diff --git includes/entity.inc includes/entity.inc
index 8ba2e70..80af87e 100644
--- includes/entity.inc
+++ includes/entity.inc
@@ -126,7 +126,6 @@ class DrupalDefaultEntityController implements DrupalEntityControllerInterface {
         ->execute()
         ->fetchAllAssoc($this->idKey);
     }
-
     // Pass all entities loaded from the database through $this->attachLoad(),
     // which attaches fields (if supported by the entity type) and calls the
     // entity type specific load callback, for example hook_node_load().
diff --git includes/filetransfer/filetransfer.inc includes/filetransfer/filetransfer.inc
index 9efe66a..1a4f7f4 100644
--- includes/filetransfer/filetransfer.inc
+++ includes/filetransfer/filetransfer.inc
@@ -57,12 +57,18 @@ abstract class FileTransfer {
    *   The source path.
    * @param $destination
    *   The destination path.
+   * @param copyInto
+   *   If the contents of $source should be coppied into $destination
+   *   or if $source itself should be coppied into $destination.
+   *   If this is NULL, then a trailing slash in $source will indicate
+   *   that the contents of $source should be coppied.
    */
-  public final function copyDirectory($source, $destination) {
+  public final function copyDirectory($source, $destination, $copyInto = NULL) {
+    $copyInto = $copyInto ? $copyInto : (substr($source, -1) == '/');
     $source = $this->sanitizePath($source);
     $destination = $this->fixRemotePath($destination);
     $this->checkPath($destination);
-    $this->copyDirectoryJailed($source, $destination);
+    $this->copyDirectoryJailed($source, $destination, $copyInto);
   }
 
   /**
@@ -171,16 +177,15 @@ abstract class FileTransfer {
   }
 
   /**
-  * Changes backslahes to slashes, also removes a trailing slash.
-  *
-  * @param string $path
-  * @return string
-  */
+   * Changes backslahes to slashes and removes a trailing slash.
+   *
+   * @param string $path
+   * @return string;
+   */
   function sanitizePath($path) {
+    substr($path, -1, 0) == '/' && $path = substr($path, 0, 1);
+
     $path = str_replace('\\', '/', $path); // Windows path sanitiation.
-    if (substr($path, -1) == '/') {
-      $path = substr($path, 0, -1);
-    }
     return $path;
   }
 
@@ -193,16 +198,32 @@ abstract class FileTransfer {
    *   The source path.
    * @param $destination
    *   The destination path.
+   * @param copyInto
+   *   If the contents of $source should be coppied into $destination
+   *   or if $source itself should be coppied into $destination. Defaults to FALSE
    */
-  protected function copyDirectoryJailed($source, $destination) {
-    if ($this->isDirectory($destination)) {
-      $destination = $destination . '/' . basename($source);
+  protected function copyDirectoryJailed($source, $destination, $copyInto = FALSE) {
+    // If $source ends in "/", replace the contents of $destination with the contents of $source.
+    if ($copyInto) {
+      if (!$this->isDirectory($destination)) {
+        throw new FileTransferException('Cannot copy the contents of %source to %destination.  %destination does not exist.', NULL, array('%source' => $source, '%destination' => $destination));
+      }
+    }
+    else {
+      // If the destination exists, create a new directory inside of it and
+      // change the destination.
+      if ($this->isDirectory($destination)) {
+        $destination = $destination . '/' . basename($source);
+      }
+      $this->createDirectory($destination);
     }
-    $this->createDirectory($destination);
+
     foreach (new RecursiveIteratorIterator(new RecursiveDirectoryIterator($source), RecursiveIteratorIterator::SELF_FIRST) as $filename => $file) {
       $relative_path = substr($filename, strlen($source));
       if ($file->isDir()) {
-        $this->createDirectory($destination . $relative_path);
+        if (!$this->isDirectory($destination . $relative_path)) {
+          $this->createDirectory($destination . $relative_path);
+        }
       }
       else {
         $this->copyFile($file->getPathName(), $destination . $relative_path);
diff --git includes/updater.inc includes/updater.inc
index 307c305..0693fd6 100644
--- includes/updater.inc
+++ includes/updater.inc
@@ -54,17 +54,28 @@ interface DrupalUpdaterInterface {
 
