Remove bundling of stage in/out from unity-app-generator by default

[mcduffie]

App packages must be able to build existing app packages, non-default flag for building new ones (e.g. don't bundle stage_in/out)

[mcduffie]

CWL modular DAG requires that stage-out be called output.

See:
https://github.com/mike-gangl/unity-OGC-example-application/blob/main/process.ipynb

[mcduffie]

Implemented here: #25