diff --git a/.htaccess b/.htaccess
index ca10d364e0..cab4556788 100644
--- a/.htaccess
+++ b/.htaccess
@@ -136,11 +136,12 @@ DirectoryIndex index.php
   # uncomment the following line:
   # RewriteBase /
 
-  # Rewrite URLs of the form 'x' to the form 'index.php?q=x'.
+  # Pass all requests not referring directly to files in the filesystem to
+  # index.php. Clean URLs are handled in drupal_environment_initialize().
   RewriteCond %{REQUEST_FILENAME} !-f
   RewriteCond %{REQUEST_FILENAME} !-d
   RewriteCond %{REQUEST_URI} !=/favicon.ico
-  RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
+  RewriteRule ^ index.php [L]
 </IfModule>
 
 # Various header fixes.
diff --git a/includes/bootstrap.inc b/includes/bootstrap.inc
index d1bcedfa71..bea9c53247 100644
--- a/includes/bootstrap.inc
+++ b/includes/bootstrap.inc
@@ -433,8 +433,8 @@ function conf_init() {
 
     // $_SERVER['SCRIPT_NAME'] can, in contrast to $_SERVER['PHP_SELF'], not
     // be modified by a visitor.
-    if ($dir = trim(dirname($_SERVER['SCRIPT_NAME']), '\,/')) {
-      $base_path = "/$dir";
+    if ($dir = rtrim(dirname($_SERVER['SCRIPT_NAME']), '\/')) {
+      $base_path = $dir;
       $base_url .= $base_path;
       $base_path .= '/';
     }
@@ -1138,6 +1138,19 @@ function _drupal_bootstrap($phase) {
 
     case DRUPAL_BOOTSTRAP_CONFIGURATION:
       drupal_unset_globals();
+
+      // When clean URLs are enabled, emulate ?q=foo/bar using REQUEST_URI. It is
+      // not possible to append the query string using mod_rewrite without the B
+      // flag (this was added in Apache 2.2.8), because mod_rewrite unescapes the
+      // path before passing it on to PHP. This is a problem when the path contains
+      // e.g. "&" or "%" that have special meanings in URLs and must be encoded.
+      $_GET['q'] = request_path();
+
+      // The D7 patch we're backporting does not sync $_REQUEST['q'], however some contrib modules use this
+      // instead of $_GET['q'] - eg: globalredirect, imagecache_customactions.
+      // This is added to maintain support.
+      $_REQUEST['q'] = $_GET['q'];
+
       // PHP's built-in phar:// stream wrapper is not sufficiently secure. Override
       // it with a more secure one, which requires PHP 5.3.3. For lower versions,
       // unregister the built-in one without replacing it. Sites needing phar
@@ -1367,6 +1380,50 @@ function language_default($property = NULL) {
   return $property ? $language->$property : $language;
 }
 
+/**
+ * Returns the requested URL path of the page being viewed.
+ *
+ * Examples:
+ * - http://example.com/node/306 returns "node/306".
+ * - http://example.com/drupalfolder/node/306 returns "node/306" while
+ *   base_path() returns "/drupalfolder/".
+ * - http://example.com/path/alias (which is a path alias for node/306) returns
+ *   "path/alias" as opposed to the internal path.
+ *
+ * @return
+ *   The requested Drupal URL path.
+ *
+ * @see current_path()
+ */
+function request_path() {
+  static $path;
+
+  if (isset($path)) {
+    return $path;
+  }
+
+  if (isset($_GET['q'])) {
+    // This is a request with a ?q=foo/bar query string. $_GET['q'] is
+    // overwritten in drupal_path_initialize(), but request_path() is called
+    // very early in the bootstrap process, so the original value is saved in
+    // $path and returned in later calls.
+    $path = $_GET['q'];
+  }
+  elseif (isset($_SERVER['REQUEST_URI'])) {
+    // This is a request using a clean URL. Extract the path from REQUEST_URI.
+    $request_path = strtok($_SERVER['REQUEST_URI'], '?');
+    $base_path_len = strlen(rtrim(dirname($_SERVER['SCRIPT_NAME']), '\/'));
+    // Unescape and strip $base_path prefix, leaving q without a leading slash.
+    $path = substr(urldecode($request_path), $base_path_len + 1);
+  }
+  else {
+    // This is the front page.
+    $path = '';
+  }
+
+  return $path;
+}
+
 /**
  * If Drupal is behind a reverse proxy, we use the X-Forwarded-For header
  * instead of $_SERVER['REMOTE_ADDR'], which would be the IP address
diff --git a/includes/common.inc b/includes/common.inc
index 0c6af87217..44cc553f50 100644
--- a/includes/common.inc
+++ b/includes/common.inc
@@ -2691,35 +2691,18 @@ function drupal_json($var = NULL) {
 }
 
 /**
- * Wrapper around urlencode() which avoids Apache quirks.
- *
- * Should be used when placing arbitrary data in an URL. Note that Drupal paths
- * are urlencoded() when passed through url() and do not require urlencoding()
- * of individual components.
- *
- * Notes:
- * - For esthetic reasons, we do not escape slashes. This also avoids a 'feature'
- *   in Apache where it 404s on any path containing '%2F'.
- * - mod_rewrite unescapes %-encoded ampersands, hashes, and slashes when clean
- *   URLs are used, which are interpreted as delimiters by PHP. These
- *   characters are double escaped so PHP will still see the encoded version.
- * - With clean URLs, Apache changes '//' to '/', so every second slash is
- *   double escaped.
- * - This function should only be used on paths, not on query string arguments,
- *   otherwise unwanted double encoding will occur.
+ * Encodes a Drupal path for use in a URL.
  *
- * @param $text
- *   String to encode
+ * For aesthetic reasons slashes are not escaped.
+ *
+ * Note that url() takes care of calling this function, so a path passed to that
+ * function should not be encoded in advance.
+ *
+ * @param $path
+ *   The Drupal path to encode.
  */
 function drupal_urlencode($text) {
-  if (variable_get('clean_url', '0')) {
-    return str_replace(array('%2F', '%26', '%23', '//'),
-                       array('/', '%2526', '%2523', '/%252F'),
-                       rawurlencode($text));
-  }
-  else {
-    return str_replace('%2F', '/', rawurlencode($text));
-  }
+  return str_replace('%2F', '/', rawurlencode($text));
 }
 
 /**
diff --git a/includes/file.inc b/includes/file.inc
index 32371f4fb5..3697292331 100644
--- a/includes/file.inc
+++ b/includes/file.inc
@@ -521,6 +521,10 @@ function file_unmunge_filename($filename) {
  * @return
  */
 function file_create_filename($basename, $directory) {
+  // Strip control characters (ASCII value < 32). Though these are allowed in
+  // some filesystems, not many applications handle them well.
+  $basename = preg_replace('/[\x00-\x1F]/u', '_', $basename);
+
   $dest = $directory .'/'. $basename;
 
   if (file_exists($dest)) {
diff --git a/misc/drupal.js b/misc/drupal.js
index 182f069d8b..fa314bbcda 100644
--- a/misc/drupal.js
+++ b/misc/drupal.js
@@ -348,8 +348,7 @@ Drupal.unfreezeHeight = function () {
  */
 Drupal.encodeURIComponent = function (item, uri) {
   uri = uri || location.href;
-  item = encodeURIComponent(item).replace(/%2F/g, '/');
-  return (uri.indexOf('?q=') != -1) ? item : item.replace(/%26/g, '%2526').replace(/%23/g, '%2523').replace(/\/\//g, '/%252F');
+  return encodeURIComponent(item).replace(/%2F/g, '/');
 };
 
 /**