I don't use maildirs, I use mboxes. My USE flag contains "-maildir mbox" among others. When running mutt for the first time, I got this message: /home/throstur/.maildir does not exist. Create it? ([yes]/no): So I answered no, quit mutt, and found /etc/mutt/Muttrc, changed set_mbox_type to mbox and commented everything else out. Now it works for mboxes. I don't know what the other options should be set as, so perhaps someone can fix this, 'cause I don't know what the defaults for mbox should be. (Plus, I don't know how to make ebuilds). hardly
I've adjusted the ebuild not to install an /etc/Muttrc when USE="mbox" is defined. mbox is the default behavior of mutt and so it shouldn't be needed.