332,7 +1346,7 @@ describe "TextEditorComponent", ->
         editor.insertNewline()
         nextAnimationFrame()
 
-        position = editor.pixelPositionForBufferPosition([5, 0])
+        position = wrapperNode.pixelPositionForBufferPosition([5, 0])
 
         expect(overlay.style.left).toBe position.left + 'px'
         expect(overlay.style.top).toBe position.top - itemHeight + 'px'
@@ -1354,7 +1368,7 @@ describe "TextEditorComponent", ->
           decoration = editor.decorateMarker(marker, {type: 'overlay', item})
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([0, 2])
+          position = wrapperNode.pixelPositionForBufferPosition([0, 2])
 
           overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
           expect(overlay.style.left).toBe position.left + 'px'
@@ -1363,7 +1377,7 @@ describe "TextEditorComponent", ->
           editor.insertText('a')
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([0, 3])
+          position = wrapperNode.pixelPositionForBufferPosition([0, 3])
 
           expect(overlay.style.left).toBe position.left + 'px'
           expect(overlay.style.top).toBe position.top + editor.getLineHeightInPixels() + 'px'
@@ -1373,7 +1387,7 @@ describe "TextEditorComponent", ->
           decoration = editor.decorateMarker(marker, {type: 'overlay', item})
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([1, 0])
+          position = wrapperNode.pixelPositionForBufferPosition([1, 0])
 
           overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
           expect(overlay.style.left).toBe position.left + 'px'
@@ -1382,7 +1396,7 @@ describe "TextEditorComponent", ->
           editor.insertNewline()
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([2, 0])
+          position = wrapperNode.pixelPositionForBufferPosition([2, 0])
 
           expect(overlay.style.left).toBe position.left + 'px'
           expect(overlay.style.top).toBe position.top + editor.getLineHeightInPixels() + 'px'
@@ -1395,7 +1409,7 @@ describe "TextEditorComponent", ->
           decoration = editor.decorateMarker(marker, {type: 'overlay', item})
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([0, 28])
+          position = wrapperNode.pixelPositionForBufferPosition([0, 28])
 
           overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
           expect(overlay.style.left).toBe position.left + 'px'
@@ -1404,7 +1418,7 @@ describe "TextEditorComponent", ->
           editor.insertText('a')
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([0, 29])
+          position = wrapperNode.pixelPositionForBufferPosition([0, 29])
 
           expect(overlay.style.left).toBe position.left - itemWidth + 'px'
           expect(overlay.style.top).toBe position.top + editor.getLineHeightInPixels() + 'px'
@@ -1415,7 +1429,7 @@ describe "TextEditorComponent", ->
           decoration = editor.decorateMarker(marker, {type: 'overlay', item})
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([6, 0])
+          position = wrapperNode.pixelPositionForBufferPosition([6, 0])
 
           overlay = component.getTopmostDOMNode().querySelector('atom-overlay')
           expect(overlay.style.left).toBe position.left + 'px'
@@ -1424,7 +1438,7 @@ describe "TextEditorComponent", ->
           editor.insertNewline()
           nextAnimationFrame()
 
-          position = editor.pixelPositionForBufferPosition([7, 0])
+          position = wrapperNode.pixelPositionForBufferPosition([7, 0])
 
           expect(overlay.style.left).toBe position.left + 'px'
           expect(overlay.style.top).toBe position.top - itemHeight + 'px'
@@ -2048,8 +2062,6 @@ describe "TextEditorComponent", ->
         expect(component.mouseWheelScreenRow).toBe null
 
       it "clears the mouseWheelScreenRow after a delay even if the event does not cause scrolling", ->
-        spyOn(_._, 'now').andCallFake -> window.now # Ensure _.debounce is based on our fake spec timeline
-
         expect(editor.getScrollTop()).toBe 0
 
         lineNode = componentNode.querySelector('.line')
@@ -2505,7 +2517,8 @@ describe "TextEditorComponent", ->
 
   describe "when the 'mini' property is true", ->
     beforeEach ->
-      component.setProps(mini: true)
+      editor.setMini(true)
+      nextAnimationFrame()
 
     it "does not render the gutter", ->
       expect(componentNode.querySelector('.gutter')).toBeNull()
@@ -2593,9 +2606,9 @@ describe "TextEditorComponent", ->
 
     describe 'soft wrap settings', ->
       beforeEach ->
-        atom.config.set '.source.coffee', 'editor.softWrap', true
-        atom.config.set '.source.coffee', 'editor.preferredLineLength', 17
-        atom.config.set '.source.coffee', 'editor.softWrapAtPreferredLineLength', true
+        atom.config.set 'editor.softWrap', true, scopeSelector: '.source.coffee'
+        atom.config.set 'editor.preferredLineLength', 17, scopeSelector: '.source.coffee'
+        atom.config.set 'editor.softWrapAtPreferredLineLength', true, scopeSelector: '.source.coffee'
 
         editor.setEditorWidthInChars(20)
         coffeeEditor.setEditorWidthInChars(20)
@@ -2605,18 +2618,18 @@ describe "TextEditorComponent", ->
         expect(coffeeEditor.lineTextForScreenRow(3)).toEqual '    return items '
 
       it 'updates the wrapped lines when editor.preferredLineLength changes', ->
-        atom.config.set '.source.coffee', 'editor.preferredLineLength', 20
+        atom.config.set 'editor.preferredLineLength', 20, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(2)).toEqual '    return items if '
 
       it 'updates the wrapped lines when editor.softWrapAtPreferredLineLength changes', ->
-        atom.config.set '.source.coffee', 'editor.softWrapAtPreferredLineLength', false
+        atom.config.set 'editor.softWrapAtPreferredLineLength', false, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(2)).toEqual '    return items if '
 
       it 'updates the wrapped lines when editor.softWrap changes', ->
-        atom.config.set '.source.coffee', 'editor.softWrap', false
+        atom.config.set 'editor.softWrap', false, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(2)).toEqual '    return items if items.length <= 1'
 
-        atom.config.set '.source.coffee', 'editor.softWrap', true
+        atom.config.set 'editor.softWrap', true, scopeSelector: '.source.coffee'
         expect(coffeeEditor.lineTextForScreenRow(3)).toEqual '    return items '
 
       it 'updates the wrapped lines when the grammar changes', ->
@@ -2644,11 +2657,11 @@ describe "TextEditorComponent", ->
           tab: 'F'
           cr: 'E'
 
-        atom.config.set '.source.js', 'editor.showInvisibles', true
-        atom.config.set '.source.js', 'editor.invisibles', jsInvisibles
+        atom.config.set 'editor.showInvisibles', true, scopeSelector: '.source.js'
+        atom.config.set 'editor.invisibles', jsInvisibles, scopeSelector: '.source.js'
 
-        atom.config.set '.source.coffee', 'editor.showInvisibles', false
-        atom.config.set '.source.coffee', 'editor.invisibles', coffeeInvisibles
+        atom.config.set 'editor.showInvisibles', false, scopeSelector: '.source.coffee'
+        atom.config.set 'editor.invisibles', coffeeInvisibles, scopeSelector: '.source.coffee'
 
         editor.setText " a line with tabs\tand spaces \n"
         nextAnimationFrame()
@@ -2664,7 +2677,7 @@ describe "TextEditorComponent", ->
       it "re-renders the invisibles when the invisible settings change", ->
         jsGrammar = editor.getGrammar()
         editor.setGrammar(coffeeEditor.getGrammar())
-        atom.config.set '.source.coffee', 'editor.showInvisibles', true
+        atom.config.set 'editor.showInvisibles', true, scopeSelector: '.source.coffee'
         nextAnimationFrame()
         expect(component.lineNodeForScreenRow(0).textContent).toBe "#{coffeeInvisibles.space}a line with tabs#{coffeeInvisibles.tab}and spaces#{coffeeInvisibles.space}#{coffeeInvisibles.eol}"
 
@@ -2673,7 +2686,7 @@ describe "TextEditorComponent", ->
           space: 'E'
           tab: 'W'
           cr: 'I'
-        atom.config.set '.source.coffee', 'editor.invisibles', newInvisibles
+        atom.config.set 'editor.invisibles', newInvisibles, scopeSelector: '.source.coffee'
         nextAnimationFrame()
         expect(component.lineNodeForScreenRow(0).textContent).toBe "#{newInvisibles.space}a line with tabs#{newInvisibles.tab}and spaces#{newInvisibles.space}#{newInvisibles.eol}"
 
@@ -2683,8 +2696,8 @@ describe "TextEditorComponent", ->
 
     describe 'editor.showIndentGuide', ->
       beforeEach ->
-        atom.config.set '.source.js', 'editor.showIndentGuide', true
-        atom.config.set '.source.coffee', 'editor.showIndentGuide', false
+        atom.config.set 'editor.showIndentGuide', true, scopeSelector: '.source.js'
+        atom.config.set 'editor.showIndentGuide', false, scopeSelector: '.source.coffee'
 
       it "has an 'indent-guide' class when scoped editor.showIndentGuide is true, but not when scoped editor.showIndentGuide is false", ->
         line1LeafNodes = getLeafNodes(component.lineNodeForScreenRow(1))
@@ -2705,7 +2718,7 @@ describe "TextEditorComponent", ->
         expect(line1LeafNodes[0].classList.contains('indent-guide')).toBe true
         expect(line1LeafNodes[1].classList.contains('indent-guide')).toBe false
 
-        atom.config.set '.source.js', 'editor.showIndentGuide', false
+        atom.config.set 'editor.showIndentGuide', false, scopeSelector: '.source.js'
 
         line1LeafNodes = getLeafNodes(component.lineNodeForScreenRow(1))
         expect(line1LeafNodes[0].textContent).toBe '  '
@@ -2754,14 +2767,14 @@ describe "TextEditorComponent", ->
     event
 
   clientCoordinatesForScreenPosition = (screenPosition) ->
-    positionOffset = editor.pixelPositionForScreenPosition(screenPosition)
+    positionOffset = wrapperNode.pixelPositionForScreenPosition(screenPosition)
     scrollViewClientRect = componentNode.querySelector('.scroll-view').getBoundingClientRect()
     clientX = scrollViewClientRect.left + positionOffset.left - editor.getScrollLeft()
     clientY = scrollViewClientRect.top + positionOffset.top - editor.getScrollTop()
     {clientX, clientY}
 
   clientCoordinatesForScreenRowInGutter = (screenRow) ->
-    positionOffset = editor.pixelPositionForScreenPosition([screenRow, 1])
+    positionOffset = wrapperNode.pixelPositionForScreenPosition([screenRow, 1])
     gutterClientRect = componentNode.querySelector('.gutter').getBoundingClientRect()
     clientX = gutterClientRect.left + positionOffset.left - editor.getScrollLeft()
     clientY = gutterClientRect.top + positionOffset.top - editor.getScrollTop()

spec/text-editor-element-spec.coffee

@@ -10,16 +10,21 @@ describe "TextEditorElement", ->
     jasmineContent = document.body.querySelector('#jasmine-content')
 
   describe "instantiation", ->
-    it "honors the mini attribute", ->
+    it "honors the 'mini' attribute", ->
       jasmineContent.innerHTML = "<atom-text-editor mini>"
       element = jasmineContent.firstChild
       expect(element.getModel().isMini()).toBe true
 
-    it "honors the placeholder-text attribute", ->
+    it "honors the 'placeholder-text' attribute", ->
       jasmineContent.innerHTML = "<atom-text-editor placeholder-text='testing'>"
       element = jasmineContent.firstChild
       expect(element.getModel().getPlaceholderText()).toBe 'testing'
 
+    it "honors the 'gutter-hidden' attribute", ->
+      jasmineContent.innerHTML = "<atom-text-editor gutter-hidden>"
+      element = jasmineContent.firstChild
+      expect(element.getModel().isGutterVisible()).toBe false
+
     it "honors the text content", ->
       jasmineContent.innerHTML = "<atom-text-editor>testing</atom-text-editor>"
       element = jasmineContent.firstChild
@@ -42,9 +47,12 @@ describe "TextEditorElement", ->
 
         component = element.component
         expect(component.isMounted()).toBe true
-        element.getModel().destroy()
+        element.remove()
         expect(component.isMounted()).toBe false
 
+        jasmine.attachToDOM(element)
+        expect(element.component.isMounted()).toBe true
+
     describe "when the editor.useShadowDOM config option is false", ->
       it "mounts the react component and unmounts when removed from the dom", ->
         atom.config.set('editor.useShadowDOM', false)
@@ -95,6 +103,22 @@ describe "TextEditorElement", ->
         document.body.focus()
         expect(blurCalled).toBe true
 
+    describe "when focused while a parent node is being attached to the DOM", ->
+      class ElementThatFocusesChild extends HTMLDivElement
+        attachedCallback: ->
+          @firstChild.focus()
+
+      document.registerElement("element-that-focuses-child",
+        prototype: ElementThatFocusesChild.prototype
+      )
+
+      it "proxies the focus event to the hidden input", ->
+        element = new TextEditorElement
+        parentElement = document.createElement("element-that-focuses-child")
+        parentElement.appendChild(element)
+        jasmineContent.appendChild(parentElement)
+        expect(element.shadowRoot.activeElement).toBe element.shadowRoot.querySelector('input')
+
   describe "when the themes finish loading", ->
     [themeReloadCallback, initialThemeLoadComplete, element] = []
 
@@ -104,7 +128,7 @@ describe "TextEditorElement", ->
 
       spyOn(atom.themes, 'isInitialLoadComplete').andCallFake ->
         initialThemeLoadComplete
-      spyOn(atom.themes, 'onDidReloadAll').andCallFake (fn) ->
+      spyOn(atom.themes, 'onDidChangeActiveThemes').andCallFake (fn) ->
         themeReloadCallback = fn
 
       atom.config.set("editor.useShadowDOM", false)

spec/text-editor-spec.coffee

@@ -62,7 +62,6 @@ describe "TextEditor", ->
         atom.workspace.open('sample.less', initialLine: 5).then (o) -> editor = o
 
       runs ->
-        buffer = editor.buffer
         expect(editor.getLastCursor().getBufferPosition().row).toEqual 5
         expect(editor.getLastCursor().getBufferPosition().column).toEqual 0
 
@@ -74,10 +73,37 @@ describe "TextEditor", ->
         atom.workspace.open('sample.less', initialColumn: 8).then (o) -> editor = o
 
       runs ->
-        buffer = editor.buffer
         expect(editor.getLastCursor().getBufferPosition().row).toEqual 0
         expect(editor.getLastCursor().getBufferPosition().column).toEqual 8
 
+  describe "when the editor is reopened with an initialLine option", ->
+    it "positions the cursor on the specified line", ->
+      editor = null
+
+      waitsForPromise ->
+        atom.workspace.open('sample.less', initialLine: 5).then (o) -> editor = o
+
+      waitsForPromise ->
+        atom.workspace.open('sample.less', initialLine: 4).then (o) -> editor = o
+
+      runs ->
+        expect(editor.getLastCursor().getBufferPosition().row).toEqual 4
+        expect(editor.getLastCursor().getBufferPosition().column).toEqual 0
+
+  describe "when the editor is reopened with an initialColumn option", ->
+    it "positions the cursor on the specified column", ->
+      editor = null
+
+      waitsForPromise ->
+        atom.workspace.open('sample.less', initialColumn: 8).then (o) -> editor = o
+
+      waitsForPromise ->
+        atom.workspace.open('sample.less', initialColumn: 7).then (o) -> editor = o
+
+      runs ->
+        expect(editor.getLastCursor().getBufferPosition().row).toEqual 0
+        expect(editor.getLastCursor().getBufferPosition().column).toEqual 7
+
   describe ".copy()", ->
     it "returns a different edit session with the same initial state", ->
       editor.setSelectedBufferRange([[1, 2], [3, 4]])
@@ -918,6 +944,15 @@ describe "TextEditor", ->
         editor.undo()
         expect(editor.getScrollTop()).toBe 0
 
