The menu is configured in both the theme.php and the theme_functions_include.php it's the function showsublinks.
If you want to replace it completely then you can remove the code from the theme.php and put whatever you want in instead, however if your looking for specific html links somewhere you won't find any as the links are pulled from the database.
You could edit the links from within the database, or just use the admin panel > system admin > site links to edit them as it's easier, and there are options for the position of the link, navigation panel = side panel, subheader = top horizontal menu.
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