tweme\includes\menu.inc
function tweme_menu_tree__main_menu($vars)

function tweme_menu_link__main_menu($vars)

Why there has a trailing __main_menu for the override menu function?

Comments

That means these functions will be invoked only for main menu - not for all menus on the site.

I don't know there is such a function override naming in drupal.
where could I find such information ? I could not get these kind of function overriding mentioned from google

Unfortunately this feature is not documented yet.
Some information could be found here: http://drupal.org/node/254940#theme-suggestions-for-menus.