diff --git a/spec/spec-suite.coffee b/spec/spec-suite.coffee
index fd047243d..6ef97bac3 100644
--- a/spec/spec-suite.coffee
+++ b/spec/spec-suite.coffee
@@ -1,10 +1,10 @@
+fs = require 'fs'
+
 require 'window'
 
 measure 'spec suite require time', ->
-  fs = require 'fs'
   fsUtils = require 'fs-utils'
   path = require 'path'
-  _ = require 'underscore'
   require 'spec-helper'
 
   requireSpecs = (directoryPath, specType) ->
@@ -19,20 +19,15 @@ measure 'spec suite require time', ->
   requireSpecs(window.resourcePath)
   setSpecType('core')
 
-  fixturesPackagesPath = fsUtils.resolveOnLoadPath('fixtures/packages')
-  packagePaths = atom.getAvailablePackageNames().map (packageName) -> atom.resolvePackagePath(packageName)
-  packagePaths = _.groupBy packagePaths, (packagePath) ->
-    if packagePath.indexOf("#{fixturesPackagesPath}#{path.sep}") is 0
-      'fixtures'
-    else if packagePath.indexOf("#{window.resourcePath}#{path.sep}") is 0
-      'bundled'
-    else
-      'user'
-
   # Run bundled package specs
-  requireSpecs(packagePath) for packagePath in packagePaths.bundled
-  setSpecType('bundled')
+  if fsUtils.isDirectorySync(config.nodeModulesDirPath)
+    for packageName in fs.readdirSync(config.nodeModulesDirPath)
+      packagePath = path.join(config.nodeModulesDirPath, packageName)
+      requireSpecs(packagePath, 'bundled') if atom.isInternalPackage(packagePath)
+    setSpecType('bundled')
 
   # Run user package specs
-  requireSpecs(packagePath) for packagePath in packagePaths.user
-  setSpecType('user')
+  for packageDirPath in config.userPackageDirPaths when fsUtils.isDirectorySync(packageDirPath)
+    for packageName in fs.readdirSync(packageDirPath)
+      requireSpecs(path.join(packageDirPath, packageName))
+    setSpecType('user')
diff --git a/src/app/config.coffee b/src/app/config.coffee
index ec6abaa57..ecd42faf4 100644
--- a/src/app/config.coffee
+++ b/src/app/config.coffee
@@ -12,8 +12,8 @@ nodeModulesDirPath = path.join(resourcePath, "node_modules")
 bundledThemesDirPath = path.join(resourcePath, "themes")
 userThemesDirPath = path.join(configDirPath, "themes")
 userPackagesDirPath = path.join(configDirPath, "packages")
-packageDirPaths = [userPackagesDirPath]
-packageDirPaths.unshift(path.join(configDirPath, "dev", "packages")) if atom.getLoadSettings().devMode
+userPackageDirPaths = [userPackagesDirPath]
+userPackageDirPaths.unshift(path.join(configDirPath, "dev", "packages")) if atom.getLoadSettings().devMode
 userStoragePath = path.join(configDirPath, "storage")
 
 # Public: Handles all of Atom's configuration details.
@@ -26,8 +26,8 @@ class Config
   themeDirPaths: [userThemesDirPath, bundledThemesDirPath]
   bundledPackageDirPaths: [nodeModulesDirPath]
   nodeModulesDirPath: nodeModulesDirPath
-  packageDirPaths: packageDirPaths
-  userPackagesDirPath: userPackagesDirPath
+  packageDirPaths: _.clone(userPackageDirPaths)
+  userPackageDirPaths: userPackageDirPaths
   userStoragePath: userStoragePath
   lessSearchPaths: [path.join(resourcePath, 'static'), path.join(resourcePath, 'vendor')]
   defaultSettings: null