feat: add modern development tools and enhance coding standards

[ryanmccann1024]

Description:
This PR introduces a comprehensive modern development stack with tools like Black, Ruff, MyPy, and pre-commit hooks. It also updates coding and testing standards documentation for better AI optimization and includes extensive refactoring across multiple modules to comply with these new standards.

🔧 Type of Change

Primary Change Type:

• 🐛 Bug Fix - Non-breaking change that fixes an issue
• ✨ New Feature - Non-breaking change that adds functionality
• 💥 Breaking Change - Change that would cause existing functionality to break
• 🔄 Refactor - Code change that neither fixes a bug nor adds a feature
• 📚 Documentation - Documentation only changes
• 🧪 Tests - Adding missing tests or correcting existing tests
• 🏗️ Build/CI - Changes to build process or CI configuration
• 🎨 Style - Code style changes (formatting, missing semicolons, etc.)
• ⚡ Performance - Performance improvements
• 🔒 Security - Security vulnerability fixes

Component(s) Affected:

• CLI Interface (fusion/cli/)
• Configuration System (fusion/configs/)
• Simulation Core (fusion/core/)
• ML/RL Modules (fusion/modules/rl/, fusion/modules/ml/)
• Routing Algorithms (fusion/modules/routing/)
• Spectrum Assignment (fusion/modules/spectrum/)
• SNR Calculations (fusion/modules/snr/)
• Visualization (fusion/visualization/)
• GUI Interface (fusion/gui/)
• Unity/HPC Integration (fusion/unity/)
• Testing Framework (tests/)
• Documentation
• GitHub Workflows (.github/)
• Build/Dependencies

🧪 Testing

Test Coverage:

• Unit tests added/updated
• Integration tests added/updated
• Manual testing performed
• Existing tests still pass
• Performance impact assessed

Test Details:

• Verified that pre-commit hooks are functioning correctly
• Tested Black and Ruff formatting on sample files
• Confirmed MyPy type checking integration
• Ensured .gitignore properly excludes coverage and venv files

Test Configuration Used:

# Using existing test configurations
[general_settings]
# Standard test config...

Commands to Reproduce Testing:

# Install development dependencies
pip install -r requirements-dev.txt

# Run pre-commit hooks
pre-commit run --all-files

# Run tests
python -m pytest tests/

Test Results:

• Operating System: macOS (Darwin 25.0.0)
• Python Version: 3.11
• Test Environment: local

📊 Impact Analysis

Performance Impact:

• No performance impact
• Performance improved
• Minor performance decrease (acceptable)
• Significant performance impact (needs discussion)

Memory Usage:

• No change in memory usage
• Memory usage optimized
• Minor increase in memory usage
• Significant memory impact

Backward Compatibility:

• Fully backward compatible
• Minor breaking changes with migration path
• Major breaking changes (requires version bump)

Dependencies:

• No new dependencies
• New dependencies added (list in Additional Notes)
• Dependencies removed/updated

🔄 Migration Guide

Breaking Changes (if any):
None - all changes are backward compatible.

Migration Steps:

1. Install new development dependencies: pip install -r requirements-dev.txt
2. Run pre-commit install to set up git hooks
3. Optionally run formatters on existing code when ready

Before/After Examples:

# Before (manual formatting)
def function(x,y,z):
  return x+y+z

# After (auto-formatted with Black)
def function(x, y, z):
    return x + y + z

✅ Code Quality Checklist

Architecture & Design:

• Follows established architecture patterns
• Code is modular and follows separation of concerns
• Interfaces are well-defined and documented
• Error handling is comprehensive
• Logging is appropriate and informative

Code Standards:

• Code follows project style guidelines
• Variable and function names are descriptive
• Code is properly commented
• Complex logic is documented
• No dead code or unused imports

Configuration & CLI:

• CLI arguments follow established patterns
• Configuration validation updated (if needed)
• Schema updated for new config options
• Backward compatibility maintained for configs

Security:

• No sensitive information hardcoded
• Input validation performed where needed
• No security vulnerabilities introduced
• Dependencies scanned for vulnerabilities

📚 Documentation

Documentation Updates:

• Code comments added/updated
• API documentation updated
• User guide/tutorial updated
• Configuration reference updated
• CHANGELOG.md updated
• README updated (if needed)

Examples Added:

• Usage examples in docstrings
• Configuration examples
• CLI usage examples
• Integration examples

🚀 Deployment

Deployment Considerations:

• Safe to deploy to all environments
• Requires environment-specific configuration
• Needs database migration (if applicable)
• Requires manual steps (document below)

Manual Steps Required:
None - deployment is straightforward.

🔍 Review Guidelines

For Reviewers:

• PR description is clear and complete
• Code changes align with described functionality
• Tests are comprehensive and pass
• Documentation is adequate
• No obvious security issues
• Performance impact is acceptable

Review Focus Areas:

1. Pre-commit hook configuration in .pre-commit-config.yaml
2. Development workflow documentation in DEVELOPMENT_QUICKSTART.md and DEVELOPMENT_WORKFLOW.md
3. Refactored modules for coding standards compliance
4. GitHub Actions workflow in .github/workflows/quality.yml

📝 Additional Notes

New Dependencies Added:

• black: Code formatter
• ruff: Fast Python linter
• mypy: Static type checker
• pre-commit: Git hook framework
• vulture: Dead code finder
• bandit: Security linter
• pydeps: Dependency analyzer
• Additional development tools for profiling and analysis

Open Questions:

• Should we apply the formatters to all existing code immediately or gradually?
• Do we want to make pre-commit hooks mandatory for all contributors?

Future Work:

• Apply formatting standards to remaining modules not covered in this PR
• Add more comprehensive type hints throughout the codebase
• Enhance test coverage reporting integration

Related PRs:
This PR is based on commits from the release/6.0.0 branch merge.

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🏁 Final Checklist

Before submitting this PR, confirm:

• I have followed the contributing guidelines
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published