From c2f92a3fb86e2b70e943fee5f1c17debc1b264d3 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mike.carper@gmail.com>
Date: Thu, 29 Mar 2012 15:48:14 -0700
Subject: [PATCH 01/29] Issue by mikeytown2: prevent variable_init from
 returning a blank array.

---
 includes/bootstrap.inc | 62 ++++++++++++++++++++++++++++--------------
 1 file changed, 41 insertions(+), 21 deletions(-)

diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index d857f651597..6db36634625 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -561,13 +561,21 @@ function drupal_get_filename($type, $name, $filename = NULL) {
  * file.
  */
 function variable_init($conf = array(), $regenerate = FALSE, $recursion_depth = 0) {
-  // NOTE: caching the variables improves performance by 20% when serving cached pages.
+  // NOTE: caching the variables improves performance by 20% when serving
+  // cached pages.
   if (!$regenerate && $cached = cache_get('variables', 'cache')) {
     $variables = $cached->data;
   }
   else {
     if (defined('MAINTENANCE_MODE') || lock_acquire('variable_cache_regenerate')) {
       $result = db_query('SELECT * FROM {variable}');
+      // Exit here if the database went away. Do not want to pollute the cache
+      // with bad data. This request isn't going to end well anyway; end it
+      // eairly.
+      if ($result === FALSE) {
+        // This function calls exit.
+        _db_error_page();
+      }
       while ($variable = db_fetch_object($result)) {
         $variables[$variable->name] = unserialize($variable->value);
       }
@@ -580,15 +588,27 @@ function variable_init($conf = array(), $regenerate = FALSE, $recursion_depth =
       // Wait for another request that is already doing this work.
       lock_wait('variable_cache_regenerate');
 
-      // Run the function again. Try a limited number of times to avoid 
-      // infinite recursion if the database connection is invalid for  
+      // Run the function again. Try a limited number of times to avoid
+      // infinite recursion if the database connection is invalid for
       // some reason, e.g., mysqld restart, loss of network, etc.
       $recursion_depth++;
       if ($recursion_depth < 50) {
         return variable_init($conf, $regenerate, $recursion_depth);
       }
 
-      $variables = array();
+      // If the recursion_depth hit the limit, assume we aren't going to get it
+      // from the cache or the lock will be released any time soon. Give up and
+      // get variables from the database.
+      $result = db_query('SELECT * FROM {variable}');
+      // Exit here if the database went away. Do not want to pollute the cache
+      // with bad data. This request isn't going to end well.
+      if ($result === FALSE) {
+        // This function calls exit.
+        _db_error_page();
+      }
+      while ($variable = db_fetch_object($result)) {
+        $variables[$variable->name] = unserialize($variable->value);
+      }
     }
   }
 
@@ -653,7 +673,7 @@ function variable_set($name, $value) {
   if (is_string($db_prefix) && strpos($db_prefix, 'simpletest') === 0) {
     cache_clear_all('variables', 'cache');
   }
-  
+
   variable_cache_rebuild();
 }
 
@@ -682,7 +702,7 @@ function variable_del($name) {
   if (is_string($db_prefix) && strpos($db_prefix, 'simpletest') === 0) {
     cache_clear_all('variables', 'cache');
   }
-  
+
   variable_cache_rebuild();
 }
 
@@ -805,7 +825,7 @@ function drupal_set_header($name = NULL, $value = NULL, $append = FALSE) {
   if (!isset($name)) {
     return $headers;
   }
-  
+
   // Support the Drupal 6 header API
   if (!isset($value)) {
     if (strpos($name, ':') !== FALSE) {
@@ -1423,7 +1443,7 @@ function drupal_bootstrap($phase = NULL) {
       _drupal_bootstrap($current_phase);
     }
   }
-  
+
   return $phase_index;
 }
 
@@ -1483,7 +1503,7 @@ function _drupal_bootstrap($phase) {
       // those using APC or memcached.
       require_once variable_get('lock_inc', './includes/lock.inc');
       lock_init();
-      
+
       // Detect if an installation is present.
       detect_installation_or_run_installer();
 
@@ -1534,11 +1554,11 @@ function _drupal_bootstrap($phase) {
         // We are done.
         exit;
       }
-  
+
       if (!$cache && drupal_page_is_cacheable() && $cache_mode != CACHE_EXTERNAL) {
         header('X-Drupal-Cache: MISS');
       }
-      
+
       // If using an external cache and the page is cacheable, set headers.
       if ($cache_mode == CACHE_EXTERNAL && drupal_page_is_cacheable()) {
         drupal_page_cache_header_external();
@@ -1679,17 +1699,17 @@ function ip_address() {
 
   if (!isset($ip_address)) {
     $ip_address = $_SERVER['REMOTE_ADDR'];
-    
+
     // Only use parts of the X-Forwarded-For (XFF) header that have followed a trusted route.
     // Specifically, identify the leftmost IP address in the XFF header that is not one of ours.
     // An XFF header is: X-Forwarded-For: client1, proxy1, proxy2
     if (isset($_SERVER['HTTP_' . variable_get('x_forwarded_for_header', 'X_FORWARDED_FOR')]) && variable_get('reverse_proxy', 0)) {
       // Load trusted reverse proxy server IPs.
       $reverse_proxy_addresses = variable_get('reverse_proxy_addresses', array());
-      
+
       // Turn XFF header into an array.
       $forwarded = explode(',', $_SERVER['HTTP_' . variable_get('x_forwarded_for_header', 'X_FORWARDED_FOR')]);
-      
+
       // Trim the forwarded IPs; they may have been delimited by commas and spaces.
       $forwarded = array_map('trim', $forwarded);
 
@@ -1698,7 +1718,7 @@ function ip_address() {
 
       // Eliminate all trusted IPs.
       $untrusted = array_diff($forwarded, $reverse_proxy_addresses);
-      
+
       // The right-most IP is the most specific we can trust.
       $ip_address = array_pop($untrusted);
     }
@@ -1712,9 +1732,9 @@ function ip_address() {
  */
 function drupal_session_initialize() {
   global $user;
-   
+
   session_set_save_handler('sess_open', 'sess_close', 'sess_read', 'sess_write', 'sess_destroy_sid', 'sess_gc');
- 
+
   if (isset($_COOKIE[session_name()])) {
     // If a session cookie exists, initialize the session. Otherwise the
     // session is only started on demand in drupal_session_commit(), making
@@ -1776,7 +1796,7 @@ function drupal_session_commit() {
 
 /**
  * Return whether a session has been started.
- */  
+ */
 function drupal_session_started($set = NULL) {
   static $session_started = FALSE;
   if (isset($set)) {
@@ -1841,7 +1861,7 @@ function drupal_save_session($status = NULL) {
   }
   return $save_session;
 }
-	
+
 /**
  * Returns the current bootstrap phase for this Drupal process.
  *
@@ -1886,7 +1906,7 @@ function drupal_generate_test_ua($prefix) {
     // check the HMAC before the database is initialized. filectime()
     // and fileinode() are not easily determined from remote.
 //    $filepath = DRUPAL_ROOT . '/includes/bootstrap.inc';
-    $filepath = './includes/bootstrap.inc';                
+    $filepath = './includes/bootstrap.inc';
 //    $key = sha1(serialize($databases) . filectime($filepath) . fileinode($filepath), TRUE);
     $key = sha1(serialize($db_url) . filectime($filepath) . fileinode($filepath), TRUE);
   }
@@ -1914,7 +1934,7 @@ function drupal_is_cli() {
  */
 function drupal_session_destroy() {
   session_destroy();
-  
+
   // Workaround PHP 5.2 fatal error "Failed to initialize storage module".
   // @see http://bugs.php.net/bug.php?id=32330
   session_set_save_handler('sess_open', 'sess_close', 'sess_read', 'sess_write', 'sess_destroy_sid', 'sess_gc');

From 855b22040cada75101f15cfac802f30717561f0b Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 14:47:18 -0400
Subject: [PATCH 02/29] Issue #939810 by mikeytown2: Notice: Undefined index:
 key in format_xml_elements()

---
 includes/common.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/common.inc b/includes/common.inc
index 7ef1e51b1ba..5c0908ce06a 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -1148,7 +1148,7 @@ function format_xml_elements($array) {
   $output = '';
   foreach ($array as $key => $value) {
     if (is_numeric($key)) {
-      if ($value['key']) {
+      if (!empty($value['key'])) {
         $output .= ' <'. $value['key'];
         if (isset($value['attributes']) && is_array($value['attributes'])) {
           $output .= drupal_attributes($value['attributes']);

From 0fb357773c547962de65b117d9abc247e422820c Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 14:52:44 -0400
Subject: [PATCH 03/29] Issue #557542 by mikeytown2, c960657, catch, &
 glennpratt: Cache module_implements()

---
 includes/common.inc |  3 ++
 includes/module.inc | 72 ++++++++++++++++++++++++++++++++++++++++-----
 install.php         | 36 ++++++++++-------------
 update.php          |  4 ++-
 4 files changed, 86 insertions(+), 29 deletions(-)

diff --git a/includes/common.inc b/includes/common.inc
index 5c0908ce06a..739ae17b456 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -1668,6 +1668,9 @@ function drupal_page_footer() {
   }
 
   module_invoke_all('exit');
+
+  // Update the hook implementation cache.
+  module_implements('', FALSE, FALSE, TRUE);
 }
 
 /**
diff --git a/includes/module.inc b/includes/module.inc
index 79583675bd5..6fa7448e836 100644
--- a/includes/module.inc
+++ b/includes/module.inc
@@ -257,15 +257,15 @@ function module_load_install($module) {
 
 /**
  * Load a module include file.
- * 
+ *
  * Examples:
  * @code
  *   // Load node.admin.inc from the node module.
  *   module_load_include('inc', 'node', 'node.admin');
  *   // Load content_types.inc from the node module.
- *   module_load_include('inc', 'node', 'content_types');  
+ *   module_load_include('inc', 'node', 'content_types');
  * @endcode
- * 
+ *
  * Do not use this function to load an install file. Use module_load_install()
  * instead.
  *
@@ -274,7 +274,7 @@ function module_load_install($module) {
  * @param $module
  *   The module to which the include file belongs.
  * @param $name
- *   Optionally, specify the base file name (without the $type extension). 
+ *   Optionally, specify the base file name (without the $type extension).
  *   If not set, $module is used.
  */
 function module_load_include($type, $module, $name = NULL) {
@@ -420,22 +420,64 @@ function module_hook($module, $hook) {
  * @param $sort
  *   By default, modules are ordered by weight and filename, settings this option
  *   to TRUE, module list will be ordered by module name.
- * @param $refresh
+ * @param $reset
  *   For internal use only: Whether to force the stored list of hook
  *   implementations to be regenerated (such as after enabling a new module,
  *   before processing hook_enable).
+ * @param $write_cache
+ *   For internal use only: Update the persistent cache of hook implementations.
  * @return
  *   An array with the names of the modules which are implementing this hook.
  */
-function module_implements($hook, $sort = FALSE, $refresh = FALSE) {
+function module_implements($hook, $sort = FALSE, $reset = FALSE, $write_cache = FALSE) {
   static $implementations;
-
-  if ($refresh) {
+  static $verified;
+
+  // We maintain a persistent cache of hook implementations in addition to the
+  // static cache to avoid looping through every module and every hook on each
+  // request. Benchmarks show that the benefit of this caching outweighs the
+  // additional database hit even when using the default database caching
+  // backend and only a small number of modules are enabled. The cost of the
+  // cache_get() is more or less constant and reduced further when non-database
+  // caching backends are used, so there will be more significant gains when a
+  // large number of modules are installed or hooks invoked, since this can
+  // quickly lead to module_hook() being called several thousand times
+  // per request.
+  if ($reset) {
     $implementations = array();
+    $verified = array();
+    cache_set('module_implements', array());
     return;
   }
 
+  if ($write_cache) {
+    // Check whether we should write the cache. We do not want to cache hooks
+    // which are only invoked on HTTP POST requests since these do not need to
+    // be optimized as tightly, and not doing so keeps the cache entry smaller.
+    if (isset($implementations['#write_cache']) && ($_SERVER['REQUEST_METHOD'] == 'GET' || $_SERVER['REQUEST_METHOD'] == 'HEAD')) {
+      unset($implementations['#write_cache']);
+      cache_set('module_implements', $implementations);
+    }
+    return;
+  }
+
+  // Fetch implementations from cache.
+  if (empty($implementations)) {
+    if (function_exists('cache_get')) {
+      $cache = cache_get('module_implements');
+    }
+    if (empty($cache)) {
+      $implementations = array();
+    }
+    else {
+      $implementations = $cache->data;
+    }
+  }
+
   if (!isset($implementations[$hook])) {
+    // The hook is not cached, so ensure that whether or not it has
+    // implementations, that the cache is updated at the end of the request.
+    $implementations['#write_cache'] = TRUE;
     $implementations[$hook] = array();
     $list = module_list(FALSE, TRUE, $sort);
     foreach ($list as $module) {
@@ -444,6 +486,20 @@ function module_implements($hook, $sort = FALSE, $refresh = FALSE) {
       }
     }
   }
+  elseif (empty($verified[$hook])) {
+    foreach ($implementations[$hook] as $key => $module) {
+      // It is possible that a module removed a hook implementation without the
+      // implementations cache being rebuilt yet, so we check module_hook() on
+      // each request to avoid undefined function errors.
+      if (!module_hook($module, $hook)) {
+        // Clear out the stale implementation from the cache and force a cache
+        // refresh to forget about no longer existing hook implementations.
+        unset($implementations[$hook][$key]);
+        $implementations['#write_cache'] = TRUE;
+      }
+    }
+    $verified[$hook] = TRUE;
+  }
 
   // The explicit cast forces a copy to be made. This is needed because
   // $implementations[$hook] is only a reference to an element of
diff --git a/install.php b/install.php
index beb3fcb4f18..b02bb41febf 100644
--- a/install.php
+++ b/install.php
@@ -47,6 +47,18 @@ function install_main() {
   drupal_load('module', 'system');
   drupal_load('module', 'filter');
 
+  // Load the cache infrastructure using a "fake" cache implementation that
+  // does not attempt to write to the database. We need this during the initial
+  // part of the installer because the database is not available yet. We
+  // continue to use it even when the database does become available, in order
+  // to preserve consistency between interactive and command-line installations
+  // (the latter complete in one page request and therefore are forced to
+  // continue using the cache implementation they started with) and also
+  // because any data put in the cache during the installer is inherently
+  // suspect, due to the fact that Drupal is not fully set up yet.
+  require_once './includes/cache-install.inc';
+  $conf['cache_inc'] = './includes/cache-install.inc';
+
   // Install profile chosen, set the global immediately.
   // This needs to be done before the theme cache gets 
   // initialized in drupal_maintenance_theme().
@@ -61,12 +73,6 @@ function install_main() {
   $verify = install_verify_settings();
 
   if ($verify) {
-    // Since we have a database connection, we use the normal cache system.
-    // This is important, as the installer calls into the Drupal system for
-    // the clean URL checks, so we should maintain the cache properly.
-    require_once './includes/cache.inc';
-    $conf['cache_inc'] = './includes/cache.inc';
-
     // Establish a connection to the database.
     require_once './includes/database.inc';
     db_set_active();
@@ -78,13 +84,6 @@ function install_main() {
     }
   }
   else {
-    // Since no persistent storage is available yet, and functions that check
-    // for cached data will fail, we temporarily replace the normal cache
-    // system with a stubbed-out version that short-circuits the actual
-    // caching process and avoids any errors.
-    require_once './includes/cache-install.inc';
-    $conf['cache_inc'] = './includes/cache-install.inc';
-
     $task = NULL;
   }
 
@@ -821,17 +820,14 @@ function install_tasks($profile, $task) {
 
   // The end of the install process. Remember profile used.
   if ($task == 'done') {
-    // Rebuild menu to get content type links registered by the profile,
-    // and possibly any other menu items created through the tasks.
-    menu_rebuild();
+    // Flush all caches to ensure that any full bootstraps during the installer
+    // do not leave stale cached data, and that any content types or other items
+    // registered by the install profile are registered correctly.
+    drupal_flush_all_caches();
 
     // Register actions declared by any modules.
     actions_synchronize();
 
-    // Randomize query-strings on css/js files, to hide the fact that
-    // this is a new install, not upgraded yet.
-    _drupal_flush_css_js();
-
     variable_set('install_profile', $profile);
   }
 
diff --git a/update.php b/update.php
index e32547369da..44e06987717 100644
--- a/update.php
+++ b/update.php
@@ -597,7 +597,7 @@ function update_check_requirements() {
 $op = isset($_REQUEST['op']) ? $_REQUEST['op'] : '';
 if (empty($op)) {
   // Minimum load of components.
-  drupal_bootstrap(DRUPAL_BOOTSTRAP_CONFIGURATION);
+  drupal_bootstrap(DRUPAL_BOOTSTRAP_DATABASE);
 
   require_once './includes/install.inc';
   require_once './includes/file.inc';
@@ -608,6 +608,8 @@ function update_check_requirements() {
   $module_list['system']['filename'] = 'modules/system/system.module';
   $module_list['filter']['filename'] = 'modules/filter/filter.module';
   module_list(TRUE, FALSE, FALSE, $module_list);
+  module_implements('', FALSE, TRUE);
+
   drupal_load('module', 'system');
   drupal_load('module', 'filter');
 

From 707636f5139262de775d734a4f36825e81527f49 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 14:56:36 -0400
Subject: [PATCH 04/29] Issue #1317236 by mikeytown2: Race condition in
 file_delete: Warning: unlink() No such file or directory in file_delete()

---
 includes/file.inc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/includes/file.inc b/includes/file.inc
index 4a3e3fc16c5..c8058a0b108 100644
--- a/includes/file.inc
+++ b/includes/file.inc
@@ -520,7 +520,7 @@ function file_create_filename($basename, $directory) {
  */
 function file_delete($path) {
   if (is_file($path)) {
-    return unlink($path);
+    return @unlink($path);
   }
 }
 

From cdbd30096cf477180bbe1f8dc11fc640c6c9ce52 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 14:59:40 -0400
Subject: [PATCH 05/29] Issue #1004820 by mikeytown2: Notice: Undefined index:
 type in dblog_build_filter_query()

---
 modules/dblog/dblog.admin.inc | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/dblog/dblog.admin.inc b/modules/dblog/dblog.admin.inc
index 853a2ce14c8..3448bd00026 100644
--- a/modules/dblog/dblog.admin.inc
+++ b/modules/dblog/dblog.admin.inc
@@ -191,8 +191,10 @@ function dblog_build_filter_query() {
   foreach ($_SESSION['dblog_overview_filter'] as $key => $filter) {
     $filter_where = array();
     foreach ($filter as $value) {
-      $filter_where[] = $filters[$key]['where'];
-      $args[] = $value;
+      if (isset($filters[$key]['where'])) {
+        $filter_where[] = $filters[$key]['where'];
+        $args[] = $value;
+      }
     }
     if (!empty($filter_where)) {
       $where[] = '('. implode(' OR ', $filter_where) .')';

