- feat: Enhance README with setup instructions, usage, and command documentation

- fix: Update API routes to include DOI URL handling and improve route organization

- chore: Add ORCID preload rule file and ensure proper registration

- docs: Add MIT License to the project for open-source compliance

- feat: Implement command to detect and fix missing dataset cross-references

- feat: Create command for updating DataCite DOI records with detailed logging and error handling

- docs: Add comprehensive documentation for dataset indexing command

- docs: Create detailed documentation for DataCite update command with usage examples and error handling

readme.md

@@ -11,6 +11,8 @@ Welcome to the Tethys Research Repository Backend System! This is the backend co
 -   [Configuration](#configuration)
 -   [Database](#database)
 -   [API Documentation](#api-documentation)
+-   [Commands](#commands)
+-   [Documentation](#documentation)
 -   [Contributing](#contributing)
 -   [License](#license)
 
@@ -29,5 +31,175 @@ Before you begin, ensure you have met the following requirements:
 1. Clone this repository:
 
     ```bash
-    git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git
+    git clone git clone https://gitea.geologie.ac.at/geolba/tethys.backend.git
+    cd tethys-backend
     ```
+
+2. Install dependencies:
+
+    ```bash
+    npm install
+    ```
+
+3. Configure environment variables (see [Configuration](#configuration))
+
+4. Run database migrations:
+
+    ```bash
+    node ace migration:run
+    ```
+
+5. Start the development server:
+
+    ```bash
+    npm run dev
+    ```
+
+## Usage
+
+The Tethys Backend provides RESTful APIs for managing research datasets, user authentication, DOI registration, and search functionality.
+
+## Configuration
+
+Copy the `.env.example` file to `.env` and configure the following variables:
+
+### Database Configuration
+```bash
+DB_CONNECTION=pg
+DB_HOST=localhost
+DB_PORT=5432
+DB_USER=your_username
+DB_PASSWORD=your_password
+DB_DATABASE=tethys_db
+```
+
+### DataCite Configuration
+```bash
+# DataCite Credentials
+DATACITE_USERNAME=your_datacite_username
+DATACITE_PASSWORD=your_datacite_password
+DATACITE_PREFIX=10.21388
+
+# Environment-specific API endpoints
+DATACITE_API_URL=https://api.test.datacite.org      # Test environment
+DATACITE_SERVICE_URL=https://mds.test.datacite.org  # Test MDS
+
+# For production:
+# DATACITE_API_URL=https://api.datacite.org
+# DATACITE_SERVICE_URL=https://mds.datacite.org
+```
+
+### OpenSearch Configuration
+```bash
+OPENSEARCH_HOST=localhost:9200
+```
+
+### Application Configuration
+```bash
+BASE_DOMAIN=tethys.at
+APP_KEY=your_app_key
+```
+
+## Database
+
+The system uses PostgreSQL with Lucid ORM. Key models include:
+
+- **Dataset**: Research dataset metadata
+- **DatasetIdentifier**: DOI and other identifiers for datasets
+- **User**: User management and authentication
+- **XmlCache**: Cached XML metadata
+
+Run migrations and seeders:
+
+```bash
+# Run migrations
+node ace migration:run
+
+# Run seeders (if available)
+node ace db:seed
+```
+
+## API Documentation
+
+API endpoints are available for:
+
+- Dataset management (`/api/datasets`)
+- User authentication (`/api/auth`)
+- DOI registration (`/api/doi`)
+- Search functionality (`/api/search`)
+
+*Detailed API documentation can be found in the `/docs/api` directory.*
+
+## Commands
+
+The system includes several Ace commands for maintenance and data management:
+
+### Dataset Indexing
+```bash
+# Index all published datasets to OpenSearch
+node ace index:datasets
+
+# Index a specific dataset
+node ace index:datasets --publish_id 123
+```
+
+### DataCite DOI Management
+```bash
+# Update DataCite records for modified datasets
+node ace update:datacite
+
+# Show detailed statistics for datasets needing updates
+node ace update:datacite --stats
+
+# Preview what would be updated (dry run)
+node ace update:datacite --dry-run
+
+# Force update all DOI records
+node ace update:datacite --force
+
+# Update a specific dataset
+node ace update:datacite --publish_id 123
+```
+
+*For detailed command documentation, see the [Commands Documentation](docs/commands/)*
+
+## Documentation
+
+Comprehensive documentation is available in the `/docs` directory:
+
+- **[Commands Documentation](docs/commands/)** - Detailed guides for Ace commands
+  - [DataCite Update Command](docs/commands/update-datacite.md) - DOI synchronization and management
+  - [Dataset Indexing Command](docs/commands/index-datasets.md) - Search index management
+- **[API Documentation](docs/api/)** - REST API endpoints and usage
+- **[Deployment Guide](docs/deployment/)** - Production deployment instructions
+- **[Configuration Guide](docs/configuration/)** - Environment setup and configuration options
+
+## Contributing
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Commit your changes (`git commit -m 'Add some amazing feature'`)
+4. Push to the branch (`git push origin feature/amazing-feature`)
+5. Open a Pull Request
+
+### Development Guidelines
+
+- Follow the existing code style and conventions
+- Write tests for new features
+- Update documentation for any API changes
+- Ensure all commands and migrations work properly
+
+### Testing Commands
+
+```bash
+# Run tests
+npm test
+
+# Test specific commands
+node ace update:datacite --dry-run --publish_id 123
+node ace index:datasets --publish_id 123
+```
+
+## License
+
+This project is licensed under the [MIT License](LICENSE).