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/runner/mod.rs

@@ -48,7 +48,7 @@ pub struct NyashRunner {
     config: CliConfig,
 }
 
-/// Minimal task runner: read nyash.toml [env] and [tasks], run the named task via shell
+/// Minimal task runner: read hako.toml (preferred) or nyash.toml [env]/[tasks], run the named task via shell
 use tasks::run_named_task;
 
 #[cfg(not(feature = "jit-direct-only"))]
@@ -71,7 +71,7 @@ impl NyashRunner {
         dispatch::execute_file_with_backend(self, filename);
     }
 
-    /// Minimal AOT build pipeline driven by nyash.toml (mvp)
+    /// Minimal AOT build pipeline driven by hako.toml/nyash.toml (mvp)
     fn run_build_mvp(&self, cfg_path: &str) -> Result<(), String> {
         build::run_build_mvp_impl(self, cfg_path)
     }