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I noticed that my configuration files in
/home/user/.config have either been overwritten by default ones or completely wiped in some cases. for example, my desktop environment(kde) booted as if I've never used it before. Things such as my wallpaper, mouse scroll direction, keyboard shortcuts, system icons, etc. are all back to default. I realized that this isn't just my desktop environment because other applications that had files in .config are the same way. For example, my music player(strawberry), GIMP, Discord, Soulseek, and Neofetch have all been reverted to a default config. Not quite sure how this happened. The only things I've done before the issue were a simple
sudo pacman -Syu and I installed qt6-imageformats with
sudo pacman -S qt6-imageformats . I doubt that I'll be able to recover my files at this point without a backup but I just want to know what went wrong. Seems very out of the ordinary for Pacman to alter anything in /home .
If it can provide any help troubleshooting, here is my pacman log for the day this happened.
[2024-11-22T19:09:29-0600] [PACMAN] Running 'pacman -Syu'
[2024-11-22T19:09:29-0600] [PACMAN] synchronizing package lists
[2024-11-22T19:09:30-0600] [PACMAN] starting full system upgrade
[2024-11-22T19:09:42-0600] [ALPM] running '60-mkinitcpio-remove.hook'...
[2024-11-22T19:09:43-0600] [ALPM] transaction started
[2024-11-22T19:09:43-0600] [ALPM] upgraded aom (3.10.0-1 -> 3.11.0-1)
[2024-11-22T19:09:43-0600] [ALPM] upgraded archinstall (2.8.6-1 -> 3.0.0-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded linux (6.11.8.arch1-2 -> 6.11.9.arch1-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded broadcom-wl (6.30.223.271-586 -> 6.30.223.271-587)
[2024-11-22T19:09:45-0600] [ALPM] upgraded darkhttpd (1.16-1 -> 1.16-2)
[2024-11-22T19:09:45-0600] [ALPM] upgraded exfatprogs (1.2.5-1 -> 1.2.6-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded grml-zsh-config (0.19.7-1 -> 0.19.8-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded gtk-update-icon-cache (1:4.16.5-1 -> 1:4.16.6-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded libsoup3 (3.6.0-1 -> 3.6.1-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded tinysparql (3.8.0-1 -> 3.8.1-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded gtk4 (1:4.16.5-1 -> 1:4.16.6-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded imagemagick (7.1.1.40-2 -> 7.1.1.41-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded iproute2 (6.11.0-1 -> 6.12.0-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded libadwaita (1:1.6.1-1 -> 1:1.6.2-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded libfabric (1.22.0-1 -> 1.22.0-2)
[2024-11-22T19:09:45-0600] [ALPM] upgraded libheif (1.19.3-1 -> 1.19.5-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded libinput (1.26.2-1 -> 1.27.0-1)
[2024-11-22T19:09:45-0600] [ALPM] upgraded libmtp (1.1.21-2 -> 1.1.22-1)
[2024-11-22T19:09:46-0600] [ALPM] upgraded libxt (1.3.0-2 -> 1.3.1-1)
[2024-11-22T19:09:49-0600] [ALPM] upgraded linux-headers (6.11.8.arch1-2 -> 6.11.9.arch1-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded linux-lts (6.6.61-1 -> 6.6.62-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded lsof (4.99.3-2 -> 4.99.4-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded luajit (2.1.1727870382-1 -> 2.1.1731601260-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded luit (20240102-2 -> 20240910-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded mariadb-libs (11.6.2-1 -> 11.6.2-2)
[2024-11-22T19:09:50-0600] [ALPM] upgraded mtools (1:4.0.45-1 -> 1:4.0.46-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded openal (1.23.1-3 -> 1.24.0-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded openpmix (5.0.3-1 -> 5.0.4-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded power-profiles-daemon (0.23-1 -> 0.23-2)
[2024-11-22T19:09:50-0600] [ALPM] upgraded prrte (3.0.6-1 -> 3.0.7-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded python-cryptography (42.0.8-1 -> 43.0.3-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded python-httplib2 (0.22.0-6 -> 0.22.0-7)
[2024-11-22T19:09:50-0600] [ALPM] upgraded python-toolz (0.12.1-2 -> 1.0.0-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded python-urllib3 (1.26.20-1 -> 1.26.20-3)
[2024-11-22T19:09:50-0600] [ALPM] upgraded qbittorrent (5.0.1-1 -> 5.0.2-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded qt6-wayland (6.8.0-1 -> 6.8.0-2)
[2024-11-22T19:09:50-0600] [ALPM] upgraded ruby-power_assert (2.0.3-5 -> 2.0.4-1)
[2024-11-22T19:09:50-0600] [ALPM] upgraded signon-ui (0.17+20231016-2 -> 0.17+20231016-3)
[2024-11-22T19:09:51-0600] [ALPM] upgraded yt-dlp (2024.11.04-1 -> 2024.11.18-1)
[2024-11-22T19:09:51-0600] [ALPM] upgraded zbar (0.23.93-2 -> 0.23.93-3)
[2024-11-22T19:09:51-0600] [ALPM] upgraded zlib-ng (2.2.2-1 -> 2.2.2-2)
[2024-11-22T19:09:51-0600] [ALPM] transaction completed
[2024-11-22T19:09:52-0600] [ALPM] running '30-systemd-daemon-reload-system.hook'...
