diff --git a/Rakefile b/Rakefile
index 071121f0b..6f9bf7181 100644
--- a/Rakefile
+++ b/Rakefile
@@ -1,5 +1,4 @@
 ATOM_SRC_PATH = File.dirname(__FILE__)
-DOT_ATOM_PATH = ENV['HOME'] + "/.atom"
 BUILD_DIR = 'atom-build'
 
 require 'erb'
@@ -53,31 +52,11 @@ task :install => [:clean, :build] do
     f.chmod(0755)
   end
 
-  Rake::Task["create-dot-atom"].invoke()
   Rake::Task["clone-default-bundles"].invoke()
 
   puts "\033[32mType `atom` to start Atom! In Atom press `cmd-,` to edit your `~/.atom` directory\033[0m"
 end
 
-desc "Creates .atom file if non exists"
-task "create-dot-atom" do
-  dot_atom_template_path = ATOM_SRC_PATH + "/dot-atom"
-
-  if File.exists?(DOT_ATOM_PATH)
-    user_config = "#{DOT_ATOM_PATH}/user.coffee"
-    old_user_config = "#{DOT_ATOM_PATH}/atom.coffee"
-
-    if File.exists?(old_user_config)
-      `mv #{old_user_config} #{user_config}`
-      puts "\033[32mRenamed #{old_user_config} to #{user_config}\033[0m"
-    end
-  else
-    `mkdir "#{DOT_ATOM_PATH}"`
-    `cp -r "#{dot_atom_template_path}/" "#{DOT_ATOM_PATH}"/`
-    `cp -r "#{ATOM_SRC_PATH}/themes/" "#{DOT_ATOM_PATH}"/themes/`
-  end
-end
-
 desc "Clone default bundles into vendor/bundles directory"
 task "clone-default-bundles" do
   `git submodule --quiet sync`
diff --git a/spec/app/config-spec.coffee b/spec/app/config-spec.coffee
index 351aa4785..7062c4042 100644
--- a/spec/app/config-spec.coffee
+++ b/spec/app/config-spec.coffee
@@ -113,16 +113,23 @@ describe "Config", ->
   describe "initializeConfigDirectory()", ->
     beforeEach ->
       config.configDirPath = '/tmp/dot-atom-dir'
+      expect(fs.exists(config.configDirPath)).toBeFalsy()
 
     afterEach ->
       fs.remove('/tmp/dot-atom-dir') if fs.exists('/tmp/dot-atom-dir')
 
     describe "when the configDirPath doesn't exist", ->
-      it "copies the contents of dot-atom to ~/.atom if it doesn't exist", ->
-        expect(fs.exists(config.configDirPath)).toBeFalsy()
+      it "copies the contents of dot-atom to ~/.atom", ->
         config.initializeConfigDirectory()
         expect(fs.exists(config.configDirPath)).toBeTruthy()
         expect(fs.exists(fs.join(config.configDirPath, 'packages'))).toBeTruthy()
         expect(fs.exists(fs.join(config.configDirPath, 'snippets'))).toBeTruthy()
         expect(fs.exists(fs.join(config.configDirPath, 'themes'))).toBeTruthy()
         expect(fs.isFile(fs.join(config.configDirPath, 'config.cson'))).toBeTruthy()
+
+      it "copies the bundles themes to ~/.atom", ->
+        config.initializeConfigDirectory()
+        expect(fs.isFile(fs.join(config.configDirPath, 'themes/atom-dark-ui/package.cson'))).toBeTruthy()
+        expect(fs.isFile(fs.join(config.configDirPath, 'themes/atom-light-ui/package.cson'))).toBeTruthy()
+        expect(fs.isFile(fs.join(config.configDirPath, 'themes/atom-dark-syntax.css'))).toBeTruthy()
+        expect(fs.isFile(fs.join(config.configDirPath, 'themes/atom-light-syntax.css'))).toBeTruthy()
diff --git a/src/app/config.coffee b/src/app/config.coffee
index cdb9b3182..00af004e0 100644
--- a/src/app/config.coffee
+++ b/src/app/config.coffee
@@ -34,13 +34,21 @@ class Config
     return if fs.exists(@configDirPath)
 
     fs.makeDirectory(@configDirPath)
+
     templateConfigDirPath = fs.resolve(window.resourcePath, 'dot-atom')
+
     onConfigDirFile = (path) =>
       templatePath = fs.join(templateConfigDirPath, path)
       configPath = fs.join(@configDirPath, path)
       fs.write(configPath, fs.read(templatePath))
-    onConfigDirPath = (path) -> true
-    fs.traverseTree(templateConfigDirPath, onConfigDirFile, onConfigDirPath)
+    fs.traverseTree(templateConfigDirPath, onConfigDirFile, (path) -> true)
+
+    configThemeDirPath = fs.join(@configDirPath, 'themes')
+    onThemeDirFile = (path) ->
+      templatePath = fs.join(bundledThemesDirPath, path)
+      configPath = fs.join(configThemeDirPath, path)
+      fs.write(configPath, fs.read(templatePath))
+    fs.traverseTree(bundledThemesDirPath, onThemeDirFile, (path) -> true)
 
   load: ->
     @initializeConfigDirectory()