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Copy style compact has to take the database down by design. This isn't an option.
But having a central list for system databases with an option to compact the database on restart of the server with certain options, would make a lot of sense.
Compact is not only for reclaiming diskspace. Also ODS upgrade, compression, etc. The mail problem after upgrading a Domino server, is to upgrade systemdatabases' ODS. You always have to do that OFFLINE.
just use the admin client