Fix CausalAgent input handling and runtime 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. Fixed runtime error where output_dir was not created for storing log files
3. Added a conditional to run signal commands only on supported OS
4. Removed invalid input arguments that were previously causing failures
5. Added per-index result writing to the output file for better traceability and debugging
6. Implemented a fallback mechanism to use the original data file if data cleaning fails
7. Added to result objects by storing query_info for additional context and analysis