Refactor and start of reorganization

Main motivation for this change is several of the best practice articles I've perused recommend a smaller number of modules.

Modules, like the name implies, are good for importing/exporting large pieces of functionality. I look at them just like maven project modules.

This first change is recognizing that "AllWorkflows" module is an extra layer that really does not need to be separated from the overall nwcApp module.

Filename/directory structure changes are to reflect recognition of a "top level application module".

Also includes a space -> tab change for some of the indentation.
Haha, yup. just noticed. Thanks jw!