From 71e7146d5d1aa2e66a3b2027247d1dee00b17d79 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 15:00:58 -0400
Subject: [PATCH 06/29] Issue #134204 by mikeytown2: Optimize
 element_children()

---
 includes/common.inc | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/includes/common.inc b/includes/common.inc
index 739ae17b456..a0550f6949a 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -3091,10 +3091,18 @@ function element_child($key) {
 }
 
 /**
- * Get keys of a structured array tree element that are not properties (i.e., do not begin with '#').
+ * Get keys of a structured array tree element that are not properties
+ * (i.e., do not begin with '#').
  */
 function element_children($element) {
-  return array_filter(array_keys((array) $element), 'element_child');
+  $results = array();
+  foreach ((array) $element as $key => $value) {
+    // Inlined call to element_child() for performance reasons.
+    if (!isset($key[0]) || $key[0] != '#') {
+      $results[] = $key;
+    }
+  }
+  return $results;
 }
 
 /**

From e909d96e85aa029796f222adb3252c86eec93a96 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 15:02:36 -0400
Subject: [PATCH 07/29] Issue #753064 by mikeytown2: _menu_link_translate()
 might avoid calling _menu_load_objects()

---
 includes/menu.inc | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/includes/menu.inc b/includes/menu.inc
index 0d377d0d387..9b813d436aa 100644
--- a/includes/menu.inc
+++ b/includes/menu.inc
@@ -581,7 +581,7 @@ function _menu_translate(&$router_item, $map, $to_arg = FALSE) {
   $router_item['href'] = implode('/', $link_map);
   $router_item['options'] = array();
   _menu_check_access($router_item, $map);
-  
+
   // For performance, don't localize an item the user can't access.
   if ($router_item['access']) {
     _menu_item_localize($router_item, $map);
@@ -656,7 +656,11 @@ function _menu_link_translate(&$item) {
     }
     // menu_tree_check_access() may set this ahead of time for links to nodes.
     if (!isset($item['access'])) {
-      if (!_menu_load_objects($item, $map)) {
+      // Loading a views object is expensive so we have a special case for it.
+      if (isset($item['access_callback']) && $item['access_callback'] == 'views_access' && $item['access_arguments'] == 'a:1:{i:0;b:1;}' && $item['title_callback'] == 't' && empty($item['title_arguments'])) {
+        $item['access'] = TRUE;
+      }
+      elseif (!_menu_load_objects($item, $map)) {
         // An error occurred loading an object.
         $item['access'] = FALSE;
         return FALSE;
@@ -1695,7 +1699,7 @@ function menu_cache_clear_all() {
 function menu_rebuild() {
   if (!lock_acquire('menu_rebuild')) {
     // Wait for another request that is already doing this work.
-    // We choose to block here since otherwise the router item may not 
+    // We choose to block here since otherwise the router item may not
     // be avaiable in menu_execute_active_handler() resulting in a 404.
     lock_wait('menu_rebuild');
     return FALSE;
@@ -1709,7 +1713,7 @@ function menu_rebuild() {
   // Clear the menu, page and block caches.
   menu_cache_clear_all();
   _menu_clear_page_cache();
-  
+
   if (defined('MAINTENANCE_MODE')) {
     variable_set('menu_rebuild_needed', TRUE);
   }
@@ -1904,7 +1908,7 @@ function _menu_delete_item($item, $force = FALSE) {
  *   - router_path: The path of the relevant router item.
  *
  * @return
- *   The mlid of the saved menu link, or FALSE if the menu link could not be 
+ *   The mlid of the saved menu link, or FALSE if the menu link could not be
  *   saved.
  */
 function menu_link_save(&$item) {

From 471dea89de2175f6d5256751cf0b90cd389a797f Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 15:56:03 -0400
Subject: [PATCH 08/29] Issue #261148 by mikeytown2, catch, chx: menu_masks
 variable is empty (race condition)

---
 includes/menu.inc | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/includes/menu.inc b/includes/menu.inc
index 9b813d436aa..79d8843127a 100644
--- a/includes/menu.inc
+++ b/includes/menu.inc
@@ -206,7 +206,16 @@ function menu_get_ancestors($parts) {
   $ancestors = array();
   $length =  $number_parts - 1;
   $end = (1 << $number_parts) - 1;
-  $masks = variable_get('menu_masks', array());
+  $masks = variable_get('menu_masks', NULL);
+  // If the optimized menu_masks array is not available, try every character
+  // position to see if that matches up with a wildcard, slash, or the original
+  // value in order to get the correct $ancestors and $placeholders returned.
+  // Do not use this as the default value of the menu_masks variable to avoid
+  // building such a big array. Currently the maximum value for $end is 511
+  // (2^9) - 1. 9 comes from the MENU_MAX_PARTS constant.
+  if (!$masks) {
+    $masks = range($end, 1);
+  }
   // Only examine patterns that actually exist as router items (the masks).
   foreach ($masks as $i) {
     if ($i > $end) {

From 9c92a1a5804418214696ec393f97ca09b452aa5e Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 15:58:25 -0400
Subject: [PATCH 09/29] Issue #1688282 by mikeytown2: Unknown error: Function
 split() is deprecated in _filter_autop()

---
 modules/filter/filter.module | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/filter/filter.module b/modules/filter/filter.module
index b95517914ee..2ed560d26da 100644
--- a/modules/filter/filter.module
+++ b/modules/filter/filter.module
@@ -911,7 +911,7 @@ function _filter_autop($text) {
       else {
         // Opening or closing tag?
         $open = ($chunk[1] != '/');
-        list($tag) = split('[ >]', substr($chunk, 2 - $open), 2);
+        list($tag) = preg_split('/[ >]/', substr($chunk, 2 - $open), 2);
         if (!$ignore) {
           if ($open) {
             $ignore = TRUE;

From 9325a3749f632ee73656cf35cce589a3658d79e2 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:00:34 -0400
Subject: [PATCH 10/29] Issue #521838 by mikeytown2: Speedup/Clean up
 drupal_get_schema_versions()

---
 includes/install.inc | 42 +++++++++++++++++++++++++++++-------------
 1 file changed, 29 insertions(+), 13 deletions(-)

diff --git a/includes/install.inc b/includes/install.inc
index e70f87ccbaa..80e83265d0b 100644
--- a/includes/install.inc
+++ b/includes/install.inc
@@ -34,25 +34,41 @@ function drupal_load_updates() {
  * @param $module
  *   A module name.
  * @return
- *   If the module has updates, an array of available updates sorted by version. 
+ *   If the module has updates, an array of available updates sorted by version.
  *   Otherwise, FALSE.
  */
 function drupal_get_schema_versions($module) {
-  $updates = array();
-  $functions = get_defined_functions();
-  foreach ($functions['user'] as $function) {
-    if (strpos($function, $module .'_update_') === 0) {
-      $version = substr($function, strlen($module .'_update_'));
-      if (is_numeric($version)) {
-        $updates[] = $version;
+  static $updates;
+  if (!isset($updates[$module])) {
+    $updates = array();
+
+    foreach (module_list() as $loaded_module) {
+      $updates[$loaded_module] = array();
+    }
+
+    // Prepare regular expression to match all possible defined hook_update_N().
+    $regexp = '/^(?P<module>.+)_update_(?P<version>\d+)$/';
+    $functions = get_defined_functions();
+    // Narrow this down to functions ending with an integer, since all
+    // hook_update_N() functions end this way, and there are other
+    // possible functions which match '_update_'. We use preg_grep() here
+    // instead of foreaching through all defined functions, since the loop
+    // through all PHP functions can take significant page execution time
+    // and this function is called on every administrative page via
+    // system_requirements().
+    foreach (preg_grep('/_\d+$/', $functions['user']) as $function) {
+      // If this function is a module update function, add it to the list of
+      // module updates.
+      if (preg_match($regexp, $function, $matches)) {
+        $updates[$matches['module']][] = $matches['version'];
       }
     }
+    // Ensure that updates are applied in numerical order.
+    foreach ($updates as &$module_updates) {
+      sort($module_updates, SORT_NUMERIC);
+    }
   }
-  if (count($updates) == 0) {
-    return FALSE;
-  }
-  sort($updates, SORT_NUMERIC);
-  return $updates;
+  return empty($updates[$module]) ? FALSE : $updates[$module];
 }
 
 /**

From a506b7d662c810d2a9c89445453df7ca3b69c9ad Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:08:40 -0400
Subject: [PATCH 11/29] Issue #1710656 by mikeytown2: If item is hidden in
 _menu_tree_check_access() skip it right away.

---
 includes/menu.inc | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/includes/menu.inc b/includes/menu.inc
index 79d8843127a..a316048e41e 100644
--- a/includes/menu.inc
+++ b/includes/menu.inc
@@ -1038,6 +1038,11 @@ function _menu_tree_check_access(&$tree) {
   $new_tree = array();
   foreach ($tree as $key => $v) {
     $item = &$tree[$key]['link'];
+    // Do not load hidden menu items if not in active breadcrumb trail and
+    // user can't administer the menu.
+    if (!empty($item['hidden']) && empty($item['in_active_trail']) && !user_access('administer menu')) {
+      continue;
+    }
     _menu_link_translate($item);
     if ($item['access']) {
       if ($tree[$key]['below']) {
@@ -1730,9 +1735,9 @@ function menu_rebuild() {
     variable_del('menu_rebuild_needed');
   }
   lock_release('menu_rebuild');
-  
+
   db_query('COMMIT');
-  
+
   return TRUE;
 }
 

From 280a9300fe17478ce707d3ea854aa5fc41498e1d Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:33:55 -0400
Subject: [PATCH 12/29] Issue #352180 by scor: Better, multi-site friendly www.
 addition/removal in .htaccess

---
 .htaccess | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.htaccess b/.htaccess
index 4733ffa4a86..718c3bf51d4 100644
--- a/.htaccess
+++ b/.htaccess
@@ -86,15 +86,15 @@ DirectoryIndex index.php
   #
   # To redirect all users to access the site WITH the 'www.' prefix,
   # (http://example.com/... will be redirected to http://www.example.com/...)
-  # adapt and uncomment the following:
-  # RewriteCond %{HTTP_HOST} ^example\.com$ [NC]
-  # RewriteRule ^(.*)$ http://www.example.com/$1 [L,R=301]
+  # uncomment the following:
+  # RewriteCond %{HTTP_HOST} !^www\. [NC]
+  # RewriteRule ^ http://www.%{HTTP_HOST}%{REQUEST_URI} [L,R=301]
   #
   # To redirect all users to access the site WITHOUT the 'www.' prefix,
   # (http://www.example.com/... will be redirected to http://example.com/...)
-  # uncomment and adapt the following:
-  # RewriteCond %{HTTP_HOST} ^www\.example\.com$ [NC]
-  # RewriteRule ^(.*)$ http://example.com/$1 [L,R=301]
+  # uncomment the following:
+  # RewriteCond %{HTTP_HOST} ^www\.(.+)$ [NC]
+  # RewriteRule ^ http://%1%{REQUEST_URI} [L,R=301]
 
   # Modify the RewriteBase if you are using Drupal in a subdirectory or in a
   # VirtualDocumentRoot and the rewrite rules are not working properly.

From 1bfe877013bf18d6c2115c9669b840ec3ff5ec10 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:38:38 -0400
Subject: [PATCH 13/29] Issue #764726 by mikeytown2:
 hook_taxonomy_term_presave() is missing

---
 modules/taxonomy/taxonomy.module | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/modules/taxonomy/taxonomy.module b/modules/taxonomy/taxonomy.module
index 38b74e19f35..ae0208ae884 100644
--- a/modules/taxonomy/taxonomy.module
+++ b/modules/taxonomy/taxonomy.module
@@ -200,6 +200,19 @@ function taxonomy_save_vocabulary(&$edit) {
     $edit['module'] = 'taxonomy';
   }
 
+  $return = module_invoke_all('taxonomy_vocabulary_presave', $edit);
+  if (is_array($return) && !empty($return)) {
+    $update = TRUE;
+    foreach ($return as $key => $value) {
+      if (is_numeric($key) && $value == FALSE) {
+        $update = FALSE;
+      }
+    }
+    if ($update) {
+      $edit = $return;
+    }
+  }
+
   if (!empty($edit['vid']) && !empty($edit['name'])) {
     drupal_write_record('vocabulary', $edit, 'vid');
     db_query("DELETE FROM {vocabulary_node_types} WHERE vid = %d", $edit['vid']);
@@ -309,6 +322,19 @@ function taxonomy_save_term(&$form_values) {
     'weight' => 0
   );
 
+  $return = module_invoke_all('taxonomy_term_presave', $form_values);
+  if (is_array($return) && !empty($return)) {
+    $update = TRUE;
+    foreach ($return as $key => $value) {
+      if (is_numeric($key) && $value == FALSE) {
+        $update = FALSE;
+      }
+    }
+    if ($update) {
+      $form_values = $return;
+    }
+  }
+
   if (!empty($form_values['tid']) && $form_values['name']) {
     drupal_write_record('term_data', $form_values, 'tid');
     $hook = 'update';

From 4b90144507dc3e66de563ebc3cde2d6e0d0cd481 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:40:39 -0400
Subject: [PATCH 14/29] Issue #496184 by mikeytown2: db_set_active errors out
 if db_connect fails. Add in the ability to handle this gracefully (don't
 always call _db_error_page).

---
 includes/database.inc        | 52 +++++++++++++++++++++++++++++++-----
 includes/database.mysql.inc  |  4 +--
 includes/database.mysqli.inc |  4 +--
 includes/database.pgsql.inc  |  4 +--
 4 files changed, 51 insertions(+), 13 deletions(-)

diff --git a/includes/database.inc b/includes/database.inc
index efb4a90fa25..79862da6a1d 100644
--- a/includes/database.inc
+++ b/includes/database.inc
@@ -117,11 +117,13 @@ function db_prefix_tables($sql) {
  * @param $name
  *   The key in the $db_url global variable from settings.php. If omitted, the
  *   default connection will be made active.
+ * @param $abort
+ *   If database connection could not be made, should we abort here or continue.
  *
  * @return
  *   The name of the previously active database, or FALSE if none was found.
  */
-function db_set_active($name = 'default') {
+function db_set_active($name = 'default', $abort = TRUE) {
   global $db_url, $db_slave_url, $db_type, $active_db, $active_slave_db;
   static $db_conns, $db_slave_conns, $active_name = FALSE;
 
@@ -139,7 +141,7 @@ function db_set_active($name = 'default') {
         $slave_connect_url = $db_slave_url[$name][$slave_index];
       }
       else {
-        $slave_connect_url = $db_slave_url[$name];        
+        $slave_connect_url = $db_slave_url[$name];
       }
     }
     else {
@@ -149,7 +151,7 @@ function db_set_active($name = 'default') {
         $slave_connect_url = $db_slave_url[$slave_index];
       }
       else {
-        $slave_connect_url = $db_slave_url;        
+        $slave_connect_url = $db_slave_url;
       }
     }
 
@@ -163,9 +165,45 @@ function db_set_active($name = 'default') {
       _db_error_page("The database type '". $db_type ."' is unsupported. Please use either 'mysql' or 'mysqli' for MySQL, or 'pgsql' for PostgreSQL databases.");
     }
 
-    $db_conns[$name] = db_connect($connect_url);
+    $connection = db_connect($connect_url);
+    // db_connect is using array return notation.
+    if (is_array($connection)) {
+      list($success, $result) = $connection;
+      // Connection worked
+      if ($success) {
+        $db_conns[$name] = $result;
+      }
+      // Connection failed and abort page load.
+      elseif ($abort) {
+        _db_error_page($result);
+      }
+      // Connection failed but return false. Calling function will handle error.
+      else {
+        return FALSE;
+      }
+    }
+    // db_connect is not using array return notation; revert to old code style.
+    else {
+      $db_conns[$name] = $connection;
+    }
     if (!empty($slave_connect_url)) {
-      $db_slave_conns[$name] = db_connect($slave_connect_url); 
+      $connection = db_connect($slave_connect_url);
+      // db_connect is using array return notation.
+      if (is_array($connection)) {
+        list($success, $result) = $connection;
+        // Connection worked
+        if ($success) {
+          $db_slave_conns[$name] = $result;
+        }
+        // Connection failed, set to false.
+        else {
+          $db_slave_conns[$name] = FALSE;
+        }
+      }
+      // db_connect is not using array return notation; revert to old code style.
+      else {
+        $db_slave_conns[$name] = $connection;
+      }
     }
   }
 
@@ -173,7 +211,7 @@ function db_set_active($name = 'default') {
   // Set the active connection.
   $active_name = $name;
   $active_db = $db_conns[$name];
-  if (isset($db_slave_conns[$name])) {
+  if (!empty($db_slave_conns[$name])) {
     $active_slave_db = $db_slave_conns[$name];
   }
   else {
@@ -696,7 +734,7 @@ function db_ignore_slave() {
     // the old data.
     $duration = variable_get('maximum_replication_lag', 300);
     // Set session variable with amount of time to delay before using slave.
-    // This will stick around for 5 minutes by default. 
+    // This will stick around for 5 minutes by default.
     // There is another $_Session variable 'not_slavesafe' for single queries.
     $_SESSION['ignore_slave_server'] = $_SERVER['REQUEST_TIME'] + $duration;
   }
diff --git a/includes/database.mysql.inc b/includes/database.mysql.inc
index 4ff53e1fa77..73c5a7aaa9a 100644
--- a/includes/database.mysql.inc
+++ b/includes/database.mysql.inc
@@ -76,7 +76,7 @@ function db_connect($url) {
   $connection = @mysql_connect($url['host'], $url['user'], $url['pass'], TRUE, 2);
   if (!$connection || !mysql_select_db(substr($url['path'], 1))) {
     // Show error screen otherwise
-    _db_error_page(mysql_error());
+    return array(FALSE, mysql_error());
   }
 
   // Force MySQL to use the UTF-8 character set. Also set the collation, if a
@@ -89,7 +89,7 @@ function db_connect($url) {
     mysql_query('SET NAMES utf8', $connection);
   }
 
