diff --git includes/actions.inc includes/actions.inc
index 77734fe..56c94a4 100644
--- includes/actions.inc
+++ includes/actions.inc
@@ -197,7 +197,7 @@ function actions_get_all_actions() {
 }
 
 /**
- * Creates an associative array keyed by md5 hashes of function names or IDs.
+ * Creates an associative array keyed by hashes of function names or IDs.
  *
  * Hashes are used to prevent actual function names from going out into HTML
  * forms and coming back.
@@ -207,14 +207,14 @@ function actions_get_all_actions() {
  *   and associative arrays with keys 'label', 'type', etc. as values.
  *   This is usually the output of actions_list() or actions_get_all_actions().
  * @return
- *   An associative array whose keys are md5 hashes of the input array keys, and
+ *   An associative array whose keys are hashes of the input array keys, and
  *   whose corresponding values are associative arrays with components
  *   'callback', 'label', 'type', and 'configurable' from the input array.
  */
 function actions_actions_map($actions) {
   $actions_map = array();
   foreach ($actions as $callback => $array) {
-    $key = md5($callback);
+    $key = drupal_hash_base64($callback);
     $actions_map[$key]['callback']     = isset($array['callback']) ? $array['callback'] : $callback;
     $actions_map[$key]['label']        = $array['label'];
     $actions_map[$key]['type']         = $array['type'];
@@ -224,12 +224,12 @@ function actions_actions_map($actions) {
 }
 
 /**
- * Given an md5 hash of an action array key, returns the key (function or ID).
+ * Given a hash of an action array key, returns the key (function or ID).
  *
  * Faster than actions_actions_map() when you only need the function name or ID.
  *
  * @param $hash
- *   MD5 hash of a function name or action ID array key. The array key
+ *   Hash of a function name or action ID array key. The array key
  *   is a key into the return value of actions_list() (array key is the action
  *   function name) or actions_get_all_actions() (array key is the action ID).
  * @return
@@ -239,13 +239,20 @@ function actions_function_lookup($hash) {
   // Check for a function name match.
   $actions_list = actions_list();
   foreach ($actions_list as $function => $array) {
-    if (md5($function) == $hash) {
+    if (drupal_hash_base64($function) == $hash) {
       return $function;
     }
   }
-
+  $aid = FALSE;
   // Must be a configurable action; check database.
-  return db_query("SELECT aid FROM {actions} WHERE MD5(aid) = :hash AND parameters <> ''", array(':hash' => $hash))->fetchField();
+  $result = db_query("SELECT aid FROM {actions} WHERE parameters <> ''")->fetchAll(PDO::FETCH_ASSOC);
+  foreach ($result as $row) {
+    if (drupal_hash_base64($row['aid']) == $hash) {
+      $aid = $row['aid'];
+      break;
+    }
+  }
+  return $aid;
 }
 
 /**
diff --git includes/bootstrap.inc includes/bootstrap.inc
index 1cf4c4d..20288ce 100644
--- includes/bootstrap.inc
+++ includes/bootstrap.inc
@@ -622,7 +622,7 @@ function drupal_settings_initialize() {
     ini_set('session.cookie_secure', TRUE);
   }
   $prefix = ini_get('session.cookie_secure') ? 'SSESS' : 'SESS';
-  session_name($prefix . md5($session_name));
+  session_name($prefix . substr(hash('sha256', $session_name), 0, 32));
 }
 
 /**
@@ -1709,6 +1709,91 @@ function drupal_block_denied($ip) {
 }
 
 /**
+ * Returns a string of highly randomized bytes (over the full 8-bit range).
+ *
+ * This function is better than simply calling mt_rand() or any other built-in
+ * PHP function because it can return a long string of bytes (compared to < 4
+ * bytes normally from mt_rand()) and uses the best available pseudo-random source.
+ *
+ * @param $count
+ *   The number of characters (bytes) to return in the string.
+ */
+function drupal_random_bytes($count)  {
+  // $random_state does not use drupal_static as it stores random bytes.
+  static $random_state, $bytes;
+  // Initialize on the first call. The contents of $_SERVER includes a mix of
+  // user-specific and system information that varies a little with each page.
+  if (!isset($random_state)) {
+    $random_state = print_r($_SERVER, TRUE);
+    if (function_exists('getmypid')) {
+      // further initialize with the somewhat random PHP process ID.
+      $random_state .= getmypid();
+    }
+    $bytes = '';
+  }
+  if (strlen($bytes) < $count) {
+    // /dev/urandom is available on many *nix systems and is considered the
+    // best commonly available pseudo-random source.
+    if ($fh = @fopen('/dev/urandom', 'rb')) {
+      // PHP only performs buffered reads, so in reality it will always read
+      // at least 4096 bytes. Thus, it costs nothing extra to read and store
+      // that much so as to speed any additional invocations.
+      $bytes .= fread($fh, max(4096, $count));
+      fclose($fh);
+    }
+    // If /dev/urandom is not available or returns no bytes, this loop will
+    // generate a good set of pseudo-random bytes on any system.
+    // Note that it may be important that our $random_state is passed
+    // through hash() prior to being rolled into $output, that the two hash()
+    // invocations are different, and that the extra input into the first one -
+    // the microtime() - is prepended rather than appended. This is to avoid
+    // directly leaking $random_state via the $output stream, which could
+    // allow for trivial prediction of further "random" numbers.
+    while (strlen($bytes) < $count) {
+      $random_state = hash('sha256', microtime() . mt_rand() . $random_state);
+      $bytes .= hash('sha256', mt_rand() . $random_state, TRUE);
+    }
+  }
+  $output = substr($bytes, 0, $count);
+  $bytes = substr($bytes, $count);
+  return $output;
+}
+
+/**
+ * Calculate a base-64 encoded, URL-safe sha-256 hmac.
+ *
+ * @param $data
+ *   String to be validated with the hmac.
+ * @param $key
+ *   A secret string key.
+ *
+ * @return
+ *   A base-64 encoded sha-256 hmac, with + replaced with -, / with _ and
+ *   any = padding characters removed.
+ */
+function drupal_hmac_base64($data, $key) {
+  $hmac = base64_encode(hash_hmac('sha256', $data, $key, TRUE));
+  // Modify the hmac so it's safe to use in URLs.
+  return strtr($hmac, array('+' => '-', '/' => '_', '=' => ''));
+}
+
+/**
+ * Calculate a base-64 encoded, URL-safe sha-256 hash.
+ *
+ * @param $data
+ *   String to be hashed.
+ *
+ * @return
+ *   A base-64 encoded sha-256 hash, with + replaced with -, / with _ and
+ *   any = padding characters removed.
+ */
+function drupal_hash_base64($data) {
+  $hash = base64_encode(hash('sha256', $data, TRUE));
+  // Modify the hash so it's safe to use in URLs.
+  return strtr($hash, array('+' => '-', '/' => '_', '=' => ''));
+}
+
+/**
  * Generates a default anonymous $user object.
  *
  * @return Object - the user object.
@@ -2026,9 +2111,9 @@ function drupal_valid_test_ua($user_agent) {
   // the database is not yet initialized and we can't access any Drupal variables.
   // The file properties add more entropy not easily accessible to others.
   $filepath = DRUPAL_ROOT . '/includes/bootstrap.inc';
-  $key = sha1(serialize($databases) . filectime($filepath) . fileinode($filepath), TRUE);
+  $key = serialize($databases) . filectime($filepath) . fileinode($filepath);
   // The HMAC must match.
-  return $hmac == base64_encode(hash_hmac('sha1', $check_string, $key, TRUE));
+  return $hmac == drupal_hmac_base64($check_string, $key);
 }
 
