OSX 10.8.2 with Server App - Where is mail stored

I have OSX 10.8.2 with the Server App installed.
When I first started using the server, I did not have Mail services turned on. I was able to get all emails from the server (for example whenever cron jobs run) at the local users mail folder. For example, if the user is johndoe the mail would get sent to [email protected] and the actual mail box would be located at /var/mail/
I then turned on Mail services and was looking at what the options there were. I did not actually add any mail service options. Have not created a Mail server to receive or send mail. So this has nothing to do with MX records, or anything to do with external email communiciations.
This is where it got strange. Local mail stopped arriving at the /var/mail folder. If I used Terminal to check mail at [email protected] it was obvious new mail was arriving and being stored somewhere. Its just not being stored in the users /var/mail/ folder.
Can someone please tell me where the mail is being stored locally? Why did the location change. Is it because I turned Mail services ON? Can I make the mail go back to the original location in /var/mail/?
Shown below are some of the log files related to mail delivery. SMTP log and Mail Server log both look happy.
Any help greatly appreciated.
Oscar
I looked at the smtp log on the server - everything seemed to be good.
Jan 14 06:47:18 server.local postfix/pipe[37427]: 58FCDC7B83C: to=<[email protected]>, orig_to=<johndoe>, relay=dovecot, delay=0.03, delays=0/0/0/0.03, dsn=2.0.0, status=sent (delivered via dovecot service)
Jan 14 06:47:18 server.local postfix/qmgr[2788]: 58FCDC7B83C: removed
Jan 14 06:49:08 server.local postfix/pickup[37160]: 74726C7B846: uid=501 from=<johndoe>
Jan 14 06:49:08 server.local postfix/cleanup[37460]: 74726C7B846: message-id=<[email protected]>
Jan 14 06:49:08 server.local postfix/qmgr[2788]: 74726C7B846: from=<[email protected]>, size=604, nrcpt=1 (queue active)
Jan 14 06:49:08 server.local postfix/pipe[37463]: 74726C7B846: to=<[email protected]>, orig_to=<johndoe>, relay=dovecot, delay=0.2, delays=0.02/0.01/0/0.17, dsn=2.0.0, status=sent (delivered via dovecot service)
Jan 14 06:49:08 server.local postfix/qmgr[2788]: 74726C7B846: removed
Jan 14 06:49:09 server.local postfix/pickup[37160]: C1FA6C7B84B: uid=501 from=<johndoe>
Jan 14 06:49:09 server.local postfix/cleanup[37460]: C1FA6C7B84B: message-id=<[email protected]>
Jan 14 06:49:09 server.local postfix/qmgr[2788]: C1FA6C7B84B: from=<[email protected]>, size=606, nrcpt=1 (queue active)
Jan 14 06:49:09 server.local postfix/pipe[37463]: C1FA6C7B84B: to=<[email protected]>, orig_to=<johndoe>, relay=dovecot, delay=0.06, delays=0.02/0/0/0.04, dsn=2.0.0, status=sent (delivered via dovecot service)
Jan 14 06:49:09 server.local postfix/qmgr[2788]: C1FA6C7B84B: removed
Jan 14 06:49:36 server.local postfix/pickup[37160]: 9E9E7C7B850: uid=501 from=<johndoe>
Jan 14 06:49:36 server.local postfix/cleanup[37460]: 9E9E7C7B850: message-id=<[email protected]>
Jan 14 06:49:36 server.local postfix/qmgr[2788]: 9E9E7C7B850: from=<[email protected]>, size=605, nrcpt=1 (queue active)
Jan 14 06:49:36 server.local postfix/pipe[37463]: 9E9E7C7B850: to=<[email protected]>, orig_to=<johndoe>, relay=dovecot, delay=0.03, delays=0/0/0/0.03, dsn=2.0.0, status=sent (delivered via dovecot service)
Jan 14 06:49:36 server.local postfix/qmgr[2788]: 9E9E7C7B850: removed
I looked at the Mail Server Log - everything seemed good here too.
Jan 14 06:53:10 server.local dovecot-lda[37564]: lda(pid 37564 user johndoe): msgid=<[email protected]>: saved mail to INBOX
Jan 14 06:53:14 server.local dovecot-lda[37572]: lda(pid 37572 user johndoe): msgid=<[email protected]>: saved mail to INBOX
Jan 14 06:53:23 server.local dovecot-lda[37581]: lda(pid 37581 user johndoe): msgid=<[email protected]>: saved mail to INBOX
Jan 14 06:55:10 server.local dovecot-lda[37606]: lda(pid 37606 user johndoe): msgid=<[email protected]>: saved mail to INBOX
Jan 14 06:55:11 server.local dovecot-lda[37610]: lda(pid 37610 user johndoe): msgid=<[email protected]>: saved mail to INBOX
Jan 14 06:55:19 server.local dovecot-lda[37617]: lda(pid 37617 user johndoe): msgid=<[email protected]>: saved mail to INBOX

I tried what you recommended and the mail that gets sent out when the cron job runs still goes to the Library/Server/Mail/Data/mail location. When I checked the /Library/Server/Mail/Config/postfix/main.cf it actually had the mail_spool_directory = /var/mail commented out.
I uncommented to see it would send mail to /var/mail but it did not work. Am I missing something. Another parameter somewhere. Any other suggestions on where I should look?
Any online documentation that would explain more about what happens when mail services is activated by the Server App?

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No doubt others will give their opnions on what and how to back up as well as what to use.
Briefly Mail is stored in either an outgoing queue awaiting transfer to a remote server or in a local mail store accessible by local mail users. Outgoing mail messages are stored, by default, in the following spool directory on the startup disk: /var/spool/postfix. This location is temporary and the mail is stored until its transferred out. These locations can be moved to any accessible volume, either local or NFS mounted and symlinked to by the mail administrator. The Mail Service keeps track of incoming mail messages with a database, but the database doesn’t contain the messages themselves; the Mail Service stores each message as a separate file in a mail folder for each user. Incoming mail is stored on the startup disk in the following directory: /var/spool/imap/user/whatever the user name is. Cyrus puts a database index file in the folder of user messages. You can change the location of any or all of the mail folders and database indexes to another folder, disk, or disk partition. You can even specify a shared volume on another server as the location of the mail folder and database. Be careful if you decide to use a shared volume as things can slow down a bit. You should not use NFS for remotely mounted filesystems. Incoming mail remains on the server until its deleted.
You could also enable IMAP for all users that have their accounts enabled for mail. This way all mail is kept on the server until its deleted by the administrator or by the users, if you decide to go for this option as well then /var/imap is the database and /var/spool/imap is the mail store.
As for backup it depends on what you want to spend. Retrospect is a cheap solution that will do the incremental backup that you seem to want. Its been around for a long time and for most people its the first thing they turn to especially on the Mac platform. However its not perfect its slightly limited in its functions and there are problems with it running on the Intel platform, specifically Xserves. It can be ran remotely and supports a variety of devices. There are numerous others which others I’m sure will mention.

OSX 10.8.2 with Server App - Where is mail stored

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