diff --git a/core/includes/config.inc b/core/includes/config.inc
index 0011533..851479e 100644
--- a/core/includes/config.inc
+++ b/core/includes/config.inc
@@ -32,13 +32,13 @@ function config_install_default_config($type, $name) {
     // If this module defines any ConfigEntity types, then create a manifest file
     // for each of them with a listing of the objects it maintains.
     foreach (config_get_module_config_entities($name) as $entity_type => $entity_info) {
-      $manifest_config = config('manifest.' . $entity_info['config_prefix']);
+      $config_manifest = config_manifest($entity_info['module'], $entity_info['config_prefix']);
       $manifest_data = array();
       foreach ($source_storage->listAll($entity_info['config_prefix']) as $config_name) {
         list(, , $id) = explode('.', $config_name);
         $manifest_data[$id]['name'] = $config_name;
       }
-      $manifest_config->setData($manifest_data)->save();
+      $config_manifest->setData($manifest_data)->save();
     }
 
     $config_changes = array(
@@ -56,25 +56,19 @@ function config_install_default_config($type, $name) {
 }
 
 /**
- * Uninstalls the default configuration of a given extension.
+ * Uninstalls the configuration of a given extension.
  *
  * @param string $type
  *   The extension type; e.g., 'module' or 'theme'.
  * @param string $name
- *   The name of the module or theme to install default configuration for.
+ *   The name of the module or theme to uninstall configuration for.
  */
-function config_uninstall_default_config($type, $name) {
+function config_uninstall_config($type, $name) {
   $storage = drupal_container()->get('config.storage');
   $config_names = $storage->listAll($name . '.');
   foreach ($config_names as $config_name) {
     config($config_name)->delete();
   }
-
-  // If this module defines any ConfigEntity types, then delete the manifest
-  // file for each of them.
-  foreach (config_get_module_config_entities($name) as $entity_type) {
-    config('manifest.' . $entity_info['config_prefix'])->delete();
-  }
 }
 
 /**
@@ -106,6 +100,35 @@ function config($name) {
 }
 
 /**
+ * Retrieves a configuration entity manifest object.
+ *
+ * @TODO An excellent explanation of manifests should live here.
+ *
+ * @param string $module
+ *   The name of the module that provides the configuration entity type.
+ * @param string $config_prefix
+ *   The config prefix used by the configuration entity type.
+ *
+ * @return Drupal\Core\Config\Config
+ *   A configuration object.
+ */
+function config_manifest($module, $config_prefix) {
+  return config(config_manifest_name($module, $config_prefix));
+}
+
+/**
+ * Assembles a configuration entity manifest name.
+ *
+ * @param string $module
+ *   The name of the module that provides the configuration entity type.
+ * @param string $config_prefix
+ *   The config prefix used by the configuration entity type.
+ */
+function config_manifest_name($module, $config_prefix) {
+  return $module . '.manifest.' . $config_prefix;
+}
+
+/**
  * Returns a list of differences between configuration storages.
  *
  * @param Drupal\Core\Config\StorageInterface $source_storage
@@ -125,12 +148,21 @@ function config_sync_get_changes(StorageInterface $source_storage, StorageInterf
   // target storage, generate an array of the objects, and compare them.
   $source_config_data = array();
   $target_config_data = array();
-  foreach ($source_storage->listAll('manifest') as $name) {
-    if ($source_manifest_data = $source_storage->read($name)) {
+  foreach (config_get_module_config_entities() as $entity_info) {
+    $manifest_name = config_manifest_name($entity_info['module'], $entity_info['config_prefix']);
+    $source_manifest_data = $source_storage->read($manifest_name);
+    // Empty arrays need to be merged as this would indicate that all config
+    // entities of this type are to be removed.
+    if ($source_manifest_data !== FALSE) {
       $source_config_data = array_merge($source_config_data, $source_manifest_data);
     }
+    else {
+      // No manifest exists in the source directory. Therefore we can not make
+      // any assumptions about what the user wants to do.
+      continue;
+    }
 
