Add indices for slow queries / to account for deleted_at

I think there are a bunch here we can actually discuss. The most necessary ones are probably on `jobs.status` and `deploys.{stage_id,deleted_at}` (for DeploysController#active).

@zendesk/samson @zendesk/octo 
The best cheat sheet is this one http://www.percona.com/files/presentations/ppc2009/PPC2009_mysql_pagination.pdf - essentially you cannot use a later column `b` in a compound index `(a, b)` if `a` is not also used in the conditions or ordering, and even then, if `a` is used for a scan like `a IS NULL` or `a < N` then `b` won't be usable.