[Dovecot] Maildir and IMAP keywords

[Per-Erik Persson]

When a user in thunderbird toggles some flags like junk, spam or 
something similar dovecot appends these flags form a-z to the end of
the file in maildir.

I have another application that also access the maildirs which gets 
really upset with these flags and ignore those emails.

Are there any other way for dovecot to store these flags to make it 
compatible with other softwares?