intermediate lesson: workflow design choices and the 7 levels of configuration

[mr-c]

In order of visibility to users:

1. Workflow level inputs (without defaults) these are mandatory
2. Workflow level inputs (with defaults) these are optional
3. Tool inputs set at the Workflow step level
4. Tool level inputs (without defaults)
5. Tool level inputs (with defaults)
6. Tool level fixed command line arguments
7. Modifying the tool itself