-    if ($target_manifest_data = $target_storage->read($name)) {
+    if ($target_manifest_data = $target_storage->read($manifest_name)) {
       $target_config_data = array_merge($target_config_data, $target_manifest_data);
     }
   }
@@ -150,8 +182,9 @@ function config_sync_get_changes(StorageInterface $source_storage, StorageInterf
   }
 
   foreach (array_intersect($source_storage->listAll(), $target_storage->listAll()) as $name) {
-    // Ignore manifest files
-    if (substr($name, 0, 9) != 'manifest.') {
+    // Ignore manifest files which have the pattern
+    // module.manifest.config_entity.
+    if (!preg_match('/^[^.]+\.manifest\./', $name)) {
       $source_config_data = $source_storage->read($name);
       $target_config_data = $target_storage->read($name);
       if ($source_config_data !== $target_config_data) {
@@ -279,21 +312,21 @@ function config_import_invoke_owner(array $config_changes, StorageInterface $sou
 }
 
 /**
- * Return a list of all config entity types provided by a module.
+ * Returns a list of config entity types.
  *
  * @param string $module
- *   The name of the module possibly providing config entities.
+ *   (optional) The name of the module providing config entities.
  *
  * @return array
  *   An associative array containing the entity info for any config entities
  *   provided by the requested module, keyed by the entity type.
  */
-function config_get_module_config_entities($module) {
+function config_get_module_config_entities($module = NULL) {
   // While this is a lot of work to generate, it's not worth static caching
   // since this function is only called at install/uninstall, and only
   // once per module.
   $info = entity_get_info();
   return array_filter($info, function($entity_info) use ($module) {
-    return ($entity_info['module'] == $module) && is_subclass_of($entity_info['class'], 'Drupal\Core\Config\Entity\ConfigEntityInterface');
+    return ($entity_info['module'] == $module || $module === NULL) && is_subclass_of($entity_info['class'], 'Drupal\Core\Config\Entity\ConfigEntityInterface');
   });
 }
diff --git a/core/includes/module.inc b/core/includes/module.inc
index 9be96cd..e9a8652 100644
--- a/core/includes/module.inc
+++ b/core/includes/module.inc
@@ -720,7 +720,7 @@ function module_uninstall($module_list = array(), $uninstall_dependents = TRUE)
     drupal_uninstall_schema($module);
 
     // Remove all configuration belonging to the module.
-    config_uninstall_default_config('module', $module);
+    config_uninstall_config('module', $module);
 
     watchdog('system', '%module module uninstalled.', array('%module' => $module), WATCHDOG_INFO);
     $schema_store->delete($module);
diff --git a/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php b/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php
index 7f60f9d..109a96b 100644
--- a/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php
+++ b/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php
@@ -265,7 +265,7 @@ public function delete(array $entities) {
       $config->delete();
 
       // Remove the entity from the manifest file.
-      config('manifest.' . $this->entityInfo['config_prefix'])
+      config_manifest($this->entityInfo['module'], $this->entityInfo['config_prefix'])
         ->clear($entity->id())
         ->save();
     }
@@ -339,7 +339,7 @@ public function save(EntityInterface $entity) {
     }
 
     // Add this entity to the manifest file if necessary.
-    $config = config('manifest.' . $this->entityInfo['config_prefix']);
+    $config = config_manifest($this->entityInfo['module'], $this->entityInfo['config_prefix']);
     $manifest = $config->get();
     if (!in_array($this->getConfigPrefix() . $entity->id(), $manifest)) {
       $manifest[$entity->id()] = array(
diff --git a/core/modules/config/lib/Drupal/config/Tests/ConfigImportTest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigImportTest.php
index 95089f7..db8c2f2 100644
--- a/core/modules/config/lib/Drupal/config/Tests/ConfigImportTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigImportTest.php
@@ -66,7 +66,7 @@ function testDeleted() {
     $this->assertIdentical($config->get('id'), 'default');
 
     // Create an empty manifest to delete the configuration object.
-    $staging->write('manifest.config_test.dynamic', array());
+    $staging->write(config_manifest_name('config_test','config_test.dynamic'), array());
     // Import.
     config_import();
 
@@ -112,9 +112,9 @@ function testNew() {
     $staging->write($dynamic_name, $original_dynamic_data);
 
     // Create manifest for new config entity.
-    $manifest_data = config('manifest.config_test.dynamic')->get();
+    $manifest_data = config_manifest('config_test', 'config_test.dynamic')->get();
     $manifest_data[$original_dynamic_data['id']]['name'] = 'config_test.dynamic.' . $original_dynamic_data['id'];
-    $staging->write('manifest.config_test.dynamic', $manifest_data);
+    $staging->write(config_manifest_name('config_test', 'config_test.dynamic'), $manifest_data);
 
     $this->assertIdentical($staging->exists($dynamic_name), TRUE, $dynamic_name . ' found.');
 
