Most of these should be a matter of swapping a getFullURL() out for a getLocalURL().

There are places where full URLs are technical required, but <link> isn't one of them. :)

(In reply to comment #0)

href="http://en.wikipedia.org/apple-touch-icon.png

This one is due to the setting of $wgAppleTouchIcon at WMF.

href="http://en.wikipedia.org/w/index.php?title=Faraday_cage&amp;action=edit
href="http://en.wikipedia.org/w/index.php?title=Special:RecentChanges&amp;feed=atom
href="http://en.wikipedia.org/w/index.php?title=Special:RecentChanges&amp;feed=rss
href="http://en.wikipedia.org/wiki/Faraday_cage
href="http://en.wikipedia.org/wiki/Wikipedia:Text_of_the_GNU_Free_Documentation_License
They could be written just href="/..." etc. like the rest.

I fixed all of these in r47583.

• This bug has been marked as a duplicate of bug 16357 ***