fix: [#14] copy generated configuration files to persistent volume

- Add missing step to copy generated config files from application/storage/ to /var/lib/torrust/
- Copy tracker.toml, prometheus.yml, and nginx.conf to persistent volume after generation
- Fixes container startup issues where services couldn't find configuration files
- Ensures all generated configs are available in the persistent volume for Docker mounts
- Resolves Prometheus restart loop and nginx 502 errors
- Validates persistent data volume implementation with E2E tests

Problem: Configuration files were generated in application/storage/ but Docker Compose
was mounting from /var/lib/torrust/, causing containers to fail to start.

Solution: Added explicit copy step in deploy-app.sh to move generated configs
to persistent volume after configure-env.sh runs.

Author: josecelano

infrastructure/scripts/deploy-app.sh

@@ -365,6 +365,18 @@ release_stage() {
             fi
         fi
         
+        # Copy generated configuration files to persistent storage
+        # These files are generated by configure-env.sh and need to be in the persistent volume
+        if [ -f application/storage/tracker/etc/tracker.toml ]; then
+            sudo cp application/storage/tracker/etc/tracker.toml /var/lib/torrust/tracker/etc/
+        fi
+        if [ -f application/storage/prometheus/etc/prometheus.yml ]; then
+            sudo cp application/storage/prometheus/etc/prometheus.yml /var/lib/torrust/prometheus/etc/
+        fi
+        if [ -f application/storage/proxy/etc/nginx-conf/nginx.conf ]; then
+            sudo cp application/storage/proxy/etc/nginx-conf/nginx.conf /var/lib/torrust/proxy/etc/nginx-conf/
+        fi
+        
         # Ensure torrust user owns all persistent data
         sudo chown -R torrust:torrust /var/lib/torrust
     " "Setting up persistent data volume directory structure"