Does Apple Mail prevent duplicates from being created in the same folder when copying/moving messages and how

One can do this. The following shows what I've found...

Individual Apple Mail emails reside in a directory, typically something like the following:

/Users/UserName/Library/Mail/POP-myEmail@isp.com@pop.secureserver.net/INBOX.mbox/Messages

as ".emix" files readable by any text editor.

".emix" files have a sequential numbering by mails received by one's Apple Mail itself rather than the particular mailbox, something like:

18373.emix
18376.emix
18378.emix

The ".emix" files have clearly marked identifiers of their content. An abridged ".emix" file follows::

Received: (somemailprovider ...); 16 Jul 2012 00:04:00 -0000
Received: from unknown ...; 16 Jul 2012 00:04:00 -0000
X-IronPort-Anti-Spam-Result: AuEPABVXA1DR...
Received: from ....isp.com ...; 15 Jul 2012 17:03:59 -0700
Received: by qcsg1 ...; Sun, 15 Jul 2012 17:03:59 -0700 (PDT)

DKIM-Signature: ...
Received: ...; Sun, 15 Jul 2012 17:03:59 -0700 (PDT)

Return-Path: <myEmail@isp.com>
Received: from iMac-6.local ....

Date: Sun, 15 Jul 2012 20:03:54 -0400 (EDT)
From: myFromEmail@isp.com
To: myToEmail@isp.com
Message-ID: <50035a6e.02d0e00a.1fef.....com>
Subject: TEST
MIME-Version: 1.0
Content-Type: multipart/mixed;boundary="----=_Part_0_1792110529.1342397034510"
X-Nonspam: None

------=_Part_0_...
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 7bit 

------=_Part_0_...
Content-Type: image/gif; name=0001.gif
Content-Transfer-Encoding: base64
Content-Disposition: inline; filename=0001.gif

So, given all of this one needs to:

• Identify which email one wants to read (I can use date and a specific email directory) ;
• Import the text of the email into Mathematica;
• Parse the required information using the appropriate identifiers in the ".emix" file.

A little cumbersome, but workable.

Mail can be extended to mimic pretty closely the feature you mention from Outlook.

OS X provides a feature called services that can be used to extend the functionality of an application (see http://www.macosxautomation.com/services/learn/index.html for more information).

I will use Automator and AppleScript to create a service that moves sent messages to the folder of the message being replied to, and then assign the standard reply keyboard shortcut (⌘R) to the service:

• Close Mail.

• Open Automator in folder Applications and choose Service:

• Select Utilities under Library and drag Run AppleScript to the empty pane on the right:

• Configure the service to receive no input in Mail:

• Replace the contents of the Run AppleScript action with:

  on run {input, parameters}
  
  tell application "Mail"
      try
          (* Get selected messages or exit *)
          set messageSelection to selection
          set selectedMessage to item 1 of messageSelection
          set replyMessage to reply selectedMessage opening window yes
          set messageID to message id of selectedMessage
          set currentMailbox to mailbox of selectedMessage
      on error
          return
      end try
      repeat
          (* Wait until reply message is sent *)
          delay 2
          try
              if replyMessage is not visible then exit repeat
          on error
              exit repeat
          end try
      end repeat
      synchronize with (account of currentMailbox)
      (* Wait while reply message is being sent *)
      delay 10
      (* Loop over all sent messages *)
      set sentMailbox to sent mailbox of application "Mail"
      set allSentMessages to messages of sentMailbox
      repeat with sentMessage in allSentMessages
          if source of sentMessage contains messageID then
              set mailbox of sentMessage to currentMailbox
              return
          end if
      end repeat
  end tell
  
  return input
  end run
  

  • Save with a descriptive name like Reply and Move Sent Message to Current Folder. The service will be saved to ~/Library/Services/. This is what the service looks like:

• Open System Preferences, select the Keyboard preference pane and then the Keyboard Shortcuts tab.

• Select Application Shortcuts, press the + button and change for application Mail the shortcut assigned to menu item Reply to ⌥⌘R. We change it to avoid conflicts when assigning ⌘R to the service below:

• Select Services, scroll down to the service you previously added and set the keyboard shortcut to ⌘R:

• Open Mail. Notice that Reply's shortcut is no longer ⌘R, but ⌥⌘R:

• Also notice that there is a new service, accessible with ⌘R:

• Now select a message in a folder, press ⌘R, type your reply and send it, in a few seconds you should see the sent message appear in the folder.

The script has some limitations and side effects:

• The service can't tell canceled and sent messages apart. So, if you press ⌘R and then change your mind and close the window, the service will continue executing and check your Sent folder for matching IDs.

• AppleScript doesn't offer any means of getting a list of replies to a message. My workaround is to get the message id of the message being replied to and search it in the sent messages.

• The sent message can't be moved while being downloaded. AppleScript doesn't return any error message if that's the case, so I added a 10-second delay. A 5-second delay was not reliable in my tests, adapt it to your needs if necessary.

• While the service searches the Sent folder, Mail slows down.