   /**
    * Actions to run after an install has occurred.
+   * 
+   * @param FileTransfer $filetransfer
+   * @param array $args
+   * @return void
    */
-  public function postInstall();
+  public function postInstall($filetransfer, $args);
 
   /**
    * Actions to run after an update has occurred.
+   * 
+   * @param FileTransfer $filetransfer
+   * @param array $args
+   * @return void
    */
-  public function postUpdate();
+  public function postUpdate($filetransfer, $args);
+
+  public function install(&$filetransfer, $options = array());
+  public function update(&$filetransfer, $options = array());
 }
 
 /**
- * Base class for Updaters used in Drupal.
+ * Base class for Updaters used in Drupal for contributed projects.
  */
 class Updater {
 
@@ -91,12 +102,12 @@ class Updater {
    * @return Updater
    */
   public static function factory($source) {
-    if (is_dir($source)) {
-      $updater = self::getUpdaterFromDirectory($source);
-    }
-    else {
-      throw new UpdaterException(t('Unable to determine the type of the source directory.'));
+    
+    if (!is_dir($source)) {
+      throw new UpdaterException(t('Source directory (%directory) does not exist', array('%directory' => $source)));
     }
+    
+    $updater = self::getUpdaterFromDirectory($source);
     return new $updater($source);
   }
 
@@ -117,7 +128,7 @@ class Updater {
         return $class;
       }
     }
-    throw new UpdaterException(t('Cannot determine the type of project.'));
+    throw new UpdaterException(t('Unable to determine the type of the source directory.'));
   }
 
   /**
@@ -190,6 +201,7 @@ class Updater {
       'make_backup' => FALSE,
       'install_dir' => $this->getInstallDirectory(),
       'backup_dir'  => $this->getBackupDir(),
+      'replace_within_install_directory' => FALSE,
     );
     return array_merge($args, $overrides);
   }
@@ -224,23 +236,32 @@ class Updater {
       // Make sure the installation parent directory exists and is writable.
       $this->prepareInstallDirectory($filetransfer, $args['install_dir']);
 
-      // Note: If the project is installed in sites/all, it will not be
-      // deleted. It will be installed in sites/default as that will override
-      // the sites/all reference and not break other sites which are using it.
-      if (is_dir($args['install_dir'] . '/' . $this->name)) {
-        // Remove the existing installed file.
-        $filetransfer->removeDirectory($args['install_dir'] . '/' . $this->name);
+      $source = $this->source;
+      if (TRUE === $args['replace_within_install_directory']) {
+        // This will copy the contents of the directory, not the directory itself.
+        if (substr($source, -1) != '/') {
+          $source .= '/';
+        }
+      }
+      else {
+        if (substr($source, -1) == '/') {
+          $source = substr($source, 0, -1);
+        }
+        // Note: If the project is installed in sites/all, it will not be
+        // deleted. It will be installed in sites/default as that will override
+        // the sites/all reference and not break other sites which are using it.
+        if (is_dir($args['install_dir'] . '/' . $this->name)) {
+          // Remove the existing installed file.
+          $filetransfer->removeDirectory($args['install_dir'] . '/' . $this->name);
+        }
       }
 
       // Copy the directory in place.
-      $filetransfer->copyDirectory($this->source, $args['install_dir']);
-
-      // Make sure what we just installed is readable by the web server.
-      $this->makeWorldReadable($filetransfer, $args['install_dir'] . '/' . $this->name);
+      $filetransfer->copyDirectory($source, $args['install_dir']);
 
       // Run the updates.
       // @TODO: decide if we want to implement this.
-      $this->postUpdate();
+      $this->postUpdate($filetransfer, $args);
 
       // For now, just return a list of links of things to do.
       return $this->postUpdateTasks();
@@ -272,12 +293,9 @@ class Updater {
       // Copy the directory in place.
       $filetransfer->copyDirectory($this->source, $args['install_dir']);
 
