[easy] add phid to repository.query

Summary:
owners.query returns paths as (repo phid, path). That should
get fixed in some non-breaking way, but for now just add phid to
repository.query so I can support non-E repos.

Would like to sneak this in before tomorrow's push

Test Plan: http://phabricator.mkedia.dev4925.snc6.facebook.com/conduit/method/repository.query/

Reviewers: epriestley, nh, vrana

Reviewed By: nh

CC: aran, Korvin

Differential Revision: https://secure.phabricator.com/D3001