 /**
@@ -2043,12 +2128,12 @@ function drupal_generate_test_ua($prefix) {
     // check the HMAC before the database is initialized. filectime()
     // and fileinode() are not easily determined from remote.
     $filepath = DRUPAL_ROOT . '/includes/bootstrap.inc';
-    $key = sha1(serialize($databases) . filectime($filepath) . fileinode($filepath), TRUE);
+    $key = serialize($databases) . filectime($filepath) . fileinode($filepath);
   }
    // Generate a moderately secure HMAC based on the database credentials.
    $salt = uniqid('', TRUE);
    $check_string = $prefix . ';' . time() . ';' . $salt;
-   return  $check_string . ';' . base64_encode(hash_hmac('sha1', $check_string, $key, TRUE));
+   return  $check_string . ';' . drupal_hmac_base64($check_string, $key);
 }
 
 /**
diff --git includes/common.inc includes/common.inc
index 476ec8f..2f45ef9 100644
--- includes/common.inc
+++ includes/common.inc
@@ -2877,7 +2877,7 @@ function drupal_aggregate_css(&$css_groups) {
         if ($group['preprocess'] && $preprocess_css) {
           // Prefix filename to prevent blocking by firewalls which reject files
           // starting with "ad*".
-          $filename = 'css_' . md5(serialize($group['items'])) . '.css';
+          $filename = 'css_' . drupal_hash_base64(serialize($group['items'])) . '.css';
           $css_groups[$key]['data'] = drupal_build_css_cache($group['items'], $filename);
         }
         break;
@@ -3749,7 +3749,7 @@ function drupal_get_js($scope = 'header', $javascript = NULL) {
     // Prefix filename to prevent blocking by firewalls which reject files
     // starting with "ad*".
     foreach ($files as $key => $file_set) {
-      $filename = 'js_' . md5(serialize($file_set)) . '.js';
+      $filename = 'js_' . drupal_hash_base64(serialize($file_set)) . '.js';
       $uri = drupal_build_js_cache($file_set, $filename);
       // Only include the file if was written successfully. Errors are logged
       // using watchdog.
@@ -4235,45 +4235,6 @@ function drupal_json_output($var = NULL) {
 }
 
 /**
- * Returns a string of highly randomized bytes (over the full 8-bit range).
- *
- * This function is better than simply calling mt_rand() or any other built-in
- * PHP function because it can return a long string of bytes (compared to < 4
- * bytes normally from mt_rand()) and uses the best available pseudo-random source.
- *
- * @param $count
- *   The number of characters (bytes) to return in the string.
- */
-function drupal_random_bytes($count)  {
-  // $random_state does not use drupal_static as it stores random bytes.
-  static $random_state;
-  // We initialize with the somewhat random PHP process ID on the first call.
-  if (empty($random_state)) {
-    $random_state = getmypid();
-  }
-  $output = '';
-  // /dev/urandom is available on many *nix systems and is considered the best
-  // commonly available pseudo-random source.
-  if ($fh = @fopen('/dev/urandom', 'rb')) {
-    $output = fread($fh, $count);
-    fclose($fh);
-  }
-  // If /dev/urandom is not available or returns no bytes, this loop will
-  // generate a good set of pseudo-random bytes on any system.
-  // Note that it may be important that our $random_state is passed
-  // through md5() prior to being rolled into $output, that the two md5()
-  // invocations are different, and that the extra input into the first one -
-  // the microtime() - is prepended rather than appended. This is to avoid
-  // directly leaking $random_state via the $output stream, which could
-  // allow for trivial prediction of further "random" numbers.
-  while (strlen($output) < $count) {
-    $random_state = md5(microtime() . mt_rand() . $random_state);
-    $output .= md5(mt_rand() . $random_state, TRUE);
-  }
-  return substr($output, 0, $count);
-}
-
-/**
  * Get a salt useful for hardening against SQL injection.
  *
  * @return
@@ -4283,7 +4244,7 @@ function drupal_get_hash_salt() {
   global $drupal_hash_salt, $databases;
   // If the $drupal_hash_salt variable is empty, a hash of the serialized
   // database credentials is used as a fallback salt.
-  return empty($drupal_hash_salt) ? sha1(serialize($databases)) : $drupal_hash_salt;
+  return empty($drupal_hash_salt) ? hash('sha256', serialize($databases)) : $drupal_hash_salt;
 }
 
 /**
@@ -4294,7 +4255,7 @@ function drupal_get_hash_salt() {
  */
 function drupal_get_private_key() {
   if (!($key = variable_get('drupal_private_key', 0))) {
-    $key = md5(drupal_random_bytes(64));
+    $key = drupal_hash_base64(drupal_random_bytes(55));
     variable_set('drupal_private_key', $key);
   }
   return $key;
@@ -4307,10 +4268,7 @@ function drupal_get_private_key() {
  *   An additional value to base the token on.
  */
 function drupal_get_token($value = '') {
-  $private_key = drupal_get_private_key();
-  // A single md5() is vulnerable to length-extension attacks, so use it twice.
-  // @todo:  add md5 and sha1 hmac functions to core.
-  return md5(drupal_get_hash_salt() . md5(session_id() . $value . $private_key));
+  return drupal_hmac_base64($value, session_id() . drupal_get_private_key() . drupal_get_hash_salt());
 }
 
 /**
@@ -5194,7 +5152,7 @@ function drupal_render_cache_set(&$markup, $elements) {
 function drupal_render_cache_by_query($query, $function, $expire = CACHE_TEMPORARY, $granularity = NULL) {
   $cache_keys = array_merge(array($function), drupal_render_cid_parts($granularity));
   $query->preExecute();
-  $cache_keys[] = md5(serialize(array((string) $query, $query->getArguments())));
+  $cache_keys[] = hash('sha256', serialize(array((string) $query, $query->getArguments())));
   return array(
     '#query' => $query,
     '#pre_render' => array($function . '_pre_render'),
diff --git includes/form.inc includes/form.inc
index 82835a7..407c8d0 100644
--- includes/form.inc
+++ includes/form.inc
@@ -203,7 +203,7 @@ function drupal_build_form($form_id, &$form_state) {
       }
 
       $form = drupal_retrieve_form($form_id, $form_state);
-      $form_build_id = 'form-' . md5(uniqid(mt_rand(), TRUE));
+      $form_build_id = 'form-' . drupal_hash_base64(uniqid(mt_rand(), TRUE) . mt_rand());
       $form['#build_id'] = $form_build_id;
 
       // Fix the form method, if it is 'get' in $form_state, but not in $form.
@@ -331,7 +331,7 @@ function drupal_rebuild_form($form_id, &$form_state, $old_form = NULL) {
   // Otherwise, a new #build_id is generated, to not clobber the previous
   // build's data in the form cache; also allowing the user to go back to an
   // earlier build, make changes, and re-submit.
-  $form['#build_id'] = isset($old_form['#build_id']) ? $old_form['#build_id'] : 'form-' . md5(mt_rand());
+  $form['#build_id'] = isset($old_form['#build_id']) ? $old_form['#build_id'] : 'form-' . drupal_hash_base64(uniqid(mt_rand(), TRUE) . mt_rand());
 
