lowerdir is the read-only directory (composefs) containing file metadata, and datadir is the directory containing the data (erofs).
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A self-hosted Forgejo or Gitea instance is really two systems bolted together: a web application backed by Postgres, and a collection of bare git repositories on the filesystem. Anything that needs to show git data in the web UI has to shell out to the binary and parse text, which is why something as straightforward as a blame view requires spawning a subprocess rather than running a query. If the git data lived in the same Postgres instance as everything else, that boundary disappears.
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