-  return $connection;
+  return array(TRUE, $connection);
 }
 
 /**
diff --git a/includes/database.mysqli.inc b/includes/database.mysqli.inc
index 2ee710bdb75..f0ce35d4ec2 100644
--- a/includes/database.mysqli.inc
+++ b/includes/database.mysqli.inc
@@ -75,7 +75,7 @@ function db_connect($url) {
   @mysqli_real_connect($connection, $url['host'], $url['user'], $url['pass'], substr($url['path'], 1), $url['port'], NULL, MYSQLI_CLIENT_FOUND_ROWS);
 
   if (mysqli_connect_errno() > 0) {
-    _db_error_page(mysqli_connect_error());
+    return array(FALSE, mysqli_connect_error());
   }
 
   // Force MySQL to use the UTF-8 character set. Also set the collation, if a
@@ -88,7 +88,7 @@ function db_connect($url) {
     mysqli_query($connection, 'SET NAMES utf8');
   }
 
-  return $connection;
+  return array(TRUE, $connection);
 }
 
 /**
diff --git a/includes/database.pgsql.inc b/includes/database.pgsql.inc
index 161de08f513..e44bc00d7f8 100644
--- a/includes/database.pgsql.inc
+++ b/includes/database.pgsql.inc
@@ -78,14 +78,14 @@ function db_connect($url) {
   $connection = @pg_connect($conn_string);
   if (!$connection) {
     require_once './includes/unicode.inc';
-    _db_error_page(decode_entities($php_errormsg));
+    return array(FALSE, decode_entities($php_errormsg));
   }
 
   // Restore error tracking setting
   ini_set('track_errors', $track_errors_previous);
 
   pg_query($connection, "set client_encoding=\"UTF8\"");
-  return $connection;
+  return array(TRUE, $connection);
 }
 
 /**

From 91e2070b741a18bfc4069703ae142c6d537e76b2 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:44:12 -0400
Subject: [PATCH 15/29] Issue #961908 by mikeytown2: Make drupal_attributes()
 faster

---
 includes/common.inc | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/includes/common.inc b/includes/common.inc
index a0550f6949a..36b69945215 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -1572,13 +1572,11 @@ function url($path = NULL, $options = array()) {
  *   An HTML string ready for insertion in a tag.
  */
 function drupal_attributes($attributes = array()) {
-  if (is_array($attributes)) {
-    $t = '';
-    foreach ($attributes as $key => $value) {
-      $t .= " $key=".'"'. check_plain($value) .'"';
-    }
-    return $t;
+  $t = '';
+  foreach ((array) $attributes as $attribute => $data) {
+    $t .= " $attribute=".'"'. check_plain($data) .'"';
   }
+  return $t;
 }
 
 /**

From c2da748fcffae16195aeaa5c74bed79fbcfe28ca Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 16:49:57 -0400
Subject: [PATCH 16/29] Issue #1103910 by mikeytown2, catch:
 bootstrap_invoke_all() queries bootstrap modules twice

---
 includes/bootstrap.inc       | 6 +++++-
 modules/system/system.module | 9 ++++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index 72cd178e819..3a6030e4e3d 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -767,7 +767,11 @@ function drupal_page_is_cacheable($force = NULL) {
  *   The name of the bootstrap hook we wish to invoke.
  */
 function bootstrap_invoke_all($hook) {
-  foreach (module_list(TRUE, TRUE) as $module) {
+  static $bootstrap_modules;
+  if (!isset($bootstrap_modules)) {
+    $bootstrap_modules = module_list(TRUE, TRUE);
+  }
+  foreach ($bootstrap_modules as $module) {
     drupal_load('module', $module);
     module_invoke($module, $hook);
   }
diff --git a/modules/system/system.module b/modules/system/system.module
index 1df0a9160c5..ec30bdd0f9f 100644
--- a/modules/system/system.module
+++ b/modules/system/system.module
@@ -1044,9 +1044,16 @@ function system_find_base_theme($themes, $key, $used_keys = array()) {
  */
 function system_region_list($theme_key) {
   static $list = array();
+  global $theme, $theme_info;
 
   if (!array_key_exists($theme_key, $list)) {
-    $info = unserialize(db_result(db_query("SELECT info FROM {system} WHERE type = 'theme' AND name = '%s'", $theme_key)));
+    if ($theme == $theme_key) {
+      $info = $theme_info->info;
+    }
+    else {
+      $info = unserialize(db_result(db_query("SELECT info FROM {system} WHERE type = 'theme' AND name = '%s'", $theme_key)));
+    }
+
     $list[$theme_key] = array_map('t', $info['regions']);
   }
 

From 9a5b2d426d54d5cf5aef501b3487f8ae38728e78 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:40:07 -0400
Subject: [PATCH 17/29] Issue #1345402 by mikeytown2, catch: Backport
 DRUPAL_ROOT to 6.x

---
 cron.php                                      |  7 +-
 includes/batch.inc                            |  4 +-
 includes/bootstrap.inc                        | 32 ++++----
 includes/common.inc                           | 22 +++---
 includes/database.inc                         |  4 +-
 includes/database.mysql.inc                   |  2 +-
 includes/database.mysqli.inc                  |  2 +-
 includes/database.pgsql.inc                   |  2 +-
 includes/form.inc                             |  2 +-
 includes/image.inc                            |  4 +-
 includes/install.inc                          | 28 +++----
 includes/mail.inc                             |  2 +-
 includes/menu.inc                             |  4 +-
 includes/module.inc                           |  4 +-
 includes/theme.inc                            | 44 +++++------
 includes/theme.maintenance.inc                | 14 ++--
 includes/unicode.inc                          |  2 +-
 index.php                                     |  7 +-
 install.php                                   | 75 ++++++++++---------
 modules/color/color.module                    |  2 +-
 modules/locale/locale.module                  |  4 +-
 modules/poll/poll.module                      |  2 +-
 modules/system/system.admin.inc               | 12 +--
 modules/system/system.install                 |  2 +-
 modules/system/system.module                  |  4 +-
 modules/update/update.fetch.inc               |  2 +-
 modules/update/update.module                  |  4 +-
 themes/engines/phptemplate/phptemplate.engine |  2 +-
 update.php                                    | 19 +++--
 xmlrpc.php                                    | 11 ++-
 30 files changed, 175 insertions(+), 150 deletions(-)

diff --git a/cron.php b/cron.php
index 79fd2381b1f..7917fad2f06 100644
--- a/cron.php
+++ b/cron.php
@@ -5,6 +5,11 @@
  * Handles incoming requests to fire off regularly-scheduled tasks (cron jobs).
  */
 
-include_once './includes/bootstrap.inc';
+/**
+ * Root directory of Drupal installation.
+ */
+define('DRUPAL_ROOT', getcwd());
+
+include_once DRUPAL_ROOT . '/includes/bootstrap.inc';
 drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
 drupal_cron_run();
diff --git a/includes/batch.inc b/includes/batch.inc
index 63629875817..b7d0ce1495f 100644
--- a/includes/batch.inc
+++ b/includes/batch.inc
@@ -176,7 +176,7 @@ function _batch_process() {
     // request, we check if it requires an additional file for functions
     // definitions.
     if ($set_changed && isset($current_set['file']) && is_file($current_set['file'])) {
-      include_once($current_set['file']);
+      include_once DRUPAL_ROOT . '/' . $current_set['file'];
     }
 
     $finished = 1;
@@ -295,7 +295,7 @@ function _batch_finished() {
     if (isset($batch_set['finished'])) {
       // Check if the set requires an additional file for functions definitions.
       if (isset($batch_set['file']) && is_file($batch_set['file'])) {
-        include_once($batch_set['file']);
+        include_once DRUPAL_ROOT . '/' . $batch_set['file'];
       }
       if (function_exists($batch_set['finished'])) {
         $batch_set['finished']($batch_set['success'], $batch_set['results'], $batch_set['operations']);
diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index 3a6030e4e3d..cb93bc51027 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -337,7 +337,7 @@ function conf_path($require_settings = TRUE, $reset = FALSE) {
   for ($i = count($uri) - 1; $i > 0; $i--) {
     for ($j = count($server); $j > 0; $j--) {
       $dir = implode('.', array_slice($server, -$j)) . implode('.', array_slice($uri, 0, $i));
-      if (file_exists("$confdir/$dir/settings.php") || (!$require_settings && file_exists("$confdir/$dir"))) {
+      if (file_exists(DRUPAL_ROOT . "/$confdir/$dir/settings.php") || (!$require_settings && file_exists(DRUPAL_ROOT . "/$confdir/$dir"))) {
         $conf = "$confdir/$dir";
         return $conf;
       }
@@ -407,8 +407,8 @@ function conf_init() {
     $_SERVER['HTTP_HOST'] = '';
   }
 
-  if (file_exists('./'. conf_path() .'/settings.php')) {
-    include_once './'. conf_path() .'/settings.php';
+  if (file_exists(DRUPAL_ROOT . '/'. conf_path() .'/settings.php')) {
+    include_once DRUPAL_ROOT . '/'. conf_path() .'/settings.php';
   }
 
   // Ignore the placeholder URL from default.settings.php.
@@ -520,7 +520,7 @@ function drupal_get_filename($type, $name, $filename = NULL) {
     $files[$type] = array();
   }
 
-  if (!empty($filename) && file_exists($filename)) {
+  if (!empty($filename) && file_exists(DRUPAL_ROOT . '/'. $filename)) {
     $files[$type][$name] = $filename;
   }
   elseif (isset($files[$type][$name])) {
@@ -530,7 +530,7 @@ function drupal_get_filename($type, $name, $filename = NULL) {
   // the database.  This is required because this function is called both
   // before we have a database connection (i.e. during installation) and
   // when a database connection fails.
-  elseif (db_is_active() && (($file = db_result(db_query("SELECT filename FROM {system} WHERE name = '%s' AND type = '%s'", $name, $type))) && file_exists($file))) {
+  elseif (db_is_active() && (($file = db_result(db_query("SELECT filename FROM {system} WHERE name = '%s' AND type = '%s'", $name, $type))) && file_exists(DRUPAL_ROOT . '/'. $file))) {
     $files[$type][$name] = $file;
   }
   else {
@@ -541,7 +541,7 @@ function drupal_get_filename($type, $name, $filename = NULL) {
     $file = (($type == 'theme_engine') ? "$name.engine" : "$name.$type");
 
     foreach (array("$config/$dir/$file", "$config/$dir/$name/$file", "$dir/$file", "$dir/$name/$file") as $file) {
-      if (file_exists($file)) {
+      if (file_exists(DRUPAL_ROOT . '/'. $file)) {
         $files[$type][$name] = $file;
         break;
       }
@@ -799,7 +799,7 @@ function drupal_load($type, $name) {
   $filename = drupal_get_filename($type, $name);
 
   if ($filename) {
-    include_once "./$filename";
+    include_once DRUPAL_ROOT . "/$filename";
     $files[$type][$name] = TRUE;
 
     return TRUE;
@@ -1477,7 +1477,7 @@ function _drupal_bootstrap($phase) {
     case DRUPAL_BOOTSTRAP_EARLY_PAGE_CACHE:
       // Allow specifying special cache handlers in settings.php, like
       // using memcached or files for storing cache information.
-      require_once variable_get('cache_inc', './includes/cache.inc');
+      require_once DRUPAL_ROOT . '/' . variable_get('cache_inc', 'includes/cache.inc');
       // If the page_cache_fastpath is set to TRUE in settings.php and
       // page_cache_fastpath (implemented in the special implementation of
       // cache.inc) printed the page and indicated this with a returned TRUE
@@ -1501,11 +1501,11 @@ function _drupal_bootstrap($phase) {
       }
 
       // Initialize the default database.
-      require_once './includes/database.inc';
+      require_once DRUPAL_ROOT . '/includes/database.inc';
       db_set_active();
       // Allow specifying alternate lock implementations in settings.php, like
       // those using APC or memcached.
-      require_once variable_get('lock_inc', './includes/lock.inc');
+      require_once DRUPAL_ROOT . '/' . variable_get('lock_inc', 'includes/lock.inc');
       lock_init();
 
       // Detect if an installation is present.
@@ -1523,7 +1523,7 @@ function _drupal_bootstrap($phase) {
       break;
 
     case DRUPAL_BOOTSTRAP_SESSION:
-      require_once variable_get('session_inc', './includes/session.inc');
+      require_once DRUPAL_ROOT . '/' . variable_get('session_inc', 'includes/session.inc');
       drupal_session_initialize();
       break;
 
@@ -1543,7 +1543,7 @@ function _drupal_bootstrap($phase) {
       // If the skipping of the bootstrap hooks is not enforced, call hook_init.
       if (!is_object($cache) || $cache_mode != CACHE_AGGRESSIVE) {
         // Load module handling.
-        require_once './includes/module.inc';
+        require_once DRUPAL_ROOT . '/includes/module.inc';
         bootstrap_invoke_all('boot');
       }
 
@@ -1580,13 +1580,13 @@ function _drupal_bootstrap($phase) {
       break;
 
     case DRUPAL_BOOTSTRAP_PATH:
-      require_once './includes/path.inc';
+      require_once DRUPAL_ROOT . '/includes/path.inc';
       // Initialize $_GET['q'] prior to loading modules and invoking hook_init().
       drupal_init_path();
       break;
 
     case DRUPAL_BOOTSTRAP_FULL:
-      require_once './includes/common.inc';
+      require_once DRUPAL_ROOT . '/includes/common.inc';
       _drupal_bootstrap_full();
       break;
   }
@@ -1601,7 +1601,7 @@ function _drupal_bootstrap($phase) {
  * @see _drupal_maintenance_theme()
  */
 function drupal_maintenance_theme() {
-  require_once './includes/theme.maintenance.inc';
+  require_once DRUPAL_ROOT . '/includes/theme.maintenance.inc';
   _drupal_maintenance_theme();
 }
 
@@ -1629,7 +1629,7 @@ function drupal_init_language() {
     $language = language_default();
   }
   else {
-    include_once './includes/language.inc';
+    include_once DRUPAL_ROOT . '/includes/language.inc';
     $language = language_initialize();
   }
 }
diff --git a/includes/common.inc b/includes/common.inc
index 36b69945215..3ec4aefd0c4 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -2661,7 +2661,7 @@ function drupal_valid_token($token, $value = '', $skip_anonymous = FALSE) {
  *     failed. See xmlrpc_error().
  */
 function xmlrpc($url) {
-  require_once './includes/xmlrpc.inc';
+  require_once DRUPAL_ROOT . '/includes/xmlrpc.inc';
   $args = func_get_args();
   return call_user_func_array('_xmlrpc', $args);
 }
@@ -2673,16 +2673,16 @@ function _drupal_bootstrap_full() {
     return;
   }
   $called = 1;
-  require_once './includes/theme.inc';
-  require_once './includes/pager.inc';
-  require_once './includes/menu.inc';
-  require_once './includes/tablesort.inc';
-  require_once './includes/file.inc';
-  require_once './includes/unicode.inc';
-  require_once './includes/image.inc';
-  require_once './includes/form.inc';
-  require_once './includes/mail.inc';
-  require_once './includes/actions.inc';
+  require_once DRUPAL_ROOT . '/includes/theme.inc';
+  require_once DRUPAL_ROOT . '/includes/pager.inc';
+  require_once DRUPAL_ROOT . '/includes/menu.inc';
+  require_once DRUPAL_ROOT . '/includes/tablesort.inc';
+  require_once DRUPAL_ROOT . '/includes/file.inc';
+  require_once DRUPAL_ROOT . '/includes/unicode.inc';
+  require_once DRUPAL_ROOT . '/includes/image.inc';
+  require_once DRUPAL_ROOT . '/includes/form.inc';
+  require_once DRUPAL_ROOT . '/includes/mail.inc';
+  require_once DRUPAL_ROOT . '/includes/actions.inc';
   // Set the Drupal custom error handler.
   set_error_handler('_drupal_error_handler');
   set_exception_handler('_drupal_exception_handler');
diff --git a/includes/database.inc b/includes/database.inc
index 79862da6a1d..dbb86e1bc55 100644
--- a/includes/database.inc
+++ b/includes/database.inc
@@ -128,7 +128,7 @@ function db_set_active($name = 'default', $abort = TRUE) {
   static $db_conns, $db_slave_conns, $active_name = FALSE;
 
   if (empty($db_url)) {
-    include_once 'includes/install.inc';
+    include_once DRUPAL_ROOT . '/includes/install.inc';
     install_goto('install.php');
   }
 
@@ -156,7 +156,7 @@ function db_set_active($name = 'default', $abort = TRUE) {
     }
 
     $db_type = substr($connect_url, 0, strpos($connect_url, '://'));
-    $handler = "./includes/database.$db_type.inc";
+    $handler = DRUPAL_ROOT . "/includes/database.$db_type.inc";
 
     if (is_file($handler)) {
       include_once $handler;
diff --git a/includes/database.mysql.inc b/includes/database.mysql.inc
index 73c5a7aaa9a..7ff85471360 100644
--- a/includes/database.mysql.inc
+++ b/includes/database.mysql.inc
@@ -11,7 +11,7 @@
  */
 
 // Include functions shared between mysql and mysqli.
-require_once './includes/database.mysql-common.inc';
+require_once DRUPAL_ROOT . '/includes/database.mysql-common.inc';
 
 /**
  * Report database status.
diff --git a/includes/database.mysqli.inc b/includes/database.mysqli.inc
index f0ce35d4ec2..21083900716 100644
--- a/includes/database.mysqli.inc
+++ b/includes/database.mysqli.inc
@@ -14,7 +14,7 @@
  */
 
 // Include functions shared between mysql and mysqli.
-require_once './includes/database.mysql-common.inc';
+require_once DRUPAL_ROOT . '/includes/database.mysql-common.inc';
 
 /**
  * Report database status.
diff --git a/includes/database.pgsql.inc b/includes/database.pgsql.inc
index e44bc00d7f8..33166601063 100644
--- a/includes/database.pgsql.inc
+++ b/includes/database.pgsql.inc
@@ -77,7 +77,7 @@ function db_connect($url) {
 
   $connection = @pg_connect($conn_string);
   if (!$connection) {
-    require_once './includes/unicode.inc';
+    require_once DRUPAL_ROOT . '/includes/unicode.inc';
     return array(FALSE, decode_entities($php_errormsg));
   }
 
diff --git a/includes/form.inc b/includes/form.inc
index 11445b457bd..5f273fdfa4e 100644
--- a/includes/form.inc
+++ b/includes/form.inc
@@ -2551,7 +2551,7 @@ function batch_process($redirect = NULL, $url = NULL) {
     else {
       // Non-progressive execution: bypass the whole progressbar workflow
       // and execute the batch in one pass.
-      require_once './includes/batch.inc';
+      require_once DRUPAL_ROOT . '/includes/batch.inc';
       _batch_process();
     }
   }
diff --git a/includes/image.inc b/includes/image.inc
index 1580d317a96..808982666fc 100644
--- a/includes/image.inc
+++ b/includes/image.inc
@@ -40,7 +40,7 @@ function image_get_available_toolkits() {
 
