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>
Amir Alexander Abdelbaki
9107b9961a