New patch that does it. Pretty much same as the old one, just with
that one bug I mentioned fixed. This is what I've currently used to
import my Maildir. I'm now happy :)

diff --git a/notmuch-new.c b/notmuch-new.c
index f25c71f..43371a3 100644
--- a/notmuch-new.c
+++ b/notmuch-new.c
@@ -39,6 +39,7 @@ typedef struct {
     int total_files;
     int processed_files;
     int added_messages;
+    int tag_maildir;
     struct timeval tv_start;
 
     _filename_list_t *removed_files;
@@ -169,6 +170,60 @@ _entries_resemble_maildir (struct dirent **entries, int 
count)
     return 0;
 }
 
+/* Tag new mail according to its Maildir attribute flags.
+ *
+ * Test if the mail file's filename contains any of the
+ * standard Maildir attributes, and translate these to
+ * the corresponding standard notmuch tags.
+ *
+ * If the message is not marked as 'seen', or if no
+ * flags are present, tag as 'inbox, unread'.
+ */
+static void
+derive_tags_from_maildir_flags (notmuch_message_t *message,
+                               const char * path)
+{
+    int seen = FALSE;
+    int end_of_flags = FALSE;
+    size_t l = strlen(path);
+
+    /* Non-experimental message flags start with this */
+    char * i = strstr(path, ":2,");
+    i = (i) ? i : strstr(path, "!2,"); /* This format is used on VFAT */
+    if (i != NULL) {
+       i += 3;
+       for (; i < (path + l) && !end_of_flags; i++) {
+           switch (*i) {
+           case 'F' :
+               notmuch_message_add_tag (message, "flagged");
+               break;
+           case 'R': /* replied */
+               notmuch_message_add_tag (message, "answered");
+               break;
+           case 'D':
+               notmuch_message_add_tag (message, "draft");
+               break;
+           case 'S': /* seen */
+               seen = TRUE;
+               break;
+           case 'T': /* trashed */
+               notmuch_message_add_tag (message, "deleted");
+               break;
+           case 'P': /* passed */
+               notmuch_message_add_tag (message, "forwarded");
+               break;
+           default:
+               end_of_flags = TRUE;
+               break;
+           }
+       }
+    }
+
+    if (i == NULL || !seen) {
+       tag_inbox_and_unread (message);
+    }
+}
+
 /* Examine 'path' recursively as follows:
  *
  *   o Ask the filesystem for the mtime of 'path' (fs_mtime)
@@ -222,6 +277,7 @@ add_files_recursive (notmuch_database_t *notmuch,
     notmuch_filenames_t *db_subdirs = NULL;
     struct stat st;
     notmuch_bool_t is_maildir, new_directory;
+    int maildir_detected = -1;
 
     if (stat (path, &st)) {
        fprintf (stderr, "Error reading directory %s: %s\n",
@@ -301,6 +357,28 @@ add_files_recursive (notmuch_database_t *notmuch,
            continue;
        }
 
+       /* If this directory is a Maildir folder, we need to
+        * ignore any subdirectories marked tmp/, and scan for
+        * Maildir attributes on messages contained in the sub-
+        * directories 'new' and 'cur'. */
+       if (maildir_detected != 0 &&
+           (entry->d_type == DT_DIR || entry->d_type == DT_UNKNOWN) &&
+           ((strcmp (entry->d_name, "tmp") == 0) ||
+            (strcmp (entry->d_name, "new") == 0) ||
+            (strcmp (entry->d_name, "cur") == 0))) {
+
+    if (maildir_detected == -1) {
+      maildir_detected = _entries_resemble_maildir(fs_entries, num_fs_entries);
+    }
+    if (maildir_detected == 1) {
+      if (strcmp (entry->d_name, "tmp") == 0) {
+        continue;
+      } else {
+        state->tag_maildir = TRUE;
+      }
+    }
+  }
+
        next = talloc_asprintf (notmuch, "%s/%s", path, entry->d_name);
        status = add_files_recursive (notmuch, next, state);
        if (status && ret == NOTMUCH_STATUS_SUCCESS)
@@ -412,7 +490,12 @@ add_files_recursive (notmuch_database_t *notmuch,
        /* success */
        case NOTMUCH_STATUS_SUCCESS:
            state->added_messages++;
-           tag_inbox_and_unread (message);
+                       if (state->tag_maildir) {
+                           derive_tags_from_maildir_flags (message,
+                                                           entry->d_name);
+                       } else {
+                           tag_inbox_and_unread (message);
+                       }
            break;
        /* Non-fatal issues (go on to next file) */
        case NOTMUCH_STATUS_DUPLICATE_MESSAGE_ID:


-- 
Stewart Smith
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