[2024-11-22T19:09:52-0600] [ALPM] running '30-systemd-daemon-reload-user.hook'...
[2024-11-22T19:09:52-0600] [ALPM] running '30-systemd-hwdb.hook'...
[2024-11-22T19:09:53-0600] [ALPM] running '30-systemd-udev-reload.hook'...
[2024-11-22T19:09:54-0600] [ALPM] running '30-systemd-update.hook'...
[2024-11-22T19:09:54-0600] [ALPM] running '60-depmod.hook'...
[2024-11-22T19:09:57-0600] [ALPM] running '90-mkinitcpio-install.hook'...
[2024-11-22T19:09:58-0600] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'archiso'
[2024-11-22T19:09:58-0600] [ALPM-SCRIPTLET] ==> Using configuration file: '/etc/mkinitcpio.conf'
[2024-11-22T19:09:58-0600] [ALPM-SCRIPTLET] -> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
[2024-11-22T19:09:58-0600] [ALPM-SCRIPTLET] ==> Starting build: '6.11.9-arch1-1'
[2024-11-22T19:09:58-0600] [ALPM-SCRIPTLET] -> Running build hook: [base]
[2024-11-22T19:09:59-0600] [ALPM-SCRIPTLET] -> Running build hook: [udev]
[2024-11-22T19:09:59-0600] [ALPM-SCRIPTLET] -> Running build hook: [autodetect]
[2024-11-22T19:09:59-0600] [ALPM-SCRIPTLET] -> Running build hook: [kms]
[2024-11-22T19:10:03-0600] [ALPM-SCRIPTLET] -> Running build hook: [modconf]
[2024-11-22T19:10:03-0600] [ALPM-SCRIPTLET] -> Running build hook: [block]
[2024-11-22T19:10:03-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'xhci_pci'
[2024-11-22T19:10:04-0600] [ALPM-SCRIPTLET] -> Running build hook: [keyboard]
[2024-11-22T19:10:04-0600] [ALPM-SCRIPTLET] -> Running build hook: [keymap]
[2024-11-22T19:10:04-0600] [ALPM-SCRIPTLET] -> Running build hook: [consolefont]
[2024-11-22T19:10:04-0600] [ALPM-SCRIPTLET] ==> WARNING: consolefont: no font found in configuration
[2024-11-22T19:10:04-0600] [ALPM-SCRIPTLET] -> Running build hook: [filesystems]
[2024-11-22T19:10:04-0600] [ALPM-SCRIPTLET] -> Running build hook: [fsck]
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> Creating zstd-compressed initcpio image: '/boot/initramfs-linux.img'
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] -> Early uncompressed CPIO image generation successful
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> Initcpio image generation successful
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux-lts.preset: 'default'
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> Using default configuration file: '/etc/mkinitcpio.conf'
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> WARNING: Deprecated option 'ALL_microcode' found. Update '/etc/mkinitcpio.d/linux-lts.preset' to use the 'microcode' hook instead.
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] -> -k /boot/vmlinuz-linux-lts -g /boot/initramfs-linux-lts.img
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] ==> Starting build: '6.6.62-1-lts'
[2024-11-22T19:10:05-0600] [ALPM-SCRIPTLET] -> Running build hook: [base]
[2024-11-22T19:10:06-0600] [ALPM-SCRIPTLET] -> Running build hook: [udev]
[2024-11-22T19:10:06-0600] [ALPM-SCRIPTLET] -> Running build hook: [autodetect]
[2024-11-22T19:10:06-0600] [ALPM-SCRIPTLET] -> Running build hook: [kms]
[2024-11-22T19:10:10-0600] [ALPM-SCRIPTLET] -> Running build hook: [modconf]
[2024-11-22T19:10:10-0600] [ALPM-SCRIPTLET] -> Running build hook: [block]
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'xhci_pci'
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] -> Running build hook: [keyboard]
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] -> Running build hook: [keymap]
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] -> Running build hook: [consolefont]
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] ==> WARNING: consolefont: no font found in configuration
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] -> Running build hook: [filesystems]
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] -> Running build hook: [fsck]
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] ==> Creating zstd-compressed initcpio image: '/boot/initramfs-linux-lts.img'
[2024-11-22T19:10:11-0600] [ALPM-SCRIPTLET] -> Early uncompressed CPIO image generation successful
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] ==> Initcpio image generation successful
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] ==> Building image from preset: /etc/mkinitcpio.d/linux-lts.preset: 'fallback'
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] ==> Using default configuration file: '/etc/mkinitcpio.conf'
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] ==> WARNING: Deprecated option 'ALL_microcode' found. Update '/etc/mkinitcpio.d/linux-lts.preset' to use the 'microcode' hook instead.