   // #action defaults to request_uri(), but in case of AJAX and other partial
   // rebuilds, the form is submitted to an alternate URL, and the original
diff --git includes/install.core.inc includes/install.core.inc
index c9b4a8a..74e6623 100644
--- includes/install.core.inc
+++ includes/install.core.inc
@@ -1004,7 +1004,7 @@ function install_settings_form_submit($form, &$form_state) {
     'required' => TRUE,
   );
   $settings['drupal_hash_salt'] = array(
-    'value'    => sha1(drupal_random_bytes(64)),
+    'value'    => drupal_hash_base64(drupal_random_bytes(55)),
     'required' => TRUE,
   );
   drupal_rewrite_settings($settings);
diff --git includes/locale.inc includes/locale.inc
index b5fe671..8e86192 100644
--- includes/locale.inc
+++ includes/locale.inc
@@ -1680,7 +1680,7 @@ function _locale_rebuild_js($langcode = NULL) {
     }
 
     $data .= "'strings': " . drupal_json_encode($translations) . " };";
-    $data_hash = md5($data);
+    $data_hash = drupal_hash_base64($data);
   }
 
   // Construct the filepath where JS translation files are stored.
diff --git includes/menu.inc includes/menu.inc
index 8e2fb1f..8ef354e 100644
--- includes/menu.inc
+++ includes/menu.inc
@@ -407,9 +407,9 @@ function menu_get_item($path = NULL, $router_item = NULL) {
     $parts = array_slice($original_map, 0, MENU_MAX_PARTS);
     $ancestors = menu_get_ancestors($parts);
 
-    // Since there is no limit to the length of $path, but the cids are
-    // restricted to 255 characters, use md5() to keep it short yet unique.
-    $cid = 'menu_item:' . md5($path);
+    // Since there is no limit to the length of $path, use a hash to keep it
+    // short yet unique.
+    $cid = 'menu_item:' . hash('sha256', $path);
     if ($cached = cache_get($cid, 'cache_menu')) {
       $router_item = $cached->data;
     }
@@ -1238,7 +1238,7 @@ function menu_tree_page_data($menu_name, $max_depth = NULL) {
  * Helper function - compute the real cache ID for menu tree data.
  */
 function _menu_tree_cid($menu_name, $data) {
-  return 'links:' . $menu_name . ':tree-data:' . $GLOBALS['language']->language . ':' . md5(serialize($data));
+  return 'links:' . $menu_name . ':tree-data:' . $GLOBALS['language']->language . ':' . hash('sha256', serialize($data));
 }
 
 /**
diff --git includes/password.inc includes/password.inc
index 787f14b..687ed4f 100644
--- includes/password.inc
+++ includes/password.inc
@@ -16,8 +16,8 @@
 
 /**
  * The standard log2 number of iterations for password stretching. This should
- * increase by 1 at least every other Drupal version in order to counteract
- * increases in the speed and power of computers available to crack the hashes.
+ * increase by 1 every Drupal version in order to counteract increases in the
+ * speed and power of computers available to crack the hashes.
  */
 define('DRUPAL_HASH_COUNT', 14);
 
@@ -49,7 +49,7 @@ function _password_itoa64() {
  * @return
  *   Encoded string
  */
-function _password_base64_encode($input, $count)  {
+function _password_base64_encode($input, $count) {
   $output = '';
   $i = 0;
   $itoa64 = _password_itoa64();
@@ -93,7 +93,7 @@ function _password_base64_encode($input, $count)  {
  *   A 12 character string containing the iteration count and a random salt.
  */
 function _password_generate_salt($count_log2) {
-  $output = '$P$';
+  $output = '$2$';
   // Minimum log2 iterations is DRUPAL_MIN_HASH_COUNT.
   $count_log2 = max($count_log2, DRUPAL_MIN_HASH_COUNT);
   // Maximum log2 iterations is DRUPAL_MAX_HASH_COUNT.
@@ -113,19 +113,22 @@ function _password_generate_salt($count_log2) {
  * for an attacker to try to break the hash by brute-force computation of the
  * hashes of a large number of plain-text words or strings to find a match.
  *
+ * @param $algo
+ *   The string name of a hashing algorithm usable by hash(), like 'sha256'.
  * @param $password
  *   The plain-text password to hash.
  * @param $setting
- *   An existing hash or the output of _password_generate_salt().
+ *   An existing hash or the output of _password_generate_salt().  Must be
+ *   at least 12 characters (the settings and salt).
  *
  * @return
  *   A string containing the hashed password (and salt) or FALSE on failure.
  */
-function _password_crypt($password, $setting)  {
+function _password_crypt($algo, $password, $setting) {
   // The first 12 characters of an existing hash are its setting string.
   $setting = substr($setting, 0, 12);
 
-  if (substr($setting, 0, 3) != '$P$') {
+  if ($setting[0] != '$' || $setting[2] != '$') {
     return FALSE;
   }
   $count_log2 = _password_get_count_log2($setting);
@@ -139,22 +142,21 @@ function _password_crypt($password, $setting)  {
     return FALSE;
   }
 
-  // We must use md5() or sha1() here since they are the only cryptographic
-  // primitives always available in PHP 5. To implement our own low-level
-  // cryptographic function in PHP would result in much worse performance and
-  // consequently in lower iteration counts and hashes that are quicker to crack
-  // (by non-PHP code).
-
+  // Convert the base 2 logrithm into an integer.
   $count = 1 << $count_log2;
 
-  $hash = md5($salt . $password, TRUE);
+  // We rely on the hash() function being available in PHP 5.2+.
+  $hash = hash($algo, $salt . $password, TRUE);
   do {
-    $hash = md5($hash . $password, TRUE);
+    $hash = hash($algo, $hash . $password, TRUE);
   } while (--$count);
 
-  $output =  $setting . _password_base64_encode($hash, 16);
+  $len = strlen($hash);
+  $output =  $setting . _password_base64_encode($hash, $len);
   // _password_base64_encode() of a 16 byte MD5 will always be 22 characters.
-  return (strlen($output) == 34) ? $output : FALSE;
+  // _password_base64_encode() of a 32 byte sha256 will always be 43 characters.
+  $expected = 12 + ceil((8 * $len) / 6);
+  return (strlen($output) == $expected) ? $output : FALSE;
 }
 
 /**
@@ -182,7 +184,7 @@ function user_hash_password($password, $count_log2 = 0) {
     // Use the standard iteration count.
     $count_log2 = variable_get('password_count_log2', DRUPAL_HASH_COUNT);
   }
-  return _password_crypt($password, _password_generate_salt($count_log2));
+  return _password_crypt('sha256', $password, _password_generate_salt($count_log2));
 }
 
 /**
@@ -201,7 +203,7 @@ function user_hash_password($password, $count_log2 = 0) {
  *   TRUE or FALSE.
  */
 function user_check_password($password, $account) {
-  if (substr($account->pass, 0, 3) == 'U$P') {
+  if (substr($account->pass, 0, 2) == 'U$') {
     // This may be an updated password from user_update_7000(). Such hashes
     // have 'U' added as the first character and need an extra md5().
     $stored_hash = substr($account->pass, 1);
@@ -210,7 +212,23 @@ function user_check_password($password, $account) {
   else {
     $stored_hash = $account->pass;
   }
-  $hash = _password_crypt($password, $stored_hash);
+
+  $type = substr($stored_hash, 0, 3);
+  switch ($type) {
+    case '$S$':
+      // A normal Drupal 7 password.
+      $hash = _password_crypt('sha256', $password, $stored_hash);
+      break;
+    case '$H$':
+      // phpBB3 uses "$H$" for the same thing as "$P$".
+    case '$P$':
+      // A phpass password generated using md5.  This is an
+      // imported password or from an earlier Drupal version.
+      $hash = _password_crypt('md5', $password, $stored_hash);
+      break;
+    default:
+      return FALSE;
+  }
   return ($hash && $stored_hash == $hash);
 }
 
