Cleanup

What does this merge request do and why?

Our code base has gotten a little messy as we have built it. I have taken it upon myself to clean it up.

• Removing defaults that cause problems (like me loosing a week of my life)
• Making CLI flags explicit (related to above point)
• Consolidating the batch completion within the beam portion of the pipeline

The list will go on.

Merge request checklist

• I've ran the eval_codebase.py pipeline to validate that nothing is broken.
• Tests added for new functionality. If not, please raise an issue to follow up.
  • Functionality remains unchanged but I will see I actually need more tests.
• Documentation added/updated, if needed
  • Nothing from how you run this should change and if your script breaks now it will tell you