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Migrate alternate updates to physical logging protocol

Sami Hiltunen requested to merge smh-physical-log-alternate into master

This MR migrates alternate linking and unlinking operations to the physical logging protocol (#5793 (closed)).

  • This commit migrates alternate linking operations to also be handled via the physical logging protocol that just logs the file system changes to be done. The staged alternate file is recorded in the log entry, and applied from there to the repository.

  • Alternate unlinking is currently logged as a logical operation. On applying the log entry, all loose objects and the packs from the alternate are linked to the repository, and the repository's 'objects/info/alternates' file is removed.

    This commit removes the logical operation, and replaces it by logging the physical operations that perform the same operation. Logging the file system operations is a more composable approach.

Closes #5846 (closed)

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