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Is it possible to set the maildir format at mailbox level? I'd like to us Maildir++ for most of my clients, but want to emulate the other one for one of my users. Can this be done with dovecot?

"the other one"? It's possible to have some users use maildir and others mbox, but if you want to use "filesystem layout" instead of Maildir++ for maildirs, then it's not possible with v1.0. With upcoming v1.1 you could do:

mail_location = maildir:~/Maildir:LAYOUT=FS

Sorry if I was not clear. I meant the later. I want Maildir++ layout as default and change it for selected users/mailboxes. Looking forward to 1.1 then :)