Enhancement: Structured runtime logging, parameter tracking, and output handling (Issue #6)

[Shruthii7]

This PR completes and extends the functionality proposed in Issue #6 by introducing structured runtime logging and improved output handling.

### Problem
Currently, MP-BioPath primarily prints output to standard output, with no centralized logging mechanism or persistent storage of runtime information. This makes debugging, reproducibility, and tracking multiple runs difficult.

### Enhancements

• Added structured logging system with timestamps
• Automatic creation of an outputs/ directory
• Logging of execution start and completion states
• Recording of runtime parameters for reproducibility
• Logging of important execution steps and conditions
• Graceful handling of missing required inputs (e.g., pathway list)

### Benefits

• Improves reproducibility of experiments
• Makes debugging easier
• Provides better traceability of runs
• Enhances usability for users working with multiple datasets

This implementation focuses on improving the Python workflow (make_output_files.py) while maintaining compatibility with the existing pipeline.