   $output = array();
   foreach ($toolkits as $file => $toolkit) {
-    include_once "./$file";
+    include_once DRUPAL_ROOT . "/$file";
     $function = str_replace('.', '_', $toolkit->name) .'_info';
     if (function_exists($function)) {
       $info = $function();
@@ -62,7 +62,7 @@ function image_get_toolkit() {
 
   if (!$toolkit) {
     $toolkit = variable_get('image_toolkit', 'gd');
-    $toolkit_file = './includes/image.'. $toolkit .'.inc';
+    $toolkit_file = DRUPAL_ROOT . '/includes/image.'. $toolkit .'.inc';
     if (isset($toolkit) && file_exists($toolkit_file)) {
       include_once $toolkit_file;
     }
diff --git a/includes/install.inc b/includes/install.inc
index 80e83265d0b..4ceae8cd839 100644
--- a/includes/install.inc
+++ b/includes/install.inc
@@ -168,8 +168,8 @@ function drupal_detect_database_types() {
   $databases = array();
 
   foreach (array('mysql', 'mysqli', 'pgsql') as $type) {
-    if (file_exists('./includes/install.'. $type .'.inc')) {
-      include_once './includes/install.'. $type .'.inc';
+    if (file_exists(DRUPAL_ROOT . '/includes/install.'. $type .'.inc')) {
+      include_once DRUPAL_ROOT . '/includes/install.'. $type .'.inc';
       $function = $type .'_is_available';
       if ($function()) {
         $databases[$type] = $type;
@@ -188,8 +188,8 @@ function drupal_detect_database_types() {
  *   An array of settings that need to be updated.
  */
 function drupal_rewrite_settings($settings = array(), $prefix = '') {
-  $default_settings = './sites/default/default.settings.php';
-  $settings_file = './'. conf_path(FALSE, TRUE) .'/'. $prefix .'settings.php';
+  $default_settings = DRUPAL_ROOT . '/sites/default/default.settings.php';
+  $settings_file = DRUPAL_ROOT . '/' . conf_path(FALSE, TRUE) .'/'. $prefix .'settings.php';
 
   // Build list of setting names and insert the values into the global namespace.
   $keys = array();
@@ -283,10 +283,10 @@ function drupal_get_install_files($module_list = array()) {
  *   The list of modules to install.
  */
 function drupal_verify_profile($profile, $locale) {
-  include_once './includes/file.inc';
-  include_once './includes/common.inc';
+  include_once DRUPAL_ROOT . '/includes/file.inc';
+  include_once DRUPAL_ROOT . '/includes/common.inc';
 
-  $profile_file = "./profiles/$profile/$profile.profile";
+  $profile_file = DRUPAL_ROOT . "/profiles/$profile/$profile.profile";
 
   if (!isset($profile) || !file_exists($profile_file)) {
     install_no_profile_error();
@@ -371,7 +371,7 @@ function _drupal_install_module($module) {
  */
 function drupal_install_system() {
   $system_path = dirname(drupal_get_filename('module', 'system', NULL));
-  require_once './'. $system_path .'/system.install';
+  require_once DRUPAL_ROOT . '/' . $system_path . '/system.install';
   module_invoke('system', 'install');
   $system_versions = drupal_get_schema_versions('system');
   $system_version = $system_versions ? max($system_versions) : SCHEMA_INSTALLED;
@@ -646,16 +646,16 @@ function st($string, $args = array()) {
 
   if (!isset($locale_strings)) {
     $locale_strings = array();
-    $filename = './profiles/'. $profile .'/translations/'. $install_locale .'.po';
+    $filename = DRUPAL_ROOT . '/profiles/'. $profile .'/translations/'. $install_locale .'.po';
     if (file_exists($filename)) {
-      require_once './includes/locale.inc';
+      require_once DRUPAL_ROOT . '/includes/locale.inc';
       $file = (object) array('filepath' => $filename);
       _locale_import_read_po('mem-store', $file);
       $locale_strings = _locale_import_one_string('mem-report');
     }
   }
 
-  require_once './includes/theme.inc';
+  require_once DRUPAL_ROOT . '/includes/theme.inc';
   // Transform arguments before inserting them
   foreach ($args as $key => $value) {
     switch ($key[0]) {
@@ -682,9 +682,9 @@ function st($string, $args = array()) {
  *   Name of profile to check.
  */
 function drupal_check_profile($profile) {
-  include_once './includes/file.inc';
+  include_once DRUPAL_ROOT . '/includes/file.inc';
 
-  $profile_file = "./profiles/$profile/$profile.profile";
+  $profile_file = DRUPAL_ROOT . "/profiles/$profile/$profile.profile";
 
   if (!isset($profile) || !file_exists($profile_file)) {
     install_no_profile_error();
@@ -730,7 +730,7 @@ function drupal_check_module($module) {
   // Include install file
   $install = drupal_get_install_files(array($module));
   if (isset($install[$module])) {
-    require_once $install[$module]->filename;
+    require_once DRUPAL_ROOT . '/' . $install->filename;
 
     // Check requirements
     $requirements = module_invoke($module, 'requirements', 'install');
diff --git a/includes/mail.inc b/includes/mail.inc
index 92540e2ea5f..9a9f7596fdf 100644
--- a/includes/mail.inc
+++ b/includes/mail.inc
@@ -172,7 +172,7 @@ function drupal_mail($module, $key, $to, $language, $params = array(), $from = N
 function drupal_mail_send($message) {
   // Allow for a custom mail backend.
   if (variable_get('smtp_library', '') && file_exists(variable_get('smtp_library', ''))) {
-    include_once './'. variable_get('smtp_library', '');
+    include_once DRUPAL_ROOT . '/'. variable_get('smtp_library', '');
     return drupal_mail_wrapper($message);
   }
   else {
diff --git a/includes/menu.inc b/includes/menu.inc
index a316048e41e..e11de864856 100644
--- a/includes/menu.inc
+++ b/includes/menu.inc
@@ -354,7 +354,7 @@ function menu_execute_active_handler($path = NULL) {
   if ($router_item = menu_get_item($path)) {
     if ($router_item['access']) {
       if ($router_item['file']) {
-        require_once($router_item['file']);
+        require_once DRUPAL_ROOT . '/' . $router_item['file'];
       }
       return call_user_func_array($router_item['page_callback'], $router_item['page_arguments']);
     }
@@ -2537,7 +2537,7 @@ function _menu_site_is_offline() {
         return $_GET['q'] != 'user' && $_GET['q'] != 'user/login';
       }
       // Logged in users are unprivileged here, so they are logged out.
-      require_once drupal_get_path('module', 'user') .'/user.pages.inc';
+      require_once DRUPAL_ROOT . '/' . drupal_get_path('module', 'user') .'/user.pages.inc';
       user_logout();
     }
   }
diff --git a/includes/module.inc b/includes/module.inc
index 6fa7448e836..402da24bc7c 100644
--- a/includes/module.inc
+++ b/includes/module.inc
@@ -250,7 +250,7 @@ function module_exists($module) {
  */
 function module_load_install($module) {
   // Make sure the installation API is available
-  include_once './includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
 
   module_load_include('install', $module);
 }
@@ -282,7 +282,7 @@ function module_load_include($type, $module, $name = NULL) {
     $name = $module;
   }
 
-  $file = './'. drupal_get_path('module', $module) ."/$name.$type";
+  $file = DRUPAL_ROOT . '/'. drupal_get_path('module', $module) ."/$name.$type";
 
   if (is_file($file)) {
     require_once $file;
diff --git a/includes/theme.inc b/includes/theme.inc
index 0b25f710e54..fb6ff58907d 100644
--- a/includes/theme.inc
+++ b/includes/theme.inc
@@ -164,7 +164,7 @@ function _init_theme($theme, $base_theme = array(), $registry_callback = '_theme
   // Initialize the theme.
   if (isset($theme->engine)) {
     // Include the engine.
-    include_once './'. $theme->owner;
+    include_once DRUPAL_ROOT . '/'. $theme->owner;
 
     $theme_engine = $theme->engine;
     if (function_exists($theme_engine .'_init')) {
@@ -179,12 +179,12 @@ function _init_theme($theme, $base_theme = array(), $registry_callback = '_theme
     foreach ($base_theme as $base) {
       // Include the theme file or the engine.
       if (!empty($base->owner)) {
-        include_once './'. $base->owner;
+        include_once DRUPAL_ROOT . '/'. $base->owner;
       }
     }
     // and our theme gets one too.
     if (!empty($theme->owner)) {
-      include_once './'. $theme->owner;
+      include_once DRUPAL_ROOT . '/'. $theme->owner;
     }
   }
 
@@ -298,23 +298,23 @@ function _theme_process_registry(&$cache, $name, $type, $theme, $path) {
       // files can prevent them from getting registered.
       if (isset($info['file']) && !isset($info['path'])) {
         // First, check to see if the fully qualified file exists.
-        $filename = './'. $path .'/'. $info['file'];
-        if (file_exists($filename)) {
-          require_once $filename;
+        $filename = $path .'/'. $info['file'];
+        if (file_exists(DRUPAL_ROOT . '/' . $filename)) {
+          require_once DRUPAL_ROOT . '/' . $filename;
           $result[$hook]['include files'][] = $filename;
         }
         else {
-          $filename = './'. $info['file'];
-          if (file_exists($filename)) {
-            require_once $filename;
+          $filename = $info['file'];
+          if (file_exists(DRUPAL_ROOT . '/' . $filename)) {
+            require_once DRUPAL_ROOT . '/' . $filename;
             $result[$hook]['include files'][] = $filename;
           }
         }
       }
       elseif (isset($info['file']) && isset($info['path'])) {
-        $filename = './'. $info['path'] .'/'. $info['file'];
-        if (file_exists($filename)) {
-          require_once $filename;
+        $filename = $info['path'] .'/'. $info['file'];
+        if (file_exists(DRUPAL_ROOT . '/' . $filename)) {
+          require_once DRUPAL_ROOT . '/' . $filename;
           $result[$hook]['include files'][] = $filename;
         }
       }
@@ -482,7 +482,7 @@ function list_themes($refresh = FALSE) {
     if (db_is_active() && !defined('MAINTENANCE_MODE')) {
       $result = db_query("SELECT * FROM {system} WHERE type = '%s'", 'theme');
       while ($theme = db_fetch_object($result)) {
-        if (file_exists($theme->filename)) {
+        if (file_exists(DRUPAL_ROOT . '/' . $theme->filename)) {
           $theme->info = unserialize($theme->info);
           $themes[] = $theme;
         }
@@ -500,7 +500,7 @@ function list_themes($refresh = FALSE) {
         }
       }
       foreach ($theme->info['scripts'] as $script => $path) {
-        if (file_exists($path)) {
+        if (file_exists(DRUPAL_ROOT . '/' . $path)) {
           $theme->scripts[$script] = $path;
         }
       }
@@ -606,7 +606,7 @@ function list_themes($refresh = FALSE) {
  *   implementations for named objects.
  * @param ...
  *   Additional arguments to pass along to the theme function.
- * 
+ *
  * @return
  *   An HTML string that generates the themed output.
  */
@@ -642,7 +642,7 @@ function theme() {
   // Include a file if the theme function or preprocess function is held elsewhere.
   if (!empty($info['include files'])) {
     foreach ($info['include files'] as $include_file) {
-      include_once($include_file);
+      include_once DRUPAL_ROOT . '/' . $include_file;
     }
   }
 
@@ -658,8 +658,8 @@ function theme() {
       // Statically cache files we've already tried to include so we don't
       // run unnecessary file_exists calls.
       $included_files[$include_file] = TRUE;
-      if (file_exists('./'. $include_file)) {
-        include_once('./'. $include_file);
+      if (file_exists(DRUPAL_ROOT . '/' . $include_file)) {
+        include_once DRUPAL_ROOT . '/' . $include_file;
       }
     }
   }
@@ -765,8 +765,8 @@ function drupal_discover_template($paths, $suggestions, $extension = '.tpl.php')
     if (!empty($suggestion)) {
       $suggestion = str_replace(array("/", "\\", "\0"), '', $suggestion);
       foreach ($paths as $path) {
-        if (file_exists($file = $path .'/'. $suggestion . $extension)) {
-          return $file;
+        if (file_exists(DRUPAL_ROOT . '/' . $path .'/'. $suggestion . $extension)) {
+          return $path .'/'. $suggestion . $extension;
         }
       }
     }
@@ -1076,7 +1076,7 @@ function theme_get_setting($setting_name, $refresh = FALSE) {
 function theme_render_template($template_file, $variables) {
   extract($variables, EXTR_SKIP);  // Extract the variables to a local namespace
   ob_start();                      // Start output buffering
-  include "./$template_file";      // Include the template file
+  include DRUPAL_ROOT . '/' . "$template_file";      // Include the template file
   $contents = ob_get_contents();   // Get the contents of the buffer
   ob_end_clean();                  // End buffering and discard
   return $contents;                // Return the contents
@@ -1279,7 +1279,7 @@ function theme_links($links, $attributes = array('class' => 'links')) {
  * @param $getsize
  *   If set to TRUE, the image's dimension are fetched and added as width/height attributes.
  *   Defaults to TRUE. Must be set to FALSE if $path is a full URL.
- * 
+ *
  * @return
  *   A string containing the image tag.
  */
diff --git a/includes/theme.maintenance.inc b/includes/theme.maintenance.inc
index 2725057d8b2..60c54daa36c 100644
--- a/includes/theme.maintenance.inc
+++ b/includes/theme.maintenance.inc
@@ -21,13 +21,13 @@ function _drupal_maintenance_theme() {
     return;
   }
 
-  require_once './includes/path.inc';
-  require_once './includes/theme.inc';
-  require_once './includes/common.inc';
-  require_once './includes/unicode.inc';
-  require_once './includes/file.inc';
-  require_once './includes/module.inc';
-  require_once './includes/database.inc';
+  require_once DRUPAL_ROOT . '/includes/path.inc';
+  require_once DRUPAL_ROOT . '/includes/theme.inc';
+  require_once DRUPAL_ROOT . '/includes/common.inc';
+  require_once DRUPAL_ROOT . '/includes/unicode.inc';
+  require_once DRUPAL_ROOT . '/includes/file.inc';
+  require_once DRUPAL_ROOT . '/includes/module.inc';
+  require_once DRUPAL_ROOT . '/includes/database.inc';
   unicode_check();
 
   // Install and update pages are treated differently to prevent theming overrides.
diff --git a/includes/unicode.inc b/includes/unicode.inc
index b1ce75760b9..9a1ba799c6b 100644
--- a/includes/unicode.inc
+++ b/includes/unicode.inc
@@ -336,7 +336,7 @@ function _mime_header_decode($matches) {
 function decode_entities($text, $exclude = array()) {
   static $html_entities;
   if (!isset($html_entities)) {
-    include_once './includes/unicode.entities.inc';
+    include_once DRUPAL_ROOT . '/includes/unicode.entities.inc';
   }
 
   // Flip the exclude list so that we can do quick lookups later.
diff --git a/index.php b/index.php
index cc504603123..58af9149327 100644
--- a/index.php
+++ b/index.php
@@ -11,7 +11,12 @@
  * See COPYRIGHT.txt and LICENSE.txt.
  */
 
-require_once './includes/bootstrap.inc';
+/**
+ * Root directory of Drupal installation.
+ */
+define('DRUPAL_ROOT', getcwd());
+
+require_once DRUPAL_ROOT . '/includes/bootstrap.inc';
 drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
 
 $return = menu_execute_active_handler();
diff --git a/install.php b/install.php
index b02bb41febf..a44bbbe0d9e 100644
--- a/install.php
+++ b/install.php
@@ -1,6 +1,11 @@
 <?php
 
-require_once './includes/install.inc';
+/**
+ * Root directory of Drupal installation.
+ */
+define('DRUPAL_ROOT', getcwd());
+
+require_once DRUPAL_ROOT . '/includes/install.inc';
 
 define('MAINTENANCE_MODE', 'install');
 
@@ -16,7 +21,7 @@
  *   The installation phase we should proceed to.
  */
 function install_main() {
-  require_once './includes/bootstrap.inc';
+  require_once DRUPAL_ROOT . '/includes/bootstrap.inc';
   drupal_bootstrap(DRUPAL_BOOTSTRAP_CONFIGURATION);
 
   // The user agent header is used to pass a database prefix in the request when
@@ -30,8 +35,8 @@ function install_main() {
   // This must go after drupal_bootstrap(), which unsets globals!
   global $profile, $install_locale, $conf;
 
-  require_once './modules/system/system.install';
-  require_once './includes/file.inc';
+  require_once DRUPAL_ROOT . '/modules/system/system.install';
+  require_once DRUPAL_ROOT . '/includes/file.inc';
 
   // Ensure correct page headers are sent (e.g. caching)
   drupal_page_header();
@@ -40,7 +45,7 @@ function install_main() {
   drupal_init_language();
 
   // Load module basics (needed for hook invokes).
-  include_once './includes/module.inc';
+  include_once DRUPAL_ROOT . '/includes/module.inc';
   $module_list['system']['filename'] = 'modules/system/system.module';
   $module_list['filter']['filename'] = 'modules/filter/filter.module';
   module_list(TRUE, FALSE, FALSE, $module_list);
@@ -56,11 +61,11 @@ function install_main() {
   // continue using the cache implementation they started with) and also
   // because any data put in the cache during the installer is inherently
   // suspect, due to the fact that Drupal is not fully set up yet.
-  require_once './includes/cache-install.inc';
-  $conf['cache_inc'] = './includes/cache-install.inc';
+  require_once DRUPAL_ROOT . '/includes/cache-install.inc';
+  $conf['cache_inc'] = DRUPAL_ROOT . '/includes/cache-install.inc';
 
   // Install profile chosen, set the global immediately.
-  // This needs to be done before the theme cache gets 
+  // This needs to be done before the theme cache gets
   // initialized in drupal_maintenance_theme().
   if (!empty($_GET['profile'])) {
     $profile = preg_replace('/[^a-zA-Z_0-9]/', '', $_GET['profile']);
@@ -74,7 +79,7 @@ function install_main() {
 
   if ($verify) {
     // Establish a connection to the database.
-    require_once './includes/database.inc';
+    require_once DRUPAL_ROOT . '/includes/database.inc';
     db_set_active();
 
     // Check if Drupal is installed.
@@ -98,7 +103,7 @@ function install_main() {
   }
 
