Always return real package paths

⬆️ bump tree view for new sort option

CONTRIBUTING.md

@@ -74,7 +74,7 @@ For more information on how to work with Atom's official packages, see
 * Limit the first line to 72 characters or less
 * Reference issues and pull requests liberally
 * Consider starting the commit message with an applicable emoji:
-    * :lipstick: `:lipstick:` when improving the format/structure of the code
+    * :art: `:art:` when improving the format/structure of the code
     * :racehorse: `:racehorse:` when improving performance
     * :non-potable_water: `:non-potable_water:` when plugging memory leaks
     * :memo: `:memo:` when writing docs

apm/package.json

@@ -6,6 +6,6 @@
     "url": "https://github.com/atom/atom.git"
   },
   "dependencies": {
-    "atom-package-manager": "0.120.0"
+    "atom-package-manager": "0.128"
   }
 }

build/package.json

@@ -24,7 +24,7 @@
     "grunt-peg": "~1.1.0",
     "grunt-shell": "~0.3.1",
     "harmony-collections": "~0.3.8",
-    "legal-eagle": "~0.8.0",
+    "legal-eagle": "~0.9.0",
     "minidump": "~0.8",
     "npm": "~1.4.5",
     "rcedit": "~0.3.0",

build/tasks/build-task.coffee

@@ -144,7 +144,10 @@ module.exports = (grunt) ->
     cp 'spec', path.join(appDir, 'spec')
     cp 'src', path.join(appDir, 'src'), filter: /.+\.(cson|coffee)$/
     cp 'static', path.join(appDir, 'static')
-    cp 'apm', path.join(appDir, 'apm'), filter: filterNodeModule
+
+    cp path.join('apm', 'node_modules', 'atom-package-manager'), path.join(appDir, 'apm'), filter: filterNodeModule
+    if process.platform isnt 'win32'
+      fs.symlinkSync(path.join('..', '..', 'bin', 'apm'), path.join(appDir, 'apm', 'node_modules', '.bin', 'apm'))
 
     if process.platform is 'darwin'
       grunt.file.recurse path.join('resources', 'mac'), (sourcePath, rootDirectory, subDirectory='', filename) ->

build/tasks/license-overrides.coffee

@@ -35,6 +35,10 @@ module.exports =
 
       MIT/X11
     """
+  'cheerio@0.15.0':
+    repository: "https://github.com/cheeriojs/cheerio"
+    license: 'MIT'
+    source: 'https://github.com/cheeriojs/cheerio/blob/master/package.json'
   'specificity@0.1.3':
     repository: 'https://github.com/keeganstreet/specificity'
     license: 'MIT'

build/tasks/prebuild-less-task.coffee

@@ -8,14 +8,35 @@ module.exports = (grunt) ->
     prebuiltConfigurations = [
       ['atom-dark-ui', 'atom-dark-syntax']
       ['atom-dark-ui', 'atom-light-syntax']
+      ['atom-dark-ui', 'one-dark-syntax']
+      ['atom-dark-ui', 'one-light-syntax']
       ['atom-dark-ui', 'solarized-dark-syntax']
       ['atom-dark-ui', 'base16-tomorrow-dark-theme']
       ['atom-dark-ui', 'base16-tomorrow-light-theme']
+
       ['atom-light-ui', 'atom-light-syntax']
       ['atom-light-ui', 'atom-dark-syntax']
+      ['atom-light-ui', 'one-dark-syntax']
+      ['atom-light-ui', 'one-light-syntax']
       ['atom-light-ui', 'solarized-dark-syntax']
       ['atom-light-ui', 'base16-tomorrow-dark-theme']
       ['atom-light-ui', 'base16-tomorrow-light-theme']
+
+      ['one-dark-ui', 'one-dark-syntax']
+      ['one-dark-ui', 'one-light-syntax']
+      ['one-dark-ui', 'atom-dark-syntax']
+      ['one-dark-ui', 'atom-light-syntax']
+      ['one-dark-ui', 'solarized-dark-syntax']
+      ['one-dark-ui', 'base16-tomorrow-dark-theme']
+      ['one-dark-ui', 'base16-tomorrow-light-theme']
+
+      ['one-light-ui', 'one-light-syntax']
+      ['one-light-ui', 'one-dark-syntax']
+      ['one-light-ui', 'atom-light-syntax']
+      ['one-light-ui', 'atom-dark-syntax']
+      ['one-light-ui', 'solarized-dark-syntax']
+      ['one-light-ui', 'base16-tomorrow-dark-theme']
+      ['one-light-ui', 'base16-tomorrow-light-theme']
     ]
 
     directory = path.join(grunt.config.get('atom.appDir'), 'less-compile-cache')
@@ -42,10 +63,18 @@ module.exports = (grunt) ->
         resourcePath: path.resolve('.')
         importPaths: importPaths
 
+      cssForFile = (file) ->
+        baseVarImports = """
+        @import "variables/ui-variables";
+        @import "variables/syntax-variables";
+        """
+        less = fs.readFileSync(file, 'utf8')
+        lessCache.cssForFile(file, [baseVarImports, less].join('\n'))
+
       for file in @filesSrc
         grunt.verbose.writeln("File #{file.cyan} created in cache.")
-        lessCache.readFileSync(file)
+        cssForFile(file)
 
       for file in themeMains
         grunt.verbose.writeln("File #{file.cyan} created in cache.")
-        lessCache.readFileSync(file)
+        cssForFile(file)

docs/converting-a-text-mate-bundle.md

@@ -45,7 +45,7 @@ the editor to see it in action!
 
 [atomio]: https://atom.io
 [CSS]: http://en.wikipedia.org/wiki/Cascading_Style_Sheets
-[LESS]: http://lesscss.org
+[Less]: http://lesscss.org
 [plist]: http://en.wikipedia.org/wiki/Property_list
 [R]: http://en.wikipedia.org/wiki/R_(programming_language)
 [TextMate]: http://macromates.com

docs/converting-a-text-mate-theme.md

@@ -6,7 +6,7 @@ theme.
 ### Differences
 
 TextMate themes use [plist][plist] files while Atom themes use [CSS][CSS] or
-[LESS][LESS] to style the UI and syntax in the editor.
+[Less][Less] to style the UI and syntax in the editor.
 
 The utility that converts the theme first parses the theme's plist file and
 then creates comparable CSS rules and properties that will style Atom similarly.
@@ -62,7 +62,7 @@ __Syntax Theme__ dropdown menu to enable your new theme.
 
 [atomio]: https://atom.io
 [CSS]: http://en.wikipedia.org/wiki/Cascading_Style_Sheets
-[LESS]: http://lesscss.org
+[Less]: http://lesscss.org
 [plist]: http://en.wikipedia.org/wiki/Property_list
 [TextMate]: http://macromates.com
 [TextMateThemes]: http://wiki.macromates.com/Themes/UserSubmittedThemes

docs/creating-a-package.md

@@ -123,8 +123,8 @@ like you.
 
 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
@@ -418,7 +418,7 @@ all the other available commands.
 [underscore]: http://underscorejs.org/
 [jasmine]: http://jasmine.github.io
 [cson]: https://github.com/atom/season
-[LESS]: http://lesscss.org
+[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

docs/creating-a-theme.md

@@ -1,7 +1,7 @@
 # Creating a Theme
 
-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
+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
@@ -17,7 +17,7 @@ section on the left hand side.
 Themes are pretty straightforward but it's still helpful to be familiar with
 a few things before starting:
 
-* LESS is a superset of CSS, but it has some really handy features like
+* Less is a superset of CSS, but it has some really handy features like
   variables. If you aren't familiar with its syntax, take a few minutes
   to [familiarize yourself][less-tutorial].
 * You may also want to review the concept of a _[package.json]_, too. This file
@@ -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

