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The problem with moving directory in podman (fuse-overlayfs) was catched in microdnf too: https://bugzilla.redhat.com/show_bug.cgi?id=1700341 .

I implemented a "copy+delete fallback " in the libdnf. And also made some workaround in the librepo.
PR https://github.com/rpm-software-management/libdnf/pull/787
PR https://github.com/rpm-software-management/libdnf/pull/789
PR https://github.com/rpm-software-management/librepo/pull/166

The new libdnf code is used by DNF too. So, the "cross-device link" problem is fixed.

But I see other message "Directory not empty" instead of "Invalid cross-device link" in this bug. Another anomaly of overlayfs? I do not know, but "copy+delete fallback" will be used in this case too. So, I hope that this bug is fixed too.

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory, and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://access.redhat.com/errata/RHBA-2020:1823