Public bug reported: Bug Report: GNOME Shell 49 ignores newly added .desktop files in both user and system directories Summary After installing applications and creating .desktop launchers in ~/.local/share/applications/, none of them appear in the GNOME application overview (Super key search). New .desktop files added to /usr/share/applications/ are also ignored. Only applications that were already indexed before the issue manifested, plus Snap and Flatpak apps, remain visible. The issue persists across reboots, TimeShift restorations, and a freshly created user account, indicating a system-level problem. System Information
Distribution: Ubuntu 25.10 (Questing) GNOME Shell version: 49.0 Kernel: 6.17.0-23 Session type: Wayland Indexer: localsearch (replacement for tracker3 in Ubuntu 25.10) Hardware: AMD Ryzen 9 9950X, NVIDIA RTX 5080, ASUS ROG STRIX B650E-E Steps to Reproduce Create a valid .desktop file in ~/.local/share/applications/ (or /usr/share/applications/ with sudo). Set executable permission: chmod +x file.desktop. Mark as trusted: gio set file.desktop metadata::trusted true. Run update-desktop-database. Log out and log back in. Press the Super key and search for the application name. Expected behavior: The application appears in the GNOME application overview. Actual behavior: The application does not appear. Only previously indexed apps and Snap/Flatpak entries are shown. Minimal example .desktop file used for testing [Desktop Entry] Version=1.0 Type=Application Name=Nmap GenericName=Network Scanner Comment=Network exploration tool and security scanner Exec=gnome-terminal -- bash -c "/usr/bin/nmap -h; exec bash" Icon=/home/stronk/Imagens/Icones/nmap.jpeg Terminal=false Categories=Network;Security; Keywords=network;scanner;security; StartupNotify=false The file passes desktop-file-validate cleanly (only an informational hint about Categories, no errors). It is correctly typed as application/x-desktop by xdg-mime query filetype. The MIME default handler for application/x-desktop is unset, which is the expected behavior. gio info confirms metadata::trusted: true. Diagnostic Tests Performed The following hypotheses have been ruled out through systematic testing: File-level checks (all passed) Syntax validation via desktop-file-validate: clean. Encoding check via file and xxd: pure ASCII, LF line endings, no BOM. Permission +x applied (-rwxr-xr-x). GIO trusted attribute set (metadata::trusted: true). Folder permissions (755 on ~/.local/share/applications/). All required Desktop Entry fields present (Type, Name, Exec, Icon, Terminal, Categories). Optional fields added for completeness (Version, GenericName, Comment, Keywords, StartupNotify). Environment checks (all corrected, no effect) XDG_DATA_HOME was empty in the session. Added XDG_DATA_HOME=/home/stronk/.local/share to /etc/environment. Variable now propagates correctly to gnome-shell (verified via cat /proc/$(pidof gnome-shell)/environ). No effect on the issue. ~/.config/mimeapps.list had application/x-desktop=org.gnome.TextEditor.desktop as default handler, causing .desktop files to be opened as text. Removed. No effect on the menu indexing issue. System and cache resets (all attempted, no effect) update-desktop-database ran successfully on both ~/.local/share/applications/ and /usr/share/applications/. Both mimeinfo.cache files updated correctly with timestamps reflecting the operation. Full system reboot: no change. TimeShift restoration to three different snapshot points: no change. ~/.local/share/gnome-shell/ directory renamed to force regeneration: no change. ~/.cache/gnome-shell/ removed: no change. All GNOME extensions disabled (tilingshell, blur-my-shell, just-perfection-desktop, ding, snapd-prompting, tiling-assistant, ubuntu-appindicators, ubuntu-dock): no change. dconf reset -f /org/gnome/desktop/app-folders/: no change. ~/.config/menus/applications-merged/xdg-desktop-menu-dummy.menu (empty file, owned by docker group) removed: no change. Reinstalled packages: sudo apt install --reinstall gnome-shell gnome-shell-common: no change. Cross-user verification (definitive) A brand new user account was created via sudo adduser teste and logged into via GDM. The same issue occurs in the new user's clean session: newly added .desktop files in /usr/share/applications/ (which were created system-wide and visible to the new user) do not appear in their menu either. This confirms the issue is system-level, not tied to any user-specific state in /home. Observed Anomalies in Logs journalctl --user -f while