@@ -174,12 +174,12 @@ atom-text-editor.is-focused .cursor {
 }
 ```
 
-Unfamiliar with LESS? Read more about it [here][LESS].
+Unfamiliar with Less? Read more about it [here][Less].
 
 This file can also be named _styles.css_ and contain CSS.
 
 [creating-a-package]: creating-a-package.md
 [create-theme]: creating-a-theme.md
-[LESS]: http://www.lesscss.org
+[Less]: http://www.lesscss.org
 [CSON]: https://github.com/atom/season
 [CoffeeScript]: http://coffeescript.org/

docs/debugging.md

@@ -100,6 +100,21 @@ When an error is thrown in Atom, the developer tools are automatically shown wit
 
 If you can reproduce the error, use this approach to get the full stack trace. The stack trace might point to a problem in your [Init script][init script or stylesheet] or a specific package you installed, which you can then disable and report an issue on its GitHub repository.
 
+## Check that you have a build toolchain installed
+
+If you are having issues installing a package using `apm install`, this could be
+because the package has dependencies on libraries that contain native code
+and so you will need to have a C++ compiler and Python installed to be able to
+install it.
+
+You can run `apm install --check` to see if [apm][apm] can build native code on
+your machine.
+
+Check out the pre-requisites in the [build instructions][build-instructions] for
+your platform for more details.
+
+[apm]: https://github.com/atom/apm
+[build-instructions]: https://github.com/atom/atom/tree/master/docs/build-instructions
 [submitting issues]: https://github.com/atom/atom/blob/master/CONTRIBUTING.md#submitting-issues
 [building atom]: https://github.com/atom/atom#building
 [atom releases]: https://github.com/atom/atom/releases

docs/getting-started.md

@@ -34,7 +34,7 @@ files. If you are using Git you can use `cmd-shift-b` to search the list of
 files modified and untracked in your project's repository.
 
 You can also use the tree view to navigate to a file. To open and focus the
-the tree view, press `ctrl-0`. The tree view can be toggled open and closed with
+tree view, press `ctrl-0`. The tree view can be toggled open and closed with
 `cmd-\`.
 
 #### Adding, Moving, Deleting Files

docs/upgrading/upgrading-your-package.md

@@ -63,7 +63,7 @@ When you are deprecation free and all done converting, upgrade the `engines` fie
 ```json
 {
   "engines": {
-    "atom": ">=0.x.0, <2.0.0"
+    "atom": ">=0.174.0, <2.0.0"
   }
 }
 ```

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

@@ -6,19 +6,16 @@ Syntax themes are specifically intended to style only text editor content, so th
 
 When theme style sheets are loaded into the text editor's shadow DOM, selectors intended to target the editor from the *outside* no longer make sense. Styles targeting the `.editor` and `.editor-colors` classes instead need to target the `:host` pseudo-element, which matches against the containing `atom-text-editor` node. Check out the [Shadow DOM 201][host-pseudo-element] article for more information about the `:host` pseudo-element.
 
-Here's an example from Atom's light syntax theme. Note that the previous selectors intended to target the editor from the outside have been retained to allow the theme to keep working during the transition phase when it is possible to disable the shadow DOM.
+Here's an example from Atom's light syntax theme. Note that the `atom-text-editor` selector intended to target the editor from the outside has been retained to allow the theme to keep working during the transition phase when it is possible to disable the shadow DOM.
 
 ```css
-.editor-colors, :host { /* :host added */
+atom-text-editor, :host { /* :host added */
   background-color: @syntax-background-color;
   color: @syntax-text-color;
-}
 
-.editor, :host { /* :host added */
   .invisible-character {
     color: @syntax-invisible-character-color;
   }
-
   /* more nested selectors... */
 }
 ```

docs/your-first-package.md

@@ -88,17 +88,17 @@ run the `ascii-art:convert` command it will output 'Hello, World!'
 Now let's add a key binding to trigger the `ascii-art:convert` command. Open
 _keymaps/ascii-art.cson_ and add a key binding linking `ctrl-alt-a` to the
 `ascii-art:convert` command. You can delete the pre-existing key binding since
-you don't need it anymore. When finished, the file will look like this:
+you don't need it anymore. When finished, the file will have this:
 
 ```coffeescript
 'atom-text-editor':
-  'cmd-alt-a': 'ascii-art:convert'
+  'ctrl-alt-a': 'ascii-art:convert'
 ```
 
 Notice `atom-text-editor` on the first line. Just like CSS, keymap selectors
 *scope* key bindings so they only apply to specific elements. In this case, our
 binding is only active for elements matching the `atom-text-editor` selector. If
-the Tree View has focus, pressing `cmd-alt-a` won't trigger the
+the Tree View has focus, pressing `ctrl-alt-a` won't trigger the
 `ascii-art:convert` command. But if the editor has focus, the
 `ascii-art:convert` method *will* be triggered. More information on key bindings
 can be found in the [keymaps](advanced/keymaps.html) documentation.
@@ -142,7 +142,7 @@ convert: ->
       selection.insertText("\n#{asciiArt}\n")
 ```
 
-Select some text in an editor window and hit `cmd-alt-a`. :tada: You're now an
+Select some text in an editor window and hit `ctrl-alt-a`. :tada: You're now an
 ASCII art professional!
 
 ## Further reading

package.json

@@ -1,7 +1,7 @@
 {
   "name": "atom",
   "productName": "Atom",
-  "version": "0.174.0",
+  "version": "0.177.0",
   "description": "A hackable text editor for the 21st Century.",
   "main": "./src/browser/main.js",
   "repository": {
@@ -17,7 +17,7 @@
       "url": "http://github.com/atom/atom/raw/master/LICENSE.md"
     }
   ],
-  "atomShellVersion": "0.20.5",
+  "atomShellVersion": "0.20.7",
   "dependencies": {
     "async": "0.2.6",
     "atom-keymap": "^2.5.2",
@@ -29,7 +29,7 @@
     "delegato": "^1",
     "emissary": "^1.3.1",
     "event-kit": "^1.0.1",
-    "first-mate": "^2.2.4",
+    "first-mate": "^2.2.5",
     "fs-plus": "^2.3.2",
     "fstream": "0.1.24",
     "fuzzaldrin": "^2.1",
@@ -39,14 +39,14 @@
     "jasmine-json": "~0.0",
     "jasmine-tagged": "^1.1.2",
     "jquery": "^2.1.1",
-    "less-cache": "0.19.0",
+    "less-cache": "git+https://github.com/atom/less-cache.git#018b1739ae03ee35aae9827d7d7b16d0799c5d42",
     "marked": "^0.3",
     "mixto": "^1",
     "mkdirp": "0.3.5",
     "nslog": "^1.0.1",
-    "oniguruma": "^3.0.4",
+    "oniguruma": "^3.0.6",
     "optimist": "0.4.0",
-    "pathwatcher": "^2.6.0",
+    "pathwatcher": "^2.6.1",
     "property-accessors": "^1",
     "q": "^1.0.1",
     "random-words": "0.0.1",
@@ -56,14 +56,14 @@
     "scandal": "1.0.3",
     "scoped-property-store": "^0.16.2",
     "scrollbar-style": "^1.0.2",
-    "season": "^5.0.5",
+    "season": "^5.1.1",
     "semver": "2.2.1",
     "serializable": "^1",
-    "service-hub": "^0.1.0",
+    "service-hub": "^0.2.0",
     "space-pen": "3.8.2",
     "stacktrace-parser": "0.1.1",
     "temp": "0.7.0",
-    "text-buffer": "^3.10.0",
+    "text-buffer": "^3.10.1",
     "theorist": "^1.0.2",
     "underscore-plus": "^1.6.6",
     "vm-compatibility-layer": "0.1.0"
@@ -75,6 +75,10 @@
     "atom-light-ui": "0.40.0",
     "base16-tomorrow-dark-theme": "0.25.0",
     "base16-tomorrow-light-theme": "0.8.0",
+    "one-dark-ui": "0.2.0",
+    "one-dark-syntax": "0.2.0",
+    "one-light-syntax": "0.2.0",
+    "one-light-ui": "0.1.0",
     "solarized-dark-syntax": "0.32.0",
     "solarized-light-syntax": "0.19.0",
     "archive-view": "0.44.0",
@@ -85,49 +89,49 @@
     "bookmarks": "0.35.0",
     "bracket-matcher": "0.69.0",
     "command-palette": "0.34.0",
-    "deprecation-cop": "0.32.0",
-    "dev-live-reload": "0.38.0",
-    "encoding-selector": "0.15.0",
+    "deprecation-cop": "0.33.0",
+    "dev-live-reload": "0.39.0",
+    "encoding-selector": "0.17.0",
     "exception-reporting": "0.21.0",
     "find-and-replace": "0.156.0",
     "fuzzy-finder": "0.65.0",
-    "git-diff": "0.49.0",
+    "git-diff": "0.50.0",
     "go-to-line": "0.30.0",
-    "grammar-selector": "0.43.0",
+    "grammar-selector": "0.44.0",
     "image-view": "0.47.0",
-    "incompatible-packages": "0.20.0",
-    "keybinding-resolver": "0.26.0",
+    "incompatible-packages": "0.21.0",
+    "keybinding-resolver": "0.27.0",
     "link": "0.29.0",
-    "markdown-preview": "0.120.0",
-    "metrics": "0.40.0",
-    "notifications": "0.25.0",
+    "markdown-preview": "0.126.0",
+    "metrics": "0.41.0",
+    "notifications": "0.26.0",
     "open-on-github": "0.32.0",
     "package-generator": "0.37.0",
-    "release-notes": "0.46.0",
-    "settings-view": "0.173.0",
-    "snippets": "0.69.0",
+    "release-notes": "0.47.0",
+    "settings-view": "0.174.0",
+    "snippets": "0.70.0",
     "spell-check": "0.51.0",
-    "status-bar": "0.57.0",
+    "status-bar": "0.58.0",
     "styleguide": "0.42.0",
     "symbols-view": "0.79.0",
     "tabs": "0.64.0",
-    "timecop": "0.27.0",
-    "tree-view": "0.148.0",
+    "timecop": "0.28.0",
+    "tree-view": "0.149.0",
     "update-package-dependencies": "0.7.0",
     "welcome": "0.21.0",
     "whitespace": "0.28.0",
-    "wrap-guide": "0.30.0",
+    "wrap-guide": "0.31.0",
     "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-gfm": "0.63.0",
     "language-git": "0.10.0",
     "language-go": "0.21.0",
     "language-html": "0.28.0",
     "language-hyperlink": "0.12.2",
     "language-java": "0.14.0",
-    "language-javascript": "0.54.0",
+    "language-javascript": "0.55.0",
     "language-json": "0.11.0",
     "language-less": "0.24.0",
     "language-make": "0.13.0",
@@ -142,7 +146,7 @@
     "language-sass": "0.31.0",
     "language-shellscript": "0.12.0",
     "language-source": "0.9.0",
-    "language-sql": "0.13.0",
+    "language-sql": "0.14.0",
     "language-text": "0.6.0",
     "language-todo": "0.15.0",
     "language-toml": "0.15.0",

