1

Is there another way the primary navigation is supposed to printed out besides how it is done in the core system template?

print theme('links__system_main_menu', array('links' => $main_menu));` 

None of the changes I made via the theme_menu_link() function are recognized when the links are printed this way. Are they only seen if I manually put the primary links block into a region?

Which is the function that I could use to override the primary links when printed out this way? Everything I have with theme_menu_link() does nothing.

3

That syntax (two underscores) means that it first looks for a theme_links__system_main_menu()theme function and then falls back to theme_links() if that doesn't exist.

So to override only the main menu, create the following theme function for your theme: yourtheme_links__system_main_menu().

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