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Regular maintenance helps keep your Zirconium system healthy and ensures optimal performance. Most maintenance tasks are automated, but understanding them helps you manage your system effectively.

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System maintenance overview

Zirconium handles most maintenance automatically:
  • Flatpak updates: Managed by uupd (Universal Update) service
  • Container storage: Automatically cleaned up by systemd timers
  • Deployment cleanup: Old bootc deployments are removed to save space
  • System logs: Rotated automatically by journald

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Container storage management

If you use Podman or Docker for containers, storage can accumulate over time.

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Checking container storage usage

View storage used by containers: 
podman system df
This shows:
  • Images: Container images you’ve pulled or built
  • Containers: Stopped and running containers
  • Volumes: Persistent data volumes
  • Build cache: Cached layers from image builds

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Cleaning up container storage

1

Remove unused containers

Remove all stopped containers:
podman container prune
Confirm when prompted to free up space.
2

Remove unused images

Remove dangling images (untagged images no longer used):
podman image prune
To remove all unused images (not just dangling ones):
podman image prune -a
3

Clean up volumes and cache

Remove unused volumes:
podman volume prune
For a complete cleanup including build cache:
podman system prune -a --volumes
podman system prune -a removes all unused images, not just dangling ones. Make sure you don’t need to restart any containers that use these images.

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Flatpak management

Zirconium includes automatic Flatpak management services.

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Understanding Flatpak services

Zirconium includes these systemd services for Flatpak:
  • flatpak-add-flathub-repos.service: Adds Flathub repository on first boot
  • flatpak-preinstall.service: Installs pre-configured Flatpaks on first boot
  • uupd.timer: Regularly updates Flatpaks and system packages

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Manual Flatpak updates

While updates are automatic, you can manually update Flatpaks: 
flatpak update
To update without prompts: 
flatpak update -y

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Cleaning up Flatpak storage

Remove unused Flatpak runtimes and extensions: 
flatpak uninstall --unused
This safely removes runtimes that are no longer needed by any installed applications.

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Checking Flatpak storage usage

View storage used by Flatpaks: 
du -sh ~/.local/share/flatpak /var/lib/flatpak
Run flatpak list --app to see only installed applications, or flatpak list to see applications and runtimes.

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Cleaning up old deployments

bootc keeps previous deployments for rollback, but you may want to clean up old ones to save space.

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Checking deployment usage

View all deployments and their storage: 
bootc status
Deployments are stored in /sysroot/ostree/deploy/default/deploy/.

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Manual deployment cleanup

bootc automatically keeps a limited number of deployments. To manually clean up: 
sudo ostree admin cleanup
This removes old deployments while keeping:
  • Current deployment (the one you’re running)
  • Previous deployment (for rollback)
  • Staged deployment (pending update)
You cannot remove the currently booted deployment or the staged deployment.

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Managing system logs

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Checking log storage usage

View space used by system logs: 
journalctl --disk-usage

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Cleaning up old logs

Limit logs to the last 7 days: 
sudo journalctl --vacuum-time=7d
Limit logs to 500MB: 
sudo journalctl --vacuum-size=500M

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Persistent log configuration

To permanently limit log storage, edit /etc/systemd/journald.conf: 
[Journal]
SystemMaxUse=500M
SystemKeepFree=1G
MaxRetentionSec=7day
Then restart the journal service: 
sudo systemctl restart systemd-journald

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Disk space overview

Get a complete overview of disk usage: 
df -h
For a detailed breakdown of what’s using space: 
sudo du -h --max-depth=1 / 2>/dev/null | sort -h
Most space issues on bootc systems come from:
  • Multiple bootc deployments
  • Container images and volumes
  • User home directories
  • Flatpak applications and runtimes

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Automated maintenance tasks

Zirconium runs these maintenance tasks automatically:
Runs regularly via uupd.timer to update Flatpaks and check for system updates. Check status:
systemctl status uupd.timer
systemctl list-timers uupd.timer
Note: uupd is configured with --disable-module-distrobox as set in /usr/lib/systemd/system/uupd.service.
Checks for system updates weekly via bootc-fetch-apply-updates.timer. Updates are staged but not applied until you reboot. Check status:
systemctl status bootc-fetch-apply-updates.timer
systemctl list-timers bootc-fetch-apply-updates.timer
Automatically cleans up temporary files in /tmp and /var/tmp. Check configuration:
systemctl status systemd-tmpfiles-clean.timer