It seems that synchronize flags just pushes Notmuch tags onto the
maildir flags (e.g. marking as unread messages that you'd read using
an external MUA). I'd thought that the synchronization would work
both ways (e.g. Notmuch reading maildir flags and updating its tags
accordingly). Since I do most of my mail reading in Mutt, the
push-only synchronization is not very helpful.
ignore=
-[maildir]
-synchronize_flags=true
+#[maildir]
+#synchronize_flags=true
[search]
exclude_tags=deleted;spam;