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] -> -k /boot/vmlinuz-linux-lts -g /boot/initramfs-linux-lts-fallback.img -S autodetect
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] ==> Starting build: '6.6.62-1-lts'
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] -> Running build hook: [base]
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] -> Running build hook: [udev]
[2024-11-22T19:10:12-0600] [ALPM-SCRIPTLET] -> Running build hook: [kms]
[2024-11-22T19:10:18-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'ast'
[2024-11-22T19:10:20-0600] [ALPM-SCRIPTLET] -> Running build hook: [modconf]
[2024-11-22T19:10:20-0600] [ALPM-SCRIPTLET] -> Running build hook: [block]
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'qla2xxx'
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'qed'
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'aic94xx'
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'bfa'
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'qla1280'
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'wd719x'
[2024-11-22T19:10:21-0600] [ALPM-SCRIPTLET] ==> WARNING: Possibly missing firmware for module: 'xhci_pci'
[2024-11-22T19:10:23-0600] [ALPM-SCRIPTLET] -> Running build hook: [keyboard]
[2024-11-22T19:10:24-0600] [ALPM-SCRIPTLET] -> Running build hook: [keymap]
[2024-11-22T19:10:24-0600] [ALPM-SCRIPTLET] -> Running build hook: [consolefont]
[2024-11-22T19:10:24-0600] [ALPM-SCRIPTLET] ==> WARNING: consolefont: no font found in configuration
[2024-11-22T19:10:24-0600] [ALPM-SCRIPTLET] -> Running build hook: [filesystems]
[2024-11-22T19:10:25-0600] [ALPM-SCRIPTLET] -> Running build hook: [fsck]
[2024-11-22T19:10:28-0600] [ALPM-SCRIPTLET] ==> Generating module dependencies
[2024-11-22T19:10:28-0600] [ALPM-SCRIPTLET] ==> Creating zstd-compressed initcpio image: '/boot/initramfs-linux-lts-fallback.img'
[2024-11-22T19:10:30-0600] [ALPM-SCRIPTLET] -> Early uncompressed CPIO image generation successful
[2024-11-22T19:10:30-0600] [ALPM-SCRIPTLET] ==> Initcpio image generation successful
[2024-11-22T19:10:30-0600] [ALPM] running 'dbus-reload.hook'...
[2024-11-22T19:10:30-0600] [ALPM] running 'detect-old-perl-modules.hook'...
[2024-11-22T19:10:31-0600] [ALPM] running 'gdk-pixbuf-query-loaders.hook'...
[2024-11-22T19:10:31-0600] [ALPM] running 'glib-compile-schemas.hook'...
[2024-11-22T19:10:31-0600] [ALPM] running 'gtk-update-icon-cache.hook'...
[2024-11-22T19:10:32-0600] [ALPM] running 'gtk4-querymodules.hook'...
[2024-11-22T19:10:32-0600] [ALPM] running 'texinfo-install.hook'...
[2024-11-22T19:10:32-0600] [ALPM] running 'update-desktop-database.hook'...
[2024-11-23T02:04:32-0600] [PACMAN] Running 'pacman -S qt6-imageformats'
[2024-11-23T02:04:37-0600] [ALPM] transaction started
[2024-11-23T02:04:37-0600] [ALPM] installed qt6-imageformats (6.8.0-1)
[2024-11-23T02:04:37-0600] [ALPM] transaction completed
[2024-11-23T02:04:37-0600] [ALPM] running '30-systemd-update.hook'...
