feat: advance repository records and provenance

Assistant: codex
Assistant-Model: gpt-5.6-sol
Assistant-Session: 01a023c0-a0a3-7c03-b395-5a0d2757214d

src/repo_manager/commands/scaffold.py

@@ -187,4 +187,6 @@ def scaffold_repository(
         except GitError as exc:
             return CommandResult("failed", evidence, {"message": str(exc)}, cid)
 
-    return CommandResult("applied" if written else "rejected", evidence, None, cid)
+    if not written:
+        evidence["noop"] = True
+    return CommandResult("applied", evidence, None, cid)