+    describe '.logCursorScope()', ->
+      beforeEach ->
+        spyOn(atom.notifications, 'addInfo')
+
+      it 'opens a notification', ->
+        editor.logCursorScope()
+
+        expect(atom.notifications.addInfo).toHaveBeenCalled()
+
   describe "selection", ->
     selection = null
 
@@ -1327,7 +1362,7 @@ describe "TextEditor", ->
           coffeeEditor.selectWordsContainingCursors()
           expect(coffeeEditor.getSelectedBufferRange()).toEqual [[0, 6], [0, 15]]
 
-          atom.config.set '.source.coffee', 'editor.nonWordCharacters', 'qusort'
+          atom.config.set 'editor.nonWordCharacters', 'qusort', scopeSelector: '.source.coffee'
 
           coffeeEditor.setCursorBufferPosition [0, 9]
           coffeeEditor.selectWordsContainingCursors()
@@ -3276,7 +3311,7 @@ describe "TextEditor", ->
         atom.packages.unloadPackages()
 
       it 'returns correct values based on the scope of the set grammars', ->
-        atom.config.set '.source.coffee', 'editor.tabLength', 6
+        atom.config.set 'editor.tabLength', 6, scopeSelector: '.source.coffee'
 
         expect(editor.getTabLength()).toBe 2
         expect(coffeeEditor.getTabLength()).toBe 6
@@ -3298,12 +3333,12 @@ describe "TextEditor", ->
         expect(editor.getTabLength()).toBe 2
         expect(editor.tokenizedLineForScreenRow(5).tokens[0].firstNonWhitespaceIndex).toBe 2
 
-        atom.config.set '.source.js', 'editor.tabLength', 6
+        atom.config.set 'editor.tabLength', 6, scopeSelector: '.source.js'
         expect(editor.getTabLength()).toBe 6
         expect(editor.tokenizedLineForScreenRow(5).tokens[0].firstNonWhitespaceIndex).toBe 6
 
       it 'updates the tab length when the grammar changes', ->
-        atom.config.set '.source.coffee', 'editor.tabLength', 6
+        atom.config.set 'editor.tabLength', 6, scopeSelector: '.source.coffee'
 
         expect(editor.getTabLength()).toBe 2
         expect(editor.tokenizedLineForScreenRow(5).tokens[0].firstNonWhitespaceIndex).toBe 2
@@ -3473,8 +3508,8 @@ describe "TextEditor", ->
           atom.project.open('coffee.coffee', autoIndent: false).then (o) -> coffeeEditor = o
 
         runs ->
-          atom.config.set('.source.js', 'editor.autoIndent', true)
-          atom.config.set('.source.coffee', 'editor.autoIndent', false)
+          atom.config.set('editor.autoIndent', true, scopeSelector: '.source.js')
+          atom.config.set('editor.autoIndent', false, scopeSelector: '.source.coffee')
 
       afterEach: ->
         atom.packages.deactivatePackages()
@@ -3766,8 +3801,12 @@ describe "TextEditor", ->
     it "updates the grammar based on grammar overrides", ->
       expect(editor.getGrammar().name).toBe 'JavaScript'
       atom.grammars.setGrammarOverrideForPath(editor.getPath(), 'source.coffee')
+      callback = jasmine.createSpy('callback')
+      editor.onDidChangeGrammar(callback)
       editor.reloadGrammar()
       expect(editor.getGrammar().name).toBe 'CoffeeScript'
+      expect(callback.callCount).toBe 1
+      expect(callback.argsForCall[0][0]).toBe atom.grammars.grammarForScopeName('source.coffee')
 
   describe "when the editor's grammar has an injection selector", ->
     beforeEach ->

spec/theme-manager-spec.coffee

@@ -73,65 +73,90 @@ describe "ThemeManager", ->
 
   describe "when the core.themes config value changes", ->
     it "add/removes stylesheets to reflect the new config value", ->
-      themeManager.onDidReloadAll reloadHandler = jasmine.createSpy()
+      themeManager.onDidChangeActiveThemes didChangeActiveThemesHandler = jasmine.createSpy()
       spyOn(atom.styles, 'getUserStyleSheetPath').andCallFake -> null
 
       waitsForPromise ->
         themeManager.activateThemes()
 
       runs ->
-        reloadHandler.reset()
+        didChangeActiveThemesHandler.reset()
         atom.config.set('core.themes', [])
 
       waitsFor ->
-        reloadHandler.callCount == 1
+        didChangeActiveThemesHandler.callCount == 1
 
       runs ->
-        reloadHandler.reset()
+        didChangeActiveThemesHandler.reset()
         expect($('style.theme')).toHaveLength 0
         atom.config.set('core.themes', ['atom-dark-ui'])
 
       waitsFor ->
-        reloadHandler.callCount == 1
+        didChangeActiveThemesHandler.callCount == 1
 
       runs ->
-        reloadHandler.reset()
-        expect($('style[group=theme]')).toHaveLength 2
-        expect($('style[group=theme]:eq(0)').attr('source-path')).toMatch /atom-dark-ui/
+        didChangeActiveThemesHandler.reset()
+        expect($('style[priority=1]')).toHaveLength 2
+        expect($('style[priority=1]:eq(0)').attr('source-path')).toMatch /atom-dark-ui/
         atom.config.set('core.themes', ['atom-light-ui', 'atom-dark-ui'])
 
       waitsFor ->
-        reloadHandler.callCount == 1
+        didChangeActiveThemesHandler.callCount == 1
 
       runs ->
-        reloadHandler.reset()
-        expect($('style[group=theme]')).toHaveLength 2
-        expect($('style[group=theme]:eq(0)').attr('source-path')).toMatch /atom-dark-ui/
-        expect($('style[group=theme]:eq(1)').attr('source-path')).toMatch /atom-light-ui/
+        didChangeActiveThemesHandler.reset()
+        expect($('style[priority=1]')).toHaveLength 2
+        expect($('style[priority=1]:eq(0)').attr('source-path')).toMatch /atom-dark-ui/
+        expect($('style[priority=1]:eq(1)').attr('source-path')).toMatch /atom-light-ui/
         atom.config.set('core.themes', [])
 
       waitsFor ->
-        reloadHandler.callCount == 1
+        didChangeActiveThemesHandler.callCount == 1
 
       runs ->
-        reloadHandler.reset()
-        expect($('style[group=theme]')).toHaveLength 2
+        didChangeActiveThemesHandler.reset()
+        expect($('style[priority=1]')).toHaveLength 2
         # 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
+        didChangeActiveThemesHandler.callCount == 1
 
       runs ->
-        expect($('style[group=theme]')).toHaveLength 2
+        expect($('style[priority=1]')).toHaveLength 2
         importPaths = themeManager.getImportPaths()
         expect(importPaths.length).toBe 1
         expect(importPaths[0]).toContain 'atom-dark-ui'
 
+    it 'adds theme-* classes to the workspace for each active theme', ->
+      workspaceElement = atom.views.getView(atom.workspace)
+      themeManager.onDidChangeActiveThemes didChangeActiveThemesHandler = jasmine.createSpy()
+
+      waitsForPromise ->
+        themeManager.activateThemes()
+
+      runs ->
+        expect(workspaceElement).toHaveClass 'theme-atom-dark-ui'
+
+        themeManager.onDidChangeActiveThemes didChangeActiveThemesHandler = jasmine.createSpy()
+        atom.config.set('core.themes', ['theme-with-ui-variables', 'theme-with-syntax-variables'])
+
+      waitsFor ->
+        didChangeActiveThemesHandler.callCount > 0
+
+      runs ->
+        # `theme-` twice as it prefixes the name with `theme-`
+        expect(workspaceElement).toHaveClass 'theme-theme-with-ui-variables'
+        expect(workspaceElement).toHaveClass 'theme-theme-with-syntax-variables'
+        expect(workspaceElement).not.toHaveClass 'theme-atom-dark-ui'
+        expect(workspaceElement).not.toHaveClass 'theme-atom-dark-syntax'
+
   describe "when a theme fails to load", ->
     it "logs a warning", ->
       spyOn(console, 'warn')
-      expect(-> atom.packages.activatePackage('a-theme-that-will-not-be-found')).toThrow()
+      atom.packages.activatePackage('a-theme-that-will-not-be-found')
+      expect(console.warn.callCount).toBe 1
+      expect(console.warn.argsForCall[0][0]).toContain "Could not resolve 'a-theme-that-will-not-be-found'"
 
   describe "::requireStylesheet(path)", ->
     beforeEach ->
@@ -145,7 +170,7 @@ describe "ThemeManager", ->
       themeManager.onDidChangeStylesheets stylesheetsChangedHandler = jasmine.createSpy("stylesheetsChangedHandler")
       themeManager.onDidAddStylesheet stylesheetAddedHandler = jasmine.createSpy("stylesheetAddedHandler")
 
-      cssPath = atom.project.resolve('css.css')
+      cssPath = atom.project.getDirectories()[0]?.resolve('css.css')
       lengthBefore = $('head style').length
 
       themeManager.requireStylesheet(cssPath)
@@ -169,7 +194,7 @@ describe "ThemeManager", ->
       $('head style[id*="css.css"]').remove()
 
     it "synchronously loads and parses less files at the given path and installs a style tag for it in the head", ->
-      lessPath = atom.project.resolve('sample.less')
+      lessPath = atom.project.getDirectories()[0]?.resolve('sample.less')
       lengthBefore = $('head style').length
       themeManager.requireStylesheet(lessPath)
       expect($('head style').length).toBe lengthBefore + 1
@@ -193,9 +218,9 @@ describe "ThemeManager", ->
 
     it "supports requiring css and less stylesheets without an explicit extension", ->
       themeManager.requireStylesheet path.join(__dirname, 'fixtures', 'css')
-      expect($('head style[source-path*="css.css"]').attr('source-path')).toBe themeManager.stringToId(atom.project.resolve('css.css'))
+      expect($('head style[source-path*="css.css"]').attr('source-path')).toBe themeManager.stringToId(atom.project.getDirectories()[0]?.resolve('css.css'))
       themeManager.requireStylesheet path.join(__dirname, 'fixtures', 'sample')
-      expect($('head style[source-path*="sample.less"]').attr('source-path')).toBe themeManager.stringToId(atom.project.resolve('sample.less'))
+      expect($('head style[source-path*="sample.less"]').attr('source-path')).toBe themeManager.stringToId(atom.project.getDirectories()[0]?.resolve('sample.less'))
 
       $('head style[id*="css.css"]').remove()
       $('head style[id*="sample.less"]').remove()
@@ -223,11 +248,9 @@ describe "ThemeManager", ->
 
       expect(stylesheetsChangedHandler).toHaveBeenCalled()
 
-  describe "base stylesheet loading", ->
+  describe "base style sheet loading", ->
     workspaceElement = null
     beforeEach ->
-      jasmine.snapshotDeprecations()
-
       workspaceElement = atom.views.getView(atom.workspace)
       jasmine.attachToDOM(workspaceElement)
       workspaceElement.appendChild document.createElement('atom-text-editor')
@@ -235,15 +258,12 @@ describe "ThemeManager", ->
       waitsForPromise ->
         themeManager.activateThemes()
 
-    beforeEach ->
-      jasmine.restoreDeprecationsSnapshot()
-
     it "loads the correct values from the theme's ui-variables file", ->
-      themeManager.onDidReloadAll reloadHandler = jasmine.createSpy()
+      themeManager.onDidChangeActiveThemes didChangeActiveThemesHandler = jasmine.createSpy()
       atom.config.set('core.themes', ['theme-with-ui-variables', 'theme-with-syntax-variables'])
 
       waitsFor ->
-        reloadHandler.callCount > 0
+        didChangeActiveThemesHandler.callCount > 0
 
       runs ->
         # an override loaded in the base css
@@ -256,11 +276,11 @@ describe "ThemeManager", ->
 
     describe "when there is a theme with incomplete variables", ->
       it "loads the correct values from the fallback ui-variables", ->
-        themeManager.onDidReloadAll reloadHandler = jasmine.createSpy()
+        themeManager.onDidChangeActiveThemes didChangeActiveThemesHandler = jasmine.createSpy()
         atom.config.set('core.themes', ['theme-with-incomplete-ui-variables', 'theme-with-syntax-variables'])
 
         waitsFor ->
-          reloadHandler.callCount > 0
+          didChangeActiveThemesHandler.callCount > 0
 
         runs ->
           # an override loaded in the base css
@@ -269,22 +289,6 @@ describe "ThemeManager", ->
           # from within the theme itself
           expect($("atom-text-editor").css("background-color")).toBe "rgb(0, 152, 255)"
 
-    describe "theme classes on the workspace", ->
-      it 'adds theme-* classes to the workspace for each active theme', ->
-        expect(workspaceElement).toHaveClass 'theme-atom-dark-ui'
-
-        themeManager.onDidReloadAll reloadHandler = jasmine.createSpy()
-        atom.config.set('core.themes', ['theme-with-ui-variables', 'theme-with-syntax-variables'])
-
-        waitsFor ->
-          reloadHandler.callCount > 0
-
-        runs ->
-          # `theme-` twice as it prefixes the name with `theme-`
-          expect(workspaceElement).toHaveClass 'theme-theme-with-ui-variables'
-          expect(workspaceElement).toHaveClass 'theme-theme-with-syntax-variables'
-          expect(workspaceElement).not.toHaveClass 'theme-atom-dark-ui'
-          expect(workspaceElement).not.toHaveClass 'theme-atom-dark-syntax'
 
   describe "when the user stylesheet changes", ->
     beforeEach ->
@@ -358,7 +362,7 @@ describe "ThemeManager", ->
         themeManager.activateThemes()
 
     it 'uses the default dark UI and syntax themes and logs a warning', ->
-      activeThemeNames = themeManager.getActiveNames()
+      activeThemeNames = themeManager.getActiveThemeNames()
       expect(console.warn.callCount).toBe 2
       expect(activeThemeNames.length).toBe(2)
       expect(activeThemeNames).toContain('atom-dark-ui')
@@ -376,7 +380,7 @@ describe "ThemeManager", ->
           themeManager.activateThemes()
 
       it 'uses the enabled themes', ->
-        activeThemeNames = themeManager.getActiveNames()
+        activeThemeNames = themeManager.getActiveThemeNames()
         expect(activeThemeNames.length).toBe(2)
         expect(activeThemeNames).toContain('atom-light-ui')
         expect(activeThemeNames).toContain('atom-dark-syntax')
@@ -389,7 +393,7 @@ describe "ThemeManager", ->
           themeManager.activateThemes()
 
       it 'uses the default dark UI and syntax themes', ->
-        activeThemeNames = themeManager.getActiveNames()
+        activeThemeNames = themeManager.getActiveThemeNames()
         expect(activeThemeNames.length).toBe(2)
         expect(activeThemeNames).toContain('atom-dark-ui')
         expect(activeThemeNames).toContain('atom-dark-syntax')
@@ -402,7 +406,7 @@ describe "ThemeManager", ->
           themeManager.activateThemes()
 
       it 'uses the default dark UI theme', ->
-        activeThemeNames = themeManager.getActiveNames()
+        activeThemeNames = themeManager.getActiveThemeNames()
         expect(activeThemeNames.length).toBe(2)
         expect(activeThemeNames).toContain('atom-dark-ui')
         expect(activeThemeNames).toContain('atom-light-syntax')
@@ -415,7 +419,7 @@ describe "ThemeManager", ->
           themeManager.activateThemes()
 
