diff --git a/core/includes/bootstrap.inc b/core/includes/bootstrap.inc
index efe8623..c3ecd47 100644
--- a/core/includes/bootstrap.inc
+++ b/core/includes/bootstrap.inc
@@ -661,21 +661,10 @@ function drupal_settings_initialize() {
       if (strpos(request_uri(TRUE) . '/', $base_path . $script_path) !== 0) {
         $script_path = '';
       }
-      // @todo Core scripts (e.g., 'core/install.php', 'core/update.php', etc.)
-      //   currently expect url() to link to Drupal's primary front controller
-      //   (index.php), rather than back to themselves.
-      //   - Do we want to refactor them to not expect this?
-      //   - Do we want to limit the below to core scripts only, allowing
-      //     modules to add custom front controllers and having url() be
-      //     relative to them?
+      // @todo Temporary BC for install.php, update.php, and other scripts.
+      //   - http://drupal.org/node/1547184
+      //   - http://drupal.org/node/1546082
       if ($script_path !== 'index.php/') {
-        // @todo Here we're assuming that when linking from another script back
-        //   to Drupal proper, we can use clean URLs. Provide documentation
-        //   somewhere (INSTALL.txt?) letting people using a web server where
-        //   clean URLs do not work know that they can manually add 'index.php/'
-        //   in their browser's address bar to view their site without clean
-        //   URLs.
-        // @see http://drupal.org/node/1183208
         $script_path = '';
       }
     }
@@ -1522,17 +1511,10 @@ function drupal_validate_utf8($text) {
  * Because $_SERVER['REQUEST_URI'] is only available on Apache, we generate an
  * equivalent using other environment variables.
  *
- * @todo The above comment is no longer true. $_SERVER['REQUEST_URI'] is
- *   available on IIS and probably other servers. Research the current state of
- *   servers and update this documentation.
+ * @todo The above comment is incorrect: http://drupal.org/node/1547294.
  */
 function request_uri($omit_query_string = FALSE) {
   if (isset($_SERVER['REQUEST_URI'])) {
-    // @todo Some builds of IIS provide 'REQUEST_URI' without the query string
-    //   (http://www.microsoft.com/download/en/details.aspx?id=9453). While we
-    //   can make this function add back $_SERVER['QUERY_STRING'], this might be
-    //   undesirable for sites on non-broken servers with 'QUERY_STRING' coming
-    //   from rewrite rules only, and not from the requested URI.
     $uri = $_SERVER['REQUEST_URI'];
   }
   else {
diff --git a/core/includes/common.inc b/core/includes/common.inc
index ecfcaba..17c626b 100644
--- a/core/includes/common.inc
+++ b/core/includes/common.inc
@@ -4078,6 +4078,7 @@ function drupal_add_js($data = NULL, $options = NULL) {
       // url() generates the script and prefix using hook_url_outbound_alter().
       // Instead of running the hook_url_outbound_alter() again here, extract
       // them from url().
+      // @todo Make this less hacky: http://drupal.org/node/1547376.
       $scriptPath = $GLOBALS['script_path'];
       $pathPrefix = '';
       url('', array('script' => &$scriptPath, 'prefix' => &$pathPrefix));
diff --git a/robots.txt b/robots.txt
index 90bec1e..d590fbf 100644
--- a/robots.txt
+++ b/robots.txt
@@ -35,12 +35,12 @@ Disallow: /user/password/
 Disallow: /user/login/
 Disallow: /user/logout/
 # Paths (no clean URLs)
-Disallow: /?q=admin/
-Disallow: /?q=comment/reply/
-Disallow: /?q=filter/tips/
-Disallow: /?q=node/add/
-Disallow: /?q=search/
-Disallow: /?q=user/password/
-Disallow: /?q=user/register/
-Disallow: /?q=user/login/
-Disallow: /?q=user/logout/
+Disallow: /index.php/admin/
+Disallow: /index.php/comment/reply/
+Disallow: /index.php/filter/tips/
+Disallow: /index.php/node/add/
+Disallow: /index.php/search/
+Disallow: /index.php/user/password/
+Disallow: /index.php/user/register/
+Disallow: /index.php/user/login/
+Disallow: /index.php/user/logout/
diff --git a/web.config b/web.config
index e990e03..06e4cbe 100644
--- a/web.config
+++ b/web.config
@@ -57,7 +57,9 @@
         </rule>
     -->
 
-        <!-- 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(). -->
         <rule name="Short URLS" stopProcessing="true">
           <match url="^(.*)$" ignoreCase="false" />
           <conditions>
@@ -65,9 +67,6 @@
             <add input="{REQUEST_FILENAME}" matchType="IsDirectory" ignoreCase="false" negate="true" />
             <add input="{URL}" pattern="^/favicon.ico$" ignoreCase="false" negate="true" />
           </conditions>
-          <!-- Pass all requests not referring directly to files in the
-            filesystem to index.php. Clean URLs are handled in
-            drupal_environment_initialize(). -->
           <action type="Rewrite" url="index.php" />
         </rule>
       </rules>