refactor: [#28] reorganize application configuration templates

- Create organized directory structure for application templates
- Move all templates to infrastructure/config/templates/application/
- Create nginx subdirectory for nginx-specific templates
- Create crontab subdirectory for cron job templates
- Add .tpl extensions to crontab files for consistency
- Update all script references to use new template paths
- Update documentation references across all guides
- Maintain template processing functionality with new structure

Template Structure:
├── application/
│   ├── docker-compose.env.tpl
│   ├── tracker.toml.tpl
│   ├── prometheus.yml.tpl
│   ├── nginx/
│   │   ├── nginx.conf.tpl
│   │   ├── nginx-http.conf.tpl
│   │   ├── nginx-https-extension.conf.tpl
│   │   └── nginx-https-selfsigned.conf.tpl
│   └── crontab/
│       ├── mysql-backup.cron.tpl
│       └── ssl-renewal.cron.tpl

Benefits:
- Improved organization and discoverability
- Clear separation by service/component type
- Consistent .tpl naming conventions
- Better maintainability and navigation
- Validated with successful E2E test run

Author: josecelano

application/docs/backups.md

@@ -14,7 +14,7 @@ sudo crontab -e
 ```
 
 You should see the MySQL backup cron job configured from the template system in
-`infrastructure/config/templates/crontab/mysql-backup.cron`.
+`infrastructure/config/templates/application/crontab/mysql-backup.cron.tpl`.
 
 ## Check Backups
 

application/share/bin/ssl-configure-nginx.sh

@@ -40,8 +40,8 @@ fi
 NGINX_CONFIG_DIR="/var/lib/torrust/proxy/etc/nginx-conf"
 NGINX_CONFIG_FILE="${NGINX_CONFIG_DIR}/default.conf"
 TEMPLATES_DIR="${PROJECT_ROOT}/infrastructure/config/templates"
-HTTP_TEMPLATE="${TEMPLATES_DIR}/nginx-http.conf.tpl"
-HTTPS_EXTENSION_TEMPLATE="${TEMPLATES_DIR}/nginx-https-extension.conf.tpl"
+HTTP_TEMPLATE="${TEMPLATES_DIR}/application/nginx/nginx-http.conf.tpl"
+HTTPS_EXTENSION_TEMPLATE="${TEMPLATES_DIR}/application/nginx/nginx-https-extension.conf.tpl"
 
 # Check prerequisites
 check_prerequisites() {

docs/adr/007-two-level-environment-variable-structure.md

@@ -51,7 +51,7 @@ with clear separation of concerns:
 ### Level 2: Docker Compose Environment Variables
 
 **Purpose**: Container runtime configuration  
-**Template**: `infrastructure/config/templates/docker-compose.env.tpl`  
+**Template**: `infrastructure/config/templates/application/docker-compose.env.tpl`  
 **Generated File**: `.env` (in application directory)  
 **Scope**: Docker Compose and running containers only
 
@@ -80,7 +80,7 @@ Level 1: Main Environment Variables
                     │
                     ▼ (template processing)
 Level 2: Docker Environment Variables
-├── infrastructure/config/templates/docker-compose.env.tpl
+├── infrastructure/config/templates/application/docker-compose.env.tpl
 └── (generated) application/.env
 ```
 
@@ -157,7 +157,7 @@ configure_backups "$ENABLE_DB_BACKUPS" "$BACKUP_RETENTION_DAYS"
 
 ```bash
 # Generate Docker environment file from template
-envsubst < "infrastructure/config/templates/docker-compose.env.tpl" > "application/.env"
+envsubst < "infrastructure/config/templates/application/docker-compose.env.tpl" > "application/.env"
 ```
 
 ### For Container Configuration

docs/guides/ssl-testing-guide.md

@@ -28,8 +28,9 @@ The SSL/HTTPS automation has been **fully implemented** and is working end-to-en
 
 ### Architecture Components (All Implemented)
 
-- **HTTP Template**: `infrastructure/config/templates/nginx-http.conf.tpl` ✅
-- **HTTPS Template**: `infrastructure/config/templates/nginx-https-selfsigned.conf.tpl` ✅ **NEW**
+- **HTTP Template**: `infrastructure/config/templates/application/nginx/nginx-http.conf.tpl` ✅
+- **HTTPS Template**:  
+  `infrastructure/config/templates/application/nginx/nginx-https-selfsigned.conf.tpl` ✅
 - **SSL Scripts**: Located in `application/share/bin/ssl-*.sh` ✅ **IMPLEMENTED**
 - **Pebble Test Environment**: `application/compose.test.yaml`
 
@@ -89,7 +90,7 @@ source infrastructure/config/environments/local.env
 export DOLLAR='$'
 
 # Test template processing
-envsubst < infrastructure/config/templates/nginx-http.conf.tpl > /tmp/test-nginx-http.conf
+envsubst < infrastructure/config/templates/application/nginx/nginx-http.conf.tpl > /tmp/test-nginx-http.conf
 
 # Verify output
 cat /tmp/test-nginx-http.conf
@@ -219,7 +220,7 @@ ssh torrust@$VM_IP \
 source infrastructure/config/environments/local.env
 export DOLLAR='$'
 
