Implement a second round of review comments from @DouweM.

- Don't use `TableReferences` - using `.arel_table` is shorter!
- Move some database-related code to `Gitlab::Database`
- Remove the `MergeRequest#issues_closed` and
  `Issue#closed_by_merge_requests`  associations. They were either
  shadowing or were too similar to existing methods. They are not being
  used anywhere, so it's better to remove them to reduce confusion.
- Use Rails 3-style validations
- Index for `MergeRequest::Metrics#first_deployed_to_production_at`
- Only include `CycleAnalyticsHelpers::TestGeneration` for specs that
  need it.
- Other minor refactorings.