I only spotted this the other day – the Elements.xml contains an ‘Overwrite’ attribute. I was provisioning a custom Content Type and some Site Columns but when activating the feature it failed. The error message was that the Content Type already existed in the site – see screenshot below.
It turns out you can set the Overwrite attribute to TRUE to force overwrite of the Content Type – this means when you activate your feature again it will work. Kind of obvious really I just hadn’t spotted it before!
Hope this helps someone!