   // Load the profile.
-  require_once "./profiles/$profile/$profile.profile";
+  require_once DRUPAL_ROOT . "/profiles/$profile/$profile.profile";
 
   // Locale selection
   if (!empty($_GET['locale'])) {
@@ -140,8 +145,8 @@ function install_main() {
     // The default lock implementation uses a database table,
     // so we cannot use it for install, but we still need
     // the API functions available.
-    require_once './includes/lock-install.inc';
-    $conf['lock_inc'] = './includes/lock-install.inc';
+    require_once DRUPAL_ROOT . '/includes/lock-install.inc';
+    $conf['lock_inc'] = DRUPAL_ROOT . '/includes/lock-install.inc';
     lock_init();
 
     // Install system.module.
@@ -176,7 +181,7 @@ function install_verify_settings() {
   // Verify existing settings (if any).
   if (!empty($db_url)) {
     // We need this because we want to run form_get_errors.
-    include_once './includes/form.inc';
+    include_once DRUPAL_ROOT . '/includes/form.inc';
 
     $url = parse_url(is_array($db_url) ? $db_url['default'] : $db_url);
     $db_user = urldecode($url['user']);
@@ -184,7 +189,7 @@ function install_verify_settings() {
     $db_host = urldecode($url['host']);
     $db_port = isset($url['port']) ? urldecode($url['port']) : '';
     $db_path = ltrim(urldecode($url['path']), '/');
-    $settings_file = './'. conf_path(FALSE, TRUE) .'/settings.php';
+    $settings_file = DRUPAL_ROOT . '/'. conf_path(FALSE, TRUE) .'/settings.php';
 
     $form_state = array();
     _install_settings_form_validate($db_prefix, $db_type, $db_user, $db_pass, $db_host, $db_port, $db_path, $settings_file, $form_state);
@@ -207,11 +212,11 @@ function install_change_settings($profile = 'default', $install_locale = '') {
   $db_host = isset($url['host']) ? urldecode($url['host']) : '';
   $db_port = isset($url['port']) ? urldecode($url['port']) : '';
   $db_path = ltrim(urldecode($url['path']), '/');
-  $conf_path = './'. conf_path(FALSE, TRUE);
+  $conf_path = DRUPAL_ROOT . '/'. conf_path(FALSE, TRUE);
   $settings_file = $conf_path .'/settings.php';
 
   // We always need this because we want to run form_get_errors.
-  include_once './includes/form.inc';
+  include_once DRUPAL_ROOT . '/includes/form.inc';
   install_task_list('database');
 
   $output = drupal_get_form('install_settings_form', $profile, $install_locale, $settings_file, $db_url, $db_type, $db_prefix, $db_user, $db_pass, $db_host, $db_port, $db_path);
@@ -428,7 +433,7 @@ function install_settings_form_submit($form, &$form_state) {
  * Find all .profile files.
  */
 function install_find_profiles() {
-  return file_scan_directory('./profiles', '\.profile$', array('.', '..', 'CVS'), 0, TRUE, 'name', 0);
+  return file_scan_directory(DRUPAL_ROOT . '/profiles', '\.profile$', array('.', '..', 'CVS'), 0, TRUE, 'name', 0);
 }
 
 /**
@@ -438,13 +443,13 @@ function install_find_profiles() {
  *   The selected profile.
  */
 function install_select_profile() {
-  include_once './includes/form.inc';
+  include_once DRUPAL_ROOT . '/includes/form.inc';
 
   $profiles = install_find_profiles();
   // Don't need to choose profile if only one available.
   if (sizeof($profiles) == 1) {
     $profile = array_pop($profiles);
-    require_once $profile->filename;
+    require_once DRUPAL_ROOT . '/' . $profile->filename;
     return $profile->name;
   }
   elseif (sizeof($profiles) > 1) {
@@ -475,7 +480,7 @@ function install_select_profile_form(&$form_state, $profile_files) {
   $names = array();
 
   foreach ($profile_files as $profile) {
-    include_once($profile->filename);
+    include_once DRUPAL_ROOT . '/' . $profile->filename;
 
     // Load profile details and store them for later retrieval.
     $function = $profile->name .'_profile_details';
@@ -490,7 +495,7 @@ function install_select_profile_form(&$form_state, $profile_files) {
     $names[$profile->name] = $name;
   }
 
-  // Display radio buttons alphabetically by human-readable name. 
+  // Display radio buttons alphabetically by human-readable name.
   natcasesort($names);
   foreach ($names as $profile => $name) {
     $form['profile'][$name] = array(
@@ -513,7 +518,7 @@ function install_select_profile_form(&$form_state, $profile_files) {
  * Find all .po files for the current profile.
  */
 function install_find_locales($profilename) {
-  $locales = file_scan_directory('./profiles/'. $profilename .'/translations', '\.po$', array('.', '..', 'CVS'), 0, FALSE);
+  $locales = file_scan_directory(DRUPAL_ROOT . '/profiles/'. $profilename .'/translations', '\.po$', array('.', '..', 'CVS'), 0, FALSE);
   array_unshift($locales, (object) array('name' => 'en'));
   return $locales;
 }
@@ -525,8 +530,8 @@ function install_find_locales($profilename) {
  *   The selected language.
  */
 function install_select_locale($profilename) {
-  include_once './includes/file.inc';
-  include_once './includes/form.inc';
+  include_once DRUPAL_ROOT . '/includes/file.inc';
+  include_once DRUPAL_ROOT . '/includes/form.inc';
 
   // Find all available locales.
   $locales = install_find_locales($profilename);
@@ -592,7 +597,7 @@ function install_select_locale($profilename) {
  * Form API array definition for language selection.
  */
 function install_select_locale_form(&$form_state, $locales) {
-  include_once './includes/locale.inc';
+  include_once DRUPAL_ROOT . '/includes/locale.inc';
   $languages = _locale_get_predefined_list();
   foreach ($locales as $locale) {
     // Try to use verbose locale name
@@ -686,14 +691,14 @@ function install_tasks($profile, $task) {
   // to the same address, until the batch finished callback is invoked
   // and the task advances to 'locale-initial-import'.
   if ($task == 'profile-install-batch') {
-    include_once 'includes/batch.inc';
+    include_once DRUPAL_ROOT . '/includes/batch.inc';
     $output = _batch_page();
   }
 
   // Import interface translations for the enabled modules.
   if ($task == 'locale-initial-import') {
     if (!empty($install_locale) && ($install_locale != 'en')) {
-      include_once 'includes/locale.inc';
+      include_once DRUPAL_ROOT . '/includes/locale.inc';
       // Enable installation language as default site language.
       locale_add_language($install_locale, NULL, NULL, NULL, NULL, NULL, 1, TRUE);
       // Collect files to import for this language.
@@ -712,8 +717,8 @@ function install_tasks($profile, $task) {
     $task = 'configure';
   }
   if ($task == 'locale-initial-batch') {
-    include_once 'includes/batch.inc';
-    include_once 'includes/locale.inc';
+    include_once DRUPAL_ROOT . '/includes/batch.inc';
+    include_once DRUPAL_ROOT . '/includes/locale.inc';
     $output = _batch_page();
   }
 
@@ -732,7 +737,7 @@ function install_tasks($profile, $task) {
       drupal_set_title(st('Configure site'));
 
       // Warn about settings.php permissions risk
-      $settings_dir = './'. conf_path();
+      $settings_dir = DRUPAL_ROOT . '/'. conf_path();
       $settings_file = $settings_dir .'/settings.php';
       if (!drupal_verify_install_file($settings_file, FILE_EXIST|FILE_READABLE|FILE_NOT_WRITABLE) || !drupal_verify_install_file($settings_dir, FILE_NOT_WRITABLE, 'dir')) {
         drupal_set_message(st('All necessary changes to %dir and %file have been made, so you should remove write permissions to them now in order to avoid security risks. If you are unsure how to do so, please consult the <a href="@handbook_url">on-line handbook</a>.', array('%dir' => $settings_dir, '%file' => $settings_file, '@handbook_url' => 'http://drupal.org/getting-started')), 'error');
@@ -786,7 +791,7 @@ function install_tasks($profile, $task) {
   // control and proceed with importing the remaining translations.
   if ($task == 'profile-finished') {
     if (!empty($install_locale) && ($install_locale != 'en')) {
-      include_once 'includes/locale.inc';
+      include_once DRUPAL_ROOT . '/includes/locale.inc';
       // Collect files to import for this language. Skip components
       // already covered in the initial batch set.
       $batch = locale_batch_by_language($install_locale, '_install_locale_remaining_batch_finished', variable_get('install_locale_batch_components', array()));
@@ -804,8 +809,8 @@ function install_tasks($profile, $task) {
     $task = 'finished';
   }
   if ($task == 'locale-remaining-batch') {
-    include_once 'includes/batch.inc';
-    include_once 'includes/locale.inc';
+    include_once DRUPAL_ROOT . '/includes/batch.inc';
+    include_once DRUPAL_ROOT . '/includes/locale.inc';
     $output = _batch_page();
   }
 
@@ -898,7 +903,7 @@ function install_check_requirements($profile, $verify) {
   // If Drupal is not set up already, we need to create a settings file.
   if (!$verify) {
     $writable = FALSE;
-    $conf_path = './'. conf_path(FALSE, TRUE);
+    $conf_path = DRUPAL_ROOT . '/'. conf_path(FALSE, TRUE);
     $settings_file = $conf_path .'/settings.php';
     $file = $conf_path;
     $exists = FALSE;
@@ -953,7 +958,7 @@ function install_check_requirements($profile, $verify) {
         drupal_set_message($message, 'warning');
       }
     }
-  } 
+  }
 }
 
 /**
diff --git a/modules/color/color.module b/modules/color/color.module
index 63fad7af91f..a8f620f3fd6 100644
--- a/modules/color/color.module
+++ b/modules/color/color.module
@@ -121,7 +121,7 @@ function _color_page_alter(&$vars) {
  */
 function color_get_info($theme) {
   $path = drupal_get_path('theme', $theme);
-  $file = $path .'/color/color.inc';
+  $file = DRUPAL_ROOT . '/' . $path .'/color/color.inc';
   if ($path && file_exists($file)) {
     include $file;
     return $info;
diff --git a/modules/locale/locale.module b/modules/locale/locale.module
index 092eb4842ab..3a25fd62f70 100644
--- a/modules/locale/locale.module
+++ b/modules/locale/locale.module
@@ -175,7 +175,7 @@ function locale_menu() {
 function locale_inc_callback() {
   $args = func_get_args();
   $function = array_shift($args);
-  include_once './includes/locale.inc';
+  include_once DRUPAL_ROOT . '/includes/locale.inc';
   return call_user_func_array($function, $args);
 }
 
@@ -479,7 +479,7 @@ function locale_language_list($field = 'name', $all = FALSE) {
  *   translations for.
  */
 function locale_system_update($components) {
-  include_once 'includes/locale.inc';
+  include_once DRUPAL_ROOT . '/includes/locale.inc';
   if ($batch = locale_batch_by_component($components)) {
     batch_set($batch);
   }
diff --git a/modules/poll/poll.module b/modules/poll/poll.module
index 7bc5587d399..edf0246165b 100644
--- a/modules/poll/poll.module
+++ b/modules/poll/poll.module
@@ -320,7 +320,7 @@ function _poll_choice_form($delta, $value = '', $votes = 0) {
  * Menu callback for AHAH additions.
  */
 function poll_choice_js() {
-  include_once 'modules/node/node.pages.inc';
+  include_once DRUPAL_ROOT . '/modules/node/node.pages.inc';
   $form_state = array('storage' => NULL, 'submitted' => FALSE);
   $form_build_id = $_POST['form_build_id'];
   // Get the form from the cache.
diff --git a/modules/system/system.admin.inc b/modules/system/system.admin.inc
index 3086139bdf7..44ea1b87fe1 100644
--- a/modules/system/system.admin.inc
+++ b/modules/system/system.admin.inc
@@ -525,7 +525,7 @@ function system_theme_settings(&$form_state, $key = '') {
     // Process the theme and all its base themes.
     foreach ($theme_keys as $theme) {
       // Include the theme-settings.php file.
-      $filename = './'. str_replace("/$theme.info", '', $themes[$theme]->filename) .'/theme-settings.php';
+      $filename = DRUPAL_ROOT . '/'. str_replace("/$theme.info", '', $themes[$theme]->filename) .'/theme-settings.php';
       if (file_exists($filename)) {
         require_once $filename;
       }
@@ -875,7 +875,7 @@ function system_modules_confirm_form($modules, $storage) {
  * Submit callback; handles modules form submission.
  */
 function system_modules_submit($form, &$form_state) {
-  include_once './includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
   $new_modules = array();
 
   // If we are coming from the confirm form...
@@ -1027,7 +1027,7 @@ function system_module_build_dependencies($modules, $form_values) {
  */
 function system_modules_uninstall($form_state = NULL) {
   // Make sure the install API is available.
-  include_once './includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
 
   // Display the confirm form if any modules have been submitted.
   if (isset($form_state) && $confirm_form = system_modules_uninstall_confirm_form($form_state['storage'])) {
@@ -1128,7 +1128,7 @@ function system_modules_uninstall_validate($form, &$form_state) {
  */
 function system_modules_uninstall_submit($form, &$form_state) {
   // Make sure the install API is available.
-  include_once './includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
 
   if (!empty($form['#confirmed'])) {
     // Call the uninstall routine for each selected module.
@@ -1729,7 +1729,7 @@ function system_clean_url_settings() {
  */
 function system_status($check = FALSE) {
   // Load .install files
-  include_once './includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
   drupal_load_updates();
 
   // Check run-time requirements and status information.
@@ -1837,7 +1837,7 @@ function system_sql() {
  * Default page callback for batches.
  */
 function system_batch_page() {
-  require_once './includes/batch.inc';
+  require_once DRUPAL_ROOT . '/includes/batch.inc';
   $output = _batch_page();
   if ($output === FALSE) {
     drupal_access_denied();
diff --git a/modules/system/system.install b/modules/system/system.install
index 4dc6a2b6113..d0e84fb4436 100644
--- a/modules/system/system.install
+++ b/modules/system/system.install
@@ -274,7 +274,7 @@ function system_requirements($phase) {
   }
 
   // Test Unicode library
-  include_once './includes/unicode.inc';
+  include_once DRUPAL_ROOT . '/includes/unicode.inc';
   $requirements = array_merge($requirements, unicode_requirements());
 
   if ($phase == 'runtime') {
diff --git a/modules/system/system.module b/modules/system/system.module
index ec30bdd0f9f..a12d9e7d12c 100644
--- a/modules/system/system.module
+++ b/modules/system/system.module
@@ -702,7 +702,7 @@ function system_theme_select_form($description = '', $default_value = '', $weigh
         $screenshot = NULL;
         $theme_key = $info->name;
         while ($theme_key) {
-          if (file_exists($themes[$theme_key]->info['screenshot'])) {
+          if (file_exists(DRUPAL_ROOT . '/' . $themes[$theme_key]->info['screenshot'])) {
             $screenshot = $themes[$theme_key]->info['screenshot'];
             break;
           }
@@ -885,7 +885,7 @@ function _system_theme_data() {
       }
       if (empty($themes[$key]->info['engine'])) {
         $filename = dirname($themes[$key]->filename) .'/'. $themes[$key]->name .'.theme';
-        if (file_exists($filename)) {
+        if (file_exists(DRUPAL_ROOT . '/' . $filename)) {
           $themes[$key]->owner = $filename;
           $themes[$key]->prefix = $key;
         }
diff --git a/modules/update/update.fetch.inc b/modules/update/update.fetch.inc
index d1e381277ac..e25a504c4cd 100644
--- a/modules/update/update.fetch.inc
+++ b/modules/update/update.fetch.inc
@@ -148,7 +148,7 @@ function _update_get_fetch_url_base($project) {
  * @see update_requirements()
  */
 function _update_cron_notify() {
-  include_once './includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
   $status = update_requirements('runtime');
   $params = array();
   $notify_all = (variable_get('update_notification_threshold', 'all') == 'all');
diff --git a/modules/update/update.module b/modules/update/update.module
index fd45ed5df79..b4129a5adaf 100644
--- a/modules/update/update.module
+++ b/modules/update/update.module
@@ -71,7 +71,7 @@ function update_help($path, $arg) {
       return $output;
     case 'admin/build/themes':
     case 'admin/build/modules':
-      include_once './includes/install.inc';
+      include_once DRUPAL_ROOT . '/includes/install.inc';
       $status = update_requirements('runtime');
       foreach (array('core', 'contrib') as $report_type) {
         $type = 'update_'. $report_type;
@@ -103,7 +103,7 @@ function update_help($path, $arg) {
       // update missing, print an error message about it.
       if (arg(0) == 'admin' && strpos($path, '#') === FALSE
           && user_access('administer site configuration')) {
-        include_once './includes/install.inc';
+        include_once DRUPAL_ROOT . '/includes/install.inc';
         $status = update_requirements('runtime');
         foreach (array('core', 'contrib') as $report_type) {
           $type = 'update_'. $report_type;
diff --git a/themes/engines/phptemplate/phptemplate.engine b/themes/engines/phptemplate/phptemplate.engine
index 214e1a41e5f..f9b36490ada 100644
--- a/themes/engines/phptemplate/phptemplate.engine
+++ b/themes/engines/phptemplate/phptemplate.engine
@@ -11,7 +11,7 @@
 function phptemplate_init($template) {
   $file = dirname($template->filename) .'/template.php';
   if (file_exists($file)) {
-    include_once "./$file";
+    include_once DRUPAL_ROOT . "/$file";
   }
 }
 
diff --git a/update.php b/update.php
index 44e06987717..e4ef7cdff31 100644
--- a/update.php
+++ b/update.php
@@ -12,6 +12,11 @@
  * be sure to open settings.php again, and change it back to its original state!
  */
 
+/**
+ * Root directory of Drupal installation.
+ */
+define('DRUPAL_ROOT', getcwd());
+
 /**
  * Global flag to identify update.php run, and so avoid various unwanted
  * operations, such as hook_init() and hook_exit() invokes, css/js preprocessing
@@ -590,7 +595,7 @@ function update_check_requirements() {
 // Our custom error handler is not yet installed, so we just suppress them.
 ini_set('display_errors', FALSE);
 
-require_once './includes/bootstrap.inc';
+require_once DRUPAL_ROOT . '/includes/bootstrap.inc';
 
 // We only load DRUPAL_BOOTSTRAP_CONFIGURATION for the update requirements
 // check to avoid reaching the PHP memory limit.
@@ -599,12 +604,12 @@ function update_check_requirements() {
   // Minimum load of components.
   drupal_bootstrap(DRUPAL_BOOTSTRAP_DATABASE);
 