-      // Make sure what we just installed is readable by the web server.
-      $this->makeWorldReadable($filetransfer, $args['install_dir'] . '/' . $this->name);
-
       // Potentially enable something?
       // @TODO: decide if we want to implement this.
-      $this->postInstall();
+      $this->postInstall($filetransfer, $args);
       // For now, just return a list of links of things to do.
       return $this->postInstallTasks();
     }
@@ -365,13 +383,17 @@ class Updater {
   /**
    * Perform actions after new code is updated.
    */
-  public function postUpdate() {
+  public function postUpdate($filetransfer, $args) {
+    // Make sure what we just installed is readable by the web server.
+    $this->makeWorldReadable($filetransfer, $args['install_dir'] . '/' . $this->name);
   }
 
   /**
    * Perform actions after installation.
    */
-  public function postInstall() {
+  public function postInstall($filetransfer, $args) {
+    // Make sure what we just installed is readable by the web server.
+    $this->makeWorldReadable($filetransfer, $args['install_dir'] . '/' . $this->name);    
   }
 
   /**
diff --git modules/field/field.attach.inc modules/field/field.attach.inc
index 50dbe05..59e039c 100644
--- modules/field/field.attach.inc
+++ modules/field/field.attach.inc
@@ -834,6 +834,7 @@ function field_attach_insert($obj_type, $object) {
   // Collect the storage backends used by the remaining fields in the objects.
   $storages = array();
   foreach (field_info_instances($obj_type, $bundle) as $instance) {
+    dpr($instance);
     $field = field_info_field_by_id($instance['field_id']);
     $field_id = $field['id'];
     $field_name = $field['field_name'];
diff --git modules/simpletest/drupal_web_test_case.php modules/simpletest/drupal_web_test_case.php
index 03b03eb..5a89b0a 100644
--- modules/simpletest/drupal_web_test_case.php
+++ modules/simpletest/drupal_web_test_case.php
@@ -1048,8 +1048,14 @@ class DrupalWebTestCase extends DrupalTestCase {
 
     // Create test directory ahead of installation so fatal errors and debug
     // information can be logged during installation process.
-    $directory = $this->originalFileDirectory . '/simpletest/' . substr($db_prefix, 10);
+    // Use temporary files directory with the same prefix as the database.
+    $public_files_directory  = $this->originalFileDirectory . '/simpletest/' . substr($db_prefix, 10);
+    $private_files_directory = $public_files_directory . '/private';
+
+    // Create the directories
+    $directory = file_directory_path('public');
     file_prepare_directory($directory, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS);
+    file_prepare_directory($private_files_directory, FILE_CREATE_DIRECTORY);
 
     // Log fatal errors.
     ini_set('log_errors', 1);
@@ -1111,21 +1117,12 @@ class DrupalWebTestCase extends DrupalTestCase {
     unset($GLOBALS['conf']['language_default']);
     $language = language_default();
 
-    // Use the test mail class instead of the default mail handler class.
-    variable_set('mail_system', array('default-system' => 'TestingMailSystem'));
-
-    // Use temporary files directory with the same prefix as the database.
-    $public_files_directory  = $this->originalFileDirectory . '/' . $db_prefix;
-    $private_files_directory = $public_files_directory . '/private';
-
     // Set path variables
     variable_set('file_public_path', $public_files_directory);
     variable_set('file_private_path', $private_files_directory);
 
-    // Create the directories
-    $directory = file_directory_path('public');
-    file_prepare_directory($directory, FILE_CREATE_DIRECTORY | FILE_MODIFY_PERMISSIONS);
-    file_prepare_directory($private_files_directory, FILE_CREATE_DIRECTORY);
+    // Use the test mail class instead of the default mail handler class.
+    variable_set('mail_system', array('default-system' => 'TestingMailSystem'));
 
     drupal_set_time_limit($this->timeLimit);
   }
@@ -1180,7 +1177,7 @@ class DrupalWebTestCase extends DrupalTestCase {
 
     if (preg_match('/simpletest\d+/', $db_prefix)) {
       // Delete temporary files directory.
-      file_unmanaged_delete_recursive($this->originalFileDirectory . '/' . $db_prefix);
+      file_unmanaged_delete_recursive($this->originalFileDirectory . '/simpletest/' . substr($db_prefix, 10));
 