       it 'uses the default dark syntax theme', ->
-        activeThemeNames = themeManager.getActiveNames()
+        activeThemeNames = themeManager.getActiveThemeNames()
         expect(activeThemeNames.length).toBe(2)
         expect(activeThemeNames).toContain('atom-light-ui')
         expect(activeThemeNames).toContain('atom-dark-syntax')

spec/view-registry-spec.coffee

@@ -14,14 +14,14 @@ describe "ViewRegistry", ->
         expect(registry.getView(node)).toBe node
 
     describe "when passed a SpacePen view", ->
-      it "returns the root node of the view with a __spacePenView property pointing at the SpacePen view", ->
+      it "returns the root node of the view with a .spacePenView property pointing at the SpacePen view", ->
         class TestView extends View
           @content: -> @div "Hello"
 
         view = new TestView
         node = registry.getView(view)
         expect(node.textContent).toBe "Hello"
-        expect(node.__spacePenView).toBe view
+        expect(node.spacePenView).toBe view
 
     describe "when passed a model object", ->
       describe "when a view provider is registered matching the object's constructor", ->
@@ -62,7 +62,7 @@ describe "ViewRegistry", ->
             node = registry.getView(model)
 
             expect(node.textContent).toBe "hello"
-            view = node.__spacePenView
+            view = node.spacePenView
             expect(view instanceof TestView).toBe true
             expect(view.model).toBe model
 

spec/workspace-spec.coffee

@@ -2,12 +2,16 @@ path = require 'path'
 temp = require 'temp'
 Workspace = require '../src/workspace'
 {View} = require '../src/space-pen-extensions'
+platform = require './spec-helper-platform'
+_ = require 'underscore-plus'
+fstream = require 'fstream'
+fs = require 'fs-plus'
 
 describe "Workspace", ->
   workspace = null
 
   beforeEach ->
-    atom.project.setPaths([atom.project.resolve('dir')])
+    atom.project.setPaths([atom.project.getDirectories()[0]?.resolve('dir')])
     atom.workspace = workspace = new Workspace
 
   describe "::open(uri, options)", ->
@@ -66,19 +70,19 @@ describe "Workspace", ->
 
               expect(openEvents).toEqual [
                 {
-                  uri: atom.project.resolve('a')
+                  uri: atom.project.getDirectories()[0]?.resolve('a')
                   item: editor1
                   pane: atom.workspace.getActivePane()
                   index: 0
                 }
                 {
-                  uri: atom.project.resolve('b')
+                  uri: atom.project.getDirectories()[0]?.resolve('b')
                   item: editor2
                   pane: atom.workspace.getActivePane()
                   index: 1
                 }
                 {
-                  uri: atom.project.resolve('a')
+                  uri: atom.project.getDirectories()[0]?.resolve('a')
                   item: editor1
                   pane: atom.workspace.getActivePane()
                   index: 0
@@ -92,7 +96,7 @@ describe "Workspace", ->
               workspace.open('a').then (o) -> editor = o
 
             runs ->
-              expect(editor.getUri()).toBe atom.project.resolve('a')
+              expect(editor.getURI()).toBe atom.project.getDirectories()[0]?.resolve('a')
               expect(workspace.getActivePaneItem()).toBe editor
               expect(workspace.getActivePane().items).toEqual [editor]
               expect(workspace.getActivePane().activate).toHaveBeenCalled()
@@ -226,7 +230,7 @@ describe "Workspace", ->
         workspace.addOpener(barOpener)
 
         waitsForPromise ->
-          pathToOpen = atom.project.resolve('a.foo')
+          pathToOpen = atom.project.getDirectories()[0]?.resolve('a.foo')
           workspace.open(pathToOpen, hey: "there").then (item) ->
             expect(item).toEqual { foo: pathToOpen, options: {hey: "there"} }
 
@@ -257,21 +261,21 @@ describe "Workspace", ->
 
       runs ->
         # does not reopen items with no uri
-        expect(workspace.getActivePaneItem().getUri()).toBeUndefined()
+        expect(workspace.getActivePaneItem().getURI()).toBeUndefined()
         pane.destroyActiveItem()
 
       waitsForPromise ->
         workspace.reopenItem()
 
       runs ->
-        expect(workspace.getActivePaneItem().getUri()).not.toBeUndefined()
+        expect(workspace.getActivePaneItem().getURI()).not.toBeUndefined()
 
         # destroy all items
-        expect(workspace.getActivePaneItem().getUri()).toBe atom.project.resolve('file1')
+        expect(workspace.getActivePaneItem().getURI()).toBe atom.project.getDirectories()[0]?.resolve('file1')
         pane.destroyActiveItem()
-        expect(workspace.getActivePaneItem().getUri()).toBe atom.project.resolve('b')
+        expect(workspace.getActivePaneItem().getURI()).toBe atom.project.getDirectories()[0]?.resolve('b')
         pane.destroyActiveItem()
-        expect(workspace.getActivePaneItem().getUri()).toBe atom.project.resolve('a')
+        expect(workspace.getActivePaneItem().getURI()).toBe atom.project.getDirectories()[0]?.resolve('a')
         pane.destroyActiveItem()
 
         # reopens items with uris
@@ -281,20 +285,20 @@ describe "Workspace", ->
         workspace.reopenItem()
 
       runs ->
-        expect(workspace.getActivePaneItem().getUri()).toBe atom.project.resolve('a')
+        expect(workspace.getActivePaneItem().getURI()).toBe atom.project.getDirectories()[0]?.resolve('a')
 
       # does not reopen items that are already open
       waitsForPromise ->
         workspace.open('b')
 
       runs ->
-        expect(workspace.getActivePaneItem().getUri()).toBe atom.project.resolve('b')
+        expect(workspace.getActivePaneItem().getURI()).toBe atom.project.getDirectories()[0]?.resolve('b')
 
       waitsForPromise ->
         workspace.reopenItem()
 
       runs ->
-        expect(workspace.getActivePaneItem().getUri()).toBe atom.project.resolve('file1')
+        expect(workspace.getActivePaneItem().getURI()).toBe atom.project.getDirectories()[0]?.resolve('file1')
 
   describe "::increase/decreaseFontSize()", ->
     it "increases/decreases the font size without going below 1", ->
@@ -553,3 +557,287 @@ describe "Workspace", ->
 
         expect(atom.workspace.panelForItem(item)).toBe panel
         expect(atom.workspace.panelForItem(itemWithNoPanel)).toBe null
+
+  describe "::scan(regex, options, callback)", ->
+    describe "when called with a regex", ->
+      it "calls the callback with all regex results in all files in the project", ->
+        results = []
+        waitsForPromise ->
+          atom.workspace.scan /(a)+/, (result) ->
+            results.push(result)
+
+        runs ->
+          expect(results).toHaveLength(3)
+          expect(results[0].filePath).toBe atom.project.getDirectories()[0]?.resolve('a')
+          expect(results[0].matches).toHaveLength(3)
+          expect(results[0].matches[0]).toEqual
+            matchText: 'aaa'
+            lineText: 'aaa bbb'
+            lineTextOffset: 0
+            range: [[0, 0], [0, 3]]
+
+      it "works with with escaped literals (like $ and ^)", ->
+        results = []
+        waitsForPromise ->
+          atom.workspace.scan /\$\w+/, (result) -> results.push(result)
+
+        runs ->
+          expect(results.length).toBe 1
+
+          {filePath, matches} = results[0]
+          expect(filePath).toBe atom.project.getDirectories()[0]?.resolve('a')
+          expect(matches).toHaveLength 1
+          expect(matches[0]).toEqual
+            matchText: '$bill'
+            lineText: 'dollar$bill'
+            lineTextOffset: 0
+            range: [[2, 6], [2, 11]]
+
+      it "works on evil filenames", ->
+        platform.generateEvilFiles()
+        atom.project.setPaths([path.join(__dirname, 'fixtures', 'evil-files')])
+        paths = []
+        matches = []
+        waitsForPromise ->
+          atom.workspace.scan /evil/, (result) ->
+            paths.push(result.filePath)
+            matches = matches.concat(result.matches)
+
+        runs ->
+          _.each(matches, (m) -> expect(m.matchText).toEqual 'evil')
+
+          if platform.isWindows()
+            expect(paths.length).toBe 3
+            expect(paths[0]).toMatch /a_file_with_utf8.txt$/
+            expect(paths[1]).toMatch /file with spaces.txt$/
+            expect(path.basename(paths[2])).toBe "utfa\u0306.md"
+          else
+            expect(paths.length).toBe 5
+            expect(paths[0]).toMatch /a_file_with_utf8.txt$/
+            expect(paths[1]).toMatch /file with spaces.txt$/
+            expect(paths[2]).toMatch /goddam\nnewlines$/m
+            expect(paths[3]).toMatch /quote".txt$/m
+            expect(path.basename(paths[4])).toBe "utfa\u0306.md"
+
+      it "ignores case if the regex includes the `i` flag", ->
+        results = []
+        waitsForPromise ->
+          atom.workspace.scan /DOLLAR/i, (result) -> results.push(result)
+
+        runs ->
+          expect(results).toHaveLength 1
+
+      describe "when the core.excludeVcsIgnoredPaths config is truthy", ->
+        [projectPath, ignoredPath] = []
+
+        beforeEach ->
+          sourceProjectPath = path.join(__dirname, 'fixtures', 'git', 'working-dir')
+          projectPath = path.join(temp.mkdirSync("atom"))
+
+          writerStream = fstream.Writer(projectPath)
+          fstream.Reader(sourceProjectPath).pipe(writerStream)
+
+          waitsFor (done) ->
+            writerStream.on 'close', done
+            writerStream.on 'error', done
+
+          runs ->
+            fs.rename(path.join(projectPath, 'git.git'), path.join(projectPath, '.git'))
+            ignoredPath = path.join(projectPath, 'ignored.txt')
+            fs.writeFileSync(ignoredPath, 'this match should not be included')
+
+        afterEach ->
+          fs.removeSync(projectPath) if fs.existsSync(projectPath)
+
+        it "excludes ignored files", ->
+          atom.project.setPaths([projectPath])
+          atom.config.set('core.excludeVcsIgnoredPaths', true)
+          resultHandler = jasmine.createSpy("result found")
+          waitsForPromise ->
+            atom.workspace.scan /match/, (results) ->
+              resultHandler()
+
+          runs ->
+            expect(resultHandler).not.toHaveBeenCalled()
+
+      it "includes only files when a directory filter is specified", ->
+        projectPath = path.join(path.join(__dirname, 'fixtures', 'dir'))
+        atom.project.setPaths([projectPath])
+
+        filePath = path.join(projectPath, 'a-dir', 'oh-git')
+
+        paths = []
+        matches = []
+        waitsForPromise ->
+          atom.workspace.scan /aaa/, paths: ["a-dir#{path.sep}"], (result) ->
+            paths.push(result.filePath)
+            matches = matches.concat(result.matches)
+
+        runs ->
+          expect(paths.length).toBe 1
+          expect(paths[0]).toBe filePath
+          expect(matches.length).toBe 1
+
+      it "includes files and folders that begin with a '.'", ->
+        projectPath = temp.mkdirSync()
+        filePath = path.join(projectPath, '.text')
+        fs.writeFileSync(filePath, 'match this')
+        atom.project.setPaths([projectPath])
+        paths = []
+        matches = []
+        waitsForPromise ->
+          atom.workspace.scan /match this/, (result) ->
+            paths.push(result.filePath)
+            matches = matches.concat(result.matches)
+
+        runs ->
+          expect(paths.length).toBe 1
+          expect(paths[0]).toBe filePath
+          expect(matches.length).toBe 1
+
+      it "excludes values in core.ignoredNames", ->
+        projectPath = path.join(__dirname, 'fixtures', 'git', 'working-dir')
+        ignoredNames = atom.config.get("core.ignoredNames")
+        ignoredNames.push("a")
+        atom.config.set("core.ignoredNames", ignoredNames)
+
+        resultHandler = jasmine.createSpy("result found")
+        waitsForPromise ->
+          atom.workspace.scan /dollar/, (results) ->
+            resultHandler()
+
+        runs ->
+          expect(resultHandler).not.toHaveBeenCalled()
+
+      it "scans buffer contents if the buffer is modified", ->
+        editor = null
+        results = []
+
+        waitsForPromise ->
+          atom.project.open('a').then (o) ->
+            editor = o
+            editor.setText("Elephant")
+
+        waitsForPromise ->
+          atom.workspace.scan /a|Elephant/, (result) -> results.push result
+
+        runs ->
+          expect(results).toHaveLength 3
+          resultForA = _.find results, ({filePath}) -> path.basename(filePath) == 'a'
+          expect(resultForA.matches).toHaveLength 1
+          expect(resultForA.matches[0].matchText).toBe 'Elephant'
+
+      it "ignores buffers outside the project", ->
+        editor = null
+        results = []
+
+        waitsForPromise ->
+          atom.project.open(temp.openSync().path).then (o) ->
+            editor = o
+            editor.setText("Elephant")
+
+        waitsForPromise ->
+          atom.workspace.scan /Elephant/, (result) -> results.push result
+
+        runs ->
+          expect(results).toHaveLength 0
+
+  describe "::replace(regex, replacementText, paths, iterator)", ->
+    [filePath, commentFilePath, sampleContent, sampleCommentContent] = []
+
+    beforeEach ->
+      atom.project.setPaths([atom.project.getDirectories()[0]?.resolve('../')])
+
+      filePath = atom.project.getDirectories()[0]?.resolve('sample.js')
+      commentFilePath = atom.project.getDirectories()[0]?.resolve('sample-with-comments.js')
+      sampleContent = fs.readFileSync(filePath).toString()
+      sampleCommentContent = fs.readFileSync(commentFilePath).toString()
+
+    afterEach ->
+      fs.writeFileSync(filePath, sampleContent)
+      fs.writeFileSync(commentFilePath, sampleCommentContent)
+
+    describe "when a file doesn't exist", ->
+      it "calls back with an error", ->
+        errors = []
+        missingPath = path.resolve('/not-a-file.js')
+        expect(fs.existsSync(missingPath)).toBeFalsy()
+
+        waitsForPromise ->
+          atom.workspace.replace /items/gi, 'items', [missingPath], (result, error) ->
+            errors.push(error)
+
+        runs ->
+          expect(errors).toHaveLength 1
+          expect(errors[0].path).toBe missingPath
+
+    describe "when called with unopened files", ->
+      it "replaces properly", ->
+        results = []
+        waitsForPromise ->
+          atom.workspace.replace /items/gi, 'items', [filePath], (result) ->
+            results.push(result)
+
+        runs ->
+          expect(results).toHaveLength 1
+          expect(results[0].filePath).toBe filePath
+          expect(results[0].replacements).toBe 6
+
+    describe "when a buffer is already open", ->
+      it "replaces properly and saves when not modified", ->
+        editor = null
+        results = []
+
+        waitsForPromise ->
+          atom.project.open('sample.js').then (o) -> editor = o
+
+        runs ->
+          expect(editor.isModified()).toBeFalsy()
+
+        waitsForPromise ->
+          atom.workspace.replace /items/gi, 'items', [filePath], (result) ->
+            results.push(result)
+
+        runs ->
+          expect(results).toHaveLength 1
+          expect(results[0].filePath).toBe filePath
+          expect(results[0].replacements).toBe 6
+
+          expect(editor.isModified()).toBeFalsy()
+
+      it "does not replace when the path is not specified", ->
+        editor = null
+        results = []
+
+        waitsForPromise ->
+          atom.project.open('sample-with-comments.js').then (o) -> editor = o
+
+        waitsForPromise ->
+          atom.workspace.replace /items/gi, 'items', [commentFilePath], (result) ->
+            results.push(result)
+
+        runs ->
+          expect(results).toHaveLength 1
+          expect(results[0].filePath).toBe commentFilePath
+
+      it "does NOT save when modified", ->
+        editor = null
+        results = []
+
+        waitsForPromise ->
+          atom.project.open('sample.js').then (o) -> editor = o
+
+        runs ->
+          editor.buffer.setTextInRange([[0,0],[0,0]], 'omg')
+          expect(editor.isModified()).toBeTruthy()
+
+        waitsForPromise ->
+          atom.workspace.replace /items/gi, 'okthen', [filePath], (result) ->
+            results.push(result)
+
+        runs ->
+          expect(results).toHaveLength 1
+          expect(results[0].filePath).toBe filePath
+          expect(results[0].replacements).toBe 6
+
+          expect(editor.isModified()).toBeTruthy()

spec/workspace-view-spec.coffee

@@ -13,8 +13,8 @@ describe "WorkspaceView", ->
   beforeEach ->
     jasmine.snapshotDeprecations()
 