-  require_once './includes/install.inc';
-  require_once './includes/file.inc';
-  require_once './modules/system/system.install';
+  require_once DRUPAL_ROOT . '/includes/install.inc';
+  require_once DRUPAL_ROOT . '/includes/file.inc';
+  require_once DRUPAL_ROOT . '/modules/system/system.install';
 
   // Load module basics.
-  include_once './includes/module.inc';
+  include_once DRUPAL_ROOT . '/includes/module.inc';
   $module_list['system']['filename'] = 'modules/system/system.module';
   $module_list['filter']['filename'] = 'modules/filter/filter.module';
   module_list(TRUE, FALSE, FALSE, $module_list);
@@ -648,8 +653,8 @@ function update_check_requirements() {
 if (!empty($update_free_access) || $user->uid == 1) {
   drupal_session_start();
 
-  include_once './includes/install.inc';
-  include_once './includes/batch.inc';
+  include_once DRUPAL_ROOT . '/includes/install.inc';
+  include_once DRUPAL_ROOT . '/includes/batch.inc';
   drupal_load_updates();
 
   update_fix_d6_requirements();
diff --git a/xmlrpc.php b/xmlrpc.php
index 0f0300b184b..e50f276f8ce 100644
--- a/xmlrpc.php
+++ b/xmlrpc.php
@@ -1,13 +1,18 @@
 <?php
 
+/**
+ * Root directory of Drupal installation.
+ */
+define('DRUPAL_ROOT', getcwd());
+
 /**
  * @file
  * PHP page for handling incoming XML-RPC requests from clients.
  */
 
-include_once './includes/bootstrap.inc';
+include_once DRUPAL_ROOT . '/includes/bootstrap.inc';
 drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
-include_once './includes/xmlrpc.inc';
-include_once './includes/xmlrpcs.inc';
+include_once DRUPAL_ROOT . '/includes/xmlrpc.inc';
+include_once DRUPAL_ROOT . '/includes/xmlrpcs.inc';
 
 xmlrpc_server(module_invoke_all('xmlrpc'));

From d9f1d55550ff8270f39da3935349be37c428ebfc Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:41:57 -0400
Subject: [PATCH 18/29] Issue #1080964 by catch: Be more sparing with locale
 cache clears

---
 includes/bootstrap.inc                      |  7 +-
 includes/locale.inc                         |  2 +-
 modules/locale/locale.module                | 93 +++++++++++----------
 modules/simpletest/drupal_web_test_case.php |  3 +-
 4 files changed, 55 insertions(+), 50 deletions(-)

diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index cb93bc51027..dd20e18e53c 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -1889,8 +1889,7 @@ function drupal_valid_test_ua($user_agent) {
   // We use the database credentials from settings.php to make the HMAC key, since
   // 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';
-  $filepath = './includes/bootstrap.inc';
+  $filepath = DRUPAL_ROOT . '/includes/bootstrap.inc';
 //  $key = sha1(serialize($databases) . filectime($filepath) . fileinode($filepath), TRUE);
   $key = sha1(serialize($db_url) . filectime($filepath) . fileinode($filepath), TRUE);
   // The HMAC must match.
@@ -1909,9 +1908,7 @@ function drupal_generate_test_ua($prefix) {
     // We use the database credentials to make the HMAC key, since we
     // check the HMAC before the database is initialized. filectime()
     // and fileinode() are not easily determined from remote.
-//    $filepath = DRUPAL_ROOT . '/includes/bootstrap.inc';
-    $filepath = './includes/bootstrap.inc';
-//    $key = sha1(serialize($databases) . filectime($filepath) . fileinode($filepath), TRUE);
+    $filepath = DRUPAL_ROOT . '/includes/bootstrap.inc';
     $key = sha1(serialize($db_url) . filectime($filepath) . fileinode($filepath), TRUE);
   }
    // Generate a moderately secure HMAC based on the database credentials.
diff --git a/includes/locale.inc b/includes/locale.inc
index 82723701197..affc91893fa 100644
--- a/includes/locale.inc
+++ b/includes/locale.inc
@@ -2602,7 +2602,7 @@ function _locale_batch_build($files, $finished = NULL, $components = array()) {
       'title'         => $t('Importing interface translations'),
       'init_message'  => $t('Starting import'),
       'error_message' => $t('Error importing interface translations'),
-      'file'          => './includes/locale.inc',
+      'file'          => DRUPAL_ROOT . '/includes/locale.inc',
       // This is not a batch API construct, but data passed along to the
       // installer, so we know what did we import already.
       '#components'   => $components,
diff --git a/modules/locale/locale.module b/modules/locale/locale.module
index 3a25fd62f70..776525372be 100644
--- a/modules/locale/locale.module
+++ b/modules/locale/locale.module
@@ -342,59 +342,68 @@ function locale($string = NULL, $langcode = NULL, $reset = FALSE) {
 
   $langcode = isset($langcode) ? $langcode : $language->language;
 
-  // Store database cached translations in a static var.
-  if (!isset($locale_t[$langcode])) {
-    $locale_t[$langcode] = array();
-    // Disabling the usage of string caching allows a module to watch for
-    // the exact list of strings used on a page. From a performance
-    // perspective that is a really bad idea, so we have no user
-    // interface for this. Be careful when turning this option off!
-    if (variable_get('locale_cache_strings', 1) == 1) {
-      if ($cache = cache_get('locale:'. $langcode, 'cache')) {
-        $locale_t[$langcode] = $cache->data;
-      }
-      elseif (lock_acquire('locale_cache_' . $langcode)) {
-        // Refresh database stored cache of translations for given language.
-        // We only store short strings used in current version, to improve
-        // performance and consume less memory.
-        $result = db_query("SELECT s.source, t.translation, t.language FROM {locales_source} s LEFT JOIN {locales_target} t ON s.lid = t.lid AND t.language = '%s' WHERE s.textgroup = 'default' AND s.version = '%s' AND LENGTH(s.source) < 75", $langcode, VERSION);
-        while ($data = db_fetch_object($result)) {
-          $locale_t[$langcode][$data->source] = (empty($data->translation) ? TRUE : $data->translation);
-        }
-        cache_set('locale:'. $langcode, $locale_t[$langcode]);
-        lock_release('locale_cache_' . $langcode);
-      }
-    }
-  }
+  // Strings are cached by langcode and user roles, using instances of the
+  // LocaleLookup class to handle string lookup and caching.
+  if (!isset($locale_t[$langcode]) && isset($language)) {
+    $locale_t[$langcode] = new LocaleLookup($langcode);
+  } 
 
-  // If we have the translation cached, skip checking the database
-  if (!isset($locale_t[$langcode][$string])) {
+  return ($locale_t[$langcode][$string] === TRUE ? $string : $locale_t[$langcode][$string]);
+}
 
-    // We do not have this translation cached, so get it from the DB.
-    $translation = db_fetch_object(db_query("SELECT s.lid, t.translation, s.version FROM {locales_source} s LEFT JOIN {locales_target} t ON s.lid = t.lid AND t.language = '%s' WHERE s.source = '%s' AND s.textgroup = 'default'", $langcode, $string));
-    if ($translation) {
-      // We have the source string at least.
-      // Cache translation string or TRUE if no translation exists.
-      $locale_t[$langcode][$string] = (empty($translation->translation) ? TRUE : $translation->translation);
+/**
+ * Extends CacheArray to allow for dynamic building of the locale cache.
+ */
+class LocaleLookup extends DrupalCacheArray {
+
+  /**
+   * A language code.
+   * @var string
+   */
+  protected $langcode;
+
+  /**
+   * Constructs a LocaleCache object.
+   */
+  public function __construct($langcode) {
+    $this->langcode = $langcode;
+
+    // Add the current user's role IDs to the cache key, this ensures that, for
+    // example, strings for admin menu items and settings forms are not cached
+    // for anonymous users.
+    $rids = implode(':', array_keys($GLOBALS['user']->roles));
+    parent::__construct("locale:$langcode:$rids", 'cache');
+  }
 
+  /**
+   * Overrides DrupalCacheArray::resolveCacheMiss().
+   */
+  protected function resolveCacheMiss($offset) {
+    $translation = db_fetch_object(db_query("SELECT s.lid, t.translation, s.version FROM {locales_source} s LEFT JOIN {locales_target} t ON s.lid = t.lid AND t.language = '%s' WHERE s.source = '%s' AND s.textgroup = 'default'", $this->langcode, $offset));
+    if ($translation) {
       if ($translation->version != VERSION) {
-        // This is the first use of this string under current Drupal version. Save version
-        // and clear cache, to include the string into caching next time. Saved version is
-        // also a string-history information for later pruning of the tables.
+        // This is the first use of this string under current Drupal version.
+        // Update the {locales_source} table to indicate the string is current.
         db_query("UPDATE {locales_source} SET version = '%s' WHERE lid = %d", VERSION, $translation->lid);
-        cache_clear_all('locale:', 'cache', TRUE);
       }
+      $value = !empty($translation->translation) ? $translation->translation : TRUE;
     }
     else {
-      // We don't have the source string, cache this as untranslated.
+      // We don't have the source string, update the {locales_source} table to
+      // indicate the string is not translated.
       db_query("INSERT INTO {locales_source} (location, source, textgroup, version) VALUES ('%s', '%s', 'default', '%s')", request_uri(), $string, VERSION);
-      $locale_t[$langcode][$string] = TRUE;
-      // Clear locale cache so this string can be added in a later request.
-      cache_clear_all('locale:', 'cache', TRUE);
+        $value = TRUE;
     }
+    $this->storage[$offset] = $value;
+    // Disabling the usage of string caching allows a module to watch for
+    // the exact list of strings used on a page. From a performance
+    // perspective that is a really bad idea, so we have no user
+    // interface for this. Be careful when turning this option off!
+    if (variable_get('locale_cache_strings', 1)) {
+      $this->persist($offset);
+    }
+    return $value;
   }
-
-  return ($locale_t[$langcode][$string] === TRUE ? $string : $locale_t[$langcode][$string]);
 }
 
 /**
diff --git a/modules/simpletest/drupal_web_test_case.php b/modules/simpletest/drupal_web_test_case.php
index 6789a8d3e7d..aadf73220b6 100644
--- a/modules/simpletest/drupal_web_test_case.php
+++ b/modules/simpletest/drupal_web_test_case.php
@@ -1109,8 +1109,7 @@ protected function setUp() {
     ini_set('log_errors', 1);
     ini_set('error_log', $directory . '/error.log');
 
-//    include_once DRUPAL_ROOT . '/includes/install.inc';
-    include_once './includes/install.inc';
+    include_once DRUPAL_ROOT . '/includes/install.inc';
     drupal_install_system();
 
 //    $this->preloadRegistry();

From e08f3da0722b8a16ae55b6b0ea8945cbf5937e97 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:44:09 -0400
Subject: [PATCH 19/29] Issue #960056 by cedarm: trigger_get_assigned_actions()
 has no static cache.

---
 modules/trigger/trigger.module | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/modules/trigger/trigger.module b/modules/trigger/trigger.module
index 263a2a125ba..70762799a25 100644
--- a/modules/trigger/trigger.module
+++ b/modules/trigger/trigger.module
@@ -142,12 +142,16 @@ function trigger_access_check($module) {
  *   An array of action IDs.
  */
 function _trigger_get_hook_aids($hook, $op = '') {
-  $aids = array();
-  $result = db_query("SELECT aa.aid, a.type FROM {trigger_assignments} aa LEFT JOIN {actions} a ON aa.aid = a.aid WHERE aa.hook = '%s' AND aa.op = '%s' ORDER BY weight", $hook, $op);
-  while ($action = db_fetch_object($result)) {
-    $aids[$action->aid]['type'] = $action->type;
+  static $hooks;
+  if (!isset($hooks[$hook][$op])) {
+    $aids = array();
+    $result = db_query("SELECT aa.aid, a.type FROM {trigger_assignments} aa LEFT JOIN {actions} a ON aa.aid = a.aid WHERE aa.hook = '%s' AND aa.op = '%s' ORDER BY weight", $hook, $op);
+    while ($action = db_fetch_object($result)) {
+      $aids[$action->aid]['type'] = $action->type;
+    }
+    $hooks[$hook][$op] = $aids;
   }
-  return $aids;
+  return $hooks[$hook][$op];
 }
 
 /**

From 470a314738e0f384044016892e7775b61fa86ef0 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:45:43 -0400
Subject: [PATCH 20/29] Issue #353595 by hefox: node_access issues four queries
 on default install node/1 and has no static cache.

---
 modules/node/node.module | 28 ++++++++++++++++++++++++----
 1 file changed, 24 insertions(+), 4 deletions(-)

diff --git a/modules/node/node.module b/modules/node/node.module
index d0ca2142fa4..0ea58d8645f 100644
--- a/modules/node/node.module
+++ b/modules/node/node.module
@@ -2021,30 +2021,47 @@ function node_search_validate($form, &$form_state) {
  */
 function node_access($op, $node, $account = NULL) {
   global $user;
+  static $rights;
 
   if (!$node || !in_array($op, array('view', 'update', 'delete', 'create'), TRUE)) {
     // If there was no node to check against, or the $op was not one of the
     // supported ones, we return access denied.
     return FALSE;
   }
+  // If no user object is supplied, the access check is for the current user.
+  if (empty($account)) {
+    $account = $user;
+  }
+
+  // Cache ID contains user account, op, and NID or node type if op is create.
+  $cid = $account->uid . $op;
   // Convert the node to an object if necessary:
   if ($op != 'create') {
     $node = (object)$node;
+    $cid .= $node->nid;
   }
-  // If no user object is supplied, the access check is for the current user.
-  if (empty($account)) {
-    $account = $user;
+  // Checking create condition; $node is a string referencing a node type.
+  else {
+    $cid .= is_object($node) ? $node->type : $node;
+  }
+
+  // Return cached value if it exists.
+  if (isset($rights[$cid])) {
+    return $rights[$cid];
   }
   // If the node is in a restricted format, disallow editing.
   if ($op == 'update' && !filter_access($node->format)) {
+    $rights[$cid] = FALSE;
     return FALSE;
   }
 
   if (user_access('administer nodes', $account)) {
+    $rights[$cid] = TRUE;
     return TRUE;
   }
 
   if (!user_access('access content', $account)) {
+    $rights[$cid] = FALSE;
     return FALSE;
   }
 
@@ -2056,6 +2073,7 @@ function node_access($op, $node, $account = NULL) {
   }
   $access = module_invoke($module, 'access', $op, $node, $account);
   if (!is_null($access)) {
+    $rights[$cid] = $access;
     return $access;
   }
 
@@ -2076,11 +2094,13 @@ function node_access($op, $node, $account = NULL) {
 
     $sql = "SELECT 1 FROM {node_access} WHERE (nid = 0 OR nid = %d) $grants_sql AND grant_$op >= 1";
     $result = db_query_range($sql, $node->nid, 0, 1);
-    return (bool) db_result($result);
+    $rights[$cid] = (bool) db_result($result);
+    return $rights[$cid];
   }
 
   // Let authors view their own nodes.
   if ($op == 'view' && $account->uid == $node->uid && $account->uid != 0) {
+    $rights[$cid] = TRUE;
     return TRUE;
   }
 

From ba7c5b56f81293776726398fb20ebedf00366e81 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:46:57 -0400
Subject: [PATCH 21/29] Issue #163018 by catch: taxonomy_get_vocabularies needs
 static caching.

---
 modules/taxonomy/taxonomy.module | 32 ++++++++++++++++++--------------
 1 file changed, 18 insertions(+), 14 deletions(-)

diff --git a/modules/taxonomy/taxonomy.module b/modules/taxonomy/taxonomy.module
index ae0208ae884..b34b57601a2 100644
--- a/modules/taxonomy/taxonomy.module
+++ b/modules/taxonomy/taxonomy.module
@@ -497,10 +497,19 @@ function taxonomy_form_all($free_tags = 0) {
  *   If set, return only those vocabularies associated with this node type.
  */
 function taxonomy_get_vocabularies($type = NULL) {
+  static $vocabularies_cache = array();
+  static $vocabularies_null;
+
   if ($type) {
+    if (isset($vocabularies_cache[$type])) {
+      return $vocabularies_cache[$type];
+    }
     $result = db_query(db_rewrite_sql("SELECT v.vid, v.*, n.type FROM {vocabulary} v LEFT JOIN {vocabulary_node_types} n ON v.vid = n.vid WHERE n.type = '%s' ORDER BY v.weight, v.name", 'v', 'vid'), $type);
   }
   else {
+    if (is_array($vocabularies_null)) {
+      return $vocabularies_null;
+    }
     $result = db_query(db_rewrite_sql('SELECT v.*, n.type FROM {vocabulary} v LEFT JOIN {vocabulary_node_types} n ON v.vid = n.vid ORDER BY v.weight, v.name', 'v', 'vid'));
   }
 
@@ -520,7 +529,15 @@ function taxonomy_get_vocabularies($type = NULL) {
     $vocabularies[$voc->vid] = $voc;
   }
 
+  if ($type) {
+    $vocabularies_cache[$type] = $vocabularies;
+  }
+  else {
+    $vocabularies_null = $vocabularies;
+  }
+
   return $vocabularies;
+
 }
 
 /**
@@ -1075,20 +1092,7 @@ function taxonomy_vocabulary_load($vid, $reset = FALSE) {
   }
 
   if (!isset($vocabularies[$vid])) {
-    // Initialize so if this vocabulary does not exist, we have
-    // that cached, and we will not try to load this later.
-    $vocabularies[$vid] = FALSE;
-    // Try to load the data and fill up the object.
-    $result = db_query('SELECT v.*, n.type FROM {vocabulary} v LEFT JOIN {vocabulary_node_types} n ON v.vid = n.vid WHERE v.vid = %d', $vid);
-    $node_types = array();
-    while ($voc = db_fetch_object($result)) {
-      if (!empty($voc->type)) {
-        $node_types[$voc->type] = $voc->type;
-      }
-      unset($voc->type);
-      $voc->nodes = $node_types;
-      $vocabularies[$vid] = $voc;
-    }
+    $vocabularies = taxonomy_get_vocabularies();
   }
 
   // Return FALSE if this vocabulary does not exist.

From 932f1322bb0c5dd5137bf24b500ff9704b96d7bf Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:47:54 -0400
Subject: [PATCH 22/29] Issue #196862 by mikeytown2: COUNT(*) is an expensive
 query in InnoDB.

