I have taken a look at virtual folders and have it working. The couple of the folders I have set up are All Mail and Flagged by creating the respective dovecot-virtual file.
The dovecot-virtual files seems to be needed in each users mailbox.
How can I auto create the required dovecot-virtual files for every mailbox?
This is a pretty old question, but if you are still wondering, if i understood correctly what you were trying to achieve, you have to write auto = subscribe in each virtual mailbox in 15-mailboxes.conf, like so:
namespace inbox {
mailbox "Flagged messages" {
special_use = \Flagged
auto = subscribe
comment = Flagged messages
}
}