Add comprehensive documentation files

CONTRIBUTING.md

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+# Contributing to MatchY
+
+Thank you for your interest in contributing to MatchY! We welcome contributions from the community.
+
+## Table of Contents
+
+- [Code of Conduct](#code-of-conduct)
+- [Getting Started](#getting-started)
+- [Development Setup](#development-setup)
+- [How to Contribute](#how-to-contribute)
+- [Coding Standards](#coding-standards)
+- [Testing](#testing)
+- [Pull Request Process](#pull-request-process)
+- [Reporting Bugs](#reporting-bugs)
+- [Suggesting Features](#suggesting-features)
+
+## Code of Conduct
+
+This project adheres to a Code of Conduct. By participating, you are expected to uphold this code. Please read [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) before contributing.
+
+## Getting Started
+
+1. Fork the repository on GitHub
+2. Clone your fork locally:
+   ```bash
+   git clone https://github.com/your-username/MatchY.git
+   cd MatchY
+   ```
+3. Add the upstream repository:
+   ```bash
+   git remote add upstream https://github.com/genid/MatchY.git
+   ```
+
+## Development Setup
+
+### Prerequisites
+
+- Python 3.9 or higher
+- pip package manager
+- Git
+
+### Installation
+
+1. Create a virtual environment:
+   ```bash
+   python -m venv venv
+   source venv/bin/activate  # On Windows: venv\Scripts\activate
+   ```
+
+2. Install dependencies:
+   ```bash
+   pip install -r requirements.txt
+   ```
+
+3. Install development dependencies (optional):
+   ```bash
+   pip install black flake8 isort pytest
+   ```
+
+4. Install MatchY in editable mode:
+   ```bash
+   pip install -e .
+   ```
+
+### Running MatchY
+
+- **GUI Mode:**
+  ```bash
+  streamlit run 1_🧬_Home.py
+  ```
+
+- **CLI Mode:**
+  ```bash
+  python main.py --config examples/config.ini
+  ```
+
+## How to Contribute
+
+### Finding Issues to Work On
+
+- Check the [Issues](https://github.com/genid/MatchY/issues) page
+- Look for issues labeled `good first issue` or `help wanted`
+- Feel free to ask questions in issue comments
+
+### Creating a Branch
+
+Create a descriptive branch name:
+
+```bash
+git checkout -b feature/add-new-marker-set
+git checkout -b fix/haplotype-editor-bug
+git checkout -b docs/update-user-manual
+```
+
+Branch naming conventions:
+- `feature/` - New features
+- `fix/` - Bug fixes
+- `docs/` - Documentation changes
+- `refactor/` - Code refactoring
+- `test/` - Adding or updating tests
+
+## Coding Standards
+
+### Python Style Guide
+
+We follow [PEP 8](https://www.python.org/dev/peps/pep-0008/) Python style guidelines.
+
+**Key points:**
+- Use 4 spaces for indentation (not tabs)
+- Maximum line length: 100 characters
+- Use descriptive variable and function names
+- Add docstrings to functions and classes
+- Use type hints where appropriate
+
+### Code Formatting
+
+We recommend using automated formatters:
+
+```bash
+# Format code with Black
+black .
+
+# Sort imports with isort
+isort .
+
+# Check style with flake8
+flake8 .
+```
+
+### Documentation
+
+- Update docstrings when modifying functions
+- Update USER_MANUAL.md for user-facing changes
+- Update PARAMETERS_REFERENCE.md when adding/modifying parameters
+- Add inline comments for complex logic
+
+## Testing
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run specific test file
+pytest tests/test_pedigree.py
+
+# Run with coverage
+pytest --cov=pedigree_lr
+```
+
+### Writing Tests
+
+- Add tests for new features
+- Ensure tests pass before submitting PR
+- Aim for good code coverage
+- Test edge cases and error conditions
+
+## Pull Request Process
+
+1. **Update your fork:**
+   ```bash
+   git fetch upstream
+   git rebase upstream/master
+   ```
+
+2. **Make your changes:**
+   - Write clear, concise commit messages
+   - Follow the coding standards
+   - Add tests if applicable
+   - Update documentation
+
+3. **Commit your changes:**
+   ```bash
+   git add .
+   git commit -m "Add feature: description of changes"
+   ```
+
+4. **Push to your fork:**
+   ```bash
+   git push origin feature/your-feature-name
+   ```
+
+5. **Create a Pull Request:**
+   - Go to the [MatchY repository](https://github.com/genid/MatchY)
+   - Click "New Pull Request"
+   - Select your fork and branch
+   - Fill out the PR template with detailed description
+   - Link related issues using keywords (e.g., "Fixes #123")
+
+6. **PR Review Process:**
+   - Maintainers will review your PR
+   - Address any requested changes
+   - Once approved, your PR will be merged
+
+### Commit Message Guidelines
+
+Write clear commit messages:
+
+```
+Add trace mode support for multiple markers
+
+- Implement marker selection in trace analysis
+- Update report template to show marker-specific results
+- Add validation for marker compatibility
+
+Fixes #123
+```
+
+Format:
+- First line: Brief summary (50 chars or less)
+- Blank line
+- Detailed description (wrap at 72 chars)
+- Reference issues at the end
+
+## Reporting Bugs
+
+Found a bug? Please create an issue using the bug report template:
+
+1. Go to [Issues](https://github.com/genid/MatchY/issues)
+2. Click "New Issue"
+3. Select "Bug Report"
+4. Fill out all sections:
+   - Clear description of the bug
+   - Steps to reproduce
+   - Expected behavior
+   - Actual behavior
+   - Environment details (OS, Python version, etc.)
+   - Screenshots if applicable
+
+**Before reporting:**
+- Check if the issue already exists
+- Verify the bug is reproducible
+- Check if it's fixed in the latest version
+
+## Suggesting Features
+
+Have an idea for a new feature?
+
+1. Go to [Issues](https://github.com/genid/MatchY/issues)
+2. Click "New Issue"
+3. Select "Feature Request"
+4. Describe:
+   - The problem or use case
+   - Proposed solution
+   - Alternative solutions considered
+   - Why this would be useful
+
+## Questions?
+
+- Create a [Question Issue](https://github.com/genid/MatchY/issues)
+- Check existing issues for similar questions
+- Read the [User Manual](USER_MANUAL.md)
+
+## License
+
+By contributing to MatchY, you agree that your contributions will be licensed under the MIT License.
+
+## Acknowledgments
+
+Thank you for contributing to MatchY! Your efforts help make this tool better for the forensic genetics community.

LICENSE

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+MIT License
+
+Copyright (c) 2026 Department of Pathology and Clinical Bioinformatics, Erasmus MC University Medical Center Rotterdam, The Netherlands; Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, Germany; Chair of Epidemiology, Medical Biometry and Medical Informatics, Department of Medicine, Health and Medical University Erfurt, Erfurt, Germany
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.