Remove bundling of stage in/out from app-pack-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)

Acceptance Criteria

• The algorithm CWL specifies file/data inputs as Directory types, and in that directory will/can read a catalog.json file to get the data its relying on (A.2.1). This changes the input type from a catalog.json location to a Directory.
• The algorithm writes outputs to a Directory along with a stac catalog catalog.json), describing the files in that directory. (A.3.1). Outputs have always been a directory type and will continue to be one for a valid application package or workflow
• NEW Gherkin Test case added to System Test DURING THE PLANNING
• NEW Gherkin Test case implementation added to System Test during PI

[mcduffie]

CWL modular DAG requires that stage-in be called input.

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