---
 includes/locale.inc               | 2 +-
 modules/book/book.install         | 2 +-
 modules/menu/menu.admin.inc       | 2 +-
 modules/node/node.admin.inc       | 2 +-
 modules/node/node.module          | 8 +++-----
 modules/path/path.admin.inc       | 4 ++--
 modules/path/path.module          | 2 +-
 modules/ping/ping.module          | 2 +-
 modules/profile/profile.module    | 2 +-
 modules/profile/profile.pages.inc | 2 +-
 modules/system/system.module      | 4 ++--
 modules/user/user.admin.inc       | 4 ++--
 modules/user/user.module          | 4 ++--
 13 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/includes/locale.inc b/includes/locale.inc
index affc91893fa..3412ecb92b4 100644
--- a/includes/locale.inc
+++ b/includes/locale.inc
@@ -289,7 +289,7 @@ function _locale_languages_common_controls(&$form, $language = NULL) {
 function locale_languages_predefined_form_validate($form, &$form_state) {
   $langcode = $form_state['values']['langcode'];
 
-  if ($duplicate = db_result(db_query("SELECT COUNT(*) FROM {languages} WHERE language = '%s'", $langcode)) != 0) {
+  if ($duplicate = db_result(db_query_range("SELECT 1 FROM {languages} WHERE language = '%s'", $langcode, 0, 1)) != 0) {
     form_set_error('langcode', t('The language %language (%code) already exists.', array('%language' => $form_state['values']['name'], '%code' => $langcode)));
   }
 
diff --git a/modules/book/book.install b/modules/book/book.install
index e3172f8b725..94d24bc1b00 100644
--- a/modules/book/book.install
+++ b/modules/book/book.install
@@ -106,7 +106,7 @@ function book_update_6000() {
     }
 
     // Determine whether there are any existing nodes in the book hierarchy.
-    if (db_result(db_query("SELECT COUNT(*) FROM {book}"))) {
+    if (db_result(db_query_range("SELECT 1 FROM {book}", 0, 1))) {
       // Temporary table for the old book hierarchy; we'll discard revision info.
       $schema['book_temp'] = array(
         'fields' => array(
diff --git a/modules/menu/menu.admin.inc b/modules/menu/menu.admin.inc
index a62f246e196..84b1b1da21f 100644
--- a/modules/menu/menu.admin.inc
+++ b/modules/menu/menu.admin.inc
@@ -475,7 +475,7 @@ function menu_delete_menu_confirm_submit($form, &$form_state) {
   $menu = $form['#menu'];
   $form_state['redirect'] = 'admin/build/menu';
   // System-defined menus may not be deleted - only menus defined by this module.
-  if (in_array($menu['menu_name'], menu_list_system_menus())  || !db_result(db_query("SELECT COUNT(*) FROM {menu_custom} WHERE menu_name = '%s'", $menu['menu_name']))) {
+  if (in_array($menu['menu_name'], menu_list_system_menus())  || !db_result(db_query_range("SELECT 1 FROM {menu_custom} WHERE menu_name = '%s'", $menu['menu_name'], 0, 1))) {
     return;
   }
   // Reset all the menu links defined by the system via hook_menu.
diff --git a/modules/node/node.admin.inc b/modules/node/node.admin.inc
index 41f473032ce..74e0607f83d 100644
--- a/modules/node/node.admin.inc
+++ b/modules/node/node.admin.inc
@@ -455,7 +455,7 @@ function node_admin_nodes() {
   $result = pager_query(db_rewrite_sql('SELECT n.*, u.name FROM {node} n '. $filter['join'] .' INNER JOIN {users} u ON n.uid = u.uid '. $filter['where'] .' ORDER BY n.changed DESC'), 50, 0, NULL, $filter['args']);
 
   // Enable language column if locale is enabled or if we have any node with language
-  $count = db_result(db_query("SELECT COUNT(*) FROM {node} n WHERE language != ''"));
+  $count = db_result(db_query_range("SELECT 1 FROM {node} n WHERE language != ''", 0, 1));
   $multilanguage = (module_exists('locale') || $count);
 
   $form['options'] = array(
diff --git a/modules/node/node.module b/modules/node/node.module
index 0ea58d8645f..8e53e1b7a4f 100644
--- a/modules/node/node.module
+++ b/modules/node/node.module
@@ -490,7 +490,7 @@ function node_types_rebuild() {
 function node_type_save($info) {
   $is_existing = FALSE;
   $existing_type = !empty($info->old_type) ? $info->old_type : $info->type;
-  $is_existing = db_result(db_query("SELECT COUNT(*) FROM {node_type} WHERE type = '%s'", $existing_type));
+  $is_existing = db_result(db_query_range("SELECT 1 FROM {node_type} WHERE type = '%s'", $existing_type, 0, 1));
   if (!isset($info->help)) {
     $info->help = '';
   }
@@ -2206,9 +2206,7 @@ function node_access_view_all_nodes() {
       $grants_sql = 'AND ('. implode(' OR ', $grants) .')';
     }
 
-    $sql = "SELECT COUNT(*) FROM {node_access} WHERE nid = 0 $grants_sql AND grant_view >= 1";
-    $result = db_query($sql);
-    $access = db_result($result);
+    $access = db_result(db_query_range("SELECT 1 FROM {node_access} WHERE nid = 0 $grants_sql AND grant_view >= 1", 0, 1));
   }
 
   return $access;
@@ -2766,7 +2764,7 @@ function node_assign_owner_action_form($context) {
 }
 
 function node_assign_owner_action_validate($form, $form_state) {
-  $count = db_result(db_query("SELECT COUNT(*) FROM {users} WHERE name = '%s'", $form_state['values']['owner_name']));
+  $count = db_result(db_query_range("SELECT 1 FROM {users} WHERE name = '%s'", $form_state['values']['owner_name'], 0, 1));
   if (intval($count) != 1) {
     form_set_error('owner_name', t('Please enter a valid username.'));
   }
diff --git a/modules/path/path.admin.inc b/modules/path/path.admin.inc
index dba0d030037..9c3f7b87936 100644
--- a/modules/path/path.admin.inc
+++ b/modules/path/path.admin.inc
@@ -14,7 +14,7 @@ function path_admin_overview($keys = NULL) {
   // Add the filter form above the overview table.
   $output = drupal_get_form('path_admin_filter_form', $keys);
   // Enable language column if locale is enabled or if we have any alias with language
-  $count = db_result(db_query("SELECT COUNT(*) FROM {url_alias} WHERE language != ''"));
+  $count = db_result(db_query_range("SELECT 1 FROM {url_alias} WHERE language != ''", 0, 1));
   $multilanguage = (module_exists('locale') || $count);
 
   if ($keys) {
@@ -134,7 +134,7 @@ function path_admin_form_validate($form, &$form_state) {
   // Language is only set if locale module is enabled, otherwise save for all languages.
   $language = isset($form_state['values']['language']) ? $form_state['values']['language'] : '';
 
-  if (db_result(db_query("SELECT COUNT(dst) FROM {url_alias} WHERE pid != %d AND dst = '%s' AND language = '%s'", $pid, $dst, $language))) {
+  if (db_result(db_query_range("SELECT 1 FROM {url_alias} WHERE pid != %d AND dst = '%s' AND language = '%s'", $pid, $dst, $language, 0, 1))) {
     form_set_error('dst', t('The alias %alias is already in use in this language.', array('%alias' => $dst)));
   }
   $item = menu_get_item($src);
diff --git a/modules/path/path.module b/modules/path/path.module
index 953feb25337..5790c12c138 100644
--- a/modules/path/path.module
+++ b/modules/path/path.module
@@ -180,7 +180,7 @@ function path_nodeapi(&$node, $op, $arg = NULL) {
       case 'validate':
         if (isset($node->path)) {
           $node->path = trim($node->path);
-          if (db_result(db_query("SELECT COUNT(dst) FROM {url_alias} WHERE dst = '%s' AND src != '%s' AND language = '%s'", $node->path, "node/$node->nid", $language))) {
+          if (db_result(db_query_range("SELECT 1 FROM {url_alias} WHERE dst = '%s' AND src != '%s' AND language = '%s'", $node->path, "node/$node->nid", $language, 0, 1))) {
             form_set_error('path', t('The path is already in use.'));
           }
         }
diff --git a/modules/ping/ping.module b/modules/ping/ping.module
index 6553960d204..12b137028ed 100644
--- a/modules/ping/ping.module
+++ b/modules/ping/ping.module
@@ -29,7 +29,7 @@ function ping_cron() {
   if (variable_get('site_name', 0)) {
     $cron_last = variable_get('cron_last', time());
     // Query changed first since usually changed >= created.
-    if (db_result(db_query('SELECT COUNT(*) FROM {node} WHERE status = 1 AND changed > %d', $cron_last)) || db_result(db_query('SELECT COUNT(*) FROM {node} WHERE status = 1 AND created > %d', $cron_last))) {
+    if (db_result(db_query_range('SELECT 1 FROM {node} WHERE status = 1 AND changed > %d', $cron_last, 0, 1)) || db_result(db_query_range('SELECT 1 FROM {node} WHERE status = 1 AND created > %d', $cron_last, 0, 1))) {
       _ping_notify(variable_get('site_name', ''), $base_url);
     }
   }
diff --git a/modules/profile/profile.module b/modules/profile/profile.module
index e8c053904b5..61d4b303bd3 100644
--- a/modules/profile/profile.module
+++ b/modules/profile/profile.module
@@ -470,7 +470,7 @@ function profile_category_access($account, $category) {
     return TRUE;
   }
   else {
-    return user_edit_access($account) && db_result(db_query("SELECT COUNT(*) FROM {profile_fields} WHERE category = '%s' AND visibility <> %d", $category, PROFILE_HIDDEN));
+    return user_edit_access($account) && db_result(db_query_range("SELECT 1 FROM {profile_fields} WHERE category = '%s' AND visibility <> %d", $category, PROFILE_HIDDEN, 0, 1));
   }
 }
 
diff --git a/modules/profile/profile.pages.inc b/modules/profile/profile.pages.inc
index da1b8c5834d..b3c23db3a30 100644
--- a/modules/profile/profile.pages.inc
+++ b/modules/profile/profile.pages.inc
@@ -108,7 +108,7 @@ function profile_browse() {
  */
 function profile_autocomplete($field, $string) {
   $matches = array();
-  if (db_result(db_query("SELECT COUNT(*) FROM {profile_fields} WHERE fid = %d AND autocomplete = 1", $field))) {
+  if (db_result(db_query_range("SELECT 1 FROM {profile_fields} WHERE fid = %d AND autocomplete = 1", $field, 0, 1))) {
     $result = db_query_range("SELECT value FROM {profile_values} WHERE fid = %d AND value LIKE '%s%%' GROUP BY value ORDER BY value ASC", $field, $string, 0, 10);
     while ($data = db_fetch_object($result)) {
       $matches[$data->value] = check_plain($data->value);
diff --git a/modules/system/system.module b/modules/system/system.module
index a12d9e7d12c..9fa852eac75 100644
--- a/modules/system/system.module
+++ b/modules/system/system.module
@@ -654,7 +654,7 @@ function system_admin_menu_block($item) {
 function system_admin_theme_submit($form, &$form_state) {
   // If we're changing themes, make sure the theme has its blocks initialized.
   if ($form_state['values']['admin_theme'] && $form_state['values']['admin_theme'] != variable_get('admin_theme', '0')) {
-    $result = db_result(db_query("SELECT COUNT(*) FROM {blocks} WHERE theme = '%s'", $form_state['values']['admin_theme']));
+    $result = db_result(db_query_range("SELECT 1 FROM {blocks} WHERE theme = '%s'", $form_state['values']['admin_theme'], 0, 1));
     if (!$result) {
       system_initialize_theme_blocks($form_state['values']['admin_theme']);
     }
@@ -1086,7 +1086,7 @@ function system_default_region($theme) {
  */
 function system_initialize_theme_blocks($theme) {
   // Initialize theme's blocks if none already registered.
-  if (!(db_result(db_query("SELECT COUNT(*) FROM {blocks} WHERE theme = '%s'", $theme)))) {
+  if (!(db_result(db_query_range("SELECT 1 FROM {blocks} WHERE theme = '%s'", $theme, 0, 1)))) {
     $default_theme = variable_get('theme_default', 'garland');
     $regions = system_region_list($theme);
     $result = db_query("SELECT * FROM {blocks} WHERE theme = '%s'", $default_theme);
diff --git a/modules/user/user.admin.inc b/modules/user/user.admin.inc
index c84fdbcf66f..6ad978487bf 100644
--- a/modules/user/user.admin.inc
+++ b/modules/user/user.admin.inc
@@ -683,12 +683,12 @@ function user_admin_role() {
 function user_admin_role_validate($form, &$form_state) {
   if ($form_state['values']['name']) {
     if ($form_state['values']['op'] == t('Save role')) {
-      if (db_result(db_query("SELECT COUNT(*) FROM {role} WHERE name = '%s' AND rid != %d", $form_state['values']['name'], $form_state['values']['rid']))) {
+      if (db_result(db_query_range("SELECT 1 FROM {role} WHERE name = '%s' AND rid != %d", $form_state['values']['name'], $form_state['values']['rid'], 0, 1))) {
         form_set_error('name', t('The role name %name already exists. Please choose another role name.', array('%name' => $form_state['values']['name'])));
       }
     }
     else if ($form_state['values']['op'] == t('Add role')) {
-      if (db_result(db_query("SELECT COUNT(*) FROM {role} WHERE name = '%s'", $form_state['values']['name']))) {
+      if (db_result(db_query_range("SELECT 1 FROM {role} WHERE name = '%s'", $form_state['values']['name'], 0, 1))) {
         form_set_error('name', t('The role name %name already exists. Please choose another role name.', array('%name' => $form_state['values']['name'])));
       }
     }
diff --git a/modules/user/user.module b/modules/user/user.module
index 4e6364722f8..cafc94b3252 100644
--- a/modules/user/user.module
+++ b/modules/user/user.module
@@ -1616,7 +1616,7 @@ function _user_edit_validate($uid, &$edit) {
     if ($error = user_validate_name($edit['name'])) {
       form_set_error('name', $error);
     }
-    else if (db_result(db_query("SELECT COUNT(*) FROM {users} WHERE uid != %d AND name = '%s'", $uid, $edit['name'])) > 0) {
+    else if (db_result(db_query_range("SELECT 1 FROM {users} WHERE uid != %d AND name = '%s'", $uid, $edit['name'], 0, 1)) > 0) {
       form_set_error('name', t('The name %name is already taken.', array('%name' => $edit['name'])));
     }
     else if (drupal_is_denied('user', $edit['name'])) {
@@ -1628,7 +1628,7 @@ function _user_edit_validate($uid, &$edit) {
   if ($error = user_validate_mail($edit['mail'])) {
     form_set_error('mail', $error);
   }
-  else if (db_result(db_query("SELECT COUNT(*) FROM {users} WHERE uid != %d AND mail = '%s'", $uid, $edit['mail'])) > 0) {
+  else if (db_result(db_query_range("SELECT 1 FROM {users} WHERE uid != %d AND mail = '%s'", $uid, $edit['mail'], 0, 1)) > 0) {
     form_set_error('mail', t('The e-mail address %email is already registered. <a href="@password">Have you forgotten your password?</a>', array('%email' => $edit['mail'], '@password' => url('user/password'))));
   }
   else if (drupal_is_denied('mail', $edit['mail'])) {

From 907a84c6026adf458ea5ea6e88fb01112cd68e64 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 17:49:39 -0400
Subject: [PATCH 23/29] Issue #818818 by mikeytown2: Race Condition when using
 file_save_data FILE_EXISTS_REPLACE

---
 includes/file.inc | 29 ++++++++++++++++++++++++++++-
 1 file changed, 28 insertions(+), 1 deletion(-)

diff --git a/includes/file.inc b/includes/file.inc
index c8058a0b108..ced6adcfea0 100644
--- a/includes/file.inc
+++ b/includes/file.inc
@@ -311,7 +311,34 @@ function file_copy(&$source, $dest = 0, $replace = FILE_EXISTS_RENAME) {
       return FALSE;
     }
 
-    if (!@copy($source, $dest)) {
+    // Perform the replace operation. Since there could be multiple processes
+    // writing to the same file, the best option is to create a temporary file in
+    // the same directory and then rename it to the destination. A temporary file
+    // is needed if the directory is mounted on a separate machine; thus ensuring
+    // the rename command stays local.
+    $result = FALSE;
+    if ($replace == FILE_EXISTS_REPLACE) {
+      // Get a temporary filename in the destination directory.
+      $temporary_file = tempnam(dirname($dest), 'file');
+      // Place contents in the temporary file.
+      if ($temporary_file && @copy($source, $temporary_file)) {
+        if (!$result = @rename($temporary_file, $dest)) {
+          // Unlink and try again for windows. Rename on windows does not replace
+          // the file if it already exists.
+          @unlink($dest);
+          $result = @rename($temporary_file, $dest);
+        }
+        // Remove temporary_file if rename failed.
+        if (!$result) {
+          @unlink($temporary_file);
+        }
+      }
+    }
+    // Perform the copy operation.
+    else {
+      $result = @copy($source, $dest);
+    }
+    if ($result === FALSE) {
       drupal_set_message(t('The selected file %file could not be copied.', array('%file' => $source)), 'error');
       return 0;
     }

From 895f06d78e7dbca37d034afb7919041cc1815ee3 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 18:15:11 -0400
Subject: [PATCH 24/29] Issue #667714 by mikeytown2, tinker: Impossible to
 insert serialized data with update_sql()

---
 includes/database.inc              | 19 ++++++--
 includes/database.mysql-common.inc | 35 ++++++++++++++
 includes/database.mysql.inc        | 71 +++++++++++++++++++---------
 includes/database.mysqli.inc       | 74 +++++++++++++++++++++---------
 includes/database.pgsql.inc        | 35 ++++++++++++++
 5 files changed, 188 insertions(+), 46 deletions(-)

diff --git a/includes/database.inc b/includes/database.inc
index dbb86e1bc55..ff0c422da0d 100644
--- a/includes/database.inc
+++ b/includes/database.inc
@@ -53,15 +53,28 @@ define('DB_ERROR', 'a515ac9c2796ca0e23adbe92c68fc9fc');
  * Perform an SQL query and return success or failure.
  *
  * @param $sql
- *   A string containing a complete SQL query.  %-substitution
- *   parameters are not supported.
+ *   A string containing an SQL query.
+ * @param ...
+ *   A variable number of arguments which are substituted into the query
+ *   using printf() syntax. Instead of a variable number of query arguments,
+ *   you may also pass a single array containing the query arguments.
+ *
+ *   Valid %-modifiers are: %s, %d, %f, %b (binary data, do not enclose
+ *   in '') and %%.
+ *
+ *   NOTE: using this syntax will cast NULL and FALSE values to decimal 0,
+ *   and TRUE values to decimal 1.
+ *
  * @return
  *   An array containing the keys:
  *      success: a boolean indicating whether the query succeeded
  *      query: the SQL query executed, passed through check_plain()
  */
 function update_sql($sql) {
-  $result = db_query($sql, true);
+  $args = func_get_args();
+  array_shift($args);
+  $result = db_query($sql, $args);
+  $sql = db_query_get_string($sql, $args);
   return array('success' => $result !== FALSE, 'query' => check_plain($sql));
 }
 
diff --git a/includes/database.mysql-common.inc b/includes/database.mysql-common.inc
index ead7f367c94..f10f8766e2a 100644
--- a/includes/database.mysql-common.inc
+++ b/includes/database.mysql-common.inc
@@ -42,6 +42,41 @@ function db_query($query) {
   return _db_query($query);
 }
 
