Skeleton files /etc/skel/ automatic syncing of changes to all users

I know this probably feels like a non-answer, but my answer is to avoid doing that if at all possible.

The stuff under skel really should only be per-user things, and shouldn't need to be managed after they have been deployed.

If you have shell fragments and config put them in the /etc/profile, /etc/profile.d.

Drop any system wide scripts under /usr/local/bin.

System wide configuration should go under the appropriate file in /etc. Or if the app doesn't support a system wide configuration , maybe add a config file under /etc and deploy a symlink to the /etc config file via the skel.