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It is possible to reconstitute the database and/or resource index while the repository is running in read-only mode. This is called a warm rebuild. People will still be able to access (but not change) items in your repository while the rebuild is taking place, but a quick restart will be required at the end of the process.
The fedora-rebuild utility was originally designed to run cold rebuilds against offline repositories, but with some extra work, you can also use it to rebuild into a new store (resource index or database) while your repository is still handling requests using the original store. At the end of this process, you will need to tell Fedora to use the new store, which requires a restart.
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