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 
It's not obvious that this one is safe to remove, or - none of the added indices cover the use case, but if there are no existing query paths that rely on the presence of this index then sure.