       // Remove all prefixed tables (all the tables in the schema).
       $schema = drupal_get_schema(NULL, TRUE);
diff --git modules/simpletest/simpletest.module modules/simpletest/simpletest.module
index 76f0396..8f75a98 100644
--- modules/simpletest/simpletest.module
+++ modules/simpletest/simpletest.module
@@ -444,11 +444,11 @@ function simpletest_clean_database() {
  * Find all leftover temporary directories and remove them.
  */
 function simpletest_clean_temporary_directories() {
-  $files = scandir('public://');
+  $files = scandir('public://simpletest');
   $count = 0;
   foreach ($files as $file) {
-    $path = 'public://' . $file;
-    if (is_dir($path) && preg_match('/^simpletest\d+/', $file)) {
+    $path = 'public://simpletest/' . $file;
+    if (is_dir($path) && is_numeric($file)) {
       file_unmanaged_delete_recursive($path);
       $count++;
     }
diff --git modules/simpletest/tests/filetransfer.test modules/simpletest/tests/filetransfer.test
index c0a5657..ca4cb89 100644
--- modules/simpletest/tests/filetransfer.test
+++ modules/simpletest/tests/filetransfer.test
@@ -87,10 +87,41 @@ class FileTranferTest extends DrupalWebTestCase {
     }
     $this->assertTrue($gotit, 'Was able to copy a directory inside of the jailed area');
   }
+
+  function testFileCopy() {
+    $source = $this->_buildFakeModule();
+    $destination = DRUPAL_ROOT . '/'. file_directory_path();
+    $this->testConnection->shouldIsDirectoryReturnTrue = TRUE;
+
+    // Try it with no trailing slash.
+    // This should try to create $destination/fake/fake
+    $this->testConnection->copyDirectory($source, $destination . '/fake');
+    $commands = $this->testConnection->connection->flushCommands();
+    $fail = TRUE;
+    foreach ($commands as $command) {
+      if (preg_match('/mkdir/', $command)) {
+        $fail = FALSE;
+      }
+    }
+
+    $this->assertFalse($fail, 'Coppied source directory to destination');
+
+    $this->testConnection->copyDirectory($source . '/', $destination . '/fake');
+    $commands = $this->testConnection->connection->flushCommands();
+    $fail = FALSE;
+    foreach ($commands as $command) {
+      if (preg_match('/mkdir/', $command)) {
+        $this->fail('Copy into should not have created any directories');
+        $fail = TRUE;
+      }
+    }
+    $this->assertFalse($fail, 'Coppied contents of source directory into destination');
+  }
+
 }
 
 /**
- * Mock FileTransfer object for test case.
+ * Mock FileTransfer obdject for test case.
  */
 class TestFileTransfer extends FileTransfer {
   protected $host = NULL;
diff --git modules/system/system.module modules/system/system.module
index e63d5a6..7e22bf8 100644
--- modules/system/system.module
+++ modules/system/system.module
@@ -1620,6 +1620,11 @@ function system_authorized_batch_process() {
  */
 function system_updater_info() {
   return array(
+    'core' => array(
+      'class' => 'CoreUpdater',
+      'name' => t('Update Core'),
+      'weight' => -100,
+    ),
     'module' => array(
       'class' => 'ModuleUpdater',
       'name' => t('Update modules'),
diff --git modules/system/system.updater.inc modules/system/system.updater.inc
index b5f1d15..9e274c9 100644
--- modules/system/system.updater.inc
+++ modules/system/system.updater.inc
@@ -6,7 +6,7 @@
  * Subclasses of the Updater class to update Drupal core knows how to update.
  * At this time, only modules and themes are supported.
  */
- 
+
 /**
  * Class for updating modules using FileTransfer classes via authorize.php.
  */
@@ -67,14 +67,14 @@ class ModuleUpdater extends Updater implements DrupalUpdaterInterface {
 
   public function postInstallTasks() {
     return array(
-      l(t('Enable newly added modules in !project', array('!project' => $this->title)), 'admin/config/modules'),
+    l(t('Enable newly added modules in !project', array('!project' => $this->title)), 'admin/config/modules'),
     );
   }
 
   public function postUpdateTasks() {
     // @todo: If there are schema updates.
     return array(
-      l(t('Run database updates for !project', array('!project' => $this->title)), 'update.php'),
+    l(t('Run database updates for !project', array('!project' => $this->title)), 'update.php'),
     );
   }
 
