Overriding link-template.php within a theme

Hey all,

I’d like to modify the links that are being generated inside of wp-includes/link-template.php, but without actually modifying that file. The reason is that I don’t want to have to make custom changes to WordPress on every update.

Is there a way to override or hook into those calls without having to modify link-template?

Rob

p.s. On a side note, the link functions should really just be generating the href values, not the actual link tags themselves.