[2024-11-23T02:11:31-0600] [PACMAN] Running 'pacman -Syu'
[2024-11-23T02:11:31-0600] [PACMAN] synchronizing package lists
[2024-11-23T02:11:32-0600] [PACMAN] starting full system upgrade
[2024-11-23T02:11:37-0600] [ALPM] transaction started
[2024-11-23T02:11:37-0600] [ALPM] upgraded python-sentry_sdk (2.18.0-1 -> 2.19.0-1)
[2024-11-23T02:11:37-0600] [ALPM] transaction completed
[2024-11-23T02:11:37-0600] [ALPM] running '30-systemd-update.hook'...any help and tips on troubleshooting would be greatly appreciated! I've looked around the wiki and haven't found any other users with this problem as far as I know. I asked for help in other forums and received users telling me "this is just arch being arch".
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The folders in .config presumably have a "last modified" date you can look at; does that perfectly match up to the time you ran pacman -Syu? If not, check your shell history and be very sure there isn't a different command that could've caused it; or any kind of service you have enabled that regularly deletes files (if you have something automatically emptying your trash directory, for example).
My next step, assuming the dates do match up, would be to look at every single pacman hook run during the update to see if any of them references a variable that could've been unset, but it's unlikely such a bug wouldn't have been caught.
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The folders in .config presumably have a "last modified" date you can look at; does that perfectly match up to the time you ran pacman -Syu? If not, check your shell history and be very sure there isn't a different command that could've caused it; or any kind of service you have enabled that regularly deletes files (if you have something automatically emptying your trash directory, for example).
My next step, assuming the dates do match up, would be to look at every single Pacman hook run during the update to see if any of them references a variable that could've been unset, but it's unlikely such a bug wouldn't have been caught.
I'm looking at the last modified date for the folders within .config and strangely enough, not only do the modification dates line up to when the problem occurred but the creation dates too. This is not just for the folders within .config but the .config folder itself is showing up as "created on Friday, November 22, 2024, 4:01:33PM Central Standard Time" which is the date that this happened. So that further confirms that something happened that day at least but the exact time may be off. there were no other shell commands that day other than what was in my Pacman log. my previous shell commands are unrelated and from the 16th and prior Im not aware of any service that would've deleted my files and I haven't set my trash to automatically clear. my trash has files in it that were there before the date and none are .config files. Whatever happened that I'm not noticing seemed to only target .config.
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I'm looking at the last modified date for the folders within .config and strangely enough, not only do the modification dates line up to when the problem occurred but the creation dates too. This is not just for the folders within .config but the .config folder itself is showing up as "created on Friday, November 22, 2024, 4:01:33PM Central Standard Time" which is the date that this happened. So that further confirms that something happened that day at least but the exact time may be off. there were no other shell commands that day other than what was in my Pacman log. my previous shell commands are unrelated and from the 16th and prior Im not aware of any service that would've deleted my files and I haven't set my trash to automatically clear. my trash has files in it that were there before the date and none are .config files. Whatever happened that I'm not noticing seemed to only target .config.
Well, if your .config got re-created at 4:01 PM, doesn't that rule out pacman, because your pacman log shows you ran pacman -Syu later than that, at 7:09? I don't know if it could be different on your system, but on mine pacman.log uses my proper local time, as does my file manager.
(The creation date doesn't tell you when it was deleted, of course; that might have been well before 4:01 PM; on the 21st for example. If .config somehow got deleted, it'd probably remain so until an application launched that needed a file there, then it'd re-create the directory.)
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yaki_huevo wrote:I'm looking at the last modified date for the folders within .config and strangely enough, not only do the modification dates line up to when the problem occurred but the creation dates too. This is not just for the folders within .config but the .config folder itself is showing up as "created on Friday, November 22, 2024, 4:01:33PM Central Standard Time" which is the date that this happened. So that further confirms that something happened that day at least but the exact time may be off. there were no other shell commands that day other than what was in my Pacman log. my previous shell commands are unrelated and from the 16th and prior Im not aware of any service that would've deleted my files and I haven't set my trash to automatically clear. my trash has files in it that were there before the date and none are .config files. Whatever happened that I'm not noticing seemed to only target .config.
Well, if your .config got re-created at 4:01 PM, doesn't that rule out pacman, because your pacman log shows you ran pacman -Syu later than that, at 7:09? I don't know if it could be different on your system, but on mine pacman.log uses my proper local time, as does my file manager.
(The creation date doesn't tell you when it was deleted, of course; that might have been well before 4:01 PM; on the 21st for example. If .config somehow got deleted, it'd probably remain so until an application launched that needed a file there, then it'd re-create the directory.)
You're right. it should be the same on my system too. If it's not Pacman though, I'm not sure what else could've caused this. any ideas?
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Please post your journal matching the timestamps of when you ran pacman and the (I assume) eventual reboot after that. Make sure both the shutdown and startup are in the logs.
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