refactor: complete utility anti-pattern sweep — utility-reference.md 100% green
Resolves all remaining open items (☐) in docs/utility-reference.md across Patterns 2–11. Every production and test violation is now fixed or confirmed already fixed in prior sessions.
Pattern 2 (manual prefix stripping): all 11 production files confirmed fixed; all 11 test files confirmed fixed or already fixed. Pattern 3 (manual hashlib.sha256 for IDs): code/manifest.py, midi/manifest.py, midi/entity.py fixed with blob_id(); storage-boundary fix via long_id(strip=True). Pattern 4 (manual short ID truncation): all 7 production files confirmed fixed; 13 test files updated to short_id() via subagent. Pattern 5 (manual UTC timestamp): 8 test files updated to now_utc_iso(). Pattern 6 (manual JSON file loading): 3 test files updated to load_json_file(). Pattern 7 (uuid for content-addressed IDs): all 24 test files confirmed fixed. Pattern 8 (manual fake_id equivalent): test_security_agent_impersonation.py fixed. Pattern 9 (manual object path construction): test_cmd_gc_hardening.py fixed; all other listed files already used object_path(). Pattern 11 (--format flag instead of --json): intent.py replaced --format/-f with --json/-j bool; test_cmd_intent.py updated; test_cmd_reserve.py and test_cmd_watch_coord.py updated to remove --format references.
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