Enhance app cleanup and listing with Docker resource management

Expanded the cleanup and factory reset commands to remove orphaned Docker containers, networks, and volumes while preserving ServerKit infrastructure. Improved the list-apps command to optionally display all Docker containers with a new --all flag, and updated documentation and CLI help to reflect these changes.

docs/DEPLOYMENT.md

@@ -96,10 +96,13 @@ serverkit restore-db backup/serverkit-20240115-120000.db
 ### App & Cleanup Commands
 
 ```bash
-# List all installed applications
+# List all installed applications (from database)
 serverkit list-apps
 
-# Delete all apps, containers, and folders
+# Also show all Docker containers (including infrastructure)
+serverkit list-apps --all
+
+# Delete all apps, containers, folders, and orphaned Docker resources
 serverkit cleanup-apps
 
 # Also delete Docker volumes
@@ -109,9 +112,17 @@ serverkit cleanup-apps --delete-volumes
 serverkit cleanup-apps --keep-db
 
 # Complete factory reset (delete everything and start fresh)
+# Preserves only serverkit-frontend infrastructure
 serverkit factory-reset
 ```
 
+**Note:** Cleanup commands will:
+- Stop and remove all app containers
+- Remove orphaned Docker containers (not tracked in database)
+- Prune unused Docker networks
+- Delete all folders in `/var/serverkit/apps/`
+- Never touch ServerKit infrastructure (serverkit-frontend, serverkit-network)
+
 ### Utility Commands
 
 ```bash