resources/win/apm.sh

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

resources/win/atom.cmd

@@ -18,5 +18,5 @@ FOR %%a IN (%*) DO (
 IF "%EXPECT_OUTPUT%"=="YES" (
   "%~dp0\..\..\atom.exe" %*
 ) ELSE (
-  "%~dp0\..\app\apm\node_modules\atom-package-manager\bin\node.exe" "%~dp0\atom.js" %*
+  "%~dp0\..\app\apm\bin\node.exe" "%~dp0\atom.js" %*
 )

resources/win/atom.sh

@@ -18,5 +18,5 @@ done
 if [ $EXPECT_OUTPUT ]; then
   "$0/../../../atom.exe" "$@"
 else
-  "$0/../../app/apm/node_modules/atom-package-manager/bin/node.exe" "$0/../atom.js" "$@"
+  "$0/../../app/apm/bin/node.exe" "$0/../atom.js" "$@"
 fi

script/bootstrap

@@ -48,9 +48,9 @@ function bootstrap() {
   var dedupeNpmCommand = npmPath + npmFlags + 'dedupe';
 
   if (process.argv.indexOf('--no-quiet') === -1) {
-    buildInstallCommand  += ' --quiet';
-    apmInstallCommand    += ' --quiet';
-    moduleInstallCommand += ' --quiet';
+    buildInstallCommand  += ' --loglevel error';
+    apmInstallCommand    += ' --loglevel error';
+    moduleInstallCommand += ' --loglevel error';
     dedupeApmCommand     += ' --quiet';
     dedupeNpmCommand     += ' --quiet';
     buildInstallOptions.ignoreStdout = true;

spec/config-spec.coffee

@@ -226,14 +226,44 @@ describe "Config", ->
       advanceClock(500)
       expect(atom.config.save.callCount).toBe 1
 
-    describe "when a 'source' and no 'scopeSelector' is given", ->
-      it "removes all scoped settings with the given source", ->
-        atom.config.set("foo.bar.baz", 1, scopeSelector: ".a", source: "source-a")
-        atom.config.set("foo.bar.quux", 2, scopeSelector: ".b", source: "source-a")
-        expect(atom.config.get("foo.bar", scope: [".a.b"])).toEqual(baz: 1, quux: 2)
+    describe "when no 'scopeSelector' is given", ->
+      describe "when a 'source' but no key-path is given", ->
+        it "removes all scoped settings with the given source", ->
+          atom.config.set("foo.bar.baz", 1, scopeSelector: ".a", source: "source-a")
+          atom.config.set("foo.bar.quux", 2, scopeSelector: ".b", source: "source-a")
+          expect(atom.config.get("foo.bar", scope: [".a.b"])).toEqual(baz: 1, quux: 2)
 
-        atom.config.unset(null, source: "source-a")
-        expect(atom.config.get("foo.bar", scope: [".a"])).toEqual(baz: 0, ok: 0)
+          atom.config.unset(null, source: "source-a")
+          expect(atom.config.get("foo.bar", scope: [".a"])).toEqual(baz: 0, ok: 0)
+
+      describe "when a 'source' and a key-path is given", ->
+        it "removes all scoped settings with the given source and key-path", ->
+          atom.config.set("foo.bar.baz", 1)
+          atom.config.set("foo.bar.baz", 2, scopeSelector: ".a", source: "source-a")
+          atom.config.set("foo.bar.baz", 3, scopeSelector: ".a.b", source: "source-b")
+          expect(atom.config.get("foo.bar.baz", scope: [".a.b"])).toEqual(3)
+
+          atom.config.unset("foo.bar.baz", source: "source-b")
+          expect(atom.config.get("foo.bar.baz", scope: [".a.b"])).toEqual(2)
+          expect(atom.config.get("foo.bar.baz")).toEqual(1)
+
+      describe "when no 'source' is given", ->
+        it "removes all scoped and unscoped properties for that key-path", ->
+          atom.config.setDefaults("foo.bar", baz: 100)
+
+          atom.config.set("foo.bar", { baz: 1, ok: 2 }, scopeSelector: ".a")
+          atom.config.set("foo.bar", { baz: 11, ok: 12 }, scopeSelector: ".b")
+          atom.config.set("foo.bar", { baz: 21, ok: 22 })
+
+          atom.config.unset("foo.bar.baz")
+
+          expect(atom.config.get("foo.bar.baz", scope: [".a"])).toBe 100
+          expect(atom.config.get("foo.bar.baz", scope: [".b"])).toBe 100
+          expect(atom.config.get("foo.bar.baz")).toBe 100
+
+          expect(atom.config.get("foo.bar.ok", scope: [".a"])).toBe 2
+          expect(atom.config.get("foo.bar.ok", scope: [".b"])).toBe 12
+          expect(atom.config.get("foo.bar.ok")).toBe 22
 
     describe "when a 'scopeSelector' is given", ->
       it "restores the global default when no scoped default set", ->
@@ -1363,6 +1393,14 @@ describe "Config", ->
           atom.config.set('foo.bar.aColor', false)
           expect(atom.config.get('foo.bar.aColor')).toEqual {red: 255, green: 255, blue: 255, alpha: 1}
 
