Add missing # rubocop:enable comments, and fix any resulting style issues

[dmolesUC]

When I first set up RuboCop, I assumed # rubocop:disable was block scoped, but it turns out it's meant to be paired with a matching # rubocop:enable. Without that, it means "disable till further notice".

We've put # rubocop:enable in a few places (e.g. Resource::duplicate_filenames), but there are still a lot of orphan disables out there. At some point we should clean these up, and fix any style issues we discover in code where checks were unintentionally disabled.

[ryscher]

I have copied this issue to the new Dryad development tracker at datadryad/dryad-product-roadmap#23 -- it's up to @dmolesUC3 whether it should still be active here.