As discussed in this thread:
https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org/thread/RZJPOB4PWNMDV25L5MUKSTGMRZAMQNPO/#RZJPOB4PWNMDV25L5MUKSTGMRZAMQNPO
You're correct that the source repos on mirrors are empty.
However the repos as generated by Pungi are not empty: https://kojipkgs.fedoraproject.org/compose/updates/Fedora-29-updates-20190109.2/compose/Everything/source/tree/repodata/ The one for 20190111.0 is also not empty. So this is not a bug in Pungi, but somewhere between Bodhi and scripts that sync stuff to mirrors.
This ticket should be filed against releng, where there are people who know how the stuff gets to mirrors. I went ahead and opened it: https://pagure.io/releng/issue/8047
Metadata Update from @lsedlar: - Issue close_status updated to: Invalid - Issue status updated to: Closed (was: Open)
This issue has been migrated to Fedora Forge: https://forge.fedoraproject.org/pungi/pungi/issues/1111
Please continue any further discussion there.