Add comprehensive documentation files

[dionzand]

• Add CONTRIBUTING.md with contribution guidelines and development setup
• Add MIT LICENSE file with institutional copyright
• Add USER_MANUAL.md and PDF with detailed usage instructions
• Add PARAMETERS_REFERENCE.md and PDF with configuration parameter documentation

Description

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code refactoring
• Performance improvement
• Test addition/improvement

Related Issues

Fixes #

Changes Made

Testing

• Tested locally with Docker
• Tested CLI interface
• Tested GUI interface
• Added/updated unit tests
• All existing tests pass

Test Configuration:

• Python version:
• OS:
• Test cases covered:

Screenshots (if applicable)

Checklist

• My code follows the project's coding standards (PEP 8)
• 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

Documentation Updates

• README.md
• USER_MANUAL.md
• PARAMETERS_REFERENCE.md
• Code docstrings
• No documentation updates needed

Additional Notes