-    atom.project.setPaths([atom.project.resolve('dir')])
-    pathToOpen = atom.project.resolve('a')
+    atom.project.setPaths([atom.project.getDirectories()[0]?.resolve('dir')])
+    pathToOpen = atom.project.getDirectories()[0]?.resolve('a')
     atom.workspace = new Workspace
     atom.workspaceView = atom.views.getView(atom.workspace).__spacePenView
     atom.workspaceView.enableKeymap()
@@ -93,11 +93,11 @@ describe "WorkspaceView", ->
           editorView2 = atom.workspaceView.panes.find('atom-pane-axis.horizontal > atom-pane-axis.vertical > atom-pane atom-text-editor:eq(0)').view()
           editorView4 = atom.workspaceView.panes.find('atom-pane-axis.horizontal > atom-pane-axis.vertical > atom-pane atom-text-editor:eq(1)').view()
 
-          expect(editorView1.getEditor().getPath()).toBe atom.project.resolve('a')
-          expect(editorView2.getEditor().getPath()).toBe atom.project.resolve('b')
-          expect(editorView3.getEditor().getPath()).toBe atom.project.resolve('../sample.js')
+          expect(editorView1.getEditor().getPath()).toBe atom.project.getDirectories()[0]?.resolve('a')
+          expect(editorView2.getEditor().getPath()).toBe atom.project.getDirectories()[0]?.resolve('b')
+          expect(editorView3.getEditor().getPath()).toBe atom.project.getDirectories()[0]?.resolve('../sample.js')
           expect(editorView3.getEditor().getCursorScreenPosition()).toEqual [2, 4]
-          expect(editorView4.getEditor().getPath()).toBe atom.project.resolve('../sample.txt')
+          expect(editorView4.getEditor().getPath()).toBe atom.project.getDirectories()[0]?.resolve('../sample.txt')
           expect(editorView4.getEditor().getCursorScreenPosition()).toEqual [0, 2]
 
           # ensure adjust pane dimensions is called

src/atom.coffee

@@ -280,7 +280,7 @@ class Atom extends Model
       deprecate "The atom.syntax global is deprecated. Use atom.grammars instead."
       @grammars
 
-    @subscribe @packages.onDidActivateAll => @watchThemes()
+    @subscribe @packages.onDidActivateInitialPackages => @watchThemes()
 
     Project = require './project'
     TextBuffer = require 'text-buffer'
@@ -721,7 +721,7 @@ class Atom extends Model
     @themes.load()
 
   watchThemes: ->
-    @themes.onDidReloadAll =>
+    @themes.onDidChangeActiveThemes =>
       # Only reload stylesheets from non-theme packages
       for pack in @packages.getActivePackages() when pack.getType() isnt 'theme'
         pack.reloadStylesheets?()

src/browser/atom-application.coffee

@@ -359,7 +359,7 @@ class AtomApplication
 
     if existingWindow?
       openedWindow = existingWindow
-      openedWindow.openPath(pathToOpen, initialLine)
+      openedWindow.openPath(pathToOpen, initialLine, initialColumn)
       if openedWindow.isMinimized()
         openedWindow.restore()
       else

src/browser/auto-update-manager.coffee

@@ -1,6 +1,7 @@
 autoUpdater = null
 _ = require 'underscore-plus'
 {EventEmitter} = require 'events'
+path = require 'path'
 
 IdleState = 'idle'
 CheckingState = 'checking'
@@ -51,8 +52,7 @@ class AutoUpdateManager
       @emitUpdateAvailableEvent(@getWindows()...)
 
     # Only released versions should check for updates.
-    unless /\w{7}/.test(@version)
-      @check(hidePopups: true)
+    @check(hidePopups: true) unless /\w{7}/.test(@version)
 
     switch process.platform
       when 'win32'
@@ -86,12 +86,24 @@ class AutoUpdateManager
   onUpdateNotAvailable: =>
     autoUpdater.removeListener 'error', @onUpdateError
     dialog = require 'dialog'
-    dialog.showMessageBox type: 'info', buttons: ['OK'], message: 'No update available.', detail: "Version #{@version} is the latest version."
+    dialog.showMessageBox
+      type: 'info'
+      buttons: ['OK']
+      icon: path.resolve(__dirname, '..', '..', 'resources', 'atom.png')
+      message: 'No update available.'
+      title: 'No Update Available'
+      detail: "Version #{@version} is the latest version."
 
   onUpdateError: (event, message) =>
     autoUpdater.removeListener 'update-not-available', @onUpdateNotAvailable
     dialog = require 'dialog'
-    dialog.showMessageBox type: 'warning', buttons: ['OK'], message: 'There was an error checking for updates.', detail: message
+    dialog.showMessageBox
+      type: 'warning'
+      buttons: ['OK']
+      icon: path.resolve(__dirname, '..', '..', 'resources', 'atom.png')
+      message: 'There was an error checking for updates.'
+      title: 'Update Error'
+      detail: message
 
   getWindows: ->
     global.atomApplication.windows

src/browser/squirrel-update.coffee

@@ -25,9 +25,15 @@ environmentKeyPath = 'HKCU\\Environment'
 # Spawn a command and invoke the callback when it completes with an error
 # and the output from standard out.
 spawn = (command, args, callback) ->
-  spawnedProcess = ChildProcess.spawn(command, args)
-
   stdout = ''
+
+  try
+    spawnedProcess = ChildProcess.spawn(command, args)
+  catch error
+    # Spawn can throw an error
+    process.nextTick -> callback?(error, stdout)
+    return
+
   spawnedProcess.stdout.on 'data', (data) -> stdout += data
 
   error = null

src/coffee-cache.coffee

@@ -6,6 +6,11 @@ CSON = require 'season'
 fs = require 'fs-plus'
 
 cacheDir = path.join(fs.absolute('~/.atom'), 'compile-cache')
+
+# Use separate compile cache when sudo'ing as root to avoid permission issues
+if process.env.USER is 'root' and process.env.SUDO_USER and process.env.SUDO_USER isnt process.env.USER
+  cacheDir = path.join(cacheDir, 'root')
+
 coffeeCacheDir = path.join(cacheDir, 'coffee')
 CSON.setCacheDir(path.join(cacheDir, 'cson'))
 
@@ -40,11 +45,13 @@ requireCoffeeScript = (module, filePath) ->
 
 module.exports =
   cacheDir: cacheDir
+
   register: ->
     Object.defineProperty(require.extensions, '.coffee', {
       writable: false
       value: requireCoffeeScript
     })
+
   addPathToCache: (filePath) ->
     extension = path.extname(filePath)
     if extension is '.coffee'

src/color.coffee

@@ -0,0 +1,87 @@
+_ = require 'underscore-plus'
+ParsedColor = require 'color'
+
+# Essential: A simple color class returned from {Config::get} when the value
+# at the key path is of type 'color'.
+module.exports =
+class Color
+  # Essential: Parse a {String} or {Object} into a {Color}.
+  #
+  # * `value` - A {String} such as `'white'`, `#ff00ff`, or
+  #             `'rgba(255, 15, 60, .75)'` or an {Object} with `red`, `green`,
+  #             `blue`, and `alpha` properties.
+  #
+  # Returns a {Color} or `null` if it cannot be parsed.
+  @parse: (value) ->
+    return null if _.isArray(value) or _.isFunction(value)
+    return null unless _.isObject(value) or _.isString(value)
+
+    try
+      parsedColor = new ParsedColor(value)
+    catch error
+      return null
+
+    new Color(parsedColor.red(), parsedColor.green(), parsedColor.blue(), parsedColor.alpha())
+
+  constructor: (red, green, blue, alpha) ->
+    Object.defineProperties this,
+      red:
+        set: (newRed) -> red = parseColor(newRed)
+        get: -> red
+        enumerable: true
+        configurable: false
+      green:
+        set: (newGreen) -> green = parseColor(newGreen)
+        get: -> green
+        enumerable: true
+        configurable: false
+      blue:
+        set: (newBlue) -> blue = parseColor(newBlue)
+        get: -> blue
+        enumerable: true
+        configurable: false
+      alpha:
+        set: (newAlpha) -> alpha = parseAlpha(newAlpha)
+        get: -> alpha
+        enumerable: true
+        configurable: false
+
+    @red = red
+    @green = green
+    @blue = blue
+    @alpha = alpha
+
+  # Esssential: Returns a {String} in the form `'#abcdef'`.
+  toHexString: ->
+    "##{numberToHexString(@red)}#{numberToHexString(@green)}#{numberToHexString(@blue)}"
+
+  # Esssential: Returns a {String} in the form `'rgba(25, 50, 75, .9)'`.
+  toRGBAString: ->
+    "rgba(#{@red}, #{@green}, #{@blue}, #{@alpha})"
+
+  isEqual: (color) ->
+    return true if this is color
+    color = Color.parse(color) unless color instanceof Color
+    return false unless color?
+    color.red is @red and color.blue is @blue and color.green is @green and color.alpha is @alpha
+
+  clone: -> new Color(@red, @green, @blue, @alpha)
+
+parseColor = (color) ->
+  color = parseInt(color)
+  color = 0 if isNaN(color)
+  color = Math.max(color, 0)
+  color = Math.min(color, 255)
+  color
+
+parseAlpha = (alpha) ->
+  alpha = parseFloat(alpha)
+  alpha = 1 if isNaN(alpha)
+  alpha = Math.max(alpha, 0)
+  alpha = Math.min(alpha, 1)
+  alpha
+
+numberToHexString = (number) ->
+  hex = number.toString(16)
+  hex = "0#{hex}" if number < 10
+  hex

src/config-schema.coffee

@@ -98,6 +98,11 @@ module.exports =
         type: ['string', 'null']
 
       # These can be used as globals or scoped, thus defaults.
+      completions:
+        type: "array"
+        items:
+          type: "string"
+        default: []
       fontFamily:
         type: 'string'
         default: ''
@@ -163,9 +168,9 @@ module.exports =
         description: 'Disabling will improve editor font rendering but reduce scrolling performance.'
       useShadowDOM:
         type: 'boolean'
-        default: false
+        default: true
         title: 'Use Shadow DOM'
-        description: 'Enable to test out themes and packages with the new shadow DOM before it ships by default.'
+        description: 'Disable if you experience styling issues with packages or themes. Be sure to open an issue on the relevant package or theme, because this option is going away eventually.'
       confirmCheckoutHeadRevision:
         type: 'boolean'
         default: true

src/config.coffee

@@ -8,6 +8,7 @@ async = require 'async'
 pathWatcher = require 'pathwatcher'
 Grim = require 'grim'
 
+Color = require './color'
 ScopedPropertyStore = require 'scoped-property-store'
 ScopeDescriptor = require './scope-descriptor'
 
@@ -216,6 +217,21 @@ ScopeDescriptor = require './scope-descriptor'
 #         maximum: 11.5
 # ```
 #
+# #### color
+#
+# Values will be coerced into a {Color} with `red`, `green`, `blue`, and `alpha`
+# properties that all have numeric values. `red`, `green`, `blue` will be in
+# the range 0 to 255 and `value` will be in the range 0 to 1. Values can be any
+# valid CSS color format such as `#abc`, `#abcdef`, `white`,
+# `rgb(50, 100, 150)`, and `rgba(25, 75, 125, .75)`.
+#
+# ```coffee
+# config:
+#   someSetting:
+#     type: 'color'
+#     default: 'white'
+# ```
+#
 # ### Other Supported Keys
 #
 # #### enum
@@ -313,13 +329,14 @@ class Config
     @defaultSettings = {}
     @settings = {}
     @scopedSettingsStore = new ScopedPropertyStore
-    @usersScopedSettings = new CompositeDisposable
-    @usersScopedSettingPriority = {priority: 1000}
     @configFileHasErrors = false
     @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
     @configFilePath ?= path.join(@configDirPath, 'config.cson')
     @transactDepth = 0
 
+    @debouncedSave = _.debounce(@save, 100)
+    @debouncedLoad = _.debounce(@loadUserConfig, 100)
+
   ###
   Section: Config Subscription
   ###
@@ -338,32 +355,36 @@ class Config
   #   # do stuff with value
   # ```
   #
-  # * `scopeDescriptor` (optional) {ScopeDescriptor} describing a path from
-  #   the root of the syntax tree to a token. Get one by calling
-  #   {editor.getLastCursor().getScopeDescriptor()}. See {::get} for examples.
-  #   See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
-  #   for more information.
   # * `keyPath` {String} name of the key to observe
+  # * `options` {Object}
+  #   * `scopeDescriptor` (optional) {ScopeDescriptor} describing a path from
+  #     the root of the syntax tree to a token. Get one by calling
+  #     {editor.getLastCursor().getScopeDescriptor()}. See {::get} for examples.
+  #     See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
+  #     for more information.
   # * `callback` {Function} to call when the value of the key changes.
   #   * `value` the new value of the key
   #
   # Returns a {Disposable} with the following keys on which you can call
   # `.dispose()` to unsubscribe.
-  observe: (scopeDescriptor, keyPath, options, callback) ->
-    args = Array::slice.call(arguments)
-    if args.length is 2
-      # observe(keyPath, callback)
-      [keyPath, callback, scopeDescriptor, options] = args
-    else if args.length is 3 and (Array.isArray(scopeDescriptor) or scopeDescriptor instanceof ScopeDescriptor)
-      # observe(scopeDescriptor, keyPath, callback)
-      [scopeDescriptor, keyPath, callback, options] = args
-    else if args.length is 3 and _.isString(scopeDescriptor) and _.isObject(keyPath)
-      # observe(keyPath, options, callback) # Deprecated!
-      [keyPath, options, callback, scopeDescriptor] = args
-
-      message = ""
-      message = "`callNow` was set to false. Use ::onDidChange instead. Note that ::onDidChange calls back with different arguments." if options.callNow == false
-      Grim.deprecate "Config::observe no longer supports options; see https://atom.io/docs/api/latest/Config. #{message}"
+  observe: ->
+    if arguments.length is 2
+      [keyPath, callback] = arguments
+    else if arguments.length is 3 and (_.isArray(arguments[0]) or arguments[0] instanceof ScopeDescriptor)
+      Grim.deprecate """
+        Passing a scope descriptor as the first argument to Config::observe is deprecated.
+        Pass a `scope` in an options hash as the third argument instead.
+      """
+      [scopeDescriptor, keyPath, callback] = arguments
+    else if arguments.length is 3 and (_.isString(arguments[0]) and _.isObject(arguments[1]))
+      [keyPath, options, callback] = arguments
+      scopeDescriptor = options.scope
+      if options.callNow?
+        Grim.deprecate """
+          Config::observe no longer takes a `callNow` option. Use ::onDidChange instead.
+          Note that ::onDidChange passes its callback different arguments.
+          See https://atom.io/docs/api/latest/Config
+        """
     else
       console.error 'An unsupported form of Config::observe is being used. See https://atom.io/docs/api/latest/Config for details'
       return
@@ -376,13 +397,14 @@ class Config
   # Essential: Add a listener for changes to a given key path. If `keyPath` is
   # not specified, your callback will be called on changes to any key.
   #
-  # * `scopeDescriptor` (optional) {ScopeDescriptor} describing a path from
-  #   the root of the syntax tree to a token. Get one by calling
-  #   {editor.getLastCursor().getScopeDescriptor()}. See {::get} for examples.
-  #   See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
-  #   for more information.
   # * `keyPath` (optional) {String} name of the key to observe. Must be
   #   specified if `scopeDescriptor` is specified.
+  # * `optional` (optional) {Object}
+  #   * `scopeDescriptor` (optional) {ScopeDescriptor} describing a path from
+  #     the root of the syntax tree to a token. Get one by calling
+  #     {editor.getLastCursor().getScopeDescriptor()}. See {::get} for examples.
+  #     See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
+  #     for more information.
   # * `callback` {Function} to call when the value of the key changes.
   #   * `event` {Object}
   #     * `newValue` the new value of the key
@@ -391,12 +413,20 @@ class Config
   #
   # Returns a {Disposable} with the following keys on which you can call
   # `.dispose()` to unsubscribe.
-  onDidChange: (scopeDescriptor, keyPath, callback) ->
-    args = Array::slice.call(arguments)
+  onDidChange: ->
     if arguments.length is 1
-      [callback, scopeDescriptor, keyPath] = args
+      [callback] = arguments
     else if arguments.length is 2
-      [keyPath, callback, scopeDescriptor] = args
+      [keyPath, callback] = arguments
+    else if _.isArray(arguments[0]) or arguments[0] instanceof ScopeDescriptor
+      Grim.deprecate """
+        Passing a scope descriptor as the first argument to Config::onDidChange is deprecated.
+        Pass a `scope` in an options hash as the third argument instead.
+      """
+      [scopeDescriptor, keyPath, callback] = arguments
+    else
+      [keyPath, options, callback] = arguments
+      scopeDescriptor = options.scope
 