-envsubst < infrastructure/config/templates/nginx-https-extension.conf.tpl > /tmp/test-nginx-https.conf
+envsubst < infrastructure/config/templates/application/nginx/nginx-https-extension.conf.tpl > /tmp/test-nginx-https.conf
 
 # Verify output
 cat /tmp/test-nginx-https.conf
@@ -793,7 +794,7 @@ Health Check: ✅ HTTPS working, minor HTTP redirect issue in test script
 
 - **SSL Script**: `application/share/bin/ssl-generate-test-certs.sh` - Complete implementation
 - **Shell Utils**: `application/share/bin/shell-utils.sh` - Application-specific utilities
-- **Nginx Template**: `infrastructure/config/templates/nginx-https-selfsigned.conf.tpl`
+- **Nginx Template**: `infrastructure/config/templates/application/nginx/nginx-https-selfsigned.conf.tpl`
 - **Deploy Integration**: `infrastructure/scripts/deploy-app.sh` - SSL generation before services
 - **Cloud-init Update**: `infrastructure/cloud-init/user-data.yaml.tpl` - OpenSSL package installation
 

docs/issues/21-complete-application-installation-automation.md

@@ -698,7 +698,7 @@ The recommended workflow follows the [Torrust production deployment guide](https
 
 ```bash
 # Step 1: Deploy with HTTP-only nginx configuration
-cp ../infrastructure/config/templates/nginx-http.conf.tpl /var/lib/torrust/proxy/etc/nginx-conf/default.conf
+cp ../infrastructure/config/templates/application/nginx/nginx-http.conf.tpl /var/lib/torrust/proxy/etc/nginx-conf/default.conf
 sed -i "s/\${DOMAIN_NAME}/torrust-demo.com/g" /var/lib/torrust/proxy/etc/nginx-conf/default.conf
 docker compose up -d
 ```
@@ -744,7 +744,7 @@ For development and testing, use Pebble to validate the complete SSL workflow lo
 docker compose -f compose.test.yaml up -d pebble pebble-challtestsrv
 
 # Step 2: Set up test nginx configuration
-cp ../infrastructure/config/templates/nginx-http.conf.tpl /var/lib/torrust/proxy/etc/nginx-conf/default.conf
+cp ../infrastructure/config/templates/application/nginx/nginx-http.conf.tpl /var/lib/torrust/proxy/etc/nginx-conf/default.conf
 sed -i "s/\${DOMAIN_NAME}/test.local/g" /var/lib/torrust/proxy/etc/nginx-conf/default.conf
 
 # Step 3: Start application services
@@ -884,7 +884,8 @@ implemented and fully tested.
 
 **Status**: ✅ **COMPLETED** - Crontab templates exist and backup automation is fully integrated.
 
-**File**: `infrastructure/config/templates/crontab/mysql-backup.cron` ✅ **EXISTS AND FUNCTIONAL**
+**File**: `infrastructure/config/templates/application/crontab/mysql-backup.cron.tpl`  
+✅ **EXISTS AND FUNCTIONAL**
 
 ```plaintext
 # MySQL Database Backup Crontab Entry
@@ -917,7 +918,7 @@ implemented and fully tested.
 
 **Files Updated**:
 
-- `infrastructure/config/templates/docker-compose.env.tpl` - Added backup variables
+- `infrastructure/config/templates/application/docker-compose.env.tpl` - Added backup variables
 - `infrastructure/config/environments/local.env` - Local testing configuration
 - `infrastructure/config/environments/local.defaults` - Template defaults
 
@@ -946,7 +947,7 @@ BACKUP_RETENTION_DAYS=7
 
 **Testing Guide Created**: [Database Backup Testing Guide](../guides/database-backup-testing-guide.md)
 
-**File**: `infrastructure/config/templates/crontab/mysql-backup.cron` ✅ **EXISTS**
+**File**: `infrastructure/config/templates/application/crontab/mysql-backup.cron.tpl` ✅ **EXISTS**
 
 ```plaintext
 # MySQL Database Backup Crontab Entry
@@ -958,7 +959,7 @@ BACKUP_RETENTION_DAYS=7
   >> /var/log/mysql-backup.log 2>&1
 ```
 
-**File**: `infrastructure/config/templates/crontab/ssl-renewal.cron` ✅ **EXISTS**
+**File**: `infrastructure/config/templates/application/crontab/ssl-renewal.cron.tpl` ✅ **EXISTS**
 
 ```plaintext
 # SSL Certificate Renewal Crontab Entry
@@ -1232,7 +1233,7 @@ setup_ssl_automation() {
     vm_exec "${vm_ip}" "
         cd /home/torrust/github/torrust/torrust-tracker-demo/application
         source ./share/bin/crontab_utils.sh
-        add_cronjob 'ssl-renewal.cron' 'torrust'
+        add_cronjob 'ssl-renewal.cron.tpl' 'torrust'
     " "SSL renewal crontab setup"
 
     log_success "SSL setup completed"
@@ -1254,7 +1255,7 @@ setup_backup_automation() {
     vm_exec "${vm_ip}" "
         cd /home/torrust/github/torrust/torrust-tracker-demo/application
         source ./share/bin/crontab_utils.sh
-        add_cronjob 'mysql-backup.cron' 'torrust'
+        add_cronjob 'mysql-backup.cron.tpl' 'torrust'
     " "MySQL backup crontab setup"
 
     log_success "Database backup automation configured"