@@ -234,7 +252,7 @@ function user_check_password($password, $account) {
  */
 function user_needs_new_hash($account) {
   // Check whether this was an updated password.
-  if ((substr($account->pass, 0, 3) != '$P$') || (strlen($account->pass) != 34)) {
+  if ((substr($account->pass, 0, 3) != '$S$') || (strlen($account->pass) != 55)) {
     return TRUE;
   }
   // Check whether the iteration count used differs from the standard number.
diff --git includes/session.inc includes/session.inc
index 542253e..2996bd0 100644
--- includes/session.inc
+++ includes/session.inc
@@ -206,7 +206,10 @@ function drupal_session_initialize() {
     // processes (like drupal_get_token()) needs to know the future
     // session ID in advance.
     $user = drupal_anonymous_user();
-    session_id(md5(uniqid('', TRUE)));
+    // Less random sessions (which are much faster to generate) are used for
+    // anonymous users than are generated in drupal_session_regenerate() when
+    // a user becomes authenticated.
+    session_id(drupal_hash_base64(uniqid(mt_rand(), TRUE)));
   }
   date_default_timezone_set(drupal_get_user_timezone());
 }
@@ -284,7 +287,7 @@ function drupal_session_regenerate() {
   if ($is_https && variable_get('https', FALSE)) {
     $insecure_session_name = substr(session_name(), 1);
     $params = session_get_cookie_params();
-    $session_id = md5(uniqid(mt_rand(), TRUE));
+    $session_id = drupal_hash_base64(uniqid(mt_rand(), TRUE) . drupal_random_bytes(55));
     setcookie($insecure_session_name, $session_id, REQUEST_TIME + $params['lifetime'], $params['path'], $params['domain'], FALSE, $params['httponly']);
     $_COOKIE[$insecure_session_name] = $session_id;
   }
diff --git includes/update.inc includes/update.inc
index f4cc99f..321274d 100644
--- includes/update.inc
+++ includes/update.inc
@@ -265,7 +265,7 @@ function update_fix_d7_requirements() {
   global $update_rewrite_settings, $db_url;
   if (!empty($update_rewrite_settings)) {
     $databases = update_parse_db_url($db_url);
-    $salt = sha1(drupal_random_bytes(64));
+    $salt = drupal_hash_base64(drupal_random_bytes(55));
     file_put_contents(conf_path() . '/settings.php', "\n" . '$databases = ' . var_export($databases, TRUE) . ";\n\$drupal_hash_salt = '$salt';", FILE_APPEND);
   }
   if (drupal_get_installed_schema_version('system') < 7000 && !variable_get('update_d7_requirements', FALSE)) {
diff --git modules/aggregator/aggregator.install modules/aggregator/aggregator.install
index 402774e..4ed9afc 100644
--- modules/aggregator/aggregator.install
+++ modules/aggregator/aggregator.install
@@ -170,10 +170,10 @@ function aggregator_schema() {
       ),
       'hash' => array(
         'type' => 'varchar',
-        'length' => 32,
+        'length' => 64,
         'not null' => TRUE,
         'default' => '',
-        'description' => 'Calculated md5 hash of the feed data, used for validating cache.',
+        'description' => 'Calculated hash of the feed data, used for validating cache.',
       ),
       'etag' => array(
         'type' => 'varchar',
@@ -275,7 +275,7 @@ function aggregator_schema() {
  * Add hash column to aggregator_feed table.
  */
 function aggregator_update_7000() {
-  db_add_field('aggregator_feed', 'hash', array('type' => 'varchar', 'length' => 32, 'not null' => TRUE, 'default' => ''));
+  db_add_field('aggregator_feed', 'hash', array('type' => 'varchar', 'length' => 64, 'not null' => TRUE, 'default' => ''));
 }
 
 /**
@@ -297,3 +297,4 @@ function aggregator_update_7002() {
   ));
   db_add_index('aggregator_feed', 'queued', array('queued'));
 }
+
diff --git modules/aggregator/aggregator.module modules/aggregator/aggregator.module
index 467423a..d6a8872 100644
--- modules/aggregator/aggregator.module
+++ modules/aggregator/aggregator.module
@@ -614,12 +614,12 @@ function aggregator_refresh($feed) {
   list($fetcher, $parser, $processors) = _aggregator_get_variables();
   $success = module_invoke($fetcher, 'aggregator_fetch', $feed);
 
-  // We store the md5 hash of feed data in the database. When refreshing a
+  // We store the hash of feed data in the database. When refreshing a
   // feed we compare stored hash and new hash calculated from downloaded
   // data. If both are equal we say that feed is not updated.
-  $md5 = md5($feed->source_string);
+  $hash = hash('sha256', $feed->source_string);
 
-  if ($success && ($feed->hash != $md5)) {
+  if ($success && ($feed->hash != $hash)) {
     // Parse the feed.
     if (module_invoke($parser, 'aggregator_parse', $feed)) {
       // Update feed with parsed data.
@@ -630,7 +630,7 @@ function aggregator_refresh($feed) {
           'link' => empty($feed->link) ? $feed->url : $feed->link,
           'description' => empty($feed->description) ? '' : $feed->description,
           'image' => empty($feed->image) ? '' : $feed->image,
-          'hash' => $md5,
+          'hash' => $hash,
           'etag' => empty($feed->etag) ? '' : $feed->etag,
           'modified' => empty($feed->modified) ? 0 : $feed->modified,
         ))
diff --git modules/aggregator/tests/aggregator_test.module modules/aggregator/tests/aggregator_test.module
index 35d626a..172a56e 100644
--- modules/aggregator/tests/aggregator_test.module
+++ modules/aggregator/tests/aggregator_test.module
@@ -25,7 +25,7 @@ function aggregator_test_menu() {
  */
 function aggregator_test_feed($use_last_modified = FALSE, $use_etag = FALSE) {
   $last_modified = strtotime('Sun, 19 Nov 1978 05:00:00 GMT');
-  $etag = md5($last_modified);
+  $etag = drupal_hash_base64($last_modified);
 
   $if_modified_since = isset($_SERVER['HTTP_IF_MODIFIED_SINCE']) ? strtotime($_SERVER['HTTP_IF_MODIFIED_SINCE']) : FALSE;
   $if_none_match = isset($_SERVER['HTTP_IF_NONE_MATCH']) ? stripslashes($_SERVER['HTTP_IF_NONE_MATCH']) : FALSE;
diff --git modules/book/book.admin.inc modules/book/book.admin.inc
index ffdcf88..61be213 100644
--- modules/book/book.admin.inc
+++ modules/book/book.admin.inc
@@ -154,7 +154,7 @@ function _book_admin_table($node, &$form) {
   $tree = book_menu_subtree_data($node->book);
   $tree = array_shift($tree); // Do not include the book item itself.
   if ($tree['below']) {
-    $hash = sha1(serialize($tree['below']));
+    $hash = drupal_hash_base64(serialize($tree['below']));
     // Store the hash value as a hidden form element so that we can detect
     // if another user changed the book hierarchy.
     $form['tree_hash'] = array(
diff --git modules/book/book.module modules/book/book.module
index 2f6dfc0..5726090 100644
--- modules/book/book.module
+++ modules/book/book.module
@@ -1254,7 +1254,7 @@ function book_menu_subtree_data($link) {
       $data['node_links'] = array();
       menu_tree_collect_node_links($data['tree'], $data['node_links']);
       // Compute the real cid for book subtree data.
-      $tree_cid = 'links:' . $item['menu_name'] . ':subtree-data:' . md5(serialize($data));
+      $tree_cid = 'links:' . $item['menu_name'] . ':subtree-data:' . hash('sha256', serialize($data));
       // Cache the data, if it is not already in the cache.
 
