Switch to a dev branch and enable initrd regeneration:
ostree commit -b dev --fsync=no --tree=ref=$booted_commit
rpm-ostree rebase :dev
rpm-ostree initramfs --enable
reboot
Updating files:
ostree checkout -H dev --fsync=no /ostree/repo/out/
# then dump files you want to add, e.g. for ignition-dracut:
rsync --delete -a /srv/ignition-dracut/dracut/30ignition/ /ostree/repo/out/usr/lib/dracut/modules.d/30ignition
ostree commit -b dev --link-checkout-speedup --fsync=no --consume /ostree/repo/out/
rpm-ostree upgrade # will regen the initrd
reboot