If you need a customizable main menu, there is a plugin available
As a first step you need to create the appropriate Directory for the plugin if it doesn't exist.
Change to your Ilias installation directory and issue the comand

mkdir -p Customizing/global/plugins/Services/UIComponent/UserIntefaceHook

Then make this your working directory:

cd Customizing/global/plugins/Services/UIComponent/UserInterfaceHook

Now check out the plugin from the svn repository:

svn co https://svn.ilias.de/svn/ilias/branches/leifos/lf_plugins/Services/UIComponent/UserInterfaceHook/LfMainMenu LfMainMenu

After installation the plugin has to be activated and configured. Login als ILIAS-admin and go to administration-plungins,modules and services. The plugin LfMainMenu shoud appear (if not, check for typos in your directory names). Click on administrate for this plugin and update/activate it. Dont panic if your main menu disappears. In the configuration first add the standard menu items:
 
personal Desktop and last visited
Repository
 
You have to select both and activate them to appear again in your main manu.
 
and then create new Items as you need.

The Administration, Online help and Search are present automatically.
 
Your Customized Main Menu is available now.