Do not remove dependency directories entirely

Remove contents only instead. This helps when either of
`node_modules` or `bower_components` is a symlink.

Author: krasnoukhov

CHANGELOG.md

@@ -1,8 +1,10 @@
 master
 ------
 
+* Fix dependencies check for compile command. [#455]
 * Introduce the `silent` configuration value. [#445]
 
+[#455]: https://github.com/thoughtbot/ember-cli-rails/pull/455
 [#445]: https://github.com/thoughtbot/ember-cli-rails/pull/445
 
 0.7.3

lib/ember_cli/shell.rb

@@ -63,14 +63,14 @@ def invalid_ember_dependencies?
     end
 
     def clean_ember_dependencies!
-      ember_dependency_directories.select(&:exist?).each(&:rmtree)
+      ember_dependency_directories.flat_map(&:children).each(&:rmtree)
     end
 
     def ember_dependency_directories
       [
         paths.node_modules,
         paths.bower_components,
-      ]
+      ].select(&:exist?)
     end
 
     def spawn(command)