First load tools, then workflows to prevent warnings

[jvdzwaan]

When using the working_dir option.

If a workflow is copied before all of its steps, warnings are issued, because not all files used in the run field can be found. The warnings can be prevented by first copying tools and then workflows.

[jvdzwaan]

If a workflow is used as a subworkflow it must be loaded before the workflow it is a subworkflow in. This is an additional problem.