Are you trying to use hook_menu_alter in Drupal 7 and finding that hook_menu_alter is not appearing to have any effect? There is a reason. Hook_menu_alter is not called every time you run your site. Hook_menu_alter only runs when the menu module is initialized or a menu is initially constructed. If you have an existing menu and you would like hook_menu_alter to affect that menu, you must do a menu rebuild. In theory, there are two trivial ways to do this. However, the 2 trivial methods may not work for you. The trivial methods are:

• Use Devel module option to request menu rebuild
• Use drush to request menu rebuild

However, these 2 methods may not be convenient for you. I know that right now (8/2/2014), Devel will not run correctly on my install because there appears to be problem with the current combination of devel, devel_theme & simplehtmldom that is currently available seem to crash my install. At the same time, drush is inconvenient for the install I have available. My solution involved creation of a simple file that will force the menu rebuild.

To do a menu rebuild programattically:

• Create a file in your site’s base directory, perhaps menuRebuild.php
• Include the following code in the new file

  
    <?php
    
      chdir("< your-root-directory >") ;
      define("DRUPAL_ROOT", getcwd());
      require_once("./includes/bootstrap.inc") ;
      drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL) ;
      // Rebuild
      menu_rebuild() ;
      echo "rebuilt" ;
  
    ?>
  
  

• run the file … the menu will be built.