Pager wrapper markup is hardcoded and isn't easily replaced

First of all, I've gotta say this is an amazing theme, but I'm encountering this issue quite a lot with the bootstrap theme: We have many overridden core functions (for this example I'll use bootstrap_pager()), and often it's necessary to add/remove/change classes and markup for the output of these functions.

In this case, we want to add a class conditionally to the pager wrapper (currently classed with "text-center" but there is no way I can think to do this without copying the entire function into our theme and modifying that one line. This causes issues with updates to the bootstrap theme when bug fixes/feature enhancements come through as we'd have to manually merge the changes into our overridden function. What would be ideal is if there was a tpl.php file for these "wrapper" type markup, that way instead of:

    return '<div class="text-center">' . theme('item_list', array(
      'items' => $items,
      'attributes' => array('class' => array('pagination')),
    )) . '</div>';

You could have something like:

    $items = theme('item_list', array(
      'items' => $items,
      'attributes' => array('class' => array('pagination')),
    ));
    return theme('bootstrap_pager', array('items' => $items));

And bootstrap_pager would simply be a template file with:

<div class="text-center">
 <?php print $items; ?>
</div>

This would give several benefits:

1) Overriding the markup would be easy, just override the template file
2) You could do preprocessing on the $items without forking the function.
3) Probably others...

However I understand that this may add extra overhead that is not wanted/desired for the theme, and if we were to do it for 1 function, then we'd want to standardise the whole theme (which may add too much overhead). I wouldn't even know where to go about doing this as I haven't wrapped my head around the whole registry.inc style of doing things but I just wanted to raise this and see what people's opinions were. We have similar issues with panels_bootstrap_layouts as well but that's a separate thing :)

Cheers