       if (!cache_get($tree_cid, 'cache_menu')) {
diff --git modules/color/color.module modules/color/color.module
index e34b469..f6572fd 100644
--- modules/color/color.module
+++ modules/color/color.module
@@ -316,7 +316,7 @@ function color_scheme_form_submit($form, &$form_state) {
   }
 
   // Prepare target locations for generated files.
-  $id = $theme . '-' . substr(md5(serialize($palette) . microtime()), 0, 8);
+  $id = $theme . '-' . substr(hash('sha256', serialize($palette) . microtime()), 0, 8);
   $paths['color'] = 'public://color';
   $paths['target'] = $paths['color'] . '/' . $id;
   foreach ($paths as $path) {
diff --git modules/field/tests/field.test modules/field/tests/field.test
index a9b4bd2..c56cf3b 100644
--- modules/field/tests/field.test
+++ modules/field/tests/field.test
@@ -2715,7 +2715,7 @@ class FieldTranslationsTestCase extends FieldTestCase {
 
     $results = _field_invoke('test_op', $entity_type, $entity);
     foreach ($results as $langcode => $result) {
-      $hash = md5(serialize(array($entity_type, $entity, $this->field_name, $langcode, $values[$langcode])));
+      $hash = hash('sha256', serialize(array($entity_type, $entity, $this->field_name, $langcode, $values[$langcode])));
       // Check whether the parameters passed to _field_invoke() were correctly
       // forwarded to the callback function.
       $this->assertEqual($hash, $result, t('The result for %language is correctly stored.', array('%language' => $langcode)));
@@ -2757,7 +2757,7 @@ class FieldTranslationsTestCase extends FieldTestCase {
     $grouped_results = _field_invoke_multiple('test_op_multiple', $entity_type, $entities);
     foreach ($grouped_results as $id => $results) {
       foreach ($results as $langcode => $result) {
-        $hash = md5(serialize(array($entity_type, $entities[$id], $this->field_name, $langcode, $values[$id][$langcode])));
+        $hash = hash('sha256', serialize(array($entity_type, $entities[$id], $this->field_name, $langcode, $values[$id][$langcode])));
         // Check whether the parameters passed to _field_invoke() were correctly
         // forwarded to the callback function.
         $this->assertEqual($hash, $result, t('The result for entity %id/%language is correctly stored.', array('%id' => $id, '%language' => $langcode)));
diff --git modules/field/tests/field_test.module modules/field/tests/field_test.module
index 7cd2e32..03ae9a4 100644
--- modules/field/tests/field_test.module
+++ modules/field/tests/field_test.module
@@ -69,7 +69,7 @@ function field_test_menu() {
  * This simulates a field operation callback to be invoked by _field_invoke().
  */
 function field_test_field_test_op($entity_type, $entity, $field, $instance, $langcode, &$items) {
-  return array($langcode => md5(serialize(array($entity_type, $entity, $field['field_name'], $langcode, $items))));
+  return array($langcode => hash('sha256', serialize(array($entity_type, $entity, $field['field_name'], $langcode, $items))));
 }
 
 /**
@@ -81,7 +81,7 @@ function field_test_field_test_op($entity_type, $entity, $field, $instance, $lan
 function field_test_field_test_op_multiple($entity_type, $entities, $field, $instances, $langcode, &$items) {
   $result = array();
   foreach ($entities as $id => $entity) {
-    $result[$id] = array($langcode => md5(serialize(array($entity_type, $entity, $field['field_name'], $langcode, $items[$id]))));
+    $result[$id] = array($langcode => hash('sha256', serialize(array($entity_type, $entity, $field['field_name'], $langcode, $items[$id]))));
   }
   return $result;
 }
diff --git modules/file/file.module modules/file/file.module
index b8f78b7..ccbcac3 100644
--- modules/file/file.module
+++ modules/file/file.module
@@ -411,7 +411,7 @@ function file_managed_file_process($element, &$form_state, $form) {
 
   // Add progress bar support to the upload if possible.
   if ($element['#progress_indicator'] == 'bar' && $implementation = file_progress_implementation()) {
-    $upload_progress_key = md5(mt_rand());
+    $upload_progress_key = mt_rand();
 
     if ($implementation == 'uploadprogress') {
       $element['UPLOAD_IDENTIFIER'] = array(
diff --git modules/filter/filter.install modules/filter/filter.install
index e295574..6edc030 100644
--- modules/filter/filter.install
+++ modules/filter/filter.install
@@ -98,7 +98,7 @@ function filter_schema() {
   );
 
   $schema['cache_filter'] = drupal_get_schema_unprocessed('system', 'cache');
-  $schema['cache_filter']['description'] = 'Cache table for the Filter module to store already filtered pieces of text, identified by text format and md5 hash of the text.';
+  $schema['cache_filter']['description'] = 'Cache table for the Filter module to store already filtered pieces of text, identified by text format and hash of the text.';
 
   return $schema;
 }
diff --git modules/filter/filter.module modules/filter/filter.module
index 2b4bddf..5602482 100644
--- modules/filter/filter.module
+++ modules/filter/filter.module
@@ -679,7 +679,7 @@ function check_markup($text, $format_id = NULL, $langcode = '', $cache = FALSE)
   $cache = $cache && !empty($format->cache);
   $cache_id = '';
   if ($cache) {
-    $cache_id = $format->format . ':' . $langcode . ':' . md5($text);
+    $cache_id = $format->format . ':' . $langcode . ':' . hash('sha256', $text);
     if ($cached = cache_get($cache_id, 'cache_filter')) {
       return $cached->data;
     }
diff --git modules/image/image.module modules/image/image.module
index 932b32a..cdd9897 100644
--- modules/image/image.module
+++ modules/image/image.module
@@ -591,19 +591,19 @@ function image_style_generate() {
   $path = implode('/', $args);
 
   $path = $scheme . '://' . $path;
-  $path_md5 = md5($path);
+  $path_hash = drupal_hash_base64($path);
   $destination = image_style_path($style['name'], $path);
 
   // Check that it's a defined style and that access was granted by
   // image_style_url().
-  if (!$style || !cache_get('access:' . $style_name . ':' . $path_md5, 'cache_image')) {
+  if (!$style || !cache_get('access:' . $style_name . ':' . $path_hash, 'cache_image')) {
     drupal_access_denied();
     drupal_exit();
   }
 
   // Don't start generating the image if the derivate already exists or if
   // generation is in progress in another thread.
-  $lock_name = 'image_style_generate:' . $style_name . ':' . $path_md5;
+  $lock_name = 'image_style_generate:' . $style_name . ':' . $path_hash;
   if (!file_exists($destination)) {
     $lock_acquired = lock_acquire($lock_name);
     if (!$lock_acquired) {
@@ -742,7 +742,7 @@ function image_style_url($style_name, $path) {
 
