Phase 20.12b: quick green + structural cleanup

- Deprecations: add warn-once for nyash.toml (runtime::deprecations); apply in plugin loader v2 (singletons/method_resolver)
- Child env + runner hygiene: unify Stage‑3/quiet/disable-fallback env in test/runner; expand LLVM noise filters
- Docs/branding: prefer  and hako.toml in README.md/README.ja.md and smokes README
- VM: implement Map.clear in MIR interpreter (boxes_map)
- Stage‑B: gate bundle/alias/require smokes behind SMOKES_ENABLE_STAGEB; fix include cwd and resolve() call even for require-only cases
- Core‑Direct: gate rc boundary canary behind SMOKES_ENABLE_CORE_DIRECT
- Smokes: inject Stage‑3 and disable selfhost fallback for LLVM runs; filter using/* logs
- Quick profile: 168/168 PASS locally

This commit accelerates Phase 20.33 (80/20) by stabilizing quick suite, reducing noise, and gating heavy/experimental paths for speed.

src/runtime/mod.rs

@@ -20,6 +20,7 @@ pub mod unified_registry;
 pub mod provider_lock;
 pub mod provider_verify;
 pub mod observe; // Lightweight observability flags (OOB etc.)
+pub mod deprecations; // Deprecation warnings with warn-once guards
 // pub mod plugin_box;  // legacy - 古いPluginBox
 // pub mod plugin_loader;  // legacy - Host VTable使用
 pub mod extern_registry; // ExternCall (env.*) 登録・診断用レジストリ