feat: Add an overwrite argument to the pipeline script with different levels

[berntpopp]

Description:
Enhance the pipeline script to include an overwrite argument that allows different levels of overwriting, such as overwriting all steps or only specific steps.

Tasks:

• Add an overwrite argument with different levels to the pipeline script.
• Implement logic to handle different overwrite levels for each step of the pipeline.
• Update the documentation to reflect the new overwrite argument.