Improve transparency of the compatibility of stages for the user

[mdenker]

Currently, there are checks that make sure that the current stage gets inputs from the previous stage which are compatible. Incompatible stacking of stages will cause an error. Despite the ability to continue the run with the previously computed results by instead running a compatible stage, it would be nice to have a mechanism that makes the stage configuration more transparent for the user, while not making customization of the pipeline more difficult. Potential mechanisms could be:

• Tagging/annotating stage outputs, or defining MIME types
• creating a validator for stages
• making a dry run option that imitates a run using current options
• creating feedback to the user on the order of stages being executed
• make a proxy output of each stage (i.e., "empty" output) to help dry running

Goal:

• Alert the user of an invalid configuration before the run or receives help in constructing a valid stage configuration