Make atomic file replacement crash durable

docs/internal/manifest.md

@@ -48,9 +48,15 @@ The model admits these stage states:
 
 - validates loaded documents;
 - normalizes missing maps/stage records;
-- writes atomically via temp file + rename;
+- writes through a sibling temporary file, syncing the completed file and
+  destination directory after atomic replacement;
 - updates `updated_at` on save.
 
+If the operating system or filesystem cannot sync a directory, save returns an
+explicit error instead of claiming crash-durable replacement. A returned error
+after the rename can therefore leave the new manifest visible but not confirmed
+durable; callers must reload it before retrying.
+
 ## Execution Semantics
 
 The application runner marks an executing stage running and then succeeded or