Changes for POTPyRI v1.1 to make code more modular and closer to Keck DRP

[charliekilpatrick]

Updating the code to be more modular and match closer to Keck DRP framework. Goals of PR:

• Renaming stages to primitives to match convention of Keck DRP framework
• Streamline main_pipeline so as much logic as possible occurs within the primitives
• Make the pipeline modular so that stages/primitives can be re-run within main_pipeline

This will require identifying input and output datamodels from each primitive so that the primitive can be properly initialized and conditions for skipping that primitive or the stage succeeded can be identified.