Inside your

I have an extra folder here for feral bundles like MailPictures that don’t play nicely with other plug-ins, but which I like to be able to swap in and out sometimes. You might not.
DefaultCounts is just an XML file
, listing the number of messages that the Junk filter has marked as spam and the number of messages that you have manually marked as spam.
Envelope Index is a SQLite database that keeps track of the senders, subjects and dates (but not the full text) of all your emails to allow for faster searching than Spotlight can achieve.
Scott Morrison, the developer of MailTags and Mail Act-on, has written some notes on how searching works in Mail.app in the comments
on a macOSXHints article.
Deleting this file and allowing Apple Mail to rebuild it can fix a number of odd problems including the infamous “Your Home folder is full” message.
IMAP-???? Or POP-????@blahblah.com folders: Each IMAP or POP account has its own folder.

Mailboxes (mbox for POP accounts, imapbox for IMAP accounts) are stored here, with each one containing another folder, Messages, for messages and an Info.plist file to record the display setting for that particular mailbox.
You can read about the different emlx files
LSMMap2: This file is the Junk filter’s database of good and bad words and characteristics which it uses to determine whether an email is junk.
Mac-??????? is your dotmac account if you have one.
Mailboxes are all the mailboxes stored locally (the “On my Mac” option in the new mailbox dialog box). They have the same structure as the IMAP- and POP- mailboxes above.
MessageRules.plist and MessageSorting.plist are XML files that record your rules. At one stage I thought the difference between them was that the former recorded rules that didn’t move messages and the latter rules that moved emails from the Inbox to somewhere else. But that’s not right. If anyone works out the difference, I’d be glad to know.
Update: In fact, MessageRules.plist is Tiger Mail’s list of rules and MessageSorting.plist was the file used by Panther. If you have upgraded to 10.4, you can safely delete MessageSorting.plist. (Thanks, Michael and Andreas!)
OpenedAttachments.plist is a list of attachments in emails that you have opened. These are also the attachments that Mail.app stores in the ~/Library/Mail Downloads folder. These attachments can often be removed from the Mail Downloads folder to reclaim space from
The Signatues folder contains a webarchive file for each signature you have created. Editing these directly is one of the ways to create HTML signatures in Mail.app. The SignaturesByAccount.plist file in this folder simply records which signatures you have alloted to which accounts in Mail’s Signature Preferences pane.
The Signatures.plist file contains Rich Text versions of your signatures.
SmartMailboxes.plist contains the criteria which define your Smart Mailboxes, again as an XML file.
Tags: Apple Mail, Bundles, Mail folder, mail.app
I think MessageSorting.plist is where Panther stored the rules, and Tiger uses MessageRules.plist.
Re: MessageRules.plist vs. MessageSorting.plist – Michael is correct. You should be able to verify this by looking at the file dates (MessageSorting.plist should have the las modified date of when you upgraded to Tiger). You can safely delete that old file.
Also, if you upgraded from Panther, you might still have a bunch of “mbox” files (POP and local mailboxes) as well as “Cached Messages” folder with files in them (IMAP mailboxes) – you can safely delete those as well.
Thanks, guys. That’s good to know.
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How has this changed (if at all?) with Leopard?