fix(engine): bump now_iso() to microsecond precision

CI failure on python 3.11/3.12: test_update_bumps_version_and_updated_at
asserts updated_at > created_at, but ms-precision timestamps collide when
SQLite create + update fire inside the same millisecond on fast runners.

Microsecond precision (6 fractional digits) keeps ISO-8601 valid, TS
Date.parse handles it natively, and no consumer regex-binds to the
3-digit form. Fixes the repository ordering invariant.

engine/_utils.py

@@ -5,10 +5,15 @@ import datetime as _dt
 
 
 def now_iso() -> str:
-    """UTC ISO timestamp with millisecond precision and ``Z`` suffix.
+    """UTC ISO timestamp with microsecond precision and ``Z`` suffix.
 
     Used for `created_at`, `updated_at`, `library_snapshot_at`,
     migration `applied_at`, and import-export `exported_at`. Single source
     of truth so the format never drifts between callers.
+
+    Microsecond precision (vs. millisecond) prevents collisions when
+    two ops fire inside the same millisecond on fast CI runners — the
+    `updated_at > created_at` invariant in `ModuleRepository.update`
+    must hold for any sequential create+update pair.
     """
-    return _dt.datetime.now(_dt.timezone.utc).strftime("%Y-%m-%dT%H:%M:%S.%f")[:-3] + "Z"
+    return _dt.datetime.now(_dt.timezone.utc).strftime("%Y-%m-%dT%H:%M:%S.%fZ")