Currently, when the API outputs the links in an article (see URL), there is no way to see if a link is directly in an article or the result of a transclusion. An attribute on <pl> such as direct="no" or something would make these results clearer.
Version: unspecified
Severity: enhancement
URL: http://en.wikipedia.org/w/api.php?action=query&prop=links&titles=Main%20Page&format=xml