+        it "returns a clone of the Color when returned in a parent object", ->
+          color1 = atom.config.get('foo.bar').aColor
+          color2 = atom.config.get('foo.bar').aColor
+          expect(color1.toRGBAString()).toBe 'rgba(255, 255, 255, 1)'
+          expect(color2.toRGBAString()).toBe 'rgba(255, 255, 255, 1)'
+          expect(color1).not.toBe color2
+          expect(color1).toEqual color2
+
       describe 'when the `enum` key is used', ->
         beforeEach ->
           schema =

spec/fixtures/packages/package-with-config-schema/index.coffee

@@ -9,5 +9,3 @@ module.exports =
         two:
           type: 'integer'
           default: 2
-
-  activate: -> # no-op

spec/project-spec.coffee

@@ -37,6 +37,32 @@ describe "Project", ->
         deserializedProject.getBuffers()[0].destroy()
         expect(deserializedProject.getBuffers().length).toBe 0
 
+
+    it "does not deserialize buffers when their path is a directory that exists", ->
+      pathToOpen = path.join(temp.mkdirSync(), 'file.txt')
+
+      waitsForPromise ->
+        atom.project.open(pathToOpen)
+
+      runs ->
+        expect(atom.project.getBuffers().length).toBe 1
+        fs.mkdirSync(pathToOpen)
+        deserializedProject = atom.project.testSerialization()
+        expect(deserializedProject.getBuffers().length).toBe 0
+
+    it "does not deserialize buffers when their path is inaccessible", ->
+      pathToOpen = path.join(temp.mkdirSync(), 'file.txt')
+      fs.writeFileSync(pathToOpen, '')
+
+      waitsForPromise ->
+        atom.project.open(pathToOpen)
+
+      runs ->
+        expect(atom.project.getBuffers().length).toBe 1
+        fs.chmodSync(pathToOpen, '000')
+        deserializedProject = atom.project.testSerialization()
+        expect(deserializedProject.getBuffers().length).toBe 0
+
   describe "when an editor is saved and the project has no path", ->
     it "sets the project's path to the saved file's parent directory", ->
       tempFile = temp.openSync().path

spec/spec-helper.coffee

@@ -213,6 +213,11 @@ jasmine.snapshotDeprecations = ->
 jasmine.restoreDeprecationsSnapshot = ->
   Grim.deprecations = deprecationsSnapshot
 
+jasmine.useRealClock = ->
+  jasmine.unspy(window, 'setTimeout')
+  jasmine.unspy(window, 'clearTimeout')
+  jasmine.unspy(_._, 'now')
+
 addCustomMatchers = (spec) ->
   spec.addMatchers
     toBeInstanceOf: (expected) ->
@@ -298,13 +303,13 @@ window.waitsForPromise = (args...) ->
   window.waitsFor timeout, (moveOn) ->
     promise = fn()
     if shouldReject
-      promise.fail(moveOn)
-      promise.done ->
+      promise.catch(moveOn)
+      promise.then ->
         jasmine.getEnv().currentSpec.fail("Expected promise to be rejected, but it was resolved")
         moveOn()
     else
-      promise.done(moveOn)
-      promise.fail (error) ->
+      promise.then(moveOn)
+      promise.catch (error) ->
         jasmine.getEnv().currentSpec.fail("Expected promise to be resolved, but it was rejected with #{jasmine.pp(error)}")
         moveOn()
 

spec/text-editor-spec.coffee

@@ -155,6 +155,25 @@ describe "TextEditor", ->
         expect(editor2.getSoftTabs()).toBe true
         expect(editor2.getEncoding()).toBe 'macroman'
 
+    it "uses scoped `core.fileEncoding` values", ->
+      editor1 = null
+      editor2 = null
+
+      atom.config.set('core.fileEncoding', 'utf16le')
+      atom.config.set('core.fileEncoding', 'macroman', scopeSelector: '.js')
+
+      waitsForPromise ->
+        atom.workspace.open('a').then (o) -> editor1 = o
+
+      runs ->
+        expect(editor1.getEncoding()).toBe 'utf16le'
+
+      waitsForPromise ->
+        atom.workspace.open('test.js').then (o) -> editor2 = o
+
+      runs ->
+        expect(editor2.getEncoding()).toBe 'macroman'
+
   describe "title", ->
     describe ".getTitle()", ->
       it "uses the basename of the buffer's path as its title, or 'untitled' if the path is undefined", ->
@@ -2630,12 +2649,20 @@ describe "TextEditor", ->
             atom.config.set("editor.autoIndentOnPaste", true)
 
           describe "when only whitespace precedes the cursor", ->
-            it "auto-indents the lines spanned by the pasted text", ->
-              atom.clipboard.write("console.log(x);\nconsole.log(y);\n")
-              editor.setCursorBufferPosition([5, 2])
+            it "auto-indents the lines spanned by the pasted text, based on the first pasted line", ->
+              expect(editor.indentationForBufferRow(5)).toBe(3)
+
+              atom.clipboard.write("a(x);\n  b(x);\n    c(x);\n", indentBasis: 0)
+              editor.setCursorBufferPosition([5, 0])
               editor.pasteText()
-              expect(editor.lineTextForBufferRow(5)).toBe("      console.log(x);")
-              expect(editor.lineTextForBufferRow(6)).toBe("      console.log(y);")
+
+              # Adjust the indentation of the pasted block
+              expect(editor.indentationForBufferRow(5)).toBe(3)
+              expect(editor.indentationForBufferRow(6)).toBe(4)
+              expect(editor.indentationForBufferRow(7)).toBe(5)
+
+              # Preserve the indentation of the next row
+              expect(editor.indentationForBufferRow(8)).toBe(3)
 
           describe "when non-whitespace characters precede the cursor", ->
             it "does not auto-indent the first line being pasted", ->
@@ -2732,9 +2759,9 @@ describe "TextEditor", ->
               editor.setSelectedBufferRange([[1, 2], [1, Infinity]])
               editor.pasteText()
               expect(editor.lineTextForBufferRow(1)).toBe("  if (items.length <= 1) return items;")
-              expect(editor.lineTextForBufferRow(2)).toBe("  ")
+              expect(editor.lineTextForBufferRow(2)).toBe("")
               expect(editor.lineTextForBufferRow(3)).toBe("    if (items.length <= 1) return items;")
-              expect(editor.getCursorBufferPosition()).toEqual([2, 2])
+              expect(editor.getCursorBufferPosition()).toEqual([2, 0])
 
           describe "when there is no selection", ->
             it "pastes the line above the cursor and retains the cursor's column", ->

spec/workspace-spec.coffee

@@ -315,6 +315,44 @@ describe "Workspace", ->
             expect(notification.getMessage()).toContain 'Permission denied'
             expect(notification.getMessage()).toContain 'file1'
 
+      describe "when the the operation is not permitted", ->
+        beforeEach ->
+          spyOn(fs, 'openSync').andCallFake (path) ->
+            error = new Error("EPERM, operation not permitted '#{path}'")
+            error.path = path
+            error.code = 'EPERM'
+            throw error
+
+        it "creates a notification", ->
+          waitsForPromise ->
+            workspace.open('file1')
+
+          runs ->
+            expect(notificationSpy).toHaveBeenCalled()
+            notification = notificationSpy.mostRecentCall.args[0]
+            expect(notification.getType()).toBe 'warning'
+            expect(notification.getMessage()).toContain 'Unable to open'
+            expect(notification.getMessage()).toContain 'file1'
+
+      describe "when the the file is already open in windows", ->
+        beforeEach ->
+          spyOn(fs, 'openSync').andCallFake (path) ->
+            error = new Error("EBUSY, resource busy or locked '#{path}'")
+            error.path = path
+            error.code = 'EBUSY'
+            throw error
+
+        it "creates a notification", ->
+          waitsForPromise ->
+            workspace.open('file1')
+
+          runs ->
+            expect(notificationSpy).toHaveBeenCalled()
+            notification = notificationSpy.mostRecentCall.args[0]
+            expect(notification.getType()).toBe 'warning'
+            expect(notification.getMessage()).toContain 'Unable to open'
+            expect(notification.getMessage()).toContain 'file1'
+
       describe "when there is an unhandled error", ->
         beforeEach ->
           spyOn(fs, 'openSync').andCallFake (path) ->
@@ -948,6 +986,43 @@ describe "Workspace", ->
         expect(addedSpy).toHaveBeenCalled()
         expect(addedSpy.mostRecentCall.args[0].getType()).toBe 'warning'
 
