If you backup your home directory, your settings, preferences, and even your mailbox settings will be saved. However, unless you're using pop to get your mail, it's still on the server, and backup of the home directory won't get them. However, they will still be on the server for you to retrieve later. Imap leaves messages on the server, which is a real problem if you have low quotas. But, if you have them set to pop, then, yes, they're in your home dir a few levels down, so be sure you get the *whole* home directory, not just the top level.

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