@@ -114,7 +114,8 @@ class ThemeUpdater extends Updater implements DrupalUpdaterInterface {
     return (bool) drupal_get_path('theme', $project_name);
   }
 
-  public function postInstall() {
+  public function postInstall($filetransfer, $args) {
+    parent::postInstall($filetransfer, $args);
     // Update the system table.
     clearstatcache();
     drupal_static_reset('_system_rebuild_theme_data');
@@ -122,15 +123,64 @@ class ThemeUpdater extends Updater implements DrupalUpdaterInterface {
 
     // Active the theme
     db_update('system')
-      ->fields(array('status' => 1))
-      ->condition('type', 'theme')
-      ->condition('name', $this->name)
-      ->execute();
+    ->fields(array('status' => 1))
+    ->condition('type', 'theme')
+    ->condition('name', $this->name)
+    ->execute();
+  }
+
+  public function postInstallTasks() {
+    return array(
+    l(t('Set the !project theme as default', array('!project' => $this->title)), 'admin/appearance'),
+    );
+  }
+}
+
+/**
+ * Class for updating themes using FileTransfer classes via authorize.php.
+ */
+class CoreUpdater extends Updater implements DrupalUpdaterInterface {
+
+  public function getInstallDirectory() {
+    return DRUPAL_ROOT;
+  }
+
+  protected function getInstallArgs($overrides = array()) {
+    $overrides += array('replace_within_install_directory' => TRUE);
+    return parent::getInstallArgs($overrides);
+  }
+
+  public function isInstalled() {
+    return TRUE;
   }
-  
+
+  static function canUpdateDirectory($directory) {
+    return is_file($directory . '/robots.txt');
+  }
+
+  /**
+   * (non-PHPdoc)
+   * @see sites/default/private/temp/update-extraction/drupal/includes/Updater#postInstall()
+   */
+  public function postInstall($filetransfer, $args) {
+    // Pray.
+  }
+
   public function postInstallTasks() {
     return array(
-      l(t('Set the !project theme as default', array('!project' => $this->title)), 'admin/appearance'),
+    l(t('Set the !project theme as default', array('!project' => $this->title)), 'admin/appearance'),
     );
   }
+
+  static function getProjectName($directory) {
+    return 'drupal';
+  }
+
+  static function getProjectTitle() {
+    return 'Drupal';
+  }
+
+  function postUpdate($filetransfer, $args) {
+    // Pray
+  }
 }
diff --git modules/update/update.authorize.inc modules/update/update.authorize.inc
index 023f3f5..0a42e75 100644
--- modules/update/update.authorize.inc
+++ modules/update/update.authorize.inc
@@ -44,7 +44,7 @@ function update_authorize_run_update($filetransfer, $projects) {
     'finished' => 'update_authorize_update_batch_finished',
     'file' => drupal_get_path('module', 'update') . '/update.authorize.inc',
   );
-
+  
   batch_set($batch);
   // Invoke the batch via authorize.php.
   system_authorized_batch_process();
diff --git modules/update/update.manager.inc modules/update/update.manager.inc
index 649562a..5d7f1f0 100644
--- modules/update/update.manager.inc
+++ modules/update/update.manager.inc
@@ -35,7 +35,7 @@
  * sets up a batch to copy each extracted update from the temporary location
  * into the live web root.
  */
- 
+
 /**
  * @defgroup update_manager_update Update manager for updating existing code.
  * @{
@@ -157,30 +157,14 @@ function update_manager_update_form($form, $form_state = array(), $context) {
 
     $entry['#attributes'] = array('class' => array('update-' . $type));
 
