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Came up on `#fedora-iot` channel, some people are hitting
"No packages in transaction". I believe we have a bug,
but I didn't hit it with at least this simple test case.
It may be related to layering while doing this too, going to
test that next.
Gather the current diff of `/etc`, and filter out changes in
the tree which would overwrite it.
There is an OSTree API for diffs but it's a bit awkward, missing
some APIs in the Rust bindings and also `GFile` based unfortunately.
Doing this in Rust is nicer. The dirdiff code obviously needs
a lot more testing, but I think it's right.