     if scopeDescriptor?
       @onDidChangeScopedKeyPath(scopeDescriptor, keyPath, callback)
@@ -422,14 +452,14 @@ class Config
   # files.
   #
   # ```coffee
-  # atom.config.get(['source.ruby'], 'editor.tabLength') # => 2
+  # atom.config.get('editor.tabLength', scope: ['source.ruby']) # => 2
   # ```
   #
   # This setting in ruby files might be different than the global tabLength setting
   #
   # ```coffee
   # atom.config.get('editor.tabLength') # => 4
-  # atom.config.get(['source.ruby'], 'editor.tabLength') # => 2
+  # atom.config.get('editor.tabLength', scope: ['source.ruby']) # => 2
   # ```
   #
   # You can get the language scope descriptor via
@@ -437,34 +467,72 @@ class Config
   # for the editor's language.
   #
   # ```coffee
-  # atom.config.get(@editor.getRootScopeDescriptor(), 'editor.tabLength') # => 2
+  # atom.config.get('editor.tabLength', scope: @editor.getRootScopeDescriptor()) # => 2
   # ```
   #
   # Additionally, you can get the setting at the specific cursor position.
   #
   # ```coffee
   # scopeDescriptor = @editor.getLastCursor().getScopeDescriptor()
-  # atom.config.get(scopeDescriptor, 'editor.tabLength') # => 2
+  # atom.config.get('editor.tabLength', scope: scopeDescriptor) # => 2
   # ```
   #
-  # * `scopeDescriptor` (optional) {ScopeDescriptor} describing a path from
-  #   the root of the syntax tree to a token. Get one by calling
-  #   {editor.getLastCursor().getScopeDescriptor()}
-  #   See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
-  #   for more information.
   # * `keyPath` The {String} name of the key to retrieve.
+  # * `options` (optional) {Object}
+  #   * `sources` (optional) {Array} of {String} source names. If provided, only
+  #     values that were associated with these sources during {::set} will be used.
+  #   * `excludeSources` (optional) {Array} of {String} source names. If provided,
+  #     values that  were associated with these sources during {::set} will not
+  #     be used.
+  #   * `scope` (optional) {ScopeDescriptor} describing a path from
+  #     the root of the syntax tree to a token. Get one by calling
+  #     {editor.getLastCursor().getScopeDescriptor()}
+  #     See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
+  #     for more information.
   #
   # Returns the value from Atom's default settings, the user's configuration
   # file in the type specified by the configuration schema.
-  get: (scopeDescriptor, keyPath) ->
-    if arguments.length == 1
-      # cannot assign to keyPath for the sake of v8 optimization
-      globalKeyPath = scopeDescriptor
-      @getRawValue(globalKeyPath)
+  get: ->
+    if arguments.length > 1
+      if typeof arguments[0] is 'string' or not arguments[0]?
+        [keyPath, options] = arguments
+        {scope} = options
+      else
+        Grim.deprecate """
+          Passing a scope descriptor as the first argument to Config::get is deprecated.
+          Pass a `scope` in an options hash as the final argument instead.
+        """
+        [scope, keyPath] = arguments
     else
-      value = @getRawScopedValue(scopeDescriptor, keyPath)
-      value ?= @getRawValue(keyPath)
-      value
+      [keyPath] = arguments
+
+    if scope?
+      value = @getRawScopedValue(scope, keyPath, options)
+      value ? @getRawValue(keyPath, options)
+    else
+      @getRawValue(keyPath, options)
+
+  # Extended: Get all of the values for the given key-path, along with their
+  # associated scope selector.
+  #
+  # * `keyPath` The {String} name of the key to retrieve
+  # * `options` (optional) {Object} see the `options` argument to {::get}
+  #
+  # Returns an {Array} of {Object}s with the following keys:
+  #  * `scopeSelector` The scope-selector {String} with which the value is associated
+  #  * `value` The value for the key-path
+  getAll: (keyPath, options) ->
+    {scope, sources} = options if options?
+    result = []
+
+    if scope?
+      scopeDescriptor = ScopeDescriptor.fromObject(scope)
+      result = result.concat @scopedSettingsStore.getAll(scopeDescriptor.getScopeChain(), keyPath, options)
+
+    if globalValue = @getRawValue(keyPath, options)
+      result.push(scopeSelector: '*', value: globalValue)
+
+    result
 
   # Essential: Sets the value for a configuration setting.
   #
@@ -483,75 +551,113 @@ class Config
   #
   # ```coffee
   # atom.config.get('editor.tabLength') # => 4
-  # atom.config.get(['source.ruby'], 'editor.tabLength') # => 4
-  # atom.config.get(['source.js'], 'editor.tabLength') # => 4
+  # atom.config.get('editor.tabLength', scope: ['source.ruby']) # => 4
+  # atom.config.get('editor.tabLength', scope: ['source.js']) # => 4
   #
   # # Set ruby to 2
-  # atom.config.set('source.ruby', 'editor.tabLength', 2) # => true
+  # atom.config.set('editor.tabLength', 2, scopeSelector: 'source.ruby') # => true
   #
   # # Notice it's only set to 2 in the case of ruby
   # atom.config.get('editor.tabLength') # => 4
-  # atom.config.get(['source.ruby'], 'editor.tabLength') # => 2
-  # atom.config.get(['source.js'], 'editor.tabLength') # => 4
+  # atom.config.get('editor.tabLength', scope: ['source.ruby']) # => 2
+  # atom.config.get('editor.tabLength', scope: ['source.js']) # => 4
   # ```
   #
-  # * `scopeSelector` (optional) {String}. eg. '.source.ruby'
-  #   See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
-  #   for more information.
   # * `keyPath` The {String} name of the key.
   # * `value` The value of the setting. Passing `undefined` will revert the
   #   setting to the default value.
+  # * `options` (optional) {Object}
+  #   * `scopeSelector` (optional) {String}. eg. '.source.ruby'
+  #     See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
+  #     for more information.
+  #   * `source` (optional) {String} The name of a file with which the setting
+  #     is associated. Defaults to the user's config file.
   #
   # Returns a {Boolean}
   # * `true` if the value was set.
   # * `false` if the value was not able to be coerced to the type specified in the setting's schema.
-  set: (scopeSelector, keyPath, value) ->
-    if arguments.length < 3
-      value = keyPath
-      keyPath = scopeSelector
-      scopeSelector = undefined
+  set: ->
+    if arguments[0]?[0] is '.'
+      Grim.deprecate """
+        Passing a scope selector as the first argument to Config::set is deprecated.
+        Pass a `scopeSelector` in an options hash as the final argument instead.
+      """
+      [scopeSelector, keyPath, value] = arguments
+    else
+      [keyPath, value, options] = arguments
+      scopeSelector = options?.scopeSelector
+      source = options?.source
+      shouldSave = options?.save ? true
 
-    unless value == undefined
+    if source and not scopeSelector
+      throw new Error("::set with a 'source' and no 'sourceSelector' is not yet implemented!")
+
+    source ?= @getUserConfigPath()
+
+    unless value is undefined
       try
         value = @makeValueConformToSchema(keyPath, value)
       catch e
         return false
 
     if scopeSelector?
-      @setRawScopedValue(scopeSelector, keyPath, value)
+      @setRawScopedValue(source, scopeSelector, keyPath, value)
     else
       @setRawValue(keyPath, value)
 
-    @save() unless @configFileHasErrors
+    @debouncedSave() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
     true
 
-  # Extended: Restore the global setting at `keyPath` to its default value.
+  # Essential: Restore the setting at `keyPath` to its default value.
   #
-  # * `scopeSelector` (optional) {String}. eg. '.source.ruby'
-  #   See [the scopes docs](https://atom.io/docs/latest/advanced/scopes-and-scope-descriptors)
-  #   for more information.
   # * `keyPath` The {String} name of the key.
+  # * `options` (optional) {Object}
+  #   * `scopeSelector` (optional) {String}. See {::set}
+  #   * `source` (optional) {String}. See {::set}
+  unset: (keyPath, options) ->
+    if typeof options is 'string'
+      Grim.deprecate """
+        Passing a scope selector as the first argument to Config::unset is deprecated.
+        Pass a `scopeSelector` in an options hash as the second argument instead.
+      """
+      scopeSelector = keyPath
+      keyPath = options
+    else
+      {scopeSelector, source} = options ? {}
+
+    source ?= @getUserConfigPath()
+
+    if scopeSelector?
+      if keyPath?
+        settings = @scopedSettingsStore.propertiesForSourceAndSelector(source, scopeSelector)
+        if _.valueForKeyPath(settings, keyPath)?
+          @scopedSettingsStore.removePropertiesForSourceAndSelector(source, scopeSelector)
+          _.setValueForKeyPath(settings, keyPath, undefined)
+          settings = withoutEmptyObjects(settings)
+          @set(null, settings, {scopeSelector, source, priority: @priorityForSource(source)}) if settings?
+          @debouncedSave()
+      else
+        @scopedSettingsStore.removePropertiesForSourceAndSelector(source, scopeSelector)
+        @emitChangeEvent()
+    else
+      @scopedSettingsStore.removePropertiesForSource(source)
+      if keyPath?
+        @set(keyPath, _.valueForKeyPath(@defaultSettings, keyPath))
+
+  # Extended: Get an {Array} of all of the `source` {String}s with which
+  # settings have been added via {::set}.
+  getSources: ->
+    _.uniq(_.pluck(@scopedSettingsStore.propertySets, 'source')).sort()
+
+  # Deprecated: Restore the global setting at `keyPath` to its default value.
   #
   # Returns the new value.
   restoreDefault: (scopeSelector, keyPath) ->
-    if arguments.length == 1
-      keyPath = scopeSelector
-      scopeSelector = null
+    Grim.deprecate("Use ::unset instead.")
+    @unset(scopeSelector, keyPath)
+    @get(keyPath)
 
-    if scopeSelector?
-      settings = @scopedSettingsStore.propertiesForSourceAndSelector('user-config', scopeSelector)
-      if _.valueForKeyPath(settings, keyPath)?
-        @scopedSettingsStore.removePropertiesForSourceAndSelector('user-config', scopeSelector)
-        _.setValueForKeyPath(settings, keyPath, undefined)
-        settings = withoutEmptyObjects(settings)
-        @addScopedSettings('user-config', scopeSelector, settings, @usersScopedSettingPriority) if settings?
-        @save() unless @configFileHasErrors
-        @getDefault(scopeSelector, keyPath)
-    else
-      @set(keyPath, _.valueForKeyPath(@defaultSettings, keyPath))
-      @get(keyPath)
-
-  # Extended: Get the global default value of the key path. _Please note_ that in most
+  # Deprecated: Get the global default value of the key path. _Please note_ that in most
   # cases calling this is not necessary! {::get} returns the default value when
   # a custom value is not specified.
   #
@@ -559,35 +665,30 @@ class Config
   # * `keyPath` The {String} name of the key.
   #
   # Returns the default value.
-  getDefault: (scopeSelector, keyPath) ->
-    if arguments.length == 1
-      keyPath = scopeSelector
-      scopeSelector = null
-
-    if scopeSelector?
-      defaultValue = @scopedSettingsStore.getPropertyValue(scopeSelector, keyPath, excludeSources: ['user-config'])
-      defaultValue ?= _.valueForKeyPath(@defaultSettings, keyPath)
+  getDefault: ->
+    Grim.deprecate("Use `::get(keyPath, {scope, excludeSources: [atom.config.getUserConfigPath()]})` instead")
+    if arguments.length is 1
+      [keyPath] = arguments
     else
-      defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
-    _.deepClone(defaultValue)
+      [scopeSelector, keyPath] = arguments
+      scope = [scopeSelector]
+    @get(keyPath, {scope, excludeSources: [@getUserConfigPath()]})
 
-  # Extended: Is the value at `keyPath` its default value?
+  # Deprecated: Is the value at `keyPath` its default value?
   #
   # * `scopeSelector` (optional) {String}. eg. '.source.ruby'
   # * `keyPath` The {String} name of the key.
   #
   # Returns a {Boolean}, `true` if the current value is the default, `false`
   # otherwise.
-  isDefault: (scopeSelector, keyPath) ->
-    if arguments.length == 1
-      keyPath = scopeSelector
-      scopeSelector = null
-
-    if scopeSelector?
-      settings = @scopedSettingsStore.propertiesForSourceAndSelector('user-config', scopeSelector)
-      not _.valueForKeyPath(settings, keyPath)?
+  isDefault: ->
+    Grim.deprecate("Use `not ::get(keyPath, {scope, sources: [atom.config.getUserConfigPath()]})?` instead")
+    if arguments.length is 1
+      [keyPath] = arguments
     else
-      not _.valueForKeyPath(@settings, keyPath)?
+      [scopeSelector, keyPath] = arguments
+      scope = [scopeSelector]
+    not @get(keyPath, {scope, sources: [@getUserConfigPath()]})?
 
