Relocate dist files, fix path references, and misc script improvements

- Move setup_system.conf.dist to system_setup/config.dist/ and
  skel.tar.zst.dist + pack_skel.sh to system_setup/skel/; config/ now
  holds only gitignored local files
- Fix configure.sh CONF_DIST path (was pointing at non-existent
  config/setup_system.conf.dist)
- Fix skel/pack_skel.sh: remove vestigial source line whose path was
  wrong in both old and new location
- Update error messages in setup_system.inc.sh and
  sync_client_software.sh to reference new dist file location
- Move machine_uuid reading/writing into setup_system.inc.sh so all
  scripts have MACHINEID available; setup_system.conf.dist now uses
  MACHINEID conditionally with a hostname fallback
- sync_client_software.sh: fix && / typo (should be && \) that broke
  the flatpak remote-add → install chain; add network error handling
  after flatpak install; cleanup upgrade logic and chown placement
- Update CLAUDE.md and install.md to reflect new dist file locations

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

system_setup/configure.sh

@@ -5,7 +5,7 @@
 # SPDX-License-Identifier: AGPL-3.0-or-later
 
 SCRIPTDIR="$(cd "$(dirname "$0")" && pwd)"
-CONF_DIST="${SCRIPTDIR}/../config/setup_system.conf.dist"
+CONF_DIST="${SCRIPTDIR}/config.dist/setup_system.conf.dist"
 CONF_FILE="${SCRIPTDIR}/../config.d/configure.conf"
 
 if [[ "$EUID" -eq 0 ]]; then