feat: Comprehensive repository modernization and reorganization

[danindiana]

This is a major modernization update that brings the repository up to professional standards with modern Perl development practices.

Infrastructure & Build Tools

• Add cpanfile for centralized dependency management
• Add install.sh automated dependency installer
• Add Makefile for build automation and testing
• Add .gitignore with comprehensive Perl-specific patterns
• Add .perlcriticrc for code quality standards

Documentation

• Add CONTRIBUTING.md with comprehensive coding standards
• Add CHANGELOG.md for tracking changes
• Update README.md with:
  • Multiple new badges (CI/CD, code quality, testing, etc.)
  • Quick Start section
  • Updated repository structure diagram
  • Testing & Quality section
  • Project Roadmap
  • Improved Quick Reference with new paths
• Add tools/README.md documenting utility scripts

Repository Organization

• Create tools/ directory and move utility scripts:
  • Consolidate 4 file_scanner variants into single file_scanner.pl
  • Consolidate 2 merge_dirs variants into single merge_directories.pl
  • Move 8 utility scripts to tools/ for better organization
• Create t/ directory with initial test suite:
  • 00-load.t - syntax verification for all scripts
  • 01-dependencies.t - dependency availability checks
• Create examples/ and docs/ directory structure
• Remove arxiv_doi_grabber/temp/ with 10+ old development files

Testing & CI/CD

• Add Test::More framework with initial test suite
• Add comprehensive GitHub Actions CI/CD pipeline:
  • Multi-version testing (Perl 5.30-5.38)
  • Multi-platform (Ubuntu, macOS)
  • Code quality checks with Perl::Critic
  • Dependency verification
  • Module-specific testing
  • Documentation validation
  • Security scanning
  • Coverage reporting
  • Build validation

Code Quality

• Establish Perl::Critic standards (severity 3)
• Define consistent naming conventions
• Set test coverage target (70%+)
• Implement markdown linting configuration

Cleanup

• Remove duplicate file_scanner scripts (3 variants deleted)
• Remove duplicate merge_dirs scripts (1 variant deleted)
• Clean up temp/ directory with old development artifacts
• Remove versioned filenames in favor of canonical versions

This modernization establishes a solid foundation for future development while maintaining backward compatibility with existing functionality.

All tools remain functional and are now better organized, documented, and tested. The repository now follows modern Perl development practices with proper dependency management, testing, and CI/CD automation.