+      it "emits a warning notification when the operation is not permitted", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          error = new Error("EPERM, operation not permitted '/Some/dir/and-a-file.js'")
+          error.code = 'EPERM'
+          error.path = '/Some/dir/and-a-file.js'
+          throw error
+
+      it "emits a warning notification when the file is already open by another app", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          error = new Error("EBUSY, resource busy or locked '/Some/dir/and-a-file.js'")
+          error.code = 'EBUSY'
+          error.path = '/Some/dir/and-a-file.js'
+          throw error
+
+        atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
+        atom.workspace.saveActivePaneItem()
+        expect(addedSpy).toHaveBeenCalled()
+
+        notificaiton = addedSpy.mostRecentCall.args[0]
+        expect(notificaiton.getType()).toBe 'warning'
+        expect(notificaiton.getMessage()).toContain 'Unable to save'
+
+      it "emits a warning notification when the file system is read-only", ->
+        spyOn(Pane::, 'saveActiveItem').andCallFake ->
+          error = new Error("EROFS, read-only file system '/Some/dir/and-a-file.js'")
+          error.code = 'EROFS'
+          error.path = '/Some/dir/and-a-file.js'
+          throw error
+
+        atom.notifications.onDidAddNotification addedSpy = jasmine.createSpy()
+        atom.workspace.saveActivePaneItem()
+        expect(addedSpy).toHaveBeenCalled()
+
+        notification = addedSpy.mostRecentCall.args[0]
+        expect(notification.getType()).toBe 'warning'
+        expect(notification.getMessage()).toContain 'Unable to save'
+
       it "emits a warning notification when the file cannot be saved", ->
         spyOn(Pane::, 'saveActiveItem').andCallFake ->
           throw new Error("no one knows")

src/atom.coffee

@@ -3,7 +3,6 @@ ipc = require 'ipc'
 os = require 'os'
 path = require 'path'
 remote = require 'remote'
-screen = require 'screen'
 shell = require 'shell'
 
 _ = require 'underscore-plus'
@@ -280,8 +279,6 @@ class Atom extends Model
       deprecate "The atom.syntax global is deprecated. Use atom.grammars instead."
       @grammars
 
-    @subscribe @packages.onDidActivateInitialPackages => @watchThemes()
-
     Project = require './project'
     TextBuffer = require 'text-buffer'
     @deserializers.add(TextBuffer)
@@ -547,6 +544,7 @@ class Atom extends Model
     if @isValidDimensions(dimensions)
       dimensions
     else
+      screen = remote.require 'screen'
       {width, height} = screen.getPrimaryDisplay().workAreaSize
       {x: 0, y: 0, width: Math.min(1024, width), height}
 
@@ -580,7 +578,10 @@ class Atom extends Model
 
     @watchProjectPath()
 
-    @packages.activate()
+    @packages.activate().then =>
+      maximize = dimensions?.maximized and process.platform isnt 'darwin'
+      @displayWindow({maximize})
+
     @keymaps.loadUserKeymap()
     @requireUserInitScript() unless safeMode
 
@@ -589,9 +590,6 @@ class Atom extends Model
       @setAutoHideMenuBar(newValue)
     @setAutoHideMenuBar(true) if @config.get('core.autoHideMenuBar')
 
-    maximize = dimensions?.maximized and process.platform isnt 'darwin'
-    @displayWindow({maximize})
-
   unloadEditorWindow: ->
     return if not @project
 
@@ -720,13 +718,6 @@ class Atom extends Model
   loadThemes: ->
     @themes.load()
 
-  watchThemes: ->
-    @themes.onDidChangeActiveThemes =>
-      # Only reload stylesheets from non-theme packages
-      for pack in @packages.getActivePackages() when pack.getType() isnt 'theme'
-        pack.reloadStylesheets?()
-      null
-
   # Notify the browser project of the window's current project path
   watchProjectPath: ->
     onProjectPathChanged = =>

src/browser/atom-window.coffee

@@ -10,7 +10,6 @@ module.exports =
 class AtomWindow
   _.extend @prototype, EventEmitter.prototype
 
-  @iconPath: path.resolve(__dirname, '..', '..', 'resources', 'atom.png')
   @includeShellLoadTime: true
 
   browserWindow: null
@@ -26,7 +25,6 @@ class AtomWindow
     @browserWindow = new BrowserWindow
       show: false
       title: 'Atom'
-      icon: @constructor.iconPath
       'web-preferences':
         'direct-write': false
         'subpixel-font-scaling': false

src/browser/main.coffee

@@ -13,16 +13,6 @@ process.on 'uncaughtException', (error={}) ->
   nslog(error.message) if error.message?
   nslog(error.stack) if error.stack?
 
-# Patch fs.statSyncNoException/fs.lstatSyncNoException to fail for non-strings
-# https://github.com/atom/atom-shell/issues/843
-{lstatSyncNoException, statSyncNoException} = fs
-fs.statSyncNoException = (pathToStat) ->
-  return false unless pathToStat and typeof pathToStat is 'string'
-  statSyncNoException(pathToStat)
-fs.lstatSyncNoException = (pathToStat) ->
-  return false unless pathToStat and typeof pathToStat is 'string'
-  lstatSyncNoException(pathToStat)
-
 start = ->
   if process.platform is 'win32'
     SquirrelUpdate = require './squirrel-update'
@@ -50,8 +40,12 @@ start = ->
     app.removeListener 'open-file', addPathToOpen
     app.removeListener 'open-url', addUrlToOpen
 
+    cwd = args.executedFrom?.toString() or process.cwd()
     args.pathsToOpen = args.pathsToOpen.map (pathToOpen) ->
-      path.resolve(args.executedFrom ? process.cwd(), pathToOpen.toString())
+      if cwd
+        path.resolve(cwd, pathToOpen.toString())
+      else
+        path.resolve(pathToOpen.toString())
 
     setupCoffeeScript()
     if args.devMode

src/browser/squirrel-update.coffee

@@ -125,7 +125,7 @@ addCommandsToPath = (callback) ->
     atomShCommand = "#!/bin/sh\r\n\"$0/../#{relativeAtomShPath.replace(/\\/g, '/')}\" \"$@\""
 
     apmCommandPath = path.join(binFolder, 'apm.cmd')
-    relativeApmPath = path.relative(binFolder, path.join(process.resourcesPath, 'app', 'apm', 'node_modules', 'atom-package-manager', 'bin', 'apm.cmd'))
+    relativeApmPath = path.relative(binFolder, path.join(process.resourcesPath, 'app', 'apm', 'bin', 'apm.cmd'))
     apmCommand = "@echo off\r\n\"%~dp0\\#{relativeApmPath}\" %*"
 
     apmShCommandPath = path.join(binFolder, 'apm')

src/buffered-process.coffee

@@ -28,22 +28,23 @@ class BufferedProcess
   # * `options` An {Object} with the following keys:
   #   * `command` The {String} command to execute.
   #   * `args` The {Array} of arguments to pass to the command (optional).
-  #   * `options` The options {Object} to pass to Node's `ChildProcess.spawn`
-  #               method (optional).
-  #   * `stdout` The callback {Function} that receives a single argument which
-  #              contains the standard output from the command. The callback is
-  #              called as data is received but it's buffered to ensure only
-  #              complete lines are passed until the source stream closes. After
-  #              the source stream has closed all remaining data is sent in a
-  #              final call (optional).
-  #   * `stderr` The callback {Function} that receives a single argument which
-  #              contains the standard error output from the command. The
-  #              callback is called as data is received but it's buffered to
-  #              ensure only complete lines are passed until the source stream
-  #              closes. After the source stream has closed all remaining data
-  #              is sent in a final call (optional).
-  #   * `exit` The callback {Function} which receives a single argument
-  #            containing the exit status (optional).
+  #   * `options` {Object} (optional) The options {Object} to pass to Node's
+  #     `ChildProcess.spawn` method.
+  #   * `stdout` {Function} (optional) The callback that receives a single
+  #     argument which contains the standard output from the command. The
+  #     callback is called as data is received but it's buffered to ensure only
+  #     complete lines are passed until the source stream closes. After the
+  #     source stream has closed all remaining data is sent in a final call.
+  #     * `data` {String}
+  #   * `stderr` {Function} (optional) The callback that receives a single
+  #     argument which contains the standard error output from the command. The
+  #     callback is called as data is received but it's buffered to ensure only
+  #     complete lines are passed until the source stream closes. After the
+  #     source stream has closed all remaining data is sent in a final call.
+  #     * `data` {String}
+  #   * `exit` {Function} (optional) The callback which receives a single
+  #     argument containing the exit status.
+  #     * `code` {Number}
   constructor: ({command, args, options, stdout, stderr, exit}={}) ->
     @emitter = new Emitter
     options ?= {}

src/coffee-cache.coffee

@@ -7,6 +7,10 @@ fs = require 'fs-plus'
 
 cacheDir = path.join(fs.absolute('~/.atom'), 'compile-cache')
 
