In the function _forum_access_comment_view_alter, we're checking permissions and adding/removing links from the comment links array. At the end of this process, we merge the old links with the new links using:
$links = array_merge($links, $old_links);
The problem with this approach is that it does not maintain the order of links. For example, I'm using the quote module. Because we re-order the links like this, the reply button appears on the left of the quote link, rather than at the far right.
Closed: won't fix
1.2
Code
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