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

lang/src/vm/README.md

@@ -1,4 +1,4 @@
-# VM Layout (Current → Target)
+# Hakorune VM Layout (Current → Target)
 
 Current
 - `lang/src/vm/hakorune-vm/` — Hakorune VM (nyvm) implementation
@@ -56,7 +56,8 @@ Tag→RC（Core Direct）
 Core Direct Toggle
 - `HAKO_CORE_DIRECT=1`（互換: `NYASH_CORE_DIRECT`）で、Gate‑C(Core) の JSON 実行を "Core Dispatcher 直行" 子経路に切り替える。
   - 形: 一時Hakoスクリプトに `include "lang/src/vm/core/dispatcher.hako"` を埋め込み、`NyVmDispatcher.run(json)` を実行。
-  - rc: 最後の数値行を rc にマップ。数値がない場合（タグ等）は rc≠0 とする（Fail‑Fast）。
+  - rc: 子プロセスの終了コードを採用（数値戻り=rc、タグ/非数=rc≠0）。
+  - 判定: 直行は MIR(JSON v0)（`functions` と `blocks` を含む）に限定する。Stage‑B Program(JSON v0) は v1 bridge→VM 実行に迂回し、直行は行わない。
   - 用途: Core の診断タグや rc を CI で直接検証したい時に使用。
 - Runner Core toggle: `HAKO_NYVM_CORE=1` (or `NYASH_NYVM_CORE=1`) selects the
   Core bridge for the nyvm wrapper path.

lang/src/vm/core/ops/mir_call.hako

@@ -229,7 +229,7 @@ static box NyVmOpMirCall {
   _handle_console(callee, m, state) {
     local name = me._read_str(callee, "name")
     if name == "" { return me._fail(state, "[core/mir_call] console missing name") }
-    if !(name == "env.console.log" || name == "nyash.console.log" || name == "env.console.warn" || name == "nyash.console.warn" || name == "env.console.error" || name == "nyash.console.error") {
+    if !(name == "print" || name == "env.console.log" || name == "nyash.console.log" || name == "env.console.warn" || name == "nyash.console.warn" || name == "env.console.error" || name == "nyash.console.error") {
       return me._fail(state, "[core/mir_call] unsupported global: " + name)
     }
     local arg_vid = me._read_arg_vid(m, 0, "[core/mir_call] console missing arg", "[core/mir_call] console bad arg")