Implement comprehensive TODO/FIXME tracker CLI command for code analysis

[Copilot]

This PR implements a comprehensive TODO and FIXME tracker as requested in issue #169. The tracker provides powerful code analysis capabilities to help manage development tasks and track progress across the Hydrus software stack.

🎯 Features Implemented

Core Functionality

• Multi-pattern scanning: Detects TODO, FIXME, HACK, NOTE, XXX, and BUG comments
• Smart comment detection: Uses regex patterns to find actual comments while avoiding false positives
• GitHub issue linking: Automatically extracts issue references like #123, fixes #456, issue #789
• Comprehensive reporting: Statistical breakdown by pattern, directory, and file type

CLI Integration

The tracker integrates seamlessly with the existing Hydrus CLI framework:

# Full scan with summary and detailed output
hydrus-cli todo scan

# Quick statistics overview
hydrus-cli todo stats

# Show items linked to GitHub issues
hydrus-cli todo issues

# Custom patterns and output formats
hydrus-cli todo scan --patterns "TODO,FIXME" --format json --output report.json

Output Formats

• Console: Rich formatted output with tables and colors
• JSON: Machine-readable format for automation and CI/CD
• Markdown: Documentation-ready reports

Example Output

📋 TODO Tracker Summary
Total items found: 8
Items with GitHub issues: 0

🏷️  By Pattern:
┏━━━━━━━━━┳━━━━━━━┓
┃ Pattern ┃ Count ┃
┡━━━━━━━━━╇━━━━━━━┩
│ NOTE    │ 6     │
│ TODO    │ 2     │
└─────────┴───────┘

📁 By Directory:
┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━┓
┃ Directory           ┃ Count ┃
┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━┩
│ docs                │ 3     │
│ autonomy/scripts/cv │ 2     │
│ autonomy            │ 1     │
│ autonomy/src        │ 1     │
└─────────────────────┴───────┘

🔧 Technical Implementation

• Modular design: Clean separation between scanning logic, reporting, and CLI interface
• Rich dependencies: Uses rich library for beautiful console output
• Flexible configuration: Customizable file extensions, patterns, and exclusion rules
• Error handling: Graceful handling of encoding issues and inaccessible files
• Self-exclusion: Automatically excludes the todo.py file itself to avoid self-references

📊 Current Repository Analysis

The tracker identified the current state of the Hydrus codebase:

• 2 TODO items requiring attention
• 6 NOTE items providing documentation context
• Primary areas needing work: autonomy module (documentation) and controllers (buoyancy handling)
• 0 items currently linked to GitHub issues (opportunity for better issue tracking)

🧪 Testing

Comprehensive testing validates:

• Accurate pattern detection in various comment styles
• GitHub issue number extraction
• Report generation and statistics
• JSON serialization and markdown formatting
• CLI integration and help system

This implementation provides exactly what was requested: a tool to track TODO/FIXME comments, generate reports showing development progress, and identify which folders/packages need more work, with optional GitHub issue integration for enhanced project management.

Fixes #169.

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