fix: the setup card must say what setup resets

Restarting dsh with the 2.0.12 copy still in the profile re-provisioned
the bundle to 2.0.12's pin: REA went back to 6.7.0, the Ghidra gate
override went with it, and the MCP row failed with "REA could not start".
That is the card doing its job on a machine whose plugin copy was stale —
but the card never said the aligned run also wipes the override.

- client.js: third note in both languages. It names the override case and
  the command that restores it, so the card is not advice that silently
  undoes a deliberate choice.
- README (both): the "you must run setup" block says the same thing.
- ghidra-gate-override.mjs: judge a recorded override by the files on disk.
  Re-provisioning replaces rea-agents while leaving the record behind, so
  --enable now replaces a stale record instead of refusing, and --disable
  counts already-lost files instead of throwing.
- CHANGELOG: 2.0.13 records both, plus the failure that prompted them.

Verified after re-aligning this machine: setup --reuse reached
"setup complete" with its Ghidra smoke importing java.exe in 28 s on 12.2,
the shim resolves REA 6.8.0, and the MCP path through the shim returns the
same segments / procedure inventory / entry pseudocode as the 12.1.4
baseline with provider.version = 12.2.

Gates: audit 24/24 hash-pinned clean, 88 tests (85 pass / 3 skipped),
verify-branch ALL CHECKS PASSED, host-compat 10 covered / 5 outside.

CHANGELOG.md

@@ -38,6 +38,15 @@
 - **`check-updates.ps1` 认得这份记录**：盘上跑 12.2 时打印「本机覆盖 Ghidra 闸门」，而不是劝用户「重跑 setup 对齐」
   —— 后者正好会把覆盖悄悄抹掉。
 
+### 修复
+
+- **「还要跑一次 setup」卡片的说明补上覆盖这一条**：这张卡片出现在每次升级之后，而它就是叫你去跑 setup 的。
+  setup 会重新供给内置 REA，**Ghidra 闸门覆盖随之消失** —— 卡片现在明写这一点并给出恢复命令。踩到的实例：
+  本机重启后，profile 里还是 2.0.12 的旧副本，它的 shim 按自己的 pin 把 bundle 重新供给回 6.7.0，
+  覆盖与 6.8.0 一起被抹掉，MCP 行随之 `REA could not start`。
+- **`ghidra-gate-override.mjs` 处理「记录还在、补丁已被 re-provision 抹掉」的半状态**：`--enable` 现在按盘上
+  实际内容判断记录是否仍成立，陈旧记录直接替换而不是报错；`--disable` 对已失去补丁的文件只计数不抛错。
+
 ### 验证
 
 - 单测 **88 条**（85 过 / 3 平台跳过 / 0 失败）；`audit-manifest` **24/24 hash-pinned clean**；

README.md

@@ -32,6 +32,8 @@
 > does **not** move the bundle to the new pins — REA and the engines stay at the versions recorded by the last
 > setup run. Skip it on a first install and the row exits `MODULE_NOT_FOUND` with no tools and no message;
 > skip it after an upgrade and you keep running the old REA silently (`check-updates.ps1` reports the drift).
+> If you had enabled the Ghidra gate override (see §9 of the 2026-10-26 review), that setup run re-provisions the
+> bundled REA and the patch goes with it — re-enable it afterwards, or accept the pinned Ghidra again.
 > The full rule set is under [Updating](#updating--three-independent-things).
 