triggering the application search Each time the Super key is pressed and a query typed, the following sequence occurs: Activating service name='org.gnome.Settings.SearchProvider' Activating service name='org.gnome.Nautilus' Activating service name='org.gnome.Calculator.SearchProvider' Activating service name='org.gnome.Characters' Activating service name='org.gnome.clocks' Activating service name='org.gnome.seahorse.Application' [11+ recurrent activations] No AppDisplay or AppSystem-related events are logged. The shell appears to consult only registered search providers via DBus, not the local desktop file index, when handling new app queries. Repeated warning gnome-shell: Ignoring search provider /usr/share/gnome-shell/search-providers/seahorse-search-provider.ini: missing DesktopId This message persists despite: The .ini file being syntactically correct (DesktopId=org.gnome.seahorse.Application.desktop is present). The seahorse package being installed (seahorse 47.0.1-2). The seahorse .desktop file existing in /usr/share/applications/. The search provider was renamed to .disabled to remove the warning. The application indexing issue persisted unchanged. Auto-disabled extensions After each login, three extensions are silently disabled by gnome-shell, even though they were enabled in the previous session: [email protected], blur-my-shell@aunetx, just-perfection-desktop@just-perfection. They reappear in gnome-extensions list --enabled only after manual re-enabling. This may suggest underlying instability in the gnome-shell extension subsystem. State of the system after testing 14 valid .desktop files exist in ~/.local/share/applications/, all with +x permission and trusted metadata. /usr/share/applications/Nmap-test.desktop exists as a system-level test file (also invisible). localsearch reports indexing complete (340 files, 32 folders, all miners idle), but localsearch search does not return .desktop entries — confirming localsearch indexes file content, not application registration. gnome-shell process status is normal (Ssl, sleeping multi-threaded), no apparent hang. Hypothesis The AppSystem/AppDisplay subsystem of GNOME Shell 49 on Ubuntu 25.10 has stopped registering newly added .desktop files. The condition is: Persistent across reboots. Persistent across TimeShift restorations (which by default exclude /home). Persistent across ~/.local/share/gnome-shell/ reset. Persistent across dconf resets. Persistent across gnome-shell package reinstallation. Persistent across a freshly created user account on the same machine, ruling out per-user state corruption. This pattern strongly suggests either a regression in the GNOME 49 packages shipped in Ubuntu 25.10, or a corruption in shared system state (possibly in /var/, in mutter/glib caches, or in dependencies of gnome-shell beyond gnome-shell-common). Possibly related context The system was set up recently (early May 2026) with heavy software installation activity, including BloodHound via Docker, multiple Snaps, multiple Flatpaks, and pipx packages. The issue was first noticed shortly after these installations, but no specific install action has been correlated as the trigger. Workaround: None known. Affected users must launch applications via terminal or by direct file invocation in the file manager, since the application overview cannot find them. ProblemType: Bug DistroRelease: Ubuntu 25.10 Package: gnome-shell 49.0-1ubuntu1.3 ProcVersionSignature: Ubuntu 6.17.0-23.23-generic 6.17.13 Uname: Linux 6.17.0-23-generic x86_64 ApportVersion: 2.33.1-0ubuntu3 Architecture: amd64 CasperMD5CheckResult: pass CurrentDesktop: ubuntu:GNOME Date: Thu May 7 11:27:02 2026 DisplayManager: gdm3 InstallationDate: Installed on 2026-04-11 (27 days ago) InstallationMedia: Ubuntu 25.10 "Questing Quokka" - Release amd64 (20251007) ProcEnviron: LANG=pt_BR.UTF-8 PATH=(custom, no user) SHELL=/usr/bin/zsh TERM=xterm-256color XDG_RUNTIME_DIR=<set> RebootRequiredPkgs: Error: path contained symlinks. RelatedPackageVersions: mutter-common 49.0-2ubuntu5.3 SourcePackage: gnome-shell UpgradeStatus: No upgrade log present (probably fresh install) ** Affects: gnome-shell (Ubuntu) Importance: Undecided Status: New ** Tags: amd64 apport-bug questing wayland-session -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/2151805 Title: Bug Report: GNOME Shell 49 ignores newly added .desktop files in both user and system directories To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/gnome-shell/+bug/2151805/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
