Fix indexes for Reference objects.

Turns out Flow indexes work very differently from SQL
indexes in that you can't use a covering index, your index
has to match exactly the fields on which you are querying.

Was causing the following error in WMF error logs:

Flow\Data\ObjectLocator::findMulti: No index (out of 2) available
to answer query for ref_src_namespace, ref_src_title with options []

Bug: 65672
Change-Id: Ie4cfab6e5976843fc52e0a9f788a37432c18dccd
Merge "Fix indexes for Reference objects."