   // Set a cache entry to grant access to this style/image path. This will be
   // checked by image_style_generate().
-  cache_set('access:' . $style_name . ':' . md5($path), 1, 'cache_image', REQUEST_TIME + 600);
+  cache_set('access:' . $style_name . ':' . drupal_hash_base64($path), 1, 'cache_image', REQUEST_TIME + 600);
 
   $scheme = file_uri_scheme($path);
   $target = file_uri_target($path);
diff --git modules/image/image.test modules/image/image.test
index c0e3d22..4fa693d 100644
--- modules/image/image.test
+++ modules/image/image.test
@@ -113,7 +113,7 @@ class ImageStylesPathAndUrlUnitTest extends DrupalWebTestCase {
 
     // Fetch the URL that generates the file while another process appears to
     // be generating the same file (this is signaled using a lock).
-    $lock_name = 'image_style_generate:' . $this->style_name . ':' . md5($original_uri);
+    $lock_name = 'image_style_generate:' . $this->style_name . ':' . drupal_hash_base64($original_uri);
     $this->assertTrue(lock_acquire($lock_name), t('Lock was acquired.'));
     $this->drupalGet($expected_generate_url);
     $this->assertResponse(503, t('Service Unavailable response received.'));
diff --git modules/locale/locale.install modules/locale/locale.install
index 93fb793..dc1abaf 100644
--- modules/locale/locale.install
+++ modules/locale/locale.install
@@ -82,6 +82,13 @@ function locale_update_7001() {
 }
 
 /**
+ * Allow longer javascript file names.
+ */
+function locale_update_7002() {
+  db_change_field('languages', 'javascript', 'javascript', array('type' => 'varchar', 'length' => 64, 'not null' => TRUE, 'default' => ''));
+}
+
+/**
  * @} End of "defgroup updates-6.x-to-7.x"
  */
 
@@ -207,7 +214,7 @@ function locale_schema() {
       ),
       'javascript' => array(
         'type' => 'varchar',
-        'length' => 32,
+        'length' => 64,
         'not null' => TRUE,
         'default' => '',
         'description' => 'Location of JavaScript translation file.',
diff --git modules/menu/menu.test modules/menu/menu.test
index 3c99e26..7862420 100644
--- modules/menu/menu.test
+++ modules/menu/menu.test
@@ -100,7 +100,7 @@ class MenuTestCase extends DrupalWebTestCase {
    */
   function addCustomMenuCRUD() {
     // Add a new custom menu.
-    $menu_name = substr(md5($this->randomName(16)), 0, MENU_MAX_MENU_NAME_LENGTH_UI);
+    $menu_name = substr(hash('sha256', $this->randomName(16)), 0, MENU_MAX_MENU_NAME_LENGTH_UI);
     $title = $this->randomName(16);
 
     $menu = array(
@@ -130,7 +130,7 @@ class MenuTestCase extends DrupalWebTestCase {
 
     // Try adding a menu using a menu_name that is too long.
     $this->drupalGet('admin/structure/menu/add');
-    $menu_name = substr(md5($this->randomName(16)), 0, MENU_MAX_MENU_NAME_LENGTH_UI + 1);
+    $menu_name = substr(hash('sha256', $this->randomName(16)), 0, MENU_MAX_MENU_NAME_LENGTH_UI + 1);
     $title = $this->randomName(16);
     $edit = array(
       'menu_name' => $menu_name,
@@ -143,7 +143,7 @@ class MenuTestCase extends DrupalWebTestCase {
     $this->assertText(format_plural(MENU_MAX_MENU_NAME_LENGTH_UI, "The menu name can't be longer than 1 character.", "The menu name can't be longer than @count characters."), t('Validation failed when menu name is too long.'));
 
     // Change the menu_name so it no longer exceeds the maximum length.
-    $menu_name = substr(md5($this->randomName(16)), 0, MENU_MAX_MENU_NAME_LENGTH_UI);
+    $menu_name = substr(hash('sha256', $this->randomName(16)), 0, MENU_MAX_MENU_NAME_LENGTH_UI);
     $edit['menu_name'] = $menu_name;
     $this->drupalPost('admin/structure/menu/add', $edit, t('Save'));
 
diff --git modules/simpletest/drupal_web_test_case.php modules/simpletest/drupal_web_test_case.php
index 217aadc..04b9fe1 100644
--- modules/simpletest/drupal_web_test_case.php
+++ modules/simpletest/drupal_web_test_case.php
@@ -1072,7 +1072,7 @@ class DrupalWebTestCase extends DrupalTestCase {
    */
   protected function drupalGetToken($value = '') {
     $private_key = drupal_get_private_key();
-    return md5($this->session_id . $value . $private_key);
+    return drupal_hmac_base64($value, $this->session_id . $private_key);
   }
 
   /*
diff --git modules/simpletest/tests/actions.test modules/simpletest/tests/actions.test
index 3a098a8..c673d94 100644
--- modules/simpletest/tests/actions.test
+++ modules/simpletest/tests/actions.test
@@ -21,7 +21,7 @@ class ActionsConfigurationTestCase extends DrupalWebTestCase {
 
     // Make a POST request to admin/config/system/actions/manage.
     $edit = array();
-    $edit['action'] = md5('system_goto_action');
+    $edit['action'] = drupal_hash_base64('system_goto_action');
     $this->drupalPost('admin/config/system/actions/manage', $edit, t('Create'));
 
     // Make a POST request to the individual action configuration page.
@@ -29,7 +29,7 @@ class ActionsConfigurationTestCase extends DrupalWebTestCase {
     $action_label = $this->randomName();
     $edit['actions_label'] = $action_label;
     $edit['url'] = 'admin';
-    $this->drupalPost('admin/config/system/actions/configure/' . md5('system_goto_action'), $edit, t('Save'));
+    $this->drupalPost('admin/config/system/actions/configure/' . drupal_hash_base64('system_goto_action'), $edit, t('Save'));
 
     // Make sure that the new complex action was saved properly.
     $this->assertText(t('The action has been successfully saved.'), t("Make sure we get a confirmation that we've successfully saved the complex action."));
@@ -87,7 +87,7 @@ class ActionLoopTestCase extends DrupalWebTestCase {
     $user = $this->drupalCreateUser(array('administer actions'));
     $this->drupalLogin($user);
 
-    $hash = md5('actions_loop_test_log');
+    $hash = drupal_hash_base64('actions_loop_test_log');
     $edit = array('aid' => $hash);
     $this->drupalPost('admin/structure/trigger/actions_loop_test', $edit, t('Assign'));
 
diff --git modules/simpletest/tests/registry.test modules/simpletest/tests/registry.test
index f77db6d..1733f5d 100644
--- modules/simpletest/tests/registry.test
+++ modules/simpletest/tests/registry.test
@@ -11,9 +11,10 @@ class RegistryParseFileTestCase extends DrupalWebTestCase {
   }
 
   function setUp() {
-    $this->fileName = 'registry_test_' . md5(rand());
-    $this->className = 'registry_test_class' . md5(rand());
-    $this->interfaceName = 'registry_test_interface' . md5(rand());
+    $chrs = hash('sha256', microtime() . mt_rand());
+    $this->fileName = 'registry_test_' . substr($chrs, 0, 16);
+    $this->className = 'registry_test_class' . substr($chrs, 16, 16);
+    $this->interfaceName = 'registry_test_interface' . substr($chrs, 32, 16);
     parent::setUp();
   }
 
