The issue is actually the other way round. The auto linking of URLs (performed by @inline_auto_link@ in @textile/formatter@ occurs occurs first, the wiki link is only generated after than.

Thus, the above statement is transformed into:

*Current behavior*
# @[[www|www.example.org]]@
# @[[www|<a class="external" href="http://www.example.org">www.example.org</a>]]@
# @<a href="/projects/redmine/wiki/www" class="wiki-page new"><a class="external" href="http://www.example.org">www.example.org</a></a>@

*Expected*
# @[[www|www.example.org]]@
# @<a href="/projects/redmine/wiki/www" class="wiki-page new">www.example.org</a>@

This might be solved by reordering rendering methods in source:trunk/app/helpers/application_helper.rb#L453 in a way that @parse_wiki_links@ runs before @inline_auto_link@. Maybe, these methods need to be included into the textile implementation in source:trunk/lib/redmine/wiki_formatting/textile in the correct ordering.
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Redmine links (eg. wiki, ticket links...) should not be handled by the builtin text formatter so we can easily switch to another one.

Maybe we could fix inline_auto_link instead.
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This issue seems to be fixed in Textile. I could not reproduce on Redmine 3.4.6.devel.17477. But it still does not work as expected in Markdown.
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Go MAEDA wrote:
> This issue seems to be fixed in Textile. I could not reproduce on Redmine 3.4.6.devel.17477. But it still does not work as expected in Markdown.

8 years! amazing. I thought redmine was long dead, feel free to close the ticket.
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