1.0.20170510151339: Updatable inputs (#317)

* Implement mutation manager to validate that files can be safely modified in
place.

* Test workflows for mutable inputs.

* Add in-place update tests.

* Set up Docker binds to support writable items.

* Inplace update works with & without Docker.

* Add InplaceUpdateRequirement.

* Refactor job to split Docker and non-Docker execution into separate classes.

* Manage readers for inplace updates.

* Record readers, last update step.

* Downgrade validation warnings when checking input & output objects.

* Recursive copy (#356)

* Better handling for relocating directory outputs to final output.