I am creating a series of menus in a custom module. This site also has a custom theme. Is there a way in the theme, or in the module, to set a menus "Show as expanded" to true. This way, if I move my site, uninstall, or whatever, it comes back the way it should right out of the box.
According to Drupal API for hook_menu:
"expanded": Optional. If set to TRUE, and if a menu link is provided for this menu item (as a result of other properties), then the menu link is always expanded, equivalent to its 'always expanded' checkbox being set in the UI.
So while writing your custom hook simply add
$items['examples/page_example'] = array( 'title' => 'Page Example', 'page callback' => 'page_example_description', 'access callback' => TRUE, 'expanded' => TRUE, );