It is possible to create any number of schedules you wish. You can name each schedule and attach a schedule to a custom mail queue. You can also create as many custom mail queues as you want. Use the Content Filter to move messages into your custom queues based on any criteria you wish.
For example, you can create a schedule called 'Large Messages', create a queue to store those messages, and then create a Content Filter rule using the 'MOVE message to custom QUEUE' action to move messages over a certain size into that queue. If you'd like mailing list messages delivered at certain times then create a schedule called (for example) 'List Mail', create a queue, and then use a Content Filter rule to move messages with an X-MDMailing-List header into the new queue.
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MDaemon's pruning feature allows you to remove old data from the server and free up disk space. You may be familiar with the Public Folder Pruning settings under the Server Settings menu, or the Account & Mail Pruning settings under the Domain Manager, but did you know you can fine-tune your pruning settings using a Command prompt? The command line interface allows you to be very specific about what you want to prune. For example, you can prune (remove) messages that are a specified number of days old (say, 15 days) for a sub-folder of the inbox of a specific account, have those messages moved to a designated public folder, or just have the pruning information logged without actually deleting any data so that you can run this feature in test mode.