-    // Drupal core needs to be upgraded manually.
-    $needs_manual = $project['project_type'] == 'core';
-
-    if ($needs_manual) {
-      // Since it won't be tableselect, #weight will add an extra column to the
-      // table if it's defined, so just unset it. The order doesn't matter that
-      // much in the manual updates table, anyway.
-      unset($entry['#weight']);
-    }
-    else {
-      $form['project_downloads'][$name] = array(
-        '#type' => 'value',
-        '#value' => $recommended_release['download_link'],
-      );
-    }
-
     // Based on what kind of project this is, save the entry into the
     // appropriate subarray.
     switch ($project['project_type']) {
       case 'core':
         // Core needs manual updates at this time.
-        $projects['manual'][$name] = $entry;
-        break;
-        
+        //$projects['manual'][$name] = $entry;
+       // break;
+
       case 'module':
       case 'theme':
         $projects['enabled'][$name] = $entry;
@@ -241,17 +225,6 @@ function update_manager_update_form($form, $form_state = array(), $context) {
     $form['#validate'][] = 'update_manager_update_form_validate';
   }
 
-  if (!empty($projects['manual'])) {
-    $prefix = '<h2>' . t('Manual updates required') . '</h2>';
-    $prefix .= '<p>' . t('Updates of Drupal core are not supported at this time.') . '</p>';
-    $form['manual_updates'] = array(
-      '#type' => 'markup',
-      '#markup' => theme('table', array('header' => $headers, 'rows' => $projects['manual'])),
-      '#prefix' => $prefix,
-      '#weight' => 20,
-    );
-  }
-
   return $form;
 }
 
@@ -420,11 +393,23 @@ function update_manager_confirm_update_form_submit($form, &$form_state) {
     $directory = _update_manager_extract_directory();
 
     $projects = $_SESSION['update_manager_update_projects'];
-    unset($_SESSION['update_manager_update_projects']);
+
+    //@todo: Put this back
+    //unset($_SESSION['update_manager_update_projects']);
+
+    //@todo:Drupal core doesn't have "drupal" as dir name :(  I guess we should start looking in the tarballs and getting the first directory we see.
+    // Or change the package format to have a spec file.
 
     foreach ($projects as $project => $url) {
       $project_location = $directory . '/' . $project;
-      $updater = Updater::factory($project_location);
+
+      try {
+        $updater = Updater::factory($project_location);
+      } catch(Exception $e) {
+        form_set_error('submit', $e->getMessage());
+        return;
+      }
+
       $project_real_location = drupal_realpath($project_location);
       $updates[] = array(
         'project' => $project,
@@ -432,7 +417,6 @@ function update_manager_confirm_update_form_submit($form, &$form_state) {
         'local_url' => $project_real_location,
       );
     }
-
     // If the owner of the last directory we extracted is the same as the
     // owner of our configuration directory (e.g. sites/default) where we're
     // trying to install the code, there's no need to prompt for FTP/SSH
@@ -565,7 +549,7 @@ function update_manager_install_form_submit($form, &$form_state) {
     // @todo: find out if the module is already instealled, if so, throw an error.
     $local_cache = $finfo->uri;
   }
-  
+
   $directory = _update_manager_extract_directory();
   try {
     $archive = update_manager_archive_extract($local_cache, $directory);
@@ -601,12 +585,12 @@ function update_manager_install_form_submit($form, &$form_state) {
   if (!$project_title) {
     form_set_error($field, t('Unable to determine %project name.', array('%project' => $project)));
   }
-  
+
   if ($updater->isInstalled()) {
     form_set_error($field, t('%project is already installed.', array('%project' => $project_title)));
     return;
   }
-  
+
   $project_real_location = drupal_realpath($project_location);
   $arguments = array(
     'project' => $project,
@@ -733,7 +717,7 @@ function update_manager_file_get($url) {
   if (!file_exists($cache_directory)) {
     mkdir($cache_directory);
   }
-  
+
   if (!file_exists($local)) {
     return system_retrieve_file($url, $local);
   }
diff --git sites/all/modules/README.txt sites/all/modules/README.txt
deleted file mode 100644
index f503d7d..0000000
--- sites/all/modules/README.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-// $Id: README.txt,v 1.1 2009-01-22 04:33:38 webchick Exp $
-
-This directory should be used to place downloaded and custom modules
-which are common to all sites. This will allow you to more easily
-update Drupal core files.
diff --git sites/default/default.settings.php sites/default/default.settings.php
old mode 100644
new mode 100755