@@ -61,18 +62,19 @@ class RegistryParseFilesTestCase extends DrupalWebTestCase {
     // Create files with some php to parse - one 'new', one 'existing' so
     // we test all the important code paths in _registry_parse_files.
     foreach ($this->fileTypes as $fileType) {
+      $chrs = hash('sha256', microtime() . mt_rand());
       $this->$fileType = new stdClass();
-      $this->$fileType->fileName = file_directory_path() . '/registry_test_' . md5(rand());
-      $this->$fileType->className = 'registry_test_class' . md5(rand());
-      $this->$fileType->interfaceName = 'registry_test_interface' . md5(rand());
+      $this->$fileType->fileName = file_directory_path() . '/registry_test_' . substr($chrs, 0, 16);
+      $this->$fileType->className = 'registry_test_class' . substr($chrs, 16, 16);
+      $this->$fileType->interfaceName = 'registry_test_interface' . substr($chrs, 32, 16);
       $this->$fileType->contents = $this->getFileContents($fileType);
       file_save_data($this->$fileType->contents, $this->$fileType->fileName);
 
       if ($fileType == 'existing_changed') {
         db_insert('registry_file')
           ->fields(array(
-            'filectime' => rand(1, 1000000),
-            'filemtime' => rand(1, 1000000),
+            'filectime' => mt_rand(1, 1000000),
+            'filemtime' => mt_rand(1, 1000000),
             'filename' => $this->$fileType->fileName,
           ))
           ->execute();
@@ -81,7 +83,7 @@ class RegistryParseFilesTestCase extends DrupalWebTestCase {
         foreach (array('class', 'interface') as $type) {
           db_insert('registry')
             ->fields(array(
-              'name' => $type . md5(rand()),
+              'name' => $type . hash('sha256', microtime() . mt_rand()),
               'type' => $type,
               'filename' => $this->$fileType->fileName,
             ))
@@ -117,8 +119,8 @@ class RegistryParseFilesTestCase extends DrupalWebTestCase {
     foreach ($this->fileTypes as $fileType) {
       $files[$this->$fileType->fileName] = array('module' => '', 'weight' => 0);
       if ($fileType == 'existing_changed') {
-        $files[$this->$fileType->fileName]['filectime'] = rand(1, 1000000);
-        $files[$this->$fileType->fileName]['filemtime'] = rand(1, 1000000);
+        $files[$this->$fileType->fileName]['filectime'] = mt_rand(1, 1000000);
+        $files[$this->$fileType->fileName]['filemtime'] = mt_rand(1, 1000000);
       }
     }
     return $files;
diff --git modules/system/system.admin.inc modules/system/system.admin.inc
index eafa6f1..9d778be 100644
--- modules/system/system.admin.inc
+++ modules/system/system.admin.inc
@@ -2934,7 +2934,7 @@ function system_actions_manage_form_submit($form, &$form_state) {
  * on our elements.
  *
  * @param $action
- *   md5 hash of an action ID or an integer. If it is an md5 hash, we are
+ *   Hash of an action ID or an integer. If it is a hash, we are
  *   creating a new instance. If it is an integer, we are editing an existing
  *   instance.
  * @return
@@ -2959,7 +2959,7 @@ function system_actions_configure($form, &$form_state, $action = NULL) {
     $edit['actions_label'] = $data->label;
     $edit['actions_type'] = $data->type;
     $function = $data->callback;
-    $action = md5($data->callback);
+    $action = drupal_hash_base64($data->callback);
     $params = unserialize($data->parameters);
     if ($params) {
       foreach ($params as $name => $val) {
diff --git modules/system/system.install modules/system/system.install
index 4292210..d108ec7 100644
--- modules/system/system.install
+++ modules/system/system.install
@@ -414,7 +414,7 @@ function system_install() {
     ->execute();
 
   // Populate the cron key variable.
-  $cron_key = md5(mt_rand());
+  $cron_key = drupal_hash_base64(drupal_random_bytes(55));
   variable_set('cron_key', $cron_key);
 }
 
@@ -1650,7 +1650,7 @@ function system_update_7000() {
  * Generate a cron key and save it in the variables table.
  */
 function system_update_7001() {
-  variable_set('cron_key', md5(mt_rand()));
+  variable_set('cron_key', drupal_hash_base64(drupal_random_bytes(55)));
 }
 
 /**
diff --git modules/trigger/trigger.admin.inc modules/trigger/trigger.admin.inc
index a7b6bf8..15e540a 100644
--- modules/trigger/trigger.admin.inc
+++ modules/trigger/trigger.admin.inc
@@ -155,10 +155,11 @@ function trigger_assign_form($form, $form_state, $module, $hook, $label) {
   foreach ($actions as $aid => $info) {
     // If action is defined unassign it, otherwise offer to delete all orphaned
     // actions.
-    if (actions_function_lookup(md5($aid))) {
+    $hash = drupal_hash_base64($aid, TRUE);
+    if (actions_function_lookup($hash)) {
       $form[$hook]['assigned']['#value'][$aid] = array(
         'label' => $info['label'],
-        'link' => l(t('unassign'), "admin/structure/trigger/unassign/$module/$hook/" . md5($aid)),
+        'link' => l(t('unassign'), "admin/structure/trigger/unassign/$module/$hook/$hash"),
       );
     }
     else {
diff --git modules/trigger/trigger.test modules/trigger/trigger.test
index 408eb2b..0535b40 100644
--- modules/trigger/trigger.test
+++ modules/trigger/trigger.test
@@ -19,7 +19,7 @@ class TriggerWebTestCase extends DrupalWebTestCase {
    */
   protected function configureAdvancedAction($action, $edit) {
     // Create an advanced action.
-    $hash = md5($action);
+    $hash = drupal_hash_base64($action);
     $this->drupalPost("admin/config/system/actions/configure/$hash", $edit, t('Save'));
     $this->assertText(t('The action has been successfully saved.'));
 
@@ -58,7 +58,7 @@ class TriggerContentTestCase extends TriggerWebTestCase {
     $test_user = $this->drupalCreateUser(array('administer actions'));
     $web_user = $this->drupalCreateUser(array('create page content', 'access content', 'administer nodes'));
     foreach ($content_actions as $action) {
-      $hash = md5($action);
+      $hash = drupal_hash_base64($action);
       $info = $this->actionInfo($action);
 
       // Assign an action to a trigger, then pull the trigger, and make sure
@@ -112,7 +112,7 @@ class TriggerContentTestCase extends TriggerWebTestCase {
     }
 
     $action_id = 'trigger_test_generic_any_action';
-    $hash = md5($action_id);
+    $hash = drupal_hash_base64($action_id);
     $edit = array('aid' => $hash);
     $this->drupalPost('admin/structure/trigger/node', $edit, t('Assign'), array(), array(), 'trigger-node-update-assign-form');
 
@@ -200,7 +200,7 @@ class TriggerCronTestCase extends TriggerWebTestCase {
     $this->drupalLogin($test_user);
 
     // Assign a non-configurable action to the cron run trigger.
-    $edit = array('aid' => md5('trigger_test_system_cron_action'));
+    $edit = array('aid' => drupal_hash_base64('trigger_test_system_cron_action'));
     $this->drupalPost('admin/structure/trigger/system', $edit, t('Assign'), array(), array(), 'trigger-cron-assign-form');
 