+stats =
+  hits: 0
+  misses: 0
+
 # 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')
@@ -21,7 +25,10 @@ getCachePath = (coffee) ->
 getCachedJavaScript = (cachePath) ->
   if fs.isFileSync(cachePath)
     try
-      fs.readFileSync(cachePath, 'utf8')
+      cachedJavaScript = fs.readFileSync(cachePath, 'utf8')
+      stats.hits++
+      return cachedJavaScript
+  return
 
 convertFilePath = (filePath) ->
   if process.platform is 'win32'
@@ -30,6 +37,7 @@ convertFilePath = (filePath) ->
 
 compileCoffeeScript = (coffee, filePath, cachePath) ->
   {js, v3SourceMap} = CoffeeScript.compile(coffee, filename: filePath, sourceMap: true)
+  stats.misses++
   # Include source map in the web page environment.
   if btoa? and JSON? and unescape? and encodeURIComponent?
     js = "#{js}\n//# sourceMappingURL=data:application/json;base64,#{btoa unescape encodeURIComponent v3SourceMap}\n//# sourceURL=#{convertFilePath(filePath)}"
@@ -60,3 +68,7 @@ module.exports =
       compileCoffeeScript(coffee, filePath, cachePath)
     else if extension is '.cson'
       CSON.readFileSync(filePath)
+
+  getCacheMisses: -> stats.misses
+
+  getCacheHits: -> stats.hits

src/config.coffee

@@ -583,6 +583,7 @@ class Config
         Pass a `scopeSelector` in an options hash as the final argument instead.
       """
       [scopeSelector, keyPath, value] = arguments
+      shouldSave = true
     else
       [keyPath, value, options] = arguments
       scopeSelector = options?.scopeSelector
@@ -640,8 +641,9 @@ class Config
         @scopedSettingsStore.removePropertiesForSourceAndSelector(source, scopeSelector)
         @emitChangeEvent()
     else
-      @scopedSettingsStore.removePropertiesForSource(source)
-      if keyPath?
+      for scopeSelector of @scopedSettingsStore.propertiesForSource(source)
+        @unset(keyPath, {scopeSelector, source})
+      if keyPath? and source is @getUserConfigPath()
         @set(keyPath, _.valueForKeyPath(@defaultSettings, keyPath))
 
   # Extended: Get an {Array} of all of the `source` {String}s with which
@@ -898,16 +900,10 @@ class Config
       defaultValue = _.valueForKeyPath(@defaultSettings, keyPath)
 
     if value?
-      if value instanceof Color
-        value = value.clone()
-      else
-        value = _.deepClone(value)
-        _.defaults(value, defaultValue) if isPlainObject(value) and isPlainObject(defaultValue)
+      value = @deepClone(value)
+      _.defaults(value, defaultValue) if isPlainObject(value) and isPlainObject(defaultValue)
     else
-      if defaultValue instanceof Color
-        value = defaultValue.clone()
-      else
-        value = _.deepClone(defaultValue)
+      value = @deepClone(defaultValue)
 
     value
 
@@ -957,6 +953,16 @@ class Config
       catch e
         console.warn("'#{keyPath}' could not set the default. Attempted default: #{JSON.stringify(defaults)}; Schema: #{JSON.stringify(@getSchema(keyPath))}")
 
+  deepClone: (object) ->
+    if object instanceof Color
+      object.clone()
+    else if _.isArray(object)
+      object.map (value) => @deepClone(value)
+    else if isPlainObject(object)
+      _.mapObject object, (key, value) => [key, @deepClone(value)]
+    else
+      object
+
   # `schema` will look something like this
   #
   # ```coffee
@@ -1162,7 +1168,7 @@ Config.addSchemaEnforcers
       throw new Error("Validation failed at #{keyPath}, #{JSON.stringify(value)} is not one of #{JSON.stringify(possibleValues)}")
 
 isPlainObject = (value) ->
-  _.isObject(value) and not _.isArray(value) and not _.isFunction(value) and not _.isString(value)
+  _.isObject(value) and not _.isArray(value) and not _.isFunction(value) and not _.isString(value) and not (value instanceof Color)
 
 splitKeyPath = (keyPath) ->
   return [] unless keyPath?

src/less-compile-cache.coffee

@@ -30,6 +30,10 @@ class LessCompileCache
   setImportPaths: (importPaths=[]) ->
     @cache.setImportPaths(importPaths.concat(@lessSearchPaths))
 
+  clearFooters: -> @cache.clearFooters()
+
+  setFooter: (filePath, footer) -> @cache.setFooter(filePath, footer)
+
   read: (stylesheetPath) ->
     @cache.readFileSync(stylesheetPath)
 

src/package-manager.coffee

@@ -128,9 +128,15 @@ class PackageManager
   #
   # Return a {String} file path to apm.
   getApmPath: ->
+    return @apmPath if @apmPath?
+
     commandName = 'apm'
     commandName += '.cmd' if process.platform is 'win32'
-    @apmPath ?= path.resolve(__dirname, '..', 'apm', 'node_modules', 'atom-package-manager', 'bin', commandName)
+    apmRoot = path.resolve(__dirname, '..', 'apm')
+    @apmPath = path.join(apmRoot, 'bin', commandName)
+    unless fs.isFileSync(@apmPath)
+      @apmPath = path.join(apmRoot, 'node_modules', 'atom-package-manager', 'bin', commandName)
+    @apmPath
 
   # Public: Get the paths being used to look for packages.
   #
@@ -148,7 +154,7 @@ class PackageManager
   #
   # Return a {String} folder path or undefined if it could not be resolved.
   resolvePackagePath: (name) ->
-    return name if fs.isDirectorySync(name)
+    return fs.absolute(name) if fs.isDirectorySync(name)
 
     packagePath = fs.resolve(@packageDirPaths..., name)
     return packagePath if fs.isDirectorySync(packagePath)
@@ -370,6 +376,7 @@ class PackageManager
       packages = @getLoadedPackagesForTypes(types)
       promises = promises.concat(activator.activatePackages(packages))
     Q.all(promises).then =>
+      @initialPackageActivationComplete = true
       @emit 'activated'
       @emitter.emit 'did-activate-initial-packages'
 

src/package.coffee

@@ -9,6 +9,7 @@ EmitterMixin = require('emissary').Emitter
 Q = require 'q'
 {deprecate} = require 'grim'
 
+Color = require './color'
 ModuleCache = require './module-cache'
 ScopedProperties = require './scoped-properties'
 
@@ -123,7 +124,6 @@ class Package
       try
         @loadKeymaps()
         @loadMenus()
-        @loadStylesheets()
         @settingsPromise = @loadSettings()
         @requireMainModule() unless @hasActivationCommands()
 
@@ -155,9 +155,8 @@ class Package
   activateNow: ->
     try
       @activateConfig()
-      @activateStylesheets()
       if @requireMainModule()
-        @mainModule.activate(atom.packages.getPackageState(@name) ? {})
+        @mainModule.activate?(atom.packages.getPackageState(@name) ? {})
         @mainActivated = true
     catch e
       console.warn "Failed to activate package named '#{@name}'", e.stack
@@ -185,6 +184,7 @@ class Package
     @stylesheetDisposables = new CompositeDisposable
 
     priority = @getStyleSheetPriority()
+    @loadStylesheets()
     for [sourcePath, source] in @stylesheets
       if match = path.basename(sourcePath).match(/[^.]*\.([^.]*)\./)
         context = match[1]
@@ -236,8 +236,9 @@ class Package
       fs.listSync(menusDirPath, ['cson', 'json'])
 
   loadStylesheets: ->
-    @stylesheets = @getStylesheetPaths().map (stylesheetPath) ->
-      [stylesheetPath, atom.themes.loadStylesheet(stylesheetPath, true)]
+    @stylesheets = @getStylesheetPaths().map (stylesheetPath) =>
+      stylesheet = atom.themes.loadStylesheet(stylesheetPath, {importFallbackVariables: true})
+      [stylesheetPath, stylesheet]
 
   getStylesheetsPath: ->
     if fs.isDirectorySync(path.join(@path, 'stylesheets'))
@@ -257,6 +258,21 @@ class Package
     else
       fs.listSync(stylesheetDirPath, ['css', 'less'])
 