   # Extended: Retrieve the schema for a specific key path. The schema will tell
   # you what type the keyPath expects, and other metadata about the config
@@ -602,7 +703,7 @@ class Config
     schema = @schema
     for key in keys
       break unless schema?
-      schema = schema.properties[key]
+      schema = schema.properties?[key]
     schema
 
   # Deprecated: Returns a new {Object} containing all of the global settings and
@@ -736,7 +837,7 @@ class Config
   observeUserConfig: ->
     try
       @watchSubscription ?= pathWatcher.watch @configFilePath, (eventType) =>
-        @loadUserConfig() if eventType is 'change' and @watchSubscription?
+        @debouncedLoad() if eventType is 'change' and @watchSubscription?
     catch error
       @notifyFailure('Failed to watch user config', error)
 
@@ -752,8 +853,8 @@ class Config
     console.error detail
 
   save: ->
-    allSettings = global: @settings
-    allSettings = _.extend allSettings, @scopedSettingsStore.propertiesForSource('user-config')
+    allSettings = {'*': @settings}
+    allSettings = _.extend allSettings, @scopedSettingsStore.propertiesForSource(@getUserConfigPath())
     CSON.writeFileSync(@configFilePath, allSettings)
 
   ###
@@ -767,46 +868,36 @@ class Config
       return
 
     if newSettings.global?
+      newSettings['*'] = newSettings.global
+      delete newSettings.global
+
+    if newSettings['*']?
       scopedSettings = newSettings
-      newSettings = newSettings.global
-      delete scopedSettings.global
+      newSettings = newSettings['*']
+      delete scopedSettings['*']
       @resetUserScopedSettings(scopedSettings)
 
-    unsetUnspecifiedValues = (keyPath, value) =>
-      if isPlainObject(value)
-        keys = splitKeyPath(keyPath)
-        for key, childValue of value
-          continue unless value.hasOwnProperty(key)
-          unsetUnspecifiedValues(keys.concat([key]).join('.'), childValue)
-      else
-        @setRawValue(keyPath, undefined) unless _.valueForKeyPath(newSettings, keyPath)?
-      return
+    @transact =>
+      @settings = {}
+      @set(key, value, save: false) for key, value of newSettings
 
-    @setRecursive(null, newSettings)
-    unsetUnspecifiedValues(null, @settings)
-
-  setRecursive: (keyPath, value) ->
-    if isPlainObject(value)
-      keys = splitKeyPath(keyPath)
-      for key, childValue of value
-        continue unless value.hasOwnProperty(key)
-        @setRecursive(keys.concat([key]).join('.'), childValue)
-    else
-      try
-        value = @makeValueConformToSchema(keyPath, value)
-        @setRawValue(keyPath, value)
-      catch e
-        console.warn("'#{keyPath}' could not be set. Attempted value: #{JSON.stringify(value)}; Schema: #{JSON.stringify(@getSchema(keyPath))}")
-
-  getRawValue: (keyPath) ->
-    value = _.valueForKeyPath(@settings, keyPath)
-    defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
+  getRawValue: (keyPath, options) ->
+    unless options?.excludeSources?.indexOf(@getUserConfigPath()) >= 0
+      value = _.valueForKeyPath(@settings, keyPath)
+    unless options?.sources?.length > 0
+      defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
 
     if value?
-      value = _.deepClone(value)
-      _.defaults(value, defaultValue) if isPlainObject(value) and isPlainObject(defaultValue)
+      if value instanceof Color
+        value = value.clone()
+      else
+        value = _.deepClone(value)
+        _.defaults(value, defaultValue) if isPlainObject(value) and isPlainObject(defaultValue)
     else
-      value = _.deepClone(defaultValue)
+      if defaultValue instanceof Color
+        value = defaultValue.clone()
+      else
+        value = _.deepClone(defaultValue)
 
     value
 
@@ -814,7 +905,10 @@ class Config
     defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
     value = undefined if _.isEqual(defaultValue, value)
 
-    _.setValueForKeyPath(@settings, keyPath, value)
+    if keyPath?
+      _.setValueForKeyPath(@settings, keyPath, value)
+    else
+      @settings = value
     @emitChangeEvent()
 
   observeKeyPath: (keyPath, options, callback) ->
@@ -823,13 +917,12 @@ class Config
 
   onDidChangeKeyPath: (keyPath, callback) ->
     oldValue = @get(keyPath)
-
-    didChange = =>
+    @emitter.on 'did-change', =>
       newValue = @get(keyPath)
-      callback({oldValue, newValue}) unless _.isEqual(oldValue, newValue)
-      oldValue = newValue
-
-    @emitter.on 'did-change', didChange
+      unless _.isEqual(oldValue, newValue)
+        event = {oldValue, newValue}
+        oldValue = newValue
+        callback(event)
 
   isSubKeyPath: (keyPath, subKeyPath) ->
     return false unless keyPath? and subKeyPath?
@@ -897,16 +990,23 @@ class Config
   Section: Private Scoped Settings
   ###
 
+  priorityForSource: (source) ->
+    if source is @getUserConfigPath()
+      1000
+    else
+      0
+
   emitChangeEvent: ->
     @emitter.emit 'did-change' unless @transactDepth > 0
 
   resetUserScopedSettings: (newScopedSettings) ->
-    @usersScopedSettings?.dispose()
-    @usersScopedSettings = new CompositeDisposable
-    @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', newScopedSettings, @usersScopedSettingPriority)
+    source = @getUserConfigPath()
+    @scopedSettingsStore.removePropertiesForSource(source)
+    @scopedSettingsStore.addProperties(source, newScopedSettings, priority: @priorityForSource(source))
     @emitChangeEvent()
 
   addScopedSettings: (source, selector, value, options) ->
+    Grim.deprecate("Use ::set instead")
     settingsBySelector = {}
     settingsBySelector[selector] = value
     disposable = @scopedSettingsStore.addProperties(source, settingsBySelector, options)
@@ -915,7 +1015,7 @@ class Config
       disposable.dispose()
       @emitChangeEvent()
 
-  setRawScopedValue: (selector, keyPath, value) ->
+  setRawScopedValue: (source, selector, keyPath, value) ->
     if keyPath?
       newValue = {}
       _.setValueForKeyPath(newValue, keyPath, value)
@@ -923,40 +1023,30 @@ class Config
 
     settingsBySelector = {}
     settingsBySelector[selector] = value
-    @usersScopedSettings.add @scopedSettingsStore.addProperties('user-config', settingsBySelector, @usersScopedSettingPriority)
+    @scopedSettingsStore.addProperties(source, settingsBySelector, priority: @priorityForSource(source))
     @emitChangeEvent()
 
-  getRawScopedValue: (scopeDescriptor, keyPath) ->
+  getRawScopedValue: (scopeDescriptor, keyPath, options) ->
     scopeDescriptor = ScopeDescriptor.fromObject(scopeDescriptor)
-    @scopedSettingsStore.getPropertyValue(scopeDescriptor.getScopeChain(), keyPath)
+    @scopedSettingsStore.getPropertyValue(scopeDescriptor.getScopeChain(), keyPath, options)
 
-  observeScopedKeyPath: (scopeDescriptor, keyPath, callback) ->
-    oldValue = @get(scopeDescriptor, keyPath)
+  observeScopedKeyPath: (scope, keyPath, callback) ->
+    callback(@get(keyPath, {scope}))
+    @onDidChangeScopedKeyPath scope, keyPath, (event) -> callback(event.newValue)
 
-    callback(oldValue)
+  onDidChangeScopedKeyPath: (scope, keyPath, callback) ->
+    oldValue = @get(keyPath, {scope})
+    @emitter.on 'did-change', =>
+      newValue = @get(keyPath, {scope})
+      unless _.isEqual(oldValue, newValue)
+        event = {oldValue, newValue}
+        oldValue = newValue
+        callback(event)
 
-    didChange = =>
-      newValue = @get(scopeDescriptor, keyPath)
-      callback(newValue) unless _.isEqual(oldValue, newValue)
-      oldValue = newValue
-
-    @emitter.on 'did-change', didChange
-
-  onDidChangeScopedKeyPath: (scopeDescriptor, keyPath, callback) ->
-    oldValue = @get(scopeDescriptor, keyPath)
-    didChange = =>
-      newValue = @get(scopeDescriptor, keyPath)
-      callback({oldValue, newValue}) unless _.isEqual(oldValue, newValue)
-      oldValue = newValue
-
-    @emitter.on 'did-change', didChange
-
-  # TODO: figure out how to change / remove this. The return value is awkward.
-  # * language mode uses it for one thing.
-  # * autocomplete uses it for editor.completions
   settingsForScopeDescriptor: (scopeDescriptor, keyPath) ->
-    scopeDescriptor = ScopeDescriptor.fromObject(scopeDescriptor)
-    @scopedSettingsStore.getProperties(scopeDescriptor.getScopeChain(), keyPath)
+    Grim.deprecate("Use Config::getAll instead")
+    entries = @getAll(null, scope: scopeDescriptor)
+    value for {value} in entries when _.valueForKeyPath(value, keyPath)?
 
 # Base schema enforcers. These will coerce raw input into the specified type,
 # and will throw an error when the value cannot be coerced. Throwing the error
@@ -1035,6 +1125,13 @@ Config.addSchemaEnforcers
       else
         value
 
+  'color':
+    coerce: (keyPath, value, schema) ->
+      color = Color.parse(value)
+      unless color?
+        throw new Error("Validation failed at #{keyPath}, #{JSON.stringify(value)} cannot be coerced into a color")
+      color
+
   '*':
     coerceMinimumAndMaximum: (keyPath, value, schema) ->
       return value unless typeof value is 'number'

src/context-menu-manager.coffee

@@ -16,6 +16,31 @@ SpecificityCache = {}
 #
 # An instance of this class is always available as the `atom.contextMenu`
 # global.
+#
+# ## Context Menu CSON Format
+#
+# ```coffee
+# 'atom-workspace': [{label: 'Help', command: 'application:open-documentation'}]
+# 'atom-text-editor': [{
+#   label: 'History',
+#   submenu: [
+#     {label: 'Undo', command:'core:undo'}
+#     {label: 'Redo', command:'core:redo'}
+#   ]
+# }]
+# ```
+#
+# In your package's menu `.cson` file you need to specify it under a
+# `context-menu` key:
+#
+# ```coffee
+# 'context-menu':
+#   'atom-workspace': [{label: 'Help', command: 'application:open-documentation'}]
+#   ...
+# ```
+#
+# The format for use in {::add} is the same minus the `context-menu` key. See
+# {::add} for more information.
 module.exports =
 class ContextMenuManager
   constructor: ({@resourcePath, @devMode}) ->
@@ -46,8 +71,8 @@ class ContextMenuManager
   #   'atom-text-editor': [{
   #     label: 'History',
   #     submenu: [
-  #       {label: 'Undo': command:'core:undo'}
-  #       {label: 'Redo': command:'core:redo'}
+  #       {label: 'Undo', command:'core:undo'}
+  #       {label: 'Redo', command:'core:redo'}
   #     ]
   #   }]
   # }
@@ -77,14 +102,22 @@ class ContextMenuManager
   add: (itemsBySelector) ->
     # Detect deprecated file path as first argument
     if itemsBySelector? and typeof itemsBySelector isnt 'object'
-      Grim.deprecate("ContextMenuManager::add has changed to take a single object as its argument. Please consult the documentation.")
+      Grim.deprecate """
+        ContextMenuManager::add has changed to take a single object as its
+        argument. Please see
+        https://atom.io/docs/api/latest/ContextMenuManager for more info.
+      """
       itemsBySelector = arguments[1]
       devMode = arguments[2]?.devMode
 
     # Detect deprecated format for items object
     for key, value of itemsBySelector
       unless _.isArray(value)
-        Grim.deprecate("The format for declaring context menu items has changed. Please consult the documentation.")
+        Grim.deprecate """
+          ContextMenuManager::add has changed to take a single object as its
+          argument. Please see
+          https://atom.io/docs/api/latest/ContextMenuManager for more info.
+        """
         itemsBySelector = @convertLegacyItemsBySelector(itemsBySelector, devMode)
 
     addedItemSets = []
@@ -147,9 +180,6 @@ class ContextMenuManager
 
     items
 
-  # Public: Request a context menu to be displayed.
-  #
-  # * `event` A DOM event.
   showForEvent: (event) ->
     @activeElement = event.target
     menuTemplate = @templateForEvent(event)

src/cursor.coffee

@@ -202,14 +202,20 @@ class Cursor extends Model
     [before, after] = @editor.getTextInBufferRange(range)
     return false if /\s/.test(before) or /\s/.test(after)
 
-    nonWordCharacters = atom.config.get(@getScopeDescriptor(), 'editor.nonWordCharacters').split('')
+    nonWordCharacters = atom.config.get('editor.nonWordCharacters', scope: @getScopeDescriptor()).split('')
     _.contains(nonWordCharacters, before) isnt _.contains(nonWordCharacters, after)
 
   # Public: Returns whether this cursor is between a word's start and end.
-  isInsideWord: ->
+  #
+  # * `options` (optional) {Object}
+  #   * `wordRegex` A {RegExp} indicating what constitutes a "word"
+  #     (default: {::wordRegExp}).
+  #
+  # Returns a {Boolean}
+  isInsideWord: (options) ->
     {row, column} = @getBufferPosition()
     range = [[row, column], [row, Infinity]]
-    @editor.getTextInBufferRange(range).search(@wordRegExp()) == 0
+    @editor.getTextInBufferRange(range).search(options?.wordRegex ? @wordRegExp()) == 0
 
   # Public: Returns the indentation level of the current line.
   getIndentLevel: ->
@@ -544,7 +550,7 @@ class Cursor extends Model
   # Returns a {Range}
   getBeginningOfNextWordBufferPosition: (options = {}) ->
     currentBufferPosition = @getBufferPosition()
-    start = if @isInsideWord() then @getEndOfCurrentWordBufferPosition() else currentBufferPosition
+    start = if @isInsideWord(options) then @getEndOfCurrentWordBufferPosition(options) else currentBufferPosition
     scanRange = [start, @editor.getEofBufferPosition()]
 
     beginningOfNextWordPosition = null
@@ -588,10 +594,6 @@ class Cursor extends Model
   Section: Visibility
   ###
 
-  # Public: If the marker range is empty, the cursor is marked as being visible.
-  updateVisibility: ->
-    @setVisible(@marker.getBufferRange().isEmpty())
-
   # Public: Sets whether the cursor is visible.
   setVisible: (visible) ->
     if @visible != visible
@@ -603,6 +605,9 @@ class Cursor extends Model
   # Public: Returns the visibility of the cursor.
   isVisible: -> @visible
 
+  updateVisibility: ->
+    @setVisible(@marker.getBufferRange().isEmpty())
+
   ###
   Section: Comparing to another cursor
   ###
@@ -636,7 +641,7 @@ class Cursor extends Model
   # Returns a {RegExp}.
   wordRegExp: ({includeNonWordCharacters}={}) ->
     includeNonWordCharacters ?= true
-    nonWordCharacters = atom.config.get(@getScopeDescriptor(), 'editor.nonWordCharacters')
+    nonWordCharacters = atom.config.get('editor.nonWordCharacters', scope: @getScopeDescriptor())
     segments = ["^[\t ]*$"]
     segments.push("[^\\s#{_.escapeRegExp(nonWordCharacters)}]+")
     if includeNonWordCharacters

src/display-buffer.coffee

@@ -67,24 +67,24 @@ class DisplayBuffer extends Model
 
     oldConfigSettings = @configSettings
     @configSettings =
-      scrollPastEnd: atom.config.get(scopeDescriptor, 'editor.scrollPastEnd')
-      softWrap: atom.config.get(scopeDescriptor, 'editor.softWrap')
-      softWrapAtPreferredLineLength: atom.config.get(scopeDescriptor, 'editor.softWrapAtPreferredLineLength')
-      preferredLineLength: atom.config.get(scopeDescriptor, 'editor.preferredLineLength')
+      scrollPastEnd: atom.config.get('editor.scrollPastEnd', scope: scopeDescriptor)
+      softWrap: atom.config.get('editor.softWrap', scope: scopeDescriptor)
+      softWrapAtPreferredLineLength: atom.config.get('editor.softWrapAtPreferredLineLength', scope: scopeDescriptor)
+      preferredLineLength: atom.config.get('editor.preferredLineLength', scope: scopeDescriptor)
 
