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What is the best way to backup my Citadel installation?

You should back up the entire citadel/ directory. The most important files are citadel.config, citadel.control, and the data/ subdirectory, but there are other files which contain non-static data as well.

Since Citadel uses a journalling database backend, it is vitally important that you backup both the data files and the logs, and that the data files (data/cdb.* ) are always backed up before the logs (data/log.* ). The logs must always be backed up after the data files. It might be apropriate to move the logfiles to another location.You can however speed this up by using LVM and Snapshots

This section of the system administration manual goes into more detail.

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