Wikimedia Bugzilla is closed!

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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.

I don't think we can fix this. Consider:

Template:
[[Project:{{{1}}}]]

Page:
{{:Template|Target}}

What would this result? Also this is impossible to fix without fundamentally changing how MediaWiki handles pagelinks. Closing as wontfix.