-    subscriptions.add atom.config.onDidChange scopeDescriptor, 'editor.softWrap', ({newValue}) =>
+    subscriptions.add atom.config.onDidChange 'editor.softWrap', scope: scopeDescriptor, ({newValue}) =>
       @configSettings.softWrap = newValue
       @updateWrappedScreenLines()
 
-    subscriptions.add atom.config.onDidChange scopeDescriptor, 'editor.softWrapAtPreferredLineLength', ({newValue}) =>
+    subscriptions.add atom.config.onDidChange 'editor.softWrapAtPreferredLineLength', scope: scopeDescriptor, ({newValue}) =>
       @configSettings.softWrapAtPreferredLineLength = newValue
       @updateWrappedScreenLines() if @isSoftWrapped()
 
-    subscriptions.add atom.config.onDidChange scopeDescriptor, 'editor.preferredLineLength', ({newValue}) =>
+    subscriptions.add atom.config.onDidChange 'editor.preferredLineLength', scope: scopeDescriptor, ({newValue}) =>
       @configSettings.preferredLineLength = newValue
-      @updateWrappedScreenLines() if @isSoftWrapped() and atom.config.get(scopeDescriptor, 'editor.softWrapAtPreferredLineLength')
+      @updateWrappedScreenLines() if @isSoftWrapped() and atom.config.get('editor.softWrapAtPreferredLineLength', scope: scopeDescriptor)
 
-    subscriptions.add atom.config.observe scopeDescriptor, 'editor.scrollPastEnd', (value) =>
+    subscriptions.add atom.config.observe 'editor.scrollPastEnd', scope: scopeDescriptor, (value) =>
       @configSettings.scrollPastEnd = value
 
     @updateWrappedScreenLines() if oldConfigSettings? and not _.isEqual(oldConfigSettings, @configSettings)

src/git-repository.coffee

@@ -232,7 +232,10 @@ class GitRepository
   #
   # * `path` (optional) {String} path in the repository to get this information
   #   for, only needed if the repository has submodules.
-  getOriginUrl: (path) -> @getConfigValue('remote.origin.url', path)
+  getOriginURL: (path) -> @getConfigValue('remote.origin.url', path)
+  getOriginUrl: (path) ->
+    deprecate("Use ::getOriginURL instead.")
+    @getOriginUrl()
 
   # Public: Returns the upstream branch for the current HEAD, or null if there
   # is no upstream branch for the current HEAD.

src/grammar-registry.coffee

@@ -67,5 +67,5 @@ class GrammarRegistry extends FirstMate.GrammarRegistry
     atom.config.getRawScopedValue(scope, keyPath)
 
   propertiesForScope: (scope, keyPath) ->
-    deprecate 'A direct (but private) replacement is available at atom.config.scopedSettingsForScopeDescriptor().'
+    deprecate 'Use atom.config.getAll instead.'
     atom.config.settingsForScopeDescriptor(scope, keyPath)

src/language-mode.coffee

@@ -26,17 +26,16 @@ class LanguageMode
   #
   # startRow - The row {Number} to start at
   # endRow - The row {Number} to end at
-  #
-  # Returns an {Array} of the commented {Ranges}.
   toggleLineCommentsForBufferRows: (start, end) ->
-    scopeDescriptor = @editor.scopeDescriptorForBufferPosition([start, 0])
-    properties = atom.config.settingsForScopeDescriptor(scopeDescriptor, 'editor.commentStart')[0]
-    return unless properties
+    scope = @editor.scopeDescriptorForBufferPosition([start, 0])
+    commentStartEntry = atom.config.getAll('editor.commentStart', {scope})[0]
 
-    commentStartString = _.valueForKeyPath(properties, 'editor.commentStart')
-    commentEndString = _.valueForKeyPath(properties, 'editor.commentEnd')
+    return unless commentStartEntry?
 
-    return unless commentStartString
+    commentEndEntry = atom.config.getAll('editor.commentEnd', {scope}).find (entry) ->
+      entry.scopeSelector is commentStartEntry.scopeSelector
+    commentStartString = commentStartEntry?.value
+    commentEndString = commentEndEntry?.value
 
     buffer = @editor.buffer
     commentStartRegexString = _.escapeRegExp(commentStartString).replace(/(\s+)$/, '(?:$1)?')
@@ -96,6 +95,7 @@ class LanguageMode
             buffer.insert([row, indentLength], commentStartString)
           else
             buffer.setTextInRange([[row, 0], [row, indentString.length]], indentString + commentStartString)
+    return
 
   # Folds all the foldable lines in the buffer.
   foldAll: ->
@@ -113,6 +113,7 @@ class LanguageMode
   #
   # indentLevel - A {Number} indicating indentLevel; 0 based.
   foldAllAtIndentLevel: (indentLevel) ->
+    @unfoldAll()
     for currentRow in [0..@buffer.getLastRow()]
       [startRow, endRow] = @rowRangeForFoldAtBufferRow(currentRow) ? []
       continue unless startRow?
@@ -316,7 +317,7 @@ class LanguageMode
       @editor.setIndentationForBufferRow(bufferRow, desiredIndentLevel)
 
   getRegexForProperty: (scopeDescriptor, property) ->
-    if pattern = atom.config.get(scopeDescriptor, property)
+    if pattern = atom.config.get(property, scope: scopeDescriptor)
       new OnigRegExp(pattern)
 
   increaseIndentRegexForScopeDescriptor: (scopeDescriptor) ->

src/less-compile-cache.coffee

@@ -8,7 +8,7 @@ module.exports =
 class LessCompileCache
   Subscriber.includeInto(this)
 
-  @cacheDir: path.join(atom.getConfigDirPath(), 'compile-cache', 'less')
+  @cacheDir: path.join(require('./coffee-cache').cacheDir, 'less')
 
   constructor: ({resourcePath, importPaths}) ->
     @lessSearchPaths = [

src/lines-component.coffee

@@ -23,12 +23,12 @@ LinesComponent = React.createClass
     if performedInitialMeasurement
       {editor, overlayDecorations, highlightDecorations, scrollHeight, scrollWidth, placeholderText, backgroundColor} = @props
       {lineHeightInPixels, defaultCharWidth, scrollViewHeight, scopedCharacterWidthsChangeCount} = @props
-      {scrollTop, scrollLeft, cursorPixelRects, mini} = @props
+      {scrollTop, scrollLeft, cursorPixelRects} = @props
       style =
         height: Math.max(scrollHeight, scrollViewHeight)
         width: scrollWidth
         WebkitTransform: @getTransform()
-        backgroundColor: if mini then null else backgroundColor
+        backgroundColor: if editor.isMini() then null else backgroundColor
 
     div {className: 'lines', style},
       div className: 'placeholder-text', placeholderText if placeholderText?
@@ -162,7 +162,7 @@ LinesComponent = React.createClass
     @lineNodesByLineId.hasOwnProperty(lineId)
 
   buildLineHTML: (line, screenRow) ->
-    {mini, showIndentGuide, lineHeightInPixels, lineDecorations, lineWidth} = @props
+    {showIndentGuide, lineHeightInPixels, lineDecorations, lineWidth} = @props
     {tokens, text, lineEnding, fold, isSoftWrapped, indentLevel} = line
 
     classes = ''
@@ -208,7 +208,7 @@ LinesComponent = React.createClass
       @buildEndOfLineHTML(line) or ' '
 
   buildLineInnerHTML: (line) ->
-    {mini, showIndentGuide} = @props
+    {editor, showIndentGuide} = @props
     {tokens, text} = line
     innerHTML = ""
 
@@ -217,7 +217,7 @@ LinesComponent = React.createClass
     lineIsWhitespaceOnly = firstTrailingWhitespacePosition is 0
     for token in tokens
       innerHTML += @updateScopeStack(scopeStack, token.scopes)
-      hasIndentGuide = not mini and showIndentGuide and (token.hasLeadingWhitespace() or (token.hasTrailingWhitespace() and lineIsWhitespaceOnly))
+      hasIndentGuide = not editor.isMini() and showIndentGuide and (token.hasLeadingWhitespace() or (token.hasTrailingWhitespace() and lineIsWhitespaceOnly))
       innerHTML += token.getValueAsHtml({hasIndentGuide})
 
     innerHTML += @popScope(scopeStack) while scopeStack.length > 0

src/menu-manager.coffee

@@ -12,13 +12,56 @@ MenuHelpers = require './menu-helpers'
 # application menu.
 #
 # An instance of this class is always available as the `atom.menu` global.
+#
+# ## Menu CSON Format
+#
+# Here is an example from the [tree-view](https://github.com/atom/tree-view/blob/master/menus/tree-view.cson):
+#
+# ```coffee
+# [
+#   {
+#     'label': 'View'
+#     'submenu': [
+#       { 'label': 'Toggle Tree View', 'command': 'tree-view:toggle' }
+#     ]
+#   }
+#   {
+#     'label': 'Packages'
+#     'submenu': [
+#       'label': 'Tree View'
+#       'submenu': [
+#         { 'label': 'Focus', 'command': 'tree-view:toggle-focus' }
+#         { 'label': 'Toggle', 'command': 'tree-view:toggle' }
+#         { 'label': 'Reveal Active File', 'command': 'tree-view:reveal-active-file' }
+#         { 'label': 'Toggle Tree Side', 'command': 'tree-view:toggle-side' }
+#       ]
+#     ]
+#   }
+# ]
+# ```
+#
+# Use in your package's menu `.cson` file requires that you place your menu
+# structure under a `menu` key.
+#
+# ```coffee
+# 'menu': [
+#   {
+#     'label': 'View'
+#     'submenu': [
+#       { 'label': 'Toggle Tree View', 'command': 'tree-view:toggle' }
+#     ]
+#   }
+# ]
+# ```
+#
+# See {::add} for more info about adding menu's directly.
 module.exports =
 class MenuManager
   constructor: ({@resourcePath}) ->
     @pendingUpdateOperation = null
     @template = []
     atom.keymaps.onDidLoadBundledKeymaps => @loadPlatformItems()
-    atom.packages.onDidActivateAll => @sortPackagesMenu()
+    atom.packages.onDidActivateInitialPackages => @sortPackagesMenu()
 
   # Public: Adds the given items to the application menu.
   #

src/module-cache.coffee

@@ -59,6 +59,8 @@ loadDependencies = (modulePath, rootPath, rootMetadata, moduleCache) ->
     if childMetadata?.version
       try
         mainPath = require.resolve(childPath)
+      catch error
+        mainPath = null
 
       if mainPath
         moduleCache.dependencies.push

src/notification-manager.coffee

@@ -48,3 +48,10 @@ class NotificationManager
   ###
 
   getNotifications: -> @notifications
+
+  ###
+  Section: Managing Notifications
+  ###
+
+  clear: ->
+    @notifications = []

src/notification.coffee

@@ -8,10 +8,14 @@ class Notification
     @timestamp = new Date()
     @dismissed = true
     @dismissed = false if @isDismissable()
+    @displayed = false
 
   onDidDismiss: (callback) ->
     @emitter.on 'did-dismiss', callback
 
+  onDidDisplay: (callback) ->
+    @emitter.on 'did-display', callback
+
   getOptions: -> @options
 
   getType: -> @type
@@ -30,12 +34,17 @@ class Notification
   dismiss: ->
     return unless @isDismissable() and not @isDismissed()
     @dismissed = true
-    @emitter.emit 'did-dismiss'
+    @emitter.emit 'did-dismiss', this
 
   isDismissed: -> @dismissed
 
   isDismissable: -> !!@options.dismissable
 
+  wasDisplayed: -> @displayed
+
+  setDisplayed: (@displayed) ->
+    @emitter.emit 'did-display', this
+
   getIcon: ->
     return @options.icon if @options.icon?
     switch @type

src/package-manager.coffee

@@ -5,7 +5,7 @@ EmitterMixin = require('emissary').Emitter
 {Emitter} = require 'event-kit'
 fs = require 'fs-plus'
 Q = require 'q'
-{deprecate} = require 'grim'
+Grim = require 'grim'
 
 Package = require './package'
 ThemePackage = require './theme-package'
@@ -48,30 +48,76 @@ class PackageManager
   Section: Event Subscription
   ###
 
-  # Public: Invoke the given callback when all packages have been activated.
+  # Public: Invoke the given callback when all packages have been loaded.
   #
   # * `callback` {Function}
   #
   # Returns a {Disposable} on which `.dispose()` can be called to unsubscribe.
+  onDidLoadInitialPackages: (callback) ->
+    @emitter.on 'did-load-initial-packages', callback
+    @emitter.on 'did-load-all', callback # TODO: Remove once deprecated pre-1.0 APIs are gone
+
   onDidLoadAll: (callback) ->
-    @emitter.on 'did-load-all', callback
+    Grim.deprecate("Use `::onDidLoadInitialPackages` instead.")
+    @onDidLoadInitialPackages(callback)
 
   # Public: Invoke the given callback when all packages have been activated.
   #
   # * `callback` {Function}
   #
   # Returns a {Disposable} on which `.dispose()` can be called to unsubscribe.
+  onDidActivateInitialPackages: (callback) ->
+    @emitter.on 'did-activate-initial-packages', callback
+    @emitter.on 'did-activate-all', callback # TODO: Remove once deprecated pre-1.0 APIs are gone
+
   onDidActivateAll: (callback) ->
-    @emitter.on 'did-activate-all', callback
+    Grim.deprecate("Use `::onDidActivateInitialPackages` instead.")
+    @onDidActivateInitialPackages(callback)
+
+  # Public: Invoke the given callback when a package is activated.
+  #
+  # * `callback` A {Function} to be invoked when a package is activated.
+  #   * `package` The {Package} that was activated.
+  #
+  # Returns a {Disposable} on which `.dispose()` can be called to unsubscribe.
+  onDidActivatePackage: (callback) ->
+    @emitter.on 'did-activate-package', callback
+
+  # Public: Invoke the given callback when a package is deactivated.
+  #
+  # * `callback` A {Function} to be invoked when a package is deactivated.
+  #   * `package` The {Package} that was deactivated.
+  #
+  # Returns a {Disposable} on which `.dispose()` can be called to unsubscribe.
+  onDidDeactivatePackage: (callback) ->
+    @emitter.on 'did-deactivate-package', callback
+
+  # Public: Invoke the given callback when a package is loaded.
+  #
+  # * `callback` A {Function} to be invoked when a package is loaded.
+  #   * `package` The {Package} that was loaded.
+  #
+  # Returns a {Disposable} on which `.dispose()` can be called to unsubscribe.
+  onDidLoadPackage: (callback) ->
+    @emitter.on 'did-load-package', callback
+
+  # Public: Invoke the given callback when a package is unloaded.
+  #
+  # * `callback` A {Function} to be invoked when a package is unloaded.
+  #   * `package` The {Package} that was unloaded.
+  #
+  # Returns a {Disposable} on which `.dispose()` can be called to unsubscribe.
+  onDidUnloadPackage: (callback) ->
+    @emitter.on 'did-unload-package', callback
 
   on: (eventName) ->
     switch eventName
       when 'loaded'
-        deprecate 'Use PackageManager::onDidLoadAll instead'
+        Grim.deprecate 'Use PackageManager::onDidLoadInitialPackages instead'
       when 'activated'
-        deprecate 'Use PackageManager::onDidActivateAll instead'
+        Grim.deprecate 'Use PackageManager::onDidActivateInitialPackages instead'
       else
-        deprecate 'PackageManager::on is deprecated. Use event subscription methods instead.'
+        Grim.deprecate 'PackageManager::on is deprecated. Use event subscription methods instead.'
     EmitterMixin::on.apply(this, arguments)
 
