diff --git a/core/includes/bootstrap.inc b/core/includes/bootstrap.inc
index 7dc75f5..8cca48c 100644
--- a/core/includes/bootstrap.inc
+++ b/core/includes/bootstrap.inc
@@ -1416,6 +1416,7 @@ function bootstrap_hooks() {
  * more information, including recommendations on how to break up or not
  * break up strings for translation.
  *
+ * @section sec_translating_vars Translating Variables
  * You should never use t() to translate variables, such as calling
  * @code t($text); @endcode, unless the text that the variable holds has been
  * passed through t() elsewhere (e.g., $text is one of several translated
@@ -1435,6 +1436,7 @@ function bootstrap_hooks() {
  * Translators can then rearrange the string as necessary for the language
  * (e.g., in Spanish, it might be "blog de @name").
  *
+ * @section sec_alt_funcs_install Use During Installation Phase
  * During the Drupal installation phase, some resources used by t() wil not be
  * available to code that needs localization. See st() and get_t() for
  * alternatives.
diff --git a/core/includes/theme.inc b/core/includes/theme.inc
index d79ba17..2b1f7b1 100644
--- a/core/includes/theme.inc
+++ b/core/includes/theme.inc
@@ -839,7 +839,7 @@ function drupal_find_base_themes($themes, $key, $used_keys = array()) {
  * @link themeable theme function or template @endlink, by checking the theme
  * registry.
  *
- * @section sec_a Function Arguments
+ * @section sec_theme_hooks Theme Hooks
  * Most commonly, the first argument to this function is the name of the theme
  * hook. For instance, to theme a taxonomy term, the theme hook name is
  * 'taxonomy_term'. Modules register theme hooks within a hook_theme()
@@ -851,7 +851,7 @@ function drupal_find_base_themes($themes, $key, $used_keys = array()) {
  * underscores changed to hyphens, so for the 'taxonomy_term' theme hook, the
  * default template is 'taxonomy-term.tpl.php'.
  *
- * @section sec_b Implementing Theme Hooks
+ * @subsection sub_overriding_theme_hooks Overriding Theme Hooks
  * Themes may also register new theme hooks within a hook_theme()
  * implementation, but it is more common for themes to override default
  * implementations provided by modules than to register entirely new theme
@@ -864,7 +864,7 @@ function drupal_find_base_themes($themes, $key, $used_keys = array()) {
  * rendering engine, it overrides the default implementation of the 'page' theme
  * hook by containing a 'page.tpl.php' file within its folder structure).
  *
- * @subsection sub_a Template Files
+ * @subsection sub_hook_order Hook Execution Order
  * If the implementation is a template file, several functions are called
  * before the template file is invoked, to modify the $variables array. These
  * fall into the "preprocessing" phase and the "processing" phase, and are
@@ -913,12 +913,14 @@ function drupal_find_base_themes($themes, $key, $used_keys = array()) {
  * - THEME_process_HOOK(&$variables):  Allows the theme to process the
  *   variables specific to the theme hook.
  *
- * @subsection sub_b Template Callbacks
+ * @subsection sub_restriction_function Restrictions on Functions
  * If the implementation is a function, only the theme-hook-specific preprocess
  * and process functions (the ones ending in _HOOK) are called from the
  * list above. This is because theme hooks with function implementations
  * need to be fast, and calling the non-theme-hook-specific preprocess and
  * process functions for them would incur a noticeable performance penalty.
+ *
+ * @subsection sub_alternate_suggestion Suggesting Alternate Functions
  * There are two special variables that these preprocess and process functions
  * can set: 'theme_hook_suggestion' and 'theme_hook_suggestions'. These will be
  * merged together to form a list of 'suggested' alternate theme hooks to use,
diff --git a/core/modules/system/system.api.php b/core/modules/system/system.api.php
index aa79df9..1deec52 100644
--- a/core/modules/system/system.api.php
+++ b/core/modules/system/system.api.php
@@ -554,6 +554,7 @@ function hook_menu_get_item_alter(&$router_item, $path, $original_map) {
  * paths and whose values are an associative array of properties for each
  * path. (The complete list of properties is in the return value section below.)
  *
+ * @section sec_callback_funcs Callback Functions
  * The definition for each path may include a page callback function, which is
  * invoked when the registered path is requested. If there is no other
  * registered path that fits the requested path better, any further path
@@ -578,6 +579,7 @@ function hook_menu_get_item_alter(&$router_item, $path, $original_map) {
  * $jkl will be 'foo'. Note that this automatic passing of optional path
  * arguments applies only to page and theme callback functions.
  *
+ * @subsection sub_callback_arguments Callback Arguments
  * In addition to optional path arguments, the page callback and other callback
  * functions may specify argument lists as arrays. These argument lists may
  * contain both fixed/hard-coded argument values and integers that correspond
@@ -620,6 +622,8 @@ function hook_menu_get_item_alter(&$router_item, $path, $original_map) {
  * @endcode
  * See @link form_api Form API documentation @endlink for details.
  *
+ * @section sec_path_opers Operators in Path
+ * @subsection sub_wildcard_sub Wildcards and Substitution
  * Wildcards within paths also work with integer substitution. For example,
  * your module could register path 'my-module/%/edit':
  * @code
@@ -632,6 +636,7 @@ function hook_menu_get_item_alter(&$router_item, $path, $original_map) {
  * with 'foo' and passed to the callback function. Note that wildcards may not
  * be used as the first component.
  *
+ * @subsection sub_load_funcs _load() Functions
  * Registered paths may also contain special "auto-loader" wildcard components
  * in the form of '%mymodule_abc', where the '%' part means that this path
  * component is a wildcard, and the 'mymodule_abc' part defines the prefix for a
@@ -663,6 +668,7 @@ function hook_menu_get_item_alter(&$router_item, $path, $original_map) {
  * return FALSE for the path 'node/999/edit' if a node with a node ID of 999
  * does not exist. The menu routing system will return a 404 error in this case.
  *
+ * @subsection sub_to_arg_funcs _to_arg() Functions
  * You can also define a %wildcard_to_arg() function (for the example menu
  * entry above this would be 'mymodule_abc_to_arg()'). The _to_arg() function
  * is invoked to retrieve a value that is used in the path in place of the
@@ -687,6 +693,7 @@ function hook_menu_get_item_alter(&$router_item, $path, $original_map) {
  * are called when the menu system is generating links to related paths, such
  * as the tabs for a set of MENU_LOCAL_TASK items.
  *
+ * @section sec_render_tabs Rendering Menu Items As Tabs
  * You can also make groups of menu items to be rendered (by default) as tabs
  * on a page. To do that, first create one menu item of type MENU_NORMAL_ITEM,
  * with your chosen path, such as 'foo'. Then duplicate that menu item, using a