“Mail cannot update your mailboxes because your home directory is full. You must free up space in your home folder before using Mail. Delete unneeded documents or move documents to another volume.”

It actually has nothing to do with the amount of space on your harddisk and it’s not hard to fix.

1. Quit Mail.
2. Navigate to your ~/Library/Mail folder.
3. Move the file called “Envelope Index” to your Desktop. It’s an SQLite databse—see “What’s in your Mail folder?” (maybe after you’ve finished).
4. Launch Apple Mail. It will prompt you to “import” your mailboxes, although it is really just rebuilding its index. Select OK.
5. Mail.app will rebuild and re-index the messages and create a new copy of the Envelope Index file.
6. When you are sure that everything is working properly again, you can delete the old Envelope Index file on your Desktop.

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