Debian – Detecting unreaded mails in Maildir

mutt also uses a global muttrc file. Typically it's in /etc/Muttrc or /usr/local/etc/Muttrc if you compiled it separately from the distro. You can just put the Maildir settings there.

This mutt & Maildir Mini-HOWTO should give you an idea of what settings you need to change. Essentially you need to set folder and mbox and spoolfile to all point to ~/Maildir for everyone, and ensure mbox_type=Maildir as well. Then there are a few other options to change the behavior.

Edit the file main.cf of Postfix and look for the setting home_mailbox and modify it to

home_mailbox=Maildir/

If you cannot find that line add it to the config. Then modify dovecot's config to use

mail_location=maildir:/var/mail/%u/Maildir

Comment out the other three. Postfix is then configured to drop one file for each email in /var/mail/username/Maildir/new. Restart postfix and dovecot afterwards. That should fix the issue with squirrelmail.

This setup is only suited for receiving and storing email for one domain. If you want to be able to effectively use and configure a the server as a mail-server for different domains, I'd recommend reading up on what you need, to set that up, how to set it up and how the different parts (dovecot for IMAP/POP3, postfix, squirrelmail) are configured.