 > **A first install and every plugin upgrade also show a one-time guide in the Web GUI.** It says whether the

README.zh-CN.md

@@ -29,7 +29,8 @@
 > 市场里的安装/更新只替换包，然后到此为止。从 **2.0.8** 起，市场升级能保证**那一行**继续可用（镜像启动器会
 > 转发执行新的那份），但它**不会**把 bundle 换到新的钉子 —— REA 与引擎仍是上一次 setup 时记下的版本。
 > 首次安装不跑：行以 `MODULE_NOT_FOUND` 退出，工具消失且没有任何提示；升级后不跑：仍旧跑旧 REA 且没有症状
->（`check-updates.ps1` 会报出这条漂移）。完整规则见[更新](#更新--三件互相独立的事)。
+>（`check-updates.ps1` 会报出这条漂移）。若你开过 Ghidra 闸门覆盖，这一次 setup 会重新供给内置 REA、覆盖随之
+> 消失 —— 跑完再 `--enable` 恢复，或者接受回到钉住的那一版。完整规则见[更新](#更新--三件互相独立的事)。
 
 > **首次安装与每次升级插件后，Web GUI 会显示一次操作指南。** 它会说明运行时是缺失、还是落后于本插件钉的版本，
 > 给出这次安装对应的完整 `node "<安装路径>/scripts/setup.mjs"` 命令，并按插件版本记住“已看过”。

client.js

@@ -56,6 +56,7 @@ window.__ModuleLoader__.load({
         hint: "跑完重启 dsh。这一步只对齐运行时，不会更新插件包本身；升级后同样再跑一次。",
         noteSmoke: "setup 结束时会用 JDK 自带的 java 跑一次真实分析来验证引擎 —— 那里 30–60 秒没有任何输出是正常的。",
         noteLock: "若它报 “another provisioning run holds …”，说明后台已有一个 setup 在跑，等它结束再试即可。",
+        noteOverride: "若你开过 Ghidra 闸门覆盖（让本机跑 REA 未验证的 Ghidra），setup 会重新供给内置 REA，那层覆盖随之消失 —— 跑完执行 node scripts/ghidra-gate-override.mjs --enable --version 12.2 恢复。",
       },
       en: {
         badge: "ONE-TIME SETUP",
@@ -77,6 +78,7 @@ window.__ModuleLoader__.load({
         hint: "Restart dsh afterwards. This only aligns the runtime; it does not update the plugin package — run it again after the next upgrade.",
         noteSmoke: "It finishes by importing a small file to prove the analysis engine works — 30–60 s with no output there is normal.",
         noteLock: "If it reports “another provisioning run holds …”, a setup is already running in the background; wait for it.",
+        noteOverride: "If you had enabled the Ghidra gate override (running a Ghidra REA has not verified), setup re-provisions the bundled REA and the patch goes with it — run node scripts/ghidra-gate-override.mjs --enable --version 12.2 afterwards to restore it.",
       },
     };
 
@@ -354,6 +356,7 @@ window.__ModuleLoader__.load({
             },
             h("li", null, t.noteSmoke),
             h("li", null, t.noteLock),
+            h("li", null, t.noteOverride),
           ),
 
           h(

scripts/ghidra-gate-override.mjs

@@ -138,11 +138,30 @@ function main() {
       console.log("no override is recorded; nothing to restore");
       return;
     }
+    let restored = 0;
+    let stale = 0;
     for (const entry of active.files) {
-      replaceValue(path.join(vendor, entry.file), entry.patched, entry.original);
+      const file = path.join(vendor, entry.file);
+      if (!existsSync(file)) {
+        stale += 1;
+        continue;
+      }
+      const text = readFileSync(file, "utf8");
+      if (new RegExp(`${CONSTANT}\\s*=\\s*"${entry.patched.replace(/\./g, "\\.")}"`).test(text)) {
+        replaceValue(file, entry.patched, entry.original);
+        restored += 1;
+      } else if (new RegExp(`${CONSTANT}\\s*=\\s*"${entry.original.replace(/\./g, "\\.")}"`).test(text)) {
+        stale += 1;
+      } else {
+        throw new Error(`${entry.file} declares neither ${entry.patched} nor ${entry.original}; inspect it before restoring`);
+      }
     }
     unlinkSync(record);
-    console.log(`restored ${CONSTANT} = "${active.originalVersion}" in ${active.files.length} file(s); override record removed`);
+    console.log(
+      `restored ${CONSTANT} = "${active.