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Log physical operations for repository creations and deletions

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

We're changing our logging protocol towards logging physical file changes instead of logical operations to perform. This keeps the logging protocol simple and flexible. Various operations that would previously require new logical operations are simple to represent as pure file changes.

This migrates both repository deletions and creations to be logged using the physical logging protocol.

Part of #5793 (closed)
Closes #5844 (closed)
Closes #5843 (closed)

Edited by Sami Hiltunen

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