Try to narrow down what part of the code adds files and directories to
the queue(s) to be deleted.

Update one test. The output is slightly confusing, but I believe it is
correct, resulting from a directory being discovered but containing only ignored files.
---
 notmuch-new.c    | 14 ++++++++++++++
 test/T050-new.sh |  1 +
 2 files changed, 15 insertions(+)

diff --git a/notmuch-new.c b/notmuch-new.c
index 8ff1ade..ee786a3 100644
--- a/notmuch-new.c
+++ b/notmuch-new.c
@@ -528,6 +528,10 @@ add_files (notmuch_database_t *notmuch,
 					      "%s/%s", path,
 					      notmuch_filenames_get (db_files));
 
+	    if (state->debug)
+		printf ("(D) add_files_recursive, pass 2: queuing passed file %s for deletion from database\n",
+			absolute);
+
 	    _filename_list_add (state->removed_files, absolute);
 
 	    notmuch_filenames_move_to_next (db_files);
@@ -542,6 +546,9 @@ add_files (notmuch_database_t *notmuch,
 	    {
 		char *absolute = talloc_asprintf (state->removed_directories,
 						  "%s/%s", path, filename);
+		if (state->debug)
+		    printf ("(D) add_files_recursive, pass 2: queuing passed directory %s for deletion from database\n",
+			absolute);
 
 		_filename_list_add (state->removed_directories, absolute);
 	    }
@@ -610,6 +617,9 @@ add_files (notmuch_database_t *notmuch,
 	char *absolute = talloc_asprintf (state->removed_files,
 					  "%s/%s", path,
 					  notmuch_filenames_get (db_files));
+	if (state->debug)
+	    printf ("(D) add_files_recursive, pass 3: queuing leftover file %s for deletion from database\n",
+		    absolute);
 
 	_filename_list_add (state->removed_files, absolute);
 
@@ -622,6 +632,10 @@ add_files (notmuch_database_t *notmuch,
 					  "%s/%s", path,
 					  notmuch_filenames_get (db_subdirs));
 
+	if (state->debug)
+	    printf ("(D) add_files_recursive, pass 3: queuing leftover directory %s for deletion from database\n",
+		    absolute);
+
 	_filename_list_add (state->removed_directories, absolute);
 
 	notmuch_filenames_move_to_next (db_subdirs);
diff --git a/test/T050-new.sh b/test/T050-new.sh
index 66ea10f..ab15ca1 100755
--- a/test/T050-new.sh
+++ b/test/T050-new.sh
@@ -238,6 +238,7 @@ test_expect_equal "$output" \
 (D) add_files_recursive, pass 2: explicitly ignoring ${MAIL_DIR}/one/two/ignored_file
 (D) add_files_recursive, pass 2: explicitly ignoring ${MAIL_DIR}/one/two/three/.git
 (D) add_files_recursive, pass 2: explicitly ignoring ${MAIL_DIR}/one/two/three/ignored_file
+(D) add_files_recursive, pass 3: queuing leftover directory ${MAIL_DIR}/two for deletion from database
 No new mail."
 
 
-- 
2.1.4