Fix CausalAgent input handling issues

[zaryabmakram]

This PR addresses issues in the refactoring branch related to incorrect input handling.

Key Changes:

1. Fixed input argument handling in CausalAgent to ensure only valid parameters are passed
2. Removed invalid input arguments that were previously causing failures
3. Added per-index result writing to the output file for better traceability and debugging
4. Implemented a fallback mechanism to use the original data file if data cleaning fails
5. Added to result objects by storing query_info for additional context and analysis

[jacobemmerson]

Changes look good, thanks!

[jacobemmerson]

commenting this out is fine since the user's can manually remove the cleaned files, but we may want to instead save it to a cleaned subset folder for easier removal if we don't want to do it already.

[jacobemmerson]

Looks good, my mistake for forgetting to update our CLI.