+  getStylesheetFooter: ->
+    return unless @isTheme()
+
+    footer = ''
+    for key, value of atom.config.get(@name)
+      if typeof value is 'object' and not (value instanceof Color)
+        value = Color.parse(value)
+      value = value?.toRGBAString?() ? value
+      switch typeof value
+        when 'string'
+          footer += "\n@#{key}: #{value};" if value
+        when 'number'
+          footer += "\n@#{key}: #{value};" if isFinite(value)
+    footer
+
   loadGrammarsSync: ->
     return if @grammarsLoaded
 
@@ -352,8 +368,6 @@ class Package
     @settingsActivated = false
 
   reloadStylesheets: ->
-    oldSheets = _.clone(@stylesheets)
-    @loadStylesheets()
     @stylesheetDisposables?.dispose()
     @stylesheetDisposables = new CompositeDisposable
     @stylesheetsActivated = false

src/project.coffee

@@ -66,9 +66,17 @@ class Project extends Model
     buffers: _.compact(@buffers.map (buffer) -> buffer.serialize() if buffer.isRetained())
 
   deserializeParams: (params) ->
-    params.buffers = params.buffers.map (bufferState) -> atom.deserializers.deserialize(bufferState)
-    params
+    params.buffers = _.compact params.buffers.map (bufferState) ->
+      # Check that buffer's file path is accessible
+      return if fs.isDirectorySync(bufferState.filePath)
+      if bufferState.filePath
+        try
+          fs.closeSync(fs.openSync(bufferState.filePath, 'r'))
+        catch error
+          return unless error.code is 'ENOENT'
 
+      atom.deserializers.deserialize(bufferState)
+    params
 
   ###
   Section: Event Subscription
@@ -219,8 +227,7 @@ class Project extends Model
 
     if filePath?
       try
-        fileDescriptor = fs.openSync(filePath, 'r+')
-        fs.closeSync(fileDescriptor)
+        fs.closeSync(fs.openSync(filePath, 'r'))
       catch error
         # allow ENOENT errors to create an editor for paths that dont exist
         throw error unless error.code is 'ENOENT'
@@ -273,7 +280,6 @@ class Project extends Model
   # Still needed when deserializing a tokenized buffer
   buildBufferSync: (absoluteFilePath) ->
     buffer = new TextBuffer({filePath: absoluteFilePath})
-    buffer.setEncoding(atom.config.get('core.fileEncoding'))
     @addBuffer(buffer)
     buffer.loadSync()
     buffer
@@ -291,7 +297,6 @@ class Project extends Model
       throw error
 
     buffer = new TextBuffer({filePath: absoluteFilePath})
-    buffer.setEncoding(atom.config.get('core.fileEncoding'))
     @addBuffer(buffer)
     buffer.load()
       .then((buffer) -> buffer)

src/selection.coffee

@@ -362,7 +362,7 @@ class Selection extends Model
     precedingText = @editor.getTextInRange([[oldBufferRange.start.row, 0], oldBufferRange.start])
     startLevel = @editor.indentLevelForLine(precedingText)
 
-    if options.indentBasis? and not options.autoIndent
+    if options.indentBasis?
       text = @adjustIndent(text, startLevel - options.indentBasis)
 
     newBufferRange = @editor.buffer.setTextInRange(oldBufferRange, text, pick(options, 'undo', 'normalizeLineEndings'))
@@ -375,8 +375,16 @@ class Selection extends Model
     if options.autoIndent
       precedingText = @editor.getTextInBufferRange([[newBufferRange.start.row, 0], newBufferRange.start])
       unless NonWhitespaceRegExp.test(precedingText)
-        @editor.autoIndentBufferRow(newBufferRange.getRows()[0])
-      @editor.autoIndentBufferRow(row) for row, i in newBufferRange.getRows() when i > 0
+        rowsToIndent = newBufferRange.getRows()
+        firstRow = rowsToIndent.shift()
+        rowsToIndent.pop() if text.endsWith("\n")
+        suggestedIndent = @editor.suggestedIndentForBufferRow(firstRow)
+        actualIndent = @editor.indentationForBufferRow(firstRow)
+        @editor.setIndentationForBufferRow(firstRow, suggestedIndent)
+        indentChange = suggestedIndent - actualIndent
+        for row in rowsToIndent
+          newIndent = @editor.indentationForBufferRow(row) + indentChange
+          @editor.setIndentationForBufferRow(row, newIndent)
     else if options.autoIndentNewline and text == '\n'
       currentIndentation = @editor.indentationForBufferRow(newBufferRange.start.row)
       @editor.autoIndentBufferRow(newBufferRange.end.row, preserveLeadingWhitespace: true, skipBlankLines: false)
@@ -595,14 +603,12 @@ class Selection extends Model
     @editor.createFold(range.start.row, range.end.row)
     @cursor.setBufferPosition([range.end.row + 1, 0])
 
-  # Public: Increases the indentation level of
-  #
-
-  # * `indentIncrease` The beginning indent level.
+  # Private: Increase the indentation level of the given text by given number
+  # of levels. Leaves the first line unchanged.
   adjustIndent: (text, indentIncrease) ->
     lines = text.split('\n')
     for line, i in lines when i > 0
-      if indentIncrease == 0
+      if indentIncrease == 0 or line is ''
         continue
       else if indentIncrease > 0
         lines[i] = @editor.buildIndentString(indentIncrease) + line

src/text-editor-component.coffee

@@ -224,7 +224,7 @@ TextEditorComponent = React.createClass
     @props.editor.setVisible(true)
     @performedInitialMeasurement = true
     @updatesPaused = false
-    @forceUpdate() if @updateRequestedWhilePaused and @canUpdate()
+    @forceUpdate() if @canUpdate()
 
   requestUpdate: ->
     return unless @canUpdate()

src/text-editor.coffee

@@ -105,6 +105,8 @@ class TextEditor extends Model
 
     @languageMode = new LanguageMode(this)
 
+    @setEncoding(atom.config.get('core.fileEncoding', scope: @getRootScopeDescriptor()))
+
     @subscribe @$scrollTop, (scrollTop) =>
       @emit 'scroll-top-changed', scrollTop
       @emitter.emit 'did-change-scroll-top', scrollTop

src/theme-manager.coffee

@@ -197,7 +197,7 @@ class ThemeManager
       ]
       themeNames = _.intersection(themeNames, builtInThemeNames)
       if themeNames.length is 0
-        themeNames = ['atom-dark-syntax', 'atom-dark-ui']
+        themeNames = ['atom-dark-ui', 'atom-dark-syntax']
       else if themeNames.length is 1
         if _.endsWith(themeNames[0], '-ui')
           themeNames.unshift('atom-dark-syntax')
@@ -266,7 +266,7 @@ class ThemeManager
       """
       atom.notifications.addError(message, dismissable: true)
 
-    userStylesheetContents = @loadStylesheet(userStylesheetPath, true)
+    userStylesheetContents = @loadStylesheet(userStylesheetPath, importFallbackVariables: true)
     @userStyleSheetDisposable = atom.styles.addStyleSheet(userStylesheetContents, sourcePath: userStylesheetPath, priority: 2)
 
   loadBaseStylesheets: ->
@@ -287,16 +287,14 @@ class ThemeManager
     else
       fs.resolveOnLoadPath(stylesheetPath, ['css', 'less'])
 
