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An article identified by uniq is considered to have the mark flag when the file .nnmaildir/marks/flag/uniq exists. When Gnus asks nnmaildir for a group's marks, nnmaildir looks for such files and reports the set of marks it finds. When Gnus asks nnmaildir to store a new set of marks, nnmaildir creates and deletes the corresponding files as needed. (Actually, rather than create a new file for each mark, it just creates hard links to .nnmaildir/markfile, to save inodes.)

You can invent new marks by creating a new directory in .nnmaildir/marks/. You can tar up a maildir and remove it from your server, untar it later, and keep your marks. You can add and remove marks yourself by creating and deleting mark files. If you do this while Gnus is running and your nnmaildir server is open, it's best to exit all summary buffers for nnmaildir groups and type s in the group buffer first, and to type g or M-g in the group buffer afterwards. Otherwise, Gnus might not pick up the changes, and might undo them.