Problem Summary
All 45 installed applications disappeared from the TrueNAS GUI after running sudo systemctl restart middlewared while apps were updating. The apps continue to run perfectly in the background via Docker, but the GUI shows “No Applications Installed” and I’ve lost all management capabilities.
System Information
- TrueNAS Version: 25.04.2.4 (Fangtooth)
- Number of Apps Affected: 45 apps (Nextcloud, Vaultwarden, N8N, Jellyfin, etc.)
- Pool: Data/
- Platform: Intel
What Happened
- Was updating multiple apps through the GUI
- Updates got stuck at 60% for extended period
- Ran
sudo systemctl restart middlewaredto unstick the process - After restart, GUI shows zero apps installed
- All Docker containers still running and accessible
midclt call app.queryreturns empty array[]
Current Status
Working:
- All 45 Docker containers running (
docker psshows all healthy) - All services accessible at their configured ports
- All data intact in
/mnt/.ix-apps/app_configs/ - All apps are on latest versions
Broken:
- TrueNAS GUI shows “No Applications Installed”
- Cannot manage, update, or configure apps through GUI
- Middleware completely ignores existing apps
Troubleshooting Already Performed
File System Check
ls /mnt/.ix-apps/
# Found:
- collective_metadata.yaml (89KB - contains all app metadata)
- collective_config.yaml (227KB - contains all app configs)
- user_config.yaml (232KB - contains user settings)
- metadata.yaml (created manually)
- app_configs/ (all 45 apps present with metadata)
Middleware Verification
midclt call app.query
# Returns: []
midclt call docker.config
# Returns: {"enable_image_updates": true, "dataset": "Data/ix-apps", ...}
sudo journalctl -u middlewared --since "5 minutes ago"
# No errors related to apps
Recovery Attempts
- Restored
collective_metadata.yamlfrom backup (Sept 25, 2025) - Restored
collective_config.yamlfrom backup - Created new
metadata.yamlwith all 45 apps listed - Restarted middlewared multiple times
- Full system reboot
- Verified all YAML files are valid and readable
- Confirmed Docker service is running
- Nothing makes apps reappear in GUI
File Contents Verified
sudo head -30 /mnt/.ix-apps/collective_metadata.yaml
# Shows: adguard-home, nextcloud10, and all other apps with full metadata
sudo grep "nextcloud10" /mnt/.ix-apps/collective_metadata.yaml
# Returns: nextcloud10:
The collective YAML files contain complete, valid data for all apps, but middleware refuses to read them.
Technical Observations
- The
app_appdatabase table doesn’t exist (KeyError when querying) - TrueNAS 25.04 appears to be fully file-based (no SQL database for apps)
- Middleware should be reading from collective_metadata.yaml but isn’t
- No cached state files found that could be cleared
- Docker containers have all correct labels and configurations
Questions
- Is there a middleware command to force re-scan of collective_metadata.yaml?
- Is there an internal cache or state file that needs to be cleared?
- Has anyone else experienced this after restarting middleware during app operations?
- Is there a recovery tool/script to rebuild app tracking from existing configs?
Request for Help
This appears to be a critical bug where middleware restart during app operations permanently corrupts app tracking, even though all underlying data remains intact. I need either:
- A way to force middleware to recognize existing apps from the YAML files
- An official recovery procedure from iXsystems
- Confirmation this is a known bug with an upcoming fix
I cannot reinstall 45 apps manually - this would take hours and risk data loss. The apps work perfectly; I just need GUI management back.
Has anyone successfully recovered from this situation? Any official guidance from the TrueNAS team would be greatly appreciated.
