docs: [#12] complete Phase 2 documentation updates for MySQL migration

- Added database configuration section to application README
- Enhanced environment file with MySQL-specific comments and headers
- Updated migration plan to mark Phase 2 as completed
- Documented all MySQL configuration details and requirements
- Preserved SQLite configurations as legacy/development options
- All linting checks pass successfully

Author: josecelano

application/.env.production

@@ -1,6 +1,11 @@
+# Torrust Tracker Demo - Production Environment Configuration
+# 
+# This configuration uses MySQL as the default database backend.
+# Make sure to change the default passwords before deployment!
+
 USER_ID=1000
 
-# Database Configuration
+# Database Configuration (MySQL)
 MYSQL_ROOT_PASSWORD=secure_root_password_change_me
 MYSQL_DATABASE=torrust_tracker
 MYSQL_USER=torrust

application/README.md

@@ -59,9 +59,30 @@ application/
 - **Nginx**: Reverse proxy and SSL termination
 - **Prometheus**: Metrics collection and storage
 - **Grafana**: Metrics visualization and dashboards
-- **MySQL**: Default database for production
+- **MySQL**: Default database backend for production
 - **Certbot**: SSL certificate management
 
+### Database Configuration
+
+The Torrust Tracker Demo uses **MySQL as the default database backend** for
+production deployments. This provides:
+
+- **Reliability**: Production-grade database with ACID compliance
+- **Scalability**: Support for high-throughput tracking operations
+- **Data Integrity**: Consistent data storage and retrieval
+- **Performance**: Optimized for concurrent tracker operations
+
+**Database Service**: The MySQL service is automatically configured with:
+
+- Database initialization scripts
+- Proper networking and security
+- Data persistence across container restarts
+- Health checks and monitoring
+
+For development and testing environments, you can optionally configure SQLite
+by modifying the tracker configuration, though MySQL is recommended for all
+production use cases.
+
 ## 🚀 Quick Start
 
 ### Application Deployment

docs/issues/12-use-mysql-instead-of-sqlite-by-default.md

@@ -263,17 +263,26 @@ cd application/
 
 ### Phase 2: Documentation and Cleanup
 
-**Status**: ⬜ **Pending**
+**Status**: ✅ **Completed** (2025-07-08)
 
 **Description**: Update all relevant documentation to reflect the MySQL migration and
 remove any outdated SQLite references.
 
-**Files to Update**:
+**Files Updated**:
+
+- ✅ `application/README.md` - Added database configuration section explaining MySQL as default
+- ✅ `application/docs/production-setup.md` - Already documented MySQL properly
+- ✅ `application/.env.production` - Added header comments about MySQL configuration
+- ✅ `docs/guides/smoke-testing-guide.md` - No database-specific changes needed (external testing)
+- ✅ `.github/copilot-instructions.md` - Already updated with smoke testing guide references
+
+**Results**:
 
-- `application/README.md`
-- `application/docs/production-setup.md`
-- `docs/guides/smoke-testing-guide.md` (if it contains database-specific instructions)
-- `.github/copilot-instructions.md` (ensure it reflects current best practices)
+- All documentation now reflects MySQL as the default database
+- Added clear explanations about database configuration and requirements
+- Maintained references to SQLite as a development/testing option
+- Updated environment file with clear MySQL configuration comments
+- Legacy SQLite configuration files preserved for reference and rollback scenarios
 
 ## ✅ Completion Checklist
 
@@ -285,8 +294,8 @@ remove any outdated SQLite references.
 - [x] Local functionality testing passed
 - [x] Local data persistence testing passed
 - [x] VM integration testing passed
-- [ ] All documentation updated
-- [ ] Old SQLite configurations removed or documented as legacy
+- [x] All documentation updated
+- [x] Old SQLite configurations documented as legacy
 - [ ] Final PR reviewed and approved
 
 ## Rollback Plan