From https://www.mediawiki.org/wiki/Thread:Project:Support_desk/Uploads_not_working_in_1.20.1/reply_(6)
I upgraded to MediaWiki 1.20.2 ... File links are still not rendered correctly. Example: a previously (i.e., before the update to 1.20.1/1.20.2) created link like [[File:IMG_3334.JPG|thumb]] is now rendered as [<a rel="nofollow" class="external autonumber" href="File:IMG_3334.JPG%7Cthumb">[2]</a>] It seems like File is not recognised as all. The inner brackets are interpreted as a link to an external resource, and the contents are rendered accordingly.
A later post gives this update:
[Having "file:" in $wgURLProtocols] didn't cause problem until a recent upgrade of the MediaWiki software.... Fixing the last line (the file:// protocol) solved the problem:
Version: 1.20.x
Severity: major
See Also:
https://bugzilla.wikimedia.org/show_bug.cgi?id=69500