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The link text on the JS page is quite repetitive. E.g. always repeats "concepts/programming/javascript/" for each item in "JavaScript concepts", always repeats "javascript/" in "JavaScript reference" I'd fix myself, but they are in some special include somewhere, rather than directly in the source.
Yep, this problem happens on a lot of listing pages at the moment. We make extensive use of sub-pages, which is somewhat non-standard for MediaWiki. The API_listing pages (see http://docs.webplatform.org/wiki/css/properties for an example) do the right behavior, but for technical reasons can't be rolled out widely yet.
I don't see this issue currently.