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/setup_skel.sh

@@ -3,7 +3,7 @@
 source $(dirname "$0")/setup_system.inc.sh
 EXECDIR=$(pwd)
 SRCFILE="${SYSCONFIGPATH}/config/skel.tar.zst"
-SRCFILEDIST="${SYSCONFIGPATH}/config/skel.tar.zst.dist"
+SRCFILEDIST="$(dirname "$0")/skel/skel.tar.zst.dist"
 
 #Check for root
 if [ "$EUID" -ne 0 ]; then