[JOSS Review] Improve documentation and use cases

[praneethd7]

Thank you @lauritowal for implementing the changes. I successfully ran the code locally, encountering only a minor issue with numpy>2, which was resolved by downgrading. Consider specifying numpy<2 in pyproject.toml to prevent similar issues.
I'm now reviewing other checklist criteria:

• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)

While the statement of need is clear, I find it challenging to connect it directly to solving real-world problems. I would recommend the following:

• Provide examples demonstrating how the tool addresses practical analysis challenges. I am not an expert in this domain but perhaps some examples of where supervised probing techniques fall short and CCS offers advantages would be great.
• Please clarify the purpose of each file generated by elicit and explain how they can be used in further analysis or applications.
  

Cross reference: openjournals/joss-reviews#6511