     // Assign a configurable action to the cron trigger.
@@ -212,7 +212,7 @@ class TriggerCronTestCase extends TriggerWebTestCase {
     $aid = $this->configureAdvancedAction('trigger_test_system_cron_conf_action', $edit);
     // $aid is likely 3 but if we add more uses for the sequences table in
     // core it might break, so it is easier to get the value from the database.
-    $edit = array('aid' => md5($aid));
+    $edit = array('aid' => drupal_hash_base64($aid));
     $this->drupalPost('admin/structure/trigger/system', $edit, t('Assign'), array(), array(), 'trigger-cron-assign-form');
 
     // Add a second configurable action to the cron trigger.
@@ -222,7 +222,7 @@ class TriggerCronTestCase extends TriggerWebTestCase {
       'subject' => $action_label,
     );
     $aid = $this->configureAdvancedAction('trigger_test_system_cron_conf_action', $edit);
-    $edit = array('aid' => md5($aid));
+    $edit = array('aid' => drupal_hash_base64($aid));
     $this->drupalPost('admin/structure/trigger/system', $edit, t('Assign'), array(), array(), 'trigger-cron-assign-form');
 
     // Force a cron run.
@@ -265,7 +265,7 @@ class TriggerOtherTestCase extends TriggerWebTestCase {
     $test_user = $this->drupalCreateUser(array('administer actions'));
     $this->drupalLogin($test_user);
     $action_id = 'trigger_test_generic_action';
-    $hash = md5($action_id);
+    $hash = drupal_hash_base64($action_id);
     $edit = array('aid' => $hash);
     $this->drupalPost('admin/structure/trigger/user', $edit, t('Assign'), array(), array(), 'trigger-user-insert-assign-form');
 
@@ -300,7 +300,7 @@ class TriggerOtherTestCase extends TriggerWebTestCase {
 
     // Configure an advanced action that we can assign.
     $aid = $this->configureAdvancedAction('system_message_action', $action_edit);
-    $edit = array('aid' => md5($aid));
+    $edit = array('aid' => drupal_hash_base64($aid));
     $this->drupalPost('admin/structure/trigger/user', $edit, t('Assign'), array(), array(), 'trigger-user-login-assign-form');
 
     // Verify that the action has been assigned to the correct hook.
@@ -322,7 +322,7 @@ class TriggerOtherTestCase extends TriggerWebTestCase {
     $test_user = $this->drupalCreateUser(array('administer actions'));
     $this->drupalLogin($test_user);
     $action_id = 'trigger_test_generic_action';
-    $hash = md5($action_id);
+    $hash = drupal_hash_base64($action_id);
     $edit = array('aid' => $hash);
     $this->drupalPost('admin/structure/trigger/comment', $edit, t('Assign'), array(), array(), 'trigger-comment-insert-assign-form');
 
@@ -351,7 +351,7 @@ class TriggerOtherTestCase extends TriggerWebTestCase {
     $test_user = $this->drupalCreateUser(array('administer actions'));
     $this->drupalLogin($test_user);
     $action_id = 'trigger_test_generic_action';
-    $hash = md5($action_id);
+    $hash = drupal_hash_base64($action_id);
     $edit = array('aid' => $hash);
     $this->drupalPost('admin/structure/trigger/taxonomy', $edit, t('Assign'), array(), array(), 'trigger-taxonomy-term-insert-assign-form');
 
@@ -403,7 +403,7 @@ class TriggerOrphanedActionsTestCase extends DrupalWebTestCase {
    */
   function testActionsOrphaned() {
     $action = 'trigger_test_generic_any_action';
-    $hash = md5($action);
+    $hash = drupal_hash_base64($action);
 
     // Assign an action from a disable-able module to a trigger, then pull the
     // trigger, and make sure the actions fire.
diff --git modules/update/update.fetch.inc modules/update/update.fetch.inc
index 7944828..9db4d1c 100644
--- modules/update/update.fetch.inc
+++ modules/update/update.fetch.inc
@@ -137,7 +137,7 @@ function _update_process_fetch_task($project) {
 
   $success = FALSE;
   $available = array();
-  $site_key = md5($base_url . drupal_get_private_key());
+  $site_key = drupal_hmac_base64($base_url, drupal_get_private_key());
   $url = _update_build_fetch_url($project, $site_key);
   $fetch_url_base = _update_get_fetch_url_base($project);
   $project_name = $project['name'];
diff --git modules/user/user.module modules/user/user.module
index 0b24fa2..ca23ed6 100644
--- modules/user/user.module
+++ modules/user/user.module
@@ -2079,8 +2079,7 @@ function user_cancel_url($account) {
 }
 
 function user_pass_rehash($password, $timestamp, $login) {
-  // A single md5() is vulnerable to length-extension attacks, so use it twice.
-  return md5(drupal_get_hash_salt() . md5($timestamp . $password . $login));
+  return drupal_hmac_base64($timestamp . $login, drupal_get_hash_salt() . $password);
 }
 
 /**
diff --git modules/user/user.pages.inc modules/user/user.pages.inc
index d59ded1..a51c30f 100644
--- modules/user/user.pages.inc
+++ modules/user/user.pages.inc
@@ -133,7 +133,7 @@ function user_pass_reset($form, &$form_state, $uid, $timestamp, $hashed_pass, $a
           user_login_finalize();
           drupal_set_message(t('You have just used your one-time login link. It is no longer necessary to use this link to log in. Please change your password.'));
           // Let the user's password be changed without the current password check.
-          $token = md5(drupal_random_bytes(55));
+          $token = drupal_hash_base64(drupal_random_bytes(55));
           $_SESSION['pass_reset_' . $user->uid] = $token;
           drupal_goto('user/' . $user->uid . '/edit', array('query' => array('pass-reset-token' => $token)));
         }
diff --git modules/user/user.test modules/user/user.test
index 64af9aa..ecd5d63 100644
--- modules/user/user.test
+++ modules/user/user.test
@@ -1259,7 +1259,7 @@ class UserBlocksUnitTests extends DrupalWebTestCase {
   private function insertSession(array $fields = array()) {
     $fields += array(
       'uid' => 0,
-      'sid' => md5(uniqid(mt_rand(), TRUE)),
+      'sid' => drupal_hash_base64(uniqid(mt_rand(), TRUE)),
       'timestamp' => REQUEST_TIME,
     );
     db_insert('sessions')
diff --git scripts/password-hash.sh scripts/password-hash.sh
index a7660fb..82813b9 100755
--- scripts/password-hash.sh
+++ scripts/password-hash.sh
@@ -13,10 +13,6 @@
  *  Plain-text passwords in quotes (or with spaces backslash escaped).
  */
 
-function variable_get($x, $default) {
-  return $default;
-}
-
 if (version_compare(PHP_VERSION, "5.2.0", "<")) {
   $version  = PHP_VERSION;
   echo <<<EOF
@@ -86,7 +82,7 @@ while ($param = array_shift($_SERVER['argv'])) {
 define('DRUPAL_ROOT', getcwd());
 
 include_once DRUPAL_ROOT . '/includes/password.inc';
-include_once DRUPAL_ROOT . '/includes/common.inc';
+include_once DRUPAL_ROOT . '/includes/bootstrap.inc';
 
 foreach ($passwords as $password) {
   print("\npassword: $password \t\thash: ". user_hash_password($password) ."\n");