diff --git a/benchmark/benchmark-helper.coffee b/benchmark/benchmark-helper.coffee
index fea602b9b..663ebd344 100644
--- a/benchmark/benchmark-helper.coffee
+++ b/benchmark/benchmark-helper.coffee
@@ -11,12 +11,14 @@ TextMateTheme = require 'text-mate-theme'
 require 'window'
 requireStylesheet "jasmine.css"
 
+# Load TextMate bundles, which specs rely on (but not other packages)
+atom.loadPackages(atom.getAvailableTextMateBundles())
+
 beforeEach ->
-  # don't load user configuration
+  # reset config after each benchmark; don't load or save from/to `config.json`
   window.config = new Config()
   spyOn(config, 'load')
   spyOn(config, 'save')
-  config.assignDefaults()
 
 keymap = new Keymap
 keymap.bindDefaultKeys()
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index ac65c24f0..38bdcea79 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -19,20 +19,17 @@ requireStylesheet "jasmine.css"
 
 require.paths.unshift(require.resolve('fixtures/packages'))
 
-# Temporary solution to load textmate bundles for specs
-window.config = new Config()
-config.assignDefaults()
-config.loadPackages(config.getAvailableTextMateBundles())
+# Load TextMate bundles, which specs rely on (but not other packages)
+atom.loadPackages(atom.getAvailableTextMateBundles())
 
 beforeEach ->
   window.fixturesProject = new Project(require.resolve('fixtures'))
   window.resetTimeouts()
 
-  # don't load or save user configuration
+  # reset config after each spec; don't load or save from/to `config.json`
   window.config = new Config()
   spyOn(config, 'load')
   spyOn(config, 'save')
-  config.assignDefaults()
   config.set "editor.fontSize", 16
 
   # make editor display updates synchronous
diff --git a/src/app/atom.coffee b/src/app/atom.coffee
index f0881d9a4..f37f81c8f 100644
--- a/src/app/atom.coffee
+++ b/src/app/atom.coffee
@@ -10,9 +10,26 @@ _.extend atom,
 
   pendingBrowserProcessCallbacks: {}
 
+  getAvailablePackages: ->
+    allPackageNames = []
+    for packageDirPath in config.packageDirPaths
+      packageNames = fs.list(packageDirPath).map (packagePath) -> fs.base(packagePath)
+      allPackageNames.push(packageNames...)
+    _.unique(allPackageNames)
+
+  getAvailableTextMateBundles: ->
+    @getAvailablePackages().filter (packageName) => @isTextMateBundle(packageName)
+
+  loadPackages: (packageNames=@getAvailablePackages()) ->
+    disabledPackages = config.get("core.disabledPackages") ? []
+
+    console.log packageNames
+    for packageName in packageNames
+      @loadPackage(packageName) unless _.contains(disabledPackages, packageName)
+
   loadPackage: (name) ->
     try
-      if /\.tmbundle$/.test name
+      if @isTextMateBundle(name)
         TextMateBundle.load(name)
       else
         packagePath = require.resolve(name, verifyExistence: false)
@@ -90,3 +107,5 @@ _.extend atom,
       [messageId, callbackIndex] = data.shift()
       @pendingBrowserProcessCallbacks[messageId]?[callbackIndex]?(data...)
 
+  isTextMateBundle: (packageName) ->
+    /(\.|_|-)tmbundle$/.test(packageName)
diff --git a/src/app/config.coffee b/src/app/config.coffee
index ac18ca51b..c70c37a06 100644
--- a/src/app/config.coffee
+++ b/src/app/config.coffee
@@ -13,6 +13,7 @@ require.paths.unshift userPackagesDirPath
 module.exports =
 class Config
   configDirPath: configDirPath
+  packageDirPaths: [userPackagesDirPath, bundledPackagesDirPath]
   settings: null
 
   constructor: ->
@@ -22,38 +23,14 @@ class Config
 
   load: ->
     @loadUserConfig()
-    @loadPackages(@getAvailableTextMateBundles())
-    @loadPackages(@getAvailableAtomPackages())
     @requireUserInitScript()
+    atom.loadPackages()
 
   loadUserConfig: ->
     if fs.exists(configJsonPath)
       userConfig = JSON.parse(fs.read(configJsonPath))
       _.extend(@settings, userConfig)
 
-  assignDefaults: ->
-    @settings ?= {}
-    @setDefaults "core", require('root-view').configDefaults
-    @setDefaults "editor", require('editor').configDefaults
-
-  getAvailablePackages: ->
-    atomPackages = fs.list(bundledPackagesDirPath)
-    userPackages = fs.list(userPackagesDirPath)
-    allPackageNames = atomPackages.concat(userPackages).map (path) -> fs.base(path)
-    _.unique(allPackageNames)
-
-  getAvailableTextMateBundles: ->
-    @getAvailablePackages().filter (packageName) => @isTextMateBundle(packageName)
-
-  getAvailableAtomPackages: ->
-    @getAvailablePackages().filter (packageName) => not @isTextMateBundle(packageName)
-
-  loadPackages: (packageNames) ->
-    disabledPackages = config.get("core.disabledPackages") ? []
-    for packageName in packageNames
-      continue if _.contains disabledPackages, packageName
-      atom.loadPackage(packageName)
-
   get: (keyPath) ->
     keys = @keysForKeyPath(keyPath)
     value = @settings
@@ -116,7 +93,4 @@ class Config
     catch error
       console.error "Failed to load `#{userInitScriptPath}`", error.stack, error
 
-  isTextMateBundle: (packageName) ->
-    /(\.|_)tmbundle$/.test(packageName)
-
 _.extend Config.prototype, EventEmitter