Upgrading to Fedora 44 Atomic Desktops: A Complete Migration Guide

Overview

Fedora Linux 44 has arrived, bringing a fresh wave of updates and improvements to the Atomic Desktop variants—Silverblue, Kinoite, Sway Atomic, Budgie Atomic, and COSMIC Atomic. This guide walks you through everything new in this release, from the relocation of the issue tracker to the removal of legacy FUSE 2 libraries and Polkit rule formats. Whether you're a seasoned Atomic Desktop user or new to the family, these changes affect how you manage issues, access documentation, run AppImages, and handle encrypted vaults. We'll cover what you need to know before upgrading, step-by-step actions to take, and common pitfalls to avoid. By the end, you'll be fully prepared to make the transition smoothly.

Prerequisites

Before diving into the upgrade process, ensure you meet these requirements:

• Current system: You are running Fedora Atomic Desktop 43 or earlier. This guide assumes you intend to upgrade to Fedora 44.
• Backup: Always back up important data, especially if you use Plasma Vault with EncFS or CryFS backends.
• Network connection: A stable internet connection to download the new image and updates.
• Basic command-line familiarity: Some steps require terminal commands (e.g., rpm-ostree).
• Knowledge of your AppImage runtimes: If you rely on AppImages, check whether they use the old FUSE 2 runtime.

Step-by-Step Instructions

1. Transition to the New Fedora Forge for Issue Tracking

Fedora’s Atomic Desktop community has moved its cross-variant issue tracker to the new Fedora forge. This centralizes bug reports and feature requests that affect all variants. For variant-specific issues, each SIG maintains its own tracker (links can be found in the atomic-desktops organization README).

What you need to do:

• If you regularly report issues, update your bookmarks to the new forge URL.
• When filing a new issue, choose the appropriate tracker:
  • Cross-variant: use the atomic-desktops tracker.
  • Variant-specific (e.g., only Kinoite): use the respective SIG tracker.
• If you have open issues on the old tracker, they should have been migrated automatically. Verify by searching on the new forge.

2. Access and Update Documentation

The unified documentation for all Atomic Desktop variants is now live on the new forge. However, translations from the previous wiki were not migrated. If you contributed translations before, you’ll need to re-translate content once the translation system is ready (expected soon).

Action items:

• Browse the new documentation at the atomic-desktops forge repository.
• If you find outdated or untranslated content, consider contributing translations. The tracking issue atomic-desktops#10 provides details.
• Update any internal links or bookmarks pointing to the old docs.

3. Prepare for FUSE 2 Library Removal

Fedora 44 removes FUSE version 2 libraries from Atomic Desktop images. This impacts two areas: AppImages that depend on the old FUSE 2 runtime, and legacy Plasma Vault backends (EncFS/CryFS).

Check Your AppImages

AppImages that bundle an outdated runtime will fail to launch after upgrade. To check if an AppImage is affected, run:

1. Open a terminal.
2. Run file ./your-appimage.AppImage and look for “ELF 64-bit” — if the runtime is old, it will mention “FUSE” version 1 or 2.
3. Alternatively, extract the AppImage with ./your-appimage.AppImage --appimage-extract and inspect the AppRun script for references to fuse2.

Recommended solutions:

• Prefer Flatpak: Check if the application is available as a Flatpak on Flathub. This is the preferred package format for Atomic Desktops.
• Report upstream: Contact the AppImage developer and ask them to update to a newer AppImage runtime that supports FUSE 3. Offer to help if possible.
• Workaround: If you must continue using a legacy AppImage temporarily, you can layer the FUSE 2 library (fuse2 package) via rpm-ostree install fuse2 and reboot. However, this is not recommended long-term because the library is unsupported and may be removed in future updates.

Migrate Plasma Vault Backends

KDE Plasma Vaults using EncFS or CryFS backends will break because they depend on FUSE 2. Only the gocryptfs backend is maintained.

Before upgrading to Fedora 44:

1. Open Plasma Vault and identify vaults using EncFS or CryFS.
2. Create a new vault using the gocryptfs backend.
3. Copy the contents of the old vault to the new one (using a temporary location if needed).
4. Delete the old vault.

If you already upgraded and need access:

1. Install the required packages temporarily: sudo rpm-ostree install cryfs (for CryFS) or fuse-encfs.
2. Reboot and mount the old vault to extract data.
3. Migrate data as described above.
4. Remove the layered packages: sudo rpm-ostree reset (this removes all layered packages; if you have other layered packages, you may need to reinstall them individually).

4. Handle the Removal of pkla Polkit Rules

Fedora 44 drops support for legacy pkla format Polkit rules. If you had custom .pkla files in /etc/polkit-1/rules.d/, they will now be ignored. Most users won't be affected because modern tools use JavaScript-based .rules files. To check if you have any .pkla files, run:

ls /etc/polkit-1/rules.d/*.pkla 2>/dev/null || echo "No pkla files found"

If any exist, you need to convert them to the new format. Refer to the Polkit documentation for syntax changes. This is a rare scenario, but if you rely on custom policies, test after upgrade.

Common Mistakes

• Ignoring AppImage compatibility: Don't assume all AppImages will work. Test critical ones before upgrading.
• Using rpm-ostree install as a permanent fix: Installing FUSE 2 libraries or legacy backends with rpm-ostree install should be temporary. Every layered package increases image size and may conflict with future updates.
• Forgetting to migrate Plasma Vault data before upgrade: If you upgrade first, you'll need to layer packages and then reset, which is more work. Migrate before upgrading when possible.
• Not updating documentation bookmarks: The old docs are still accessible but may not be updated. Always refer to the new unified docs for current information.
• Confusing variant-specific issues with cross-variant ones: Filing a Kinoite-only bug under the atomic-desktops tracker will delay resolution. Use the correct SIG tracker.

Summary

Upgrading to Fedora 44 Atomic Desktops brings several key changes: a new issue tracker and documentation site, removal of FUSE 2 libraries affecting AppImages and Plasma Vault backends, and discontinuation of pkla Polkit rules. By preparing in advance—migrating vault data, checking AppImage runtimes, converting Polkit rules if needed, and updating your resources—you can ensure a seamless upgrade. If issues arise, remember you can temporarily layer missing packages, but aim to adopt Flatpaks and modern configurations. This release sets the stage for a more unified and maintainable Atomic Desktop ecosystem.