@@ -160,8 +160,8 @@ function testUpdated() {
     $original_dynamic_data['label'] = 'Updated';
     $staging->write($dynamic_name, $original_dynamic_data);
     // Create manifest for updated config entity.
-    $manifest_data = config('manifest.config_test.dynamic')->get();
-    $staging->write('manifest.config_test.dynamic', $manifest_data);
+    $manifest_data = config_manifest('config_test', 'config_test.dynamic')->get();
+    $staging->write(config_manifest_name('config_test', 'config_test.dynamic'), $manifest_data);
 
     // Verify the active configuration still returns the default values.
     $config = config($name);
diff --git a/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
index dd24224..18e348a 100644
--- a/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
@@ -64,9 +64,9 @@ function testImport() {
     $staging->write($dynamic_name, $original_dynamic_data);
 
     // Create manifest for new config entity.
-    $manifest_data = config('manifest.config_test.dynamic')->get();
+    $manifest_data = config_manifest('config_test', 'config_test.dynamic')->get();
     $manifest_data[$original_dynamic_data['id']]['name'] = 'config_test.dynamic.' . $original_dynamic_data['id'];
-    $staging->write('manifest.config_test.dynamic', $manifest_data);
+    $staging->write(config_manifest_name('config_test', 'config_test.dynamic'), $manifest_data);
 
     $this->assertIdentical($staging->exists($dynamic_name), TRUE, $dynamic_name . ' found.');
 
diff --git a/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php
index b549119..6663c7c 100644
--- a/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php
@@ -7,12 +7,12 @@
 
 namespace Drupal\config\Tests;
 
-use Drupal\simpletest\DrupalUnitTestBase;
+use Drupal\simpletest\WebTestBase;
 
 /**
- * Tests installation of configuration objects in installation functionality.
+ * Tests install/uninstall of config objects during module install/uninstall.
  */
-class ConfigInstallTest extends DrupalUnitTestBase {
+class ConfigInstallTest extends WebTestBase {
   public static function getInfo() {
     return array(
       'name' => 'Installation functionality',
@@ -30,26 +30,31 @@ function setUp() {
   }
 
   /**
-   * Tests module installation.
+   * Tests module install and uninstall.
    */
-  function testModuleInstallation() {
+  function testModuleInstallAndUninstall() {
     $default_config = 'config_test.system';
     $default_configuration_entity = 'config_test.dynamic.default';
+    $default_configuration_entity_manifest = config_manifest_name('config_test', 'config_test.dynamic');
 
     // Verify that default module config does not exist before installation yet.
     $config = config($default_config);
     $this->assertIdentical($config->isNew(), TRUE);
     $config = config($default_configuration_entity);
     $this->assertIdentical($config->isNew(), TRUE);
+    $config = config($default_configuration_entity_manifest);
+    $this->assertIdentical($config->isNew(), TRUE);
 
     // Install the test module.
-    $this->enableModules(array('config_test'));
+    module_enable(array('config_test'));
 
     // Verify that default module config exists.
     $config = config($default_config);
     $this->assertIdentical($config->isNew(), FALSE);
     $config = config($default_configuration_entity);
     $this->assertIdentical($config->isNew(), FALSE);
+    $config = config($default_configuration_entity_manifest);
+    $this->assertIdentical($config->isNew(), FALSE);
 
     // Verify that configuration import callback was invoked for the dynamic
     // configuration entity.
@@ -63,5 +68,23 @@ function testModuleInstallation() {
     $this->assertFalse(isset($GLOBALS['hook_config_test']['update']));
     $this->assertFalse(isset($GLOBALS['hook_config_test']['predelete']));
     $this->assertFalse(isset($GLOBALS['hook_config_test']['delete']));
+
+    module_disable(array('config_test'));
+    // Verify that default module config exists.
+    $config = config($default_config);
+    $this->assertIdentical($config->isNew(), FALSE);
+    $config = config($default_configuration_entity);
+    $this->assertIdentical($config->isNew(), FALSE);
+    $config = config($default_configuration_entity_manifest);
+    $this->assertIdentical($config->isNew(), FALSE);
+
+    module_uninstall(array('config_test'));
+    // Verify the configuration no longer exists.
+    $config = config($default_config);
+    $this->assertIdentical($config->isNew(), TRUE);
+    $config = config($default_configuration_entity);
+    $this->assertIdentical($config->isNew(), TRUE);
+    $config = config($default_configuration_entity_manifest);
+    $this->assertIdentical($config->isNew(), TRUE);
   }
 }