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Every time I launch Mail.app it opens up a new window for each of the email messages I was checking previously. How do I stop this from happening? It only opens the emails that I launched in a new window previously, not every email message I hover over.

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1  
Close the mail viewer windows before quitting Mail.app. Seriously, it's a useful, state-preserving feature. Press Cmd-Opt-W or Opt-click the close button of one of Mail's windows to close them all, just before you quit. – Daniel Beck Apr 17 '11 at 19:03
    
Should have made that the answer Daniel. Thanks! – Eric Muyser Sep 16 '11 at 16:37

if you really want to be lazy you could put this script in your script menu and run it when you open mail

tell application "Mail"
    set window_names to name of every window
    repeat with awindow in window_names
        if awindow does not contain "messages" then close (first window whose name is awindow)
    end repeat
end tell
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Here's one (rather hacky, but working) way:

  1. Arrange the Mail App exactly how you want it to open.
  2. Quit it.
  3. Open the Terminal (Applications > Utilities > Terminal).
  4. Paste the following line and hit enter:

    chmod -w ~/Library/Saved\ Application\ State/com.apple.mail.savedState
    

If you ever want to undo it, repeat steps 3 and 4, but with +w instead of -w.

Tested on OS X 10.10.5.

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