Refactor PHP file parsing, time tracking, and logic enhancements

[erikyo]

Summary

This pull request includes various improvements and fixes across multiple areas of the codebase:

• PHP File Parsing: Improved comment parsing logic for better accuracy and efficiency.
• Time Tracking: Enhanced time tracking reliability by passing timeStart as an argument. Initialized timeStart and updated related logic to handle it properly.
• Refactoring: Simplified audit completion messages, improved console formatting, removed redundant logging, and optimized file processing logic.
• Bug Fixes: Addressed issues with JSON output, the -h help flag mapping, and consistent handling of glob patterns (Windows/Unix compatibility and catch-all syntax).
• Version Updates: Updated the codebase to v1.6.6 while fixing minor README formatting issues.

Checklist

• Unit tests updated or added for changes.
• Documentation updated (if applicable).
• Version number incremented in files affected by this change.

Additional Notes

This update improves robustness, code readability, and user-facing functionality, especially in time tracking and progress reporting areas.