feat: add CLI interface for main reconstruction pipeline

[revaarathore11]

Summary

This PR adds a command-line interface (CLI) to the main reconstruction pipeline to improve usability and reproducibility.

Changes

• Added an argparse-based CLI to main_pipeline.py
• All CLI arguments are optional to preserve backward compatibility
• Existing default behavior is unchanged when no arguments are provided
• Updated onboarding documentation with basic CLI usage examples

Usage

python3 main_pipeline.py --help
python3 main_pipeline.py --input-dir input/ --output-dir output/
python3 main_pipeline.py --visualize

### Review Notes
- This PR is intentionally limited to CLI wiring and documentation
- No changes were made to ML logic, reconstruction algorithms, or evaluation code
- `--data-path` is parsed but not wired yet by design to preserve existing behavior

[revaarathore11]

@Marmotia1 please review