[ And apparently you can't unarchive and comment on a bug report in the
same email... Resending my patches so they appear in the bug report
itself. ]

This annoyed me enough to make me dive into the code and try to fix it.
Please find attached my proposed changes, in 3 parts.  I also keep them
in a repository on Github:
https://github.com/legoscia/gnus/tree/nnmaildir-flags-may-eat-your-email

I've been using this code for a week, and despite the branch name, it
hasn't eaten my email yet.

In my change, I made the Gnus `read', `tick' and `reply' marks
correspond to the Maildir S, F and R flags, respectively.  Other marks
are kept as hardlinks in the marks directory, as before.  The new code
will read marks from both sources, and when marks are cleared, they will
be cleared in both places, but when marks that correspond to flags are
added, they will only be added to the filename.  That means that the new
nnmaildir should read directories used by old nnmaildir versions
correctly, but if you use an old nnmaildir on a directory previously
used with the new version, marks will be missing.  Is that acceptable?

My patches don't address the performance and disk space issues mentioned
in this bug report; my aim was to make it correct first, and fast later.

Regards,
Magnus