+/**
+ * Builds a query, returns string.
+ *
+ * User-supplied arguments to the query should be passed in as separate
+ * parameters so that they can be properly escaped to avoid SQL injection
+ * attacks.
+ *
+ * @param $query
+ *   A string containing an SQL query.
+ * @param ...
+ *   A variable number of arguments which are substituted into the query
+ *   using printf() syntax. Instead of a variable number of query arguments,
+ *   you may also pass a single array containing the query arguments.
+ *
+ *   Valid %-modifiers are: %s, %d, %f, %b (binary data, do not enclose
+ *   in '') and %%.
+ *
+ *   NOTE: using this syntax will cast NULL and FALSE values to decimal 0,
+ *   and TRUE values to decimal 1.
+ *
+ * @return
+ *   String of the query fully escaped and ready to run.
+ */
+function db_query_get_string($query) {
+  $args = func_get_args();
+  array_shift($args);
+  $query = db_prefix_tables($query);
+  if (isset($args[0]) and is_array($args[0])) { // 'All arguments in one array' syntax
+    $args = $args[0];
+  }
+  _db_query_callback($args, TRUE);
+  $query = preg_replace_callback(DB_QUERY_REGEXP, '_db_query_callback', $query);
+  return $query;
+}
+
 /**
  * @ingroup schemaapi
  * @{
diff --git a/includes/database.mysql.inc b/includes/database.mysql.inc
index 7ff85471360..87a6f5d1e40 100644
--- a/includes/database.mysql.inc
+++ b/includes/database.mysql.inc
@@ -134,34 +134,63 @@ function _db_query($query, $debug = 0, $slave = FALSE) {
     $query = '/* '. $name .' : '. $bt[2]['function'] .' */ '. $query;
   }
 
-  $sent_to_slave = FALSE;
-  if (isset($active_slave_db) && $slave) {
-    $result = mysql_query($query, $active_slave_db);
-    $sent_to_slave = TRUE;
-  }
-  else {
-    $result = mysql_query($query, $active_db);
-  }
+  $retry = 0;
+  do {
+    $sent_to_slave = FALSE;
+    if (isset($active_slave_db) && $slave) {
+      $result = mysql_query($query, $active_slave_db);
+      $errno = mysql_errno($active_slave_db);
+      $sent_to_slave = TRUE;
+    }
+    else {
+      $result = mysql_query($query, $active_db);
+      $errno = mysql_errno($active_db);
+    }
 
-  if (variable_get('dev_query', 0)) {
-    $query = $bt[2]['function'] ."\n". $query;
-    list($usec, $sec) = explode(' ', microtime());
-    $stop = (float)$usec + (float)$sec;
-    $diff = $stop - $timer;
-    $queries[] = array($query, $diff, $sent_to_slave);
-  }
+    if (variable_get('dev_query', 0)) {
+      $query = $bt[2]['function'] ."\n". $query;
+      list($usec, $sec) = explode(' ', microtime());
+      $stop = (float)$usec + (float)$sec;
+      $diff = $stop - $timer;
+      $queries[] = array($query, $diff, $sent_to_slave);
+    }
 
-  if (!$sent_to_slave) {
-    $active_last_db = $active_db;
-  } else {
-    $active_last_db = $active_slave_db;
-  }
+    // Handle transient errors.
+    // If we can handle this error, then increment the counter, so we run again. Otherwise
+    // use the default case to exit the while loop and return an error as per normal.
+    switch($errno) {
+      case 1205:    // Lock wait timeout exceeded; try restarting transaction
+      case 1213:    // Deadlock found when trying to get lock; try restarting transaction
+        $retry++;   // Increment counter.
+        break;
+
+      case 1614:    // Transaction branch was rolled back: deadlock was detected
+      case 2013:    // Lost connection to MySQL server during query
+        $retry++;   // Increment counter.
+        if ($sent_to_slave) {
+          $slave = FALSE; // Retry on master.
+        }
+        break;
+
+      // If not an error we can handle (or not an error!) exit the loop.
+      // We cal deal with fall-out later, as errno is set.
+      default:
+        $retry = 2;
+        break;
+    }
+
+    if (!$sent_to_slave) {
+      $active_last_db = $active_db;
+    } else {
+      $active_last_db = $active_slave_db;
+    }
+  } while ($retry < 2);
 
   if ($debug) {
     print '<p>query: '. $query .'<br />error:'. mysql_error($active_db) .'</p>';
   }
 
-  if (!mysql_errno($active_last_db)) {
+  if (!$errno) {
     return $result;
   }
   else {
diff --git a/includes/database.mysqli.inc b/includes/database.mysqli.inc
index 21083900716..6e48c70335a 100644
--- a/includes/database.mysqli.inc
+++ b/includes/database.mysqli.inc
@@ -133,34 +133,64 @@ function _db_query($query, $debug = 0, $slave = FALSE) {
     $query = '/* '. $name .' : '. $bt[2]['function'] .' */ '. $query;
   }
 
-  $sent_to_slave = FALSE;
-  if (isset($active_slave_db) && $slave) {
-    $result = mysqli_query($active_slave_db, $query);
-    $sent_to_slave = TRUE;
-  }
-  else {
-    $result = mysqli_query($active_db, $query);
-  }
+  $retry = 0;
+  do {
+    $sent_to_slave = FALSE;
+    if (isset($active_slave_db) && $slave) {
+      $result = mysqli_query($query, $active_slave_db);
+      $errno = mysqli_errno($active_slave_db);
+      $sent_to_slave = TRUE;
+    }
+    else {
+      $result = mysql_query($query, $active_db);
+      $errno = mysql_errno($active_db);
+    }
 
-  if (variable_get('dev_query', 0)) {
-    $query = $bt[2]['function'] ."\n". $query;
-    list($usec, $sec) = explode(' ', microtime());
-    $stop = (float)$usec + (float)$sec;
-    $diff = $stop - $timer;
-    $queries[] = array($query, $diff, $sent_to_slave);
-  }
+    if (variable_get('dev_query', 0)) {
+      $query = $bt[2]['function'] ."\n". $query;
+      list($usec, $sec) = explode(' ', microtime());
+      $stop = (float)$usec + (float)$sec;
+      $diff = $stop - $timer;
+      $queries[] = array($query, $diff, $sent_to_slave);
+    }
+
+    // Handle transient errors.
+    // If we can handle this error, then increment the counter, so we run again. Otherwise
+    // use the default case to exit the while loop and return an error as per normal.
+    switch($errno) {
+      case 1205:    // Lock wait timeout exceeded; try restarting transaction
+      case 1213:    // Deadlock found when trying to get lock; try restarting transaction
+        $retry++;   // Increment counter.
+        break;
+
+      case 1614:    // Transaction branch was rolled back: deadlock was detected
+      case 2013:    // Lost connection to MySQL server during query
+        $retry++;   // Increment counter.
+        if ($sent_to_slave) {
+          $slave = FALSE; // Retry on master.
+        }
+        break;
+
+      // If not an error we can handle (or not an error!) exit the loop.
+      // We cal deal with fall-out later, as errno is set.
+      default:
+        $retry = 2;
+        break;
+    }
+
+    if (!$sent_to_slave) {
+      $active_last_db = $active_db;
+    } else {
+      $active_last_db = $active_slave_db;
+    }
+  } while ($retry < 2);
 
-  if (!$sent_to_slave) {
-    $active_last_db = $active_db;
-  } else {
-    $active_last_db = $active_slave_db;
-  }
 
   if ($debug) {
     print '<p>query: '. $query .'<br />error:'. mysqli_error($active_db) .'</p>';
   }
 
-  if (!mysqli_errno($active_last_db)) {
+  if (!$errno) {
     return $result;
   }
   else {
@@ -336,7 +366,7 @@ function db_query_range_slave($query) {
  *
  * Use this as a substitute for db_query() when the results need to be stored
  * in a temporary table.
- * 
+ *
  * User-supplied arguments to the query should be passed in as separate parameters
  * so that they can be properly escaped to avoid SQL injection attacks.
  *
diff --git a/includes/database.pgsql.inc b/includes/database.pgsql.inc
index 33166601063..085015486df 100644
--- a/includes/database.pgsql.inc
+++ b/includes/database.pgsql.inc
@@ -124,6 +124,41 @@ function db_query($query) {
   return _db_query($query);
 }
 
+/**
+ * Builds a query, returns string.
+ *
+ * User-supplied arguments to the query should be passed in as separate
+ * parameters so that they can be properly escaped to avoid SQL injection
+ * attacks.
+ *
+ * @param $query
+ *   A string containing an SQL query.
+ * @param ...
+ *   A variable number of arguments which are substituted into the query
+ *   using printf() syntax. Instead of a variable number of query arguments,
+ *   you may also pass a single array containing the query arguments.
+ *
+ *   Valid %-modifiers are: %s, %d, %f, %b (binary data, do not enclose
+ *   in '') and %%.
+ *
+ *   NOTE: using this syntax will cast NULL and FALSE values to decimal 0,
+ *   and TRUE values to decimal 1.
+ *
+ * @return
+ *   String of the query fully escaped and ready to run.
+ */
+function db_query_get_string($query) {
+  $args = func_get_args();
+  array_shift($args);
+  $query = db_prefix_tables($query);
+  if (isset($args[0]) and is_array($args[0])) { // 'All arguments in one array' syntax
+    $args = $args[0];
+  }
+  _db_query_callback($args, TRUE);
+  $query = preg_replace_callback(DB_QUERY_REGEXP, '_db_query_callback', $query);
+  return $query;
+}
+
 /**
  * Helper function for db_query().
  */

From a1ef2cdab76c4edd56d267125ccd2d8580f4e987 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 18:26:59 -0400
Subject: [PATCH 25/29] Issue #972528 by mikeytown2, mkalkbrenner: dblog fails
 to log MAX_ALLOWED_PACKET errors because they're longer than
 MAX_ALLOWED_PACKET

---
 includes/database.mysql.inc  | 8 ++++++++
 includes/database.mysqli.inc | 8 ++++++++
 2 files changed, 16 insertions(+)

diff --git a/includes/database.mysql.inc b/includes/database.mysql.inc
index 87a6f5d1e40..1b5ca295528 100644
--- a/includes/database.mysql.inc
+++ b/includes/database.mysql.inc
@@ -159,6 +159,14 @@ function _db_query($query, $debug = 0, $slave = FALSE) {
     // If we can handle this error, then increment the counter, so we run again. Otherwise
     // use the default case to exit the while loop and return an error as per normal.
     switch($errno) {
+      case 1153: // Got a packet bigger than "max_allowed_packet" bytes
+        // If the MySQL Server rejected the query because it's too big,
+        // writing the query to database watchdog will fail as well
+        // Truncate the query ...
+        $retry = 2;
+        $query = substr($query, 0, 100);
+        break;
+
       case 1205:    // Lock wait timeout exceeded; try restarting transaction
       case 1213:    // Deadlock found when trying to get lock; try restarting transaction
         $retry++;   // Increment counter.
diff --git a/includes/database.mysqli.inc b/includes/database.mysqli.inc
index 6e48c70335a..2166793aa9d 100644
--- a/includes/database.mysqli.inc
+++ b/includes/database.mysqli.inc
@@ -158,6 +158,14 @@ function _db_query($query, $debug = 0, $slave = FALSE) {
     // If we can handle this error, then increment the counter, so we run again. Otherwise
     // use the default case to exit the while loop and return an error as per normal.
     switch($errno) {
+      case 1153: // Got a packet bigger than "max_allowed_packet" bytes
+        // If the MySQL Server rejected the query because it's too big,
+        // writing the query to database watchdog will fail as well
+        // Truncate the query ...
+        $retry = 2;
+        $query = substr($query, 0, 100);
+        break;
+
       case 1205:    // Lock wait timeout exceeded; try restarting transaction
       case 1213:    // Deadlock found when trying to get lock; try restarting transaction
         $retry++;   // Increment counter.

From 0dcfca3d949492f28020e94e14546bae230e017b Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 18:29:05 -0400
Subject: [PATCH 26/29] Issue #360377 by janusman: book_get_books() cache
 becomes stale when batch-inserting book pages

---
 modules/book/book.module | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/modules/book/book.module b/modules/book/book.module
index 56f839a33c6..65f17784cff 100644
--- a/modules/book/book.module
+++ b/modules/book/book.module
@@ -251,11 +251,14 @@ function theme_book_title_link($link) {
  *
  * This list may be used for generating a list of all the books, or for building
  * the options for a form select.
+ *
+ * @param $reset
+ *   Reset the cache of stored books.
  */
-function book_get_books() {
+function book_get_books($reset = FALSE) {
   static $all_books;
 
-  if (!isset($all_books)) {
+  if ($reset || !isset($all_books)) {
     $all_books = array();
     $result = db_query("SELECT DISTINCT(bid) FROM {book}");
     $nids = array();
@@ -463,12 +466,16 @@ function _book_update_outline(&$node) {
     if ($new) {
       // Insert new.
       db_query("INSERT INTO {book} (nid, mlid, bid) VALUES (%d, %d, %d)", $node->nid, $node->book['mlid'], $node->book['bid']);
+      // Reset the cache of stored books.
+      book_get_books(TRUE);
     }
     else {
       if ($node->book['bid'] != db_result(db_query("SELECT bid FROM {book} WHERE nid = %d", $node->nid))) {
         // Update the bid for this page and all children.
         book_update_bid($node->book);
       }
+      // Reset the cache of stored books.
+      book_get_books(TRUE);
     }
     return TRUE;
   }
@@ -712,6 +719,8 @@ function book_nodeapi(&$node, $op, $teaser = NULL, $page = NULL) {
         }
         menu_link_delete($node->book['mlid']);
         db_query('DELETE FROM {book} WHERE mlid = %d', $node->book['mlid']);
+        // Reset the cache of stored books.
+        book_get_books(TRUE);
       }
       break;
     case 'prepare':

From 7d8cdc5582d0c25efc0a0d036f375a597b8f3311 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Tue, 19 Mar 2013 19:35:41 -0400
Subject: [PATCH 27/29] Issue #476048 by mikeytown2: MySQL transient error
 handling

---
 includes/database.mysqli.inc | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/includes/database.mysqli.inc b/includes/database.mysqli.inc
index 2166793aa9d..0bfddf51ab2 100644
--- a/includes/database.mysqli.inc
+++ b/includes/database.mysqli.inc
@@ -137,13 +137,13 @@ function _db_query($query, $debug = 0, $slave = FALSE) {
   do {
     $sent_to_slave = FALSE;
     if (isset($active_slave_db) && $slave) {
-      $result = mysqli_query($query, $active_slave_db);
+      $result = mysqli_query($active_slave_db, $query);
       $errno = mysqli_errno($active_slave_db);
       $sent_to_slave = TRUE;
     }
     else {
-      $result = mysql_query($query, $active_db);
-      $errno = mysql_errno($active_db);
+      $result = mysqli_query($active_db, $query);
+      $errno = mysqli_errno($active_db);
     }
 
     if (variable_get('dev_query', 0)) {

From cb7df7a282fd43976ebfa88c2be79214bde208fc Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Fri, 22 Mar 2013 17:30:28 -0400
Subject: [PATCH 28/29] php 5.4 fixes

---
 includes/form.inc | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/includes/form.inc b/includes/form.inc
index 5f273fdfa4e..25baf686f98 100644
--- a/includes/form.inc
+++ b/includes/form.inc
@@ -302,7 +302,7 @@ function drupal_execute($form_id, &$form_state) {
 
   // Make sure $form_state is passed around by reference.
   $args[1] = &$form_state;
-  
+
   $form = call_user_func_array('drupal_retrieve_form', $args);
   $form['#post'] = $form_state['values'];
 
@@ -773,8 +773,8 @@ function form_execute_handlers($type, &$form, &$form_state) {
 
   foreach ($handlers as $function) {
     if (function_exists($function))  {
-      // Check to see if a previous _submit handler has set a batch, but 
-      // make sure we do not react to a batch that is already being processed 
+      // Check to see if a previous _submit handler has set a batch, but
+      // make sure we do not react to a batch that is already being processed
       // (for instance if a batch operation performs a drupal_execute()).
       if ($type == 'submit' && ($batch =& batch_get()) && !isset($batch['current_set'])) {
         // Some previous _submit handler has set a batch. We store the call
@@ -900,7 +900,7 @@ function form_builder($form_id, $form, &$form_state) {
   // Recurse through all child elements.
   $count = 0;
   foreach (element_children($form) as $key) {
-    $form[$key]['#post'] = $form['#post'];
+    $form[$key]['#post'] = isset($form['#post']) ? $form['#post'] : NULL;
     $form[$key]['#programmed'] = $form['#programmed'];
     // Don't squash an existing tree value.
     if (!isset($form[$key]['#tree'])) {
@@ -1342,6 +1342,9 @@ function form_set_value($form_item, $value, &$form_state) {
 function _form_set_value(&$form_values, $form_item, $parents, $value) {
   $parent = array_shift($parents);
   if (empty($parents)) {
+    if (!is_array($form_values)) {
+      $form_values = array();
+    }
     $form_values[$parent] = $value;
   }
   else {
@@ -2127,7 +2130,6 @@ function theme_textarea($element) {
  *
  * @ingroup themeable
  */
-
 function theme_markup($element) {
   return (isset($element['#value']) ? $element['#value'] : '') . (isset($element['#children']) ? $element['#children'] : '');
 }

From f9498387cf7593b8b07714af6b937d27bb545f43 Mon Sep 17 00:00:00 2001
From: mikeytown2 <mikeytown2@282446.no-reply.drupal.org>
Date: Fri, 22 Mar 2013 17:32:01 -0400
Subject: [PATCH 29/29] Fix file mode

---
 modules/simpletest/run-tests.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 modules/simpletest/run-tests.sh

diff --git a/modules/simpletest/run-tests.sh b/modules/simpletest/run-tests.sh
old mode 100755
new mode 100644