   ###
@@ -278,7 +324,7 @@ class PackageManager
     packagePaths = _.uniq packagePaths, (packagePath) -> path.basename(packagePath)
     @loadPackage(packagePath) for packagePath in packagePaths
     @emit 'loaded'
-    @emitter.emit 'did-load-all'
+    @emitter.emit 'did-load-initial-packages'
 
   loadPackage: (nameOrPath) ->
     return pack if pack = @getLoadedPackage(nameOrPath)
@@ -295,12 +341,13 @@ class PackageManager
           pack = new Package(packagePath, metadata)
         pack.load()
         @loadedPackages[pack.name] = pack
-        pack
+        @emitter.emit 'did-load-package', pack
+        return pack
       catch error
         console.warn "Failed to load package.json '#{path.basename(packagePath)}'", error.stack ? error
-
     else
-      throw new Error("Could not resolve '#{nameOrPath}' to a package path")
+      console.warn "Could not resolve '#{nameOrPath}' to a package path"
+    null
 
   unloadPackages: ->
     @unloadPackage(name) for name in _.keys(@loadedPackages)
@@ -312,16 +359,19 @@ class PackageManager
 
     if pack = @getLoadedPackage(name)
       delete @loadedPackages[pack.name]
+      @emitter.emit 'did-unload-package', pack
     else
       throw new Error("No loaded package for name '#{name}'")
 
   # Activate all the packages that should be activated.
   activate: ->
+    promises = []
     for [activator, types] in @packageActivators
       packages = @getLoadedPackagesForTypes(types)
-      activator.activatePackages(packages)
-    @emit 'activated'
-    @emitter.emit 'did-activate-all'
+      promises = promises.concat(activator.activatePackages(packages))
+    Q.all(promises).then =>
+      @emit 'activated'
+      @emitter.emit 'did-activate-initial-packages'
 
   # another type of package manager can handle other package types.
   # See ThemeManager
@@ -329,19 +379,25 @@ class PackageManager
     @packageActivators.push([activator, types])
 
   activatePackages: (packages) ->
+    promises = []
     atom.config.transact =>
-      @activatePackage(pack.name) for pack in packages
+      for pack in packages
+        promise = @activatePackage(pack.name)
+        promises.push(promise) unless pack.hasActivationCommands()
     @observeDisabledPackages()
+    promises
 
   # Activate a single package by name
   activatePackage: (name) ->
     if pack = @getActivePackage(name)
       Q(pack)
-    else
-      pack = @loadPackage(name)
+    else if pack = @loadPackage(name)
       pack.activate().then =>
         @activePackages[pack.name] = pack
+        @emitter.emit 'did-activate-package', pack
         pack
+    else
+      Q.reject(new Error("Failed to load package '#{name}'"))
 
   # Deactivate all packages
   deactivatePackages: ->
@@ -356,3 +412,4 @@ class PackageManager
       @setPackageState(pack.name, state) if state = pack.serialize?()
     pack.deactivate()
     delete @activePackages[pack.name]
+    @emitter.emit 'did-deactivate-package', pack

src/package.coffee

@@ -9,7 +9,6 @@ EmitterMixin = require('emissary').Emitter
 Q = require 'q'
 {deprecate} = require 'grim'
 
-$ = null # Defer require in case this is in the window-less browser process
 ModuleCache = require './module-cache'
 ScopedProperties = require './scoped-properties'
 
@@ -24,8 +23,6 @@ module.exports =
 class Package
   EmitterMixin.includeInto(this)
 
-  @stylesheetsDir: 'stylesheets'
-
   @isBundledPackagePath: (packagePath) ->
     if atom.packages.devMode
       return false unless atom.packages.resourcePath.startsWith("#{process.resourcesPath}#{path.sep}")
@@ -45,6 +42,15 @@ class Package
           throw error unless ignoreErrors
     metadata ?= {}
     metadata.name = packageName
+
+    if metadata.stylesheetMain?
+      deprecate("Use the `mainStyleSheet` key instead of `stylesheetMain` in your `package.json`", {packageName})
+      metadata.mainStyleSheet = metadata.stylesheetMain
+
+    if metadata.stylesheets?
+      deprecate("Use the `styleSheets` key instead of `stylesheets` in your `package.json`", {packageName})
+      metadata.styleSheets = metadata.stylesheets
+
     metadata
 
   keymaps: null
@@ -52,7 +58,7 @@ class Package
   stylesheets: null
   stylesheetDisposables: null
   grammars: null
-  scopedProperties: null
+  settings: null
   mainModulePath: null
   resolvedMainModulePath: false
   mainModule: null
@@ -110,7 +116,7 @@ class Package
 
   getType: -> 'atom'
 
-  getStylesheetType: -> 'bundled'
+  getStyleSheetPriority: -> 0
 
   load: ->
     @measure 'loadTime', =>
@@ -118,7 +124,7 @@ class Package
         @loadKeymaps()
         @loadMenus()
         @loadStylesheets()
-        @scopedPropertiesPromise = @loadScopedProperties()
+        @settingsPromise = @loadSettings()
         @requireMainModule() unless @hasActivationCommands()
 
       catch error
@@ -130,7 +136,7 @@ class Package
     @keymaps = []
     @menus = []
     @grammars = []
-    @scopedProperties = []
+    @settings = []
 
   activate: ->
     @grammarsPromise ?= @loadGrammars()
@@ -144,7 +150,7 @@ class Package
         else
           @activateNow()
 
-    Q.all([@grammarsPromise, @scopedPropertiesPromise, @activationDeferred.promise])
+    Q.all([@grammarsPromise, @settingsPromise, @activationDeferred.promise])
 
   activateNow: ->
     try
@@ -176,8 +182,9 @@ class Package
   activateStylesheets: ->
     return if @stylesheetsActivated
 
-    group = @getStylesheetType()
     @stylesheetDisposables = new CompositeDisposable
+
+    priority = @getStyleSheetPriority()
     for [sourcePath, source] in @stylesheets
       if match = path.basename(sourcePath).match(/[^.]*\.([^.]*)\./)
         context = match[1]
@@ -186,7 +193,7 @@ class Package
       else
         context = undefined
 
-      @stylesheetDisposables.add(atom.styles.addStyleSheet(source, {sourcePath, group, context}))
+      @stylesheetDisposables.add(atom.styles.addStyleSheet(source, {sourcePath, priority, context}))
     @stylesheetsActivated = true
 
   activateResources: ->
@@ -199,20 +206,20 @@ class Package
       grammar.activate() for grammar in @grammars
       @grammarsActivated = true
 
-    scopedProperties.activate() for scopedProperties in @scopedProperties
-    @scopedPropertiesActivated = true
+    settings.activate() for settings in @settings
+    @settingsActivated = true
 
   loadKeymaps: ->
     if @bundledPackage and packagesCache[@name]?
       @keymaps = (["#{atom.packages.resourcePath}#{path.sep}#{keymapPath}", keymapObject] for keymapPath, keymapObject of packagesCache[@name].keymaps)
     else
-      @keymaps = @getKeymapPaths().map (keymapPath) -> [keymapPath, CSON.readFileSync(keymapPath)]
+      @keymaps = @getKeymapPaths().map (keymapPath) -> [keymapPath, CSON.readFileSync(keymapPath) ? {}]
 
   loadMenus: ->
     if @bundledPackage and packagesCache[@name]?
       @menus = (["#{atom.packages.resourcePath}#{path.sep}#{menuPath}", menuObject] for menuPath, menuObject of packagesCache[@name].menus)
     else
-      @menus = @getMenuPaths().map (menuPath) -> [menuPath, CSON.readFileSync(menuPath)]
+      @menus = @getMenuPaths().map (menuPath) -> [menuPath, CSON.readFileSync(menuPath) ? {}]
 
   getKeymapPaths: ->
     keymapsDirPath = path.join(@path, 'keymaps')
@@ -233,15 +240,18 @@ class Package
       [stylesheetPath, atom.themes.loadStylesheet(stylesheetPath, true)]
 
   getStylesheetsPath: ->
-    path.join(@path, @constructor.stylesheetsDir)
+    if fs.isDirectorySync(path.join(@path, 'stylesheets'))
+      deprecate("Store package style sheets in the `styles/` directory instead of `stylesheets/`", packageName: @name)
+      path.join(@path, 'stylesheets')
+    else
+      path.join(@path, 'styles')
 
   getStylesheetPaths: ->
     stylesheetDirPath = @getStylesheetsPath()
-
-    if @metadata.stylesheetMain
-      [fs.resolve(@path, @metadata.stylesheetMain)]
-    else if @metadata.stylesheets
-      @metadata.stylesheets.map (name) -> fs.resolve(stylesheetDirPath, name, ['css', 'less', ''])
+    if @metadata.mainStyleSheet
+      [fs.resolve(@path, @metadata.mainStyleSheet)]
+    else if @metadata.styleSheets
+      @metadata.styleSheets.map (name) -> fs.resolve(stylesheetDirPath, name, ['css', 'less', ''])
     else if indexStylesheet = fs.resolve(@path, 'index', ['css', 'less'])
       [indexStylesheet]
     else
@@ -283,22 +293,28 @@ class Package
       async.each grammarPaths, loadGrammar, -> deferred.resolve()
     deferred.promise
 
-  loadScopedProperties: ->
-    @scopedProperties = []
+  loadSettings: ->
+    @settings = []
 
-    loadScopedPropertiesFile = (scopedPropertiesPath, callback) =>
-      ScopedProperties.load scopedPropertiesPath, (error, scopedProperties) =>
+    loadSettingsFile = (settingsPath, callback) =>
+      ScopedProperties.load settingsPath, (error, settings) =>
         if error?
-          console.warn("Failed to load scoped properties: #{scopedPropertiesPath}", error.stack ? error)
+          console.warn("Failed to load package settings: #{settingsPath}", error.stack ? error)
         else
-          @scopedProperties.push(scopedProperties)
-          scopedProperties.activate() if @scopedPropertiesActivated
+          @settings.push(settings)
+          settings.activate() if @settingsActivated
         callback()
 
     deferred = Q.defer()
-    scopedPropertiesDirPath = path.join(@path, 'scoped-properties')
-    fs.list scopedPropertiesDirPath, ['json', 'cson'], (error, scopedPropertiesPaths=[]) ->
-      async.each scopedPropertiesPaths, loadScopedPropertiesFile, -> deferred.resolve()
+
+    if fs.isDirectorySync(path.join(@path, 'scoped-properties'))
+      settingsDirPath = path.join(@path, 'scoped-properties')
+      deprecate("Store package settings files in the `settings/` directory instead of `scoped-properties/`", packageName: @name)
+    else
+      settingsDirPath = path.join(@path, 'settings')
+
+    fs.list settingsDirPath, ['json', 'cson'], (error, settingsPaths=[]) ->
+      async.each settingsPaths, loadSettingsFile, -> deferred.resolve()
     deferred.promise
 
   serialize: ->
@@ -328,12 +344,12 @@ class Package
 
   deactivateResources: ->
     grammar.deactivate() for grammar in @grammars
-    scopedProperties.deactivate() for scopedProperties in @scopedProperties
+    settings.deactivate() for settings in @settings
     @stylesheetDisposables?.dispose()
     @activationDisposables?.dispose()
     @stylesheetsActivated = false
     @grammarsActivated = false
-    @scopedPropertiesActivated = false
+    @settingsActivated = false
 
   reloadStylesheets: ->
     oldSheets = _.clone(@stylesheets)

src/pane-container-view.coffee

@@ -64,7 +64,7 @@ class PaneContainerView extends View
     @getActivePaneView()?.activeView
 
   paneForUri: (uri) ->
-    atom.views.getView(@model.paneForUri(uri)).__spacePenView
+    atom.views.getView(@model.paneForURI(uri)).__spacePenView
 
   focusNextPaneView: ->
     @model.activateNextPane()

src/pane-container.coffee

@@ -143,8 +143,8 @@ class PaneContainer extends Model
   getActivePaneItem: ->
     @getActivePane().getActiveItem()
 
-  paneForUri: (uri) ->
-    find @getPanes(), (pane) -> pane.itemForUri(uri)?
+  paneForURI: (uri) ->
+    find @getPanes(), (pane) -> pane.itemForURI(uri)?
 
   paneForItem: (item) ->
     @getPanes().find (pane) -> item in pane.getItems()

src/pane-view.coffee

@@ -153,7 +153,9 @@ class PaneView extends View
   activeItemModifiedChanged: =>
     @trigger 'pane:active-item-modified-status-changed'
 
-  @::accessor 'activeView', -> atom.views.getView(@activeItem)?.__spacePenView
+  @::accessor 'activeView', ->
+    element = atom.views.getView(@activeItem)
+    $(element).view() ? element
 
   splitLeft: (items...) -> atom.views.getView(@model.splitLeft({items})).__spacePenView
 

src/pane.coffee

@@ -43,14 +43,15 @@ class Pane extends Model
   serializeParams: ->
     id: @id
     items: compact(@items.map((item) -> item.serialize?()))
-    activeItemUri: @activeItem?.getUri?()
+    activeItemURI: @activeItem?.getURI?() ? @activeItem?.getUri?()
     focused: @focused
 
   # Called by the Serializable mixin during deserialization.
   deserializeParams: (params) ->
-    {items, activeItemUri} = params
+    {items, activeItemURI, activeItemUri} = params
+    activeItemURI ?= activeItemUri
     params.items = compact(items.map (itemState) -> atom.deserializers.deserialize(itemState))
-    params.activeItem = find params.items, (item) -> item.getUri?() is activeItemUri
+    params.activeItem = find params.items, (item) -> (item.getURI?() ? item.getUri?()) is activeItemURI
     params
 
   getParent: -> @parent
@@ -426,10 +427,13 @@ class Pane extends Model
     @destroyItem(item) for item in @getItems() when item isnt @activeItem
 
   promptToSaveItem: (item) ->
-    return true unless typeof item.getUri is 'function' and item.shouldPromptToSave?()
+    if typeof item.getUri is 'function' and typeof item.getURI isnt 'function'
+      Grim.deprecate("Implement `::getURI` on pane items instead of `::getUri`")
+
+    return true unless (typeof item.getURI is 'function' or typeof item.getUri is 'function') and item.shouldPromptToSave?()
 
     chosen = atom.confirm
-      message: "'#{item.getTitle?() ? item.getUri()}' has changes, do you want to save them?"
+      message: "'#{item.getTitle?() ? item.getURI?() ? item.getUri?()}' has changes, do you want to save them?"
       detailedMessage: "Your changes will be lost if you close this item without saving."
       buttons: ["Save", "Cancel", "Don't Save"]
 
@@ -456,7 +460,7 @@ class Pane extends Model
   # * `nextAction` (optional) {Function} which will be called after the item is
   #   successfully saved.
   saveItem: (item, nextAction) ->
-    if item?.getUri?()
+    if (item?.getURI?() ? item?.getUri?())
       item.save?()
       nextAction?()
     else
@@ -485,19 +489,27 @@ class Pane extends Model
   # none exists.
   #
   # * `uri` {String} containing a URI.
+  itemForURI: (uri) ->
+    find @items, (item) -> item.getURI?() is uri or item.getUri?() is uri
+
   itemForUri: (uri) ->
-    find @items, (item) -> item.getUri?() is uri
+    Grim.deprecate("Use `::itemForURI` instead.")
+    @itemForURI(uri)
 
   # Public: Activate the first item that matches the given URI.
   #
   # Returns a {Boolean} indicating whether an item matching the URI was found.
-  activateItemForUri: (uri) ->
-    if item = @itemForUri(uri)
+  activateItemForURI: (uri) ->
+    if item = @itemForURI(uri)
       @activateItem(item)
       true
     else
       false
 
+  activateItemForUri: (uri) ->
+    Grim.deprecate("Use `::activateItemForURI` instead.")
+    @activateItemForURI(uri)
+
   copyActiveItem: ->
     if @activeItem?
       @activeItem.copy?() ? atom.deserializers.deserialize(@activeItem.serialize())