-  loadStylesheet: (stylesheetPath, importFallbackVariables) ->
+  loadStylesheet: (stylesheetPath, options) ->
     if path.extname(stylesheetPath) is '.less'
-      @loadLessStylesheet(stylesheetPath, importFallbackVariables)
+      @loadLessStylesheet(stylesheetPath, options)
     else
       fs.readFileSync(stylesheetPath, 'utf8')
 
-  loadLessStylesheet: (lessStylesheetPath, importFallbackVariables=false) ->
-    unless @lessCache?
-      LessCompileCache = require './less-compile-cache'
-      @lessCache = new LessCompileCache({@resourcePath, importPaths: @getImportPaths()})
+  loadLessStylesheet: (lessStylesheetPath, {variables, importFallbackVariables}={}) ->
+    @createLessCache()
 
     try
       if importFallbackVariables
@@ -335,26 +333,7 @@ class ThemeManager
 
     # atom.config.observe runs the callback once, then on subsequent changes.
     atom.config.observe 'core.themes', =>
-      @deactivateThemes()
-
-      @refreshLessCache() # Update cache for packages in core.themes config
-
-      promises = []
-      for themeName in @getEnabledThemeNames()
-        if @packageManager.resolvePackagePath(themeName)
-          promises.push(@packageManager.activatePackage(themeName))
-        else
-          console.warn("Failed to activate theme '#{themeName}' because it isn't installed.")
-
-      Q.all(promises).then =>
-        @addActiveThemeClasses()
-        @refreshLessCache() # Update cache again now that @getActiveThemes() is populated
-        @loadUserStylesheet()
-        @reloadBaseStylesheets()
-        @initialLoadComplete = true
-        @emit 'reloaded'
-        @emitter.emit 'did-change-active-themes'
-        deferred.resolve()
+      @reloadStylesheets -> deferred.resolve()
 
     deferred.promise
 
@@ -364,6 +343,44 @@ class ThemeManager
     @packageManager.deactivatePackage(pack.name) for pack in @getActiveThemes()
     null
 
+  reloadPackageStylesheets: ->
+    for pack in @packageManager.getActivePackages()
+      pack.reloadStylesheets() if pack.getType() isnt 'theme'
+
+  reloadStylesheets: (callback) ->
+    @deactivateThemes()
+
+    @refreshLessCache() # Update cache for packages in core.themes config
+    @lessCache?.clearFooters()
+
+    loadedThemes = []
+    for themeName in @getEnabledThemeNames()
+      unless @packageManager.resolvePackagePath(themeName)
+        console.warn("Failed to activate theme '#{themeName}' because it isn't installed.")
+        continue
+
+      if theme = @packageManager.loadPackage(themeName)
+        @setFooterForTheme(theme)
+        loadedThemes.push(theme)
+
+    promises = []
+    for theme in loadedThemes
+      promises.push(@packageManager.activatePackage(theme.name))
+
+    Q.all(promises).then =>
+      @addActiveThemeClasses()
+      @refreshLessCache() # Update cache again now that @getActiveThemes() is populated
+      @loadUserStylesheet()
+      @reloadBaseStylesheets()
+      if @packageManager.initialPackageActivationComplete
+        @reloadPackageStylesheets()
+      else
+        @packageManager.onDidActivateInitialPackages => @reloadPackageStylesheets()
+      @initialLoadComplete = true
+      @emit 'reloaded'
+      @emitter.emit 'did-change-active-themes'
+      callback?()
+
   isInitialLoadComplete: -> @initialLoadComplete
 
   addActiveThemeClasses: ->
@@ -378,9 +395,32 @@ class ThemeManager
       workspaceElement.classList.remove("theme-#{pack.name}")
     return
 
+  createLessCache: ->
+    unless @lessCache?
+      LessCompileCache = require './less-compile-cache'
+      @lessCache = new LessCompileCache({@resourcePath, importPaths: @getImportPaths()})
+    @lessCache
+
   refreshLessCache: ->
     @lessCache?.setImportPaths(@getImportPaths())
 
+  setFooterForTheme: (theme) ->
+    footer = theme.getStylesheetFooter()
+    return unless footer
+
+    stylesheetPaths = []
+    try
+      stylesheetPaths = theme.getStylesheetPaths()
+
+    try
+      stylesPath = path.join(theme.path, 'styles')
+      stylesheetPaths = stylesheetPaths.concat(fs.listSync(stylesPath, ['less']))
+
+    for stylesheetPath in stylesheetPaths
+      @createLessCache().setFooter(stylesheetPath, footer)
+
+    return
+
   getImportPaths: ->
     activeThemes = @getActiveThemes()
     if activeThemes.length > 0

src/theme-package.coffee

@@ -21,12 +21,21 @@ class ThemePackage extends Package
         console.warn "Failed to load theme named '#{@name}'", error.stack ? error
     this
 
+  watchThemeConfig: ->
+    @configDisposable = atom.config.onDidChange @name, =>
+      atom.themes.reloadStylesheets()
+
   activate: ->
     return @activationDeferred.promise if @activationDeferred?
 
     @activationDeferred = Q.defer()
     @measure 'activateTime', =>
-      @loadStylesheets()
       @activateNow()
+      @reloadStylesheets()
+      @watchThemeConfig()
 
     @activationDeferred.promise
+
+  deactivate: ->
+    @configDisposable?.dispose()
+    super

src/workspace.coffee

@@ -456,6 +456,8 @@ class Workspace extends Model
           atom.notifications.addWarning("#{error.message} Large file support is being tracked at [atom/atom#307](https://github.com/atom/atom/issues/307).")
         when 'EACCES'
           atom.notifications.addWarning("Permission denied '#{error.path}'")
+        when 'EPERM', 'EBUSY'
+          atom.notifications.addWarning("Unable to open '#{error.path}'", detail: error.message)
         else
           throw error
       return Q()
@@ -498,7 +500,7 @@ class Workspace extends Model
   # ## Examples
   #
   # ```coffee
-  # atom.project.addOpener (uri) ->
+  # atom.workspace.addOpener (uri) ->
   #   if path.extname(uri) is '.toml'
   #     return new TomlEditor(uri)
   # ```
@@ -625,6 +627,12 @@ class Workspace extends Model
         atom.notifications.addWarning("Unable to save file: #{error.message}")
       else if error.code is 'EACCES' and error.path?
         atom.notifications.addWarning("Unable to save file: Permission denied '#{error.path}'")
+      else if error.code is 'EPERM' and error.path?
+        atom.notifications.addWarning("Unable to save file '#{error.path}'", detail: error.message)
+      else if error.code is 'EBUSY' and error.path?
+        atom.notifications.addWarning("Unable to save file '#{error.path}'", detail: error.message)
+      else if error.code is 'EROFS' and error.path?
+        atom.notifications.addWarning("Unable to save file: Read-only file system '#{error.path}'")
       else if errorMatch = /ENOTDIR, not a directory '([^']+)'/.exec(error.message)
         fileName = errorMatch[1]
         atom.notifications.addWarning("Unable to save file: A directory in the path '#{fileName}' could not be written to")

static/index.js

@@ -5,23 +5,6 @@ window.onload = function() {
     var fs = require('fs');
     var path = require('path');
 
-    // Patch fs.statSyncNoException/fs.lstatSyncNoException to fail for non-strings
-    // https://github.com/atom/atom-shell/issues/843
-    var statSyncNoException = fs.statSyncNoException;
-    var lstatSyncNoException = fs.lstatSyncNoException;
-    fs.statSyncNoException = function(pathToStat) {
-      if (pathToStat && typeof pathToStat === 'string')
-        return statSyncNoException(pathToStat);
-      else
-        return false;
-    };
-    fs.lstatSyncNoException = function(pathToStat) {
-      if (pathToStat && typeof pathToStat === 'string')
-        return lstatSyncNoException(pathToStat);
-      else
-        return false;
-    };
-
     // Skip "?loadSettings=".
     var rawLoadSettings = decodeURIComponent(location.search.substr(14));
     var loadSettings;

static/text-editor-light.less

@@ -12,6 +12,7 @@ atom-text-editor[mini] {
   font-size: @input-font-size;
   line-height: @component-line-height;
   max-height: @component-line-height + 2; // +2 for borders
+  overflow: auto;
 }
 
 atom-overlay {