Diagnosed from a full guided-install log plus a Hyprland startup log. Three
distinct remaining failures:
1. ~/.config left root-owned. The FIDO/Yubico setup runs `mkdir -p
~/.config/Yubico` as root (creating ~/.config itself), then chowned only
Yubico/. ~/.config stayed root-owned, so every later user step failed with
EACCES: shell-setup symlinks (starship.toml), the mail/caldav systemd --user
timers, and Hyprland creating ~/.config/hypr at startup. Chown the whole
~/.config in both Yubico spots, and defensively reclaim it in shell-setup.
2. python/wprs/plymouth/zfs sourced ../lib/logging.sh, but apps/ modules need
../../lib — so they aborted with "No such file or directory". Corrected.
3. Flatpak app modules ran `flatpak install -y` at system scope, which needs the
Flatpak SystemHelper D-Bus service + polkit (unavailable in a chroot/TTY
install) — the "The name is not activatable" failures (wireshark, xournal,
rnote, firefox-browser, …). Switch ensure_flatpak and all 19 main-flow
installs to --user scope, matching apply_flatpak_theme's --user overrides.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Policy change: graphical apps now prefer Flatpak > pacman > AUR. Non-graphical
tools keep pacman > AUR > source. This makes installed apps sandboxed, keeps
system packages clean, and gives us a single hook point (apply_flatpak_theme)
to theme every GUI app consistently.
lib/logging.sh — two new helper functions sourced by every module:
ensure_flatpak()
Checks if flatpak is installed (pacman installs it if not) and ensures the
Flathub remote is registered. Called at the top of every Flatpak script so
the module is self-contained and safe to run in any order.
apply_flatpak_theme(app_id)
Copies gtk-themes/cyberqueer/ from the Dotfiles repo into ~/.themes/, then
calls `flatpak override --user --filesystem=~/.themes:ro <id>` so the
sandbox can read it, and `flatpak override --user --env=GTK_THEME=cyberqueer
<id>` to activate it. Gracefully skips with a warning if the theme source
directory is absent.
App scripts converted (pacman/AUR → Flatpak + theme):
ardour org.ardour.Ardour
audacity org.audacityteam.Audacity
chromium org.chromium.Chromium
firefox org.mozilla.firefox
geany org.geany.Geany
gimp org.gimp.GIMP
inkscape org.inkscape.Inkscape
kate org.kde.kate
kdenlive org.kde.kdenlive
krita org.kde.krita
librewolf io.gitlab.librewolf-community.librewolf
lmms io.lmms.LMMS
localsend org.localsend.localsend
min-browser com.github.minbrowser.min
mixxx org.mixxx.Mixxx
onlyoffice org.onlyoffice.desktopeditors
openshot org.openshot.OpenShot
rdp-client org.remmina.Remmina (was pacman remmina + freerdp + libvncserver;
Flatpak bundles all protocols, including VNC and SSH tunnels)
shotcut org.shotcut.Shotcut
steam com.valvesoftware.Steam
vscodium com.vscodium.codium
wireshark org.wireshark.Wireshark
xournal com.github.xournalpp.xournalpp
zed dev.zed.Zed
zen-browser io.github.zen_browser.zen
Special cases:
blender-povray: Blender → Flatpak (org.blender.Blender) + theme; POV-Ray
stays pacman because it has no Flatpak and is a CLI renderer, not a GUI app.
prismlauncher / stuntrally: were already Flatpak installs; added
apply_flatpak_theme so they pick up the cyberqueer theme like everything else.
vesktop: switched from AUR vesktop to Flatpak dev.vencord.Vesktop. The AUR
build requires cargo and takes several minutes; the Flatpak is pre-built.
Vencord config is now deployed to ~/.var/app/dev.vencord.Vesktop/config/
(both Vencord/ and vesktop/ sub-dirs) instead of ~/.config/, which is where
the Flatpak sandbox exposes its config directory.
k8s: kubectl stays pacman (it is a CLI tool with no GUI, no Flatpak needed);
podman-desktop switches from pacman podman-desktop to Flatpak
io.podman_desktop.PodmanDesktop + theme, because it is a full GUI app.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add modules/lib/logging.sh with log(), skip(), warn(), err() helpers.
Source it in all 84 scripts (core, DEs, optional apps) and replace bare
echo calls with structured log messages. Add log file capture to install.sh.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Amir Alexander Abdelbaki