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.

lang/src/compiler/entry/compiler_stageb.hako

@@ -170,7 +170,7 @@ static box Main {
       }
     }
 
-    if bundles.length() > 0 || bundle_srcs.length() > 0 {
+    if bundles.length() > 0 || bundle_srcs.length() > 0 || require_mods.length() > 0 {
       local merged_prefix = BundleResolver.resolve(bundles, bundle_names, bundle_srcs, require_mods)
       if merged_prefix == null { return 1 }
       body_src = merged_prefix + body_src