https://bugzilla.wikimedia.org/show_bug.cgi?id=55105
--- Comment #4 from Kunal Mehta (Legoktm) legoktm.wikipedia@gmail.com --- I gave it a try with -hintsareright
If used, and a hint to an existing page is given, any interlanguage links to the site of that hint are ignored, and a note "extra interwiki on hinted site ignored" with the appropriate names is output to the console. Hints can be given on the command line, in a file, etc. and interactively. Before interactive hints are knows, i.e. concerning links in the starting page, -hintsareright has no effect.
It also does not work on hints to sites where there are no pages found. If you need that, it is an extra feature which, I believe, is a bit more complicated to implement.
Not using -hintsareright should not make a difference to what we had before, so I just submitted the change to svn as r 6341 for you to try it out. Let me know if it fits your needs. If so, this bug can be closed.