A git repository is a content-addressable object store where objects go in indexed by the SHA1 of their content, plus a set of named references pointing at specific objects by hash. The on-disk format (loose objects as individual files, packfiles as delta-compressed archives with a separate index, a ref store split between a directory of files and a packed-refs flat file with a locking protocol that breaks on NFS) is an implementation detail. The protocol for synchronising objects and refs between repositories is what actually matters, and since git-the-program is just one implementation of it, you can swap the storage backend without clients noticing.
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# Switch to agent mode
The solution is not to install packages manually with rpm-ostree but to always go through generating a new OCI image with the desired packages. This keeps a consistent state between the image and the deployed system. Let’s generate a new image with cowsay and push it to Harbor so the update service can retrieve it.