docs: Restructure documentation and enhance configuration

- Reorganize MkDocs navigation structure with new sections
- Add configuration, security, and development environment documentation
- Remove outdated development and getting started files
- Update requirements and plugin configurations
- Improve overall documentation layout and content

docs/configuration.md

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+# System Configuration
+
+This document provides detailed information about configuring the Home Assistant MCP Server.
+
+## Configuration File Structure
+
+The MCP Server uses a hierarchical configuration structure:
+
+```yaml
+server:
+  host: 0.0.0.0
+  port: 8123
+  log_level: INFO
+
+security:
+  jwt_secret: YOUR_SECRET_KEY
+  allowed_origins:
+    - http://localhost:3000
+    - https://your-domain.com
+
+devices:
+  scan_interval: 30
+  default_timeout: 10
+```
+
+## Server Settings
+
+### Basic Server Configuration
+- `host`: Server binding address (default: 0.0.0.0)
+- `port`: Server port number (default: 8123)
+- `log_level`: Logging level (INFO, DEBUG, WARNING, ERROR)
+
+### Security Settings
+- `jwt_secret`: Secret key for JWT token generation
+- `allowed_origins`: CORS allowed origins list
+- `ssl_cert`: Path to SSL certificate (optional)
+- `ssl_key`: Path to SSL private key (optional)
+
+### Device Management
+- `scan_interval`: Device state scan interval in seconds
+- `default_timeout`: Default device command timeout
+- `retry_attempts`: Number of retry attempts for failed commands
+
+## Environment Variables
+
+Environment variables override configuration file settings:
+
+```bash
+MCP_HOST=0.0.0.0
+MCP_PORT=8123
+MCP_LOG_LEVEL=INFO
+MCP_JWT_SECRET=your-secret-key
+```
+
+## Advanced Configuration
+
+### Rate Limiting
+```yaml
+rate_limit:
+  enabled: true
+  requests_per_minute: 100
+  burst: 20
+```
+
+### Caching
+```yaml
+cache:
+  enabled: true
+  ttl: 300  # seconds
+  max_size: 1000  # entries
+```
+
+### Logging
+```yaml
+logging:
+  file: /var/log/mcp-server.log
+  max_size: 10MB
+  backup_count: 5
+  format: "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+```
+
+## Best Practices
+
+1. Always use environment variables for sensitive information
+2. Keep configuration files in a secure location
+3. Regularly backup your configuration
+4. Use SSL in production environments
+5. Monitor log files for issues
+
+## Validation
+
+The server validates configuration on startup:
+- Required fields are checked
+- Value types are verified
+- Ranges are validated
+- Security settings are assessed
+
+## Troubleshooting
+
+Common configuration issues:
+1. Permission denied accessing files
+2. Invalid YAML syntax
+3. Missing required fields
+4. Type mismatches in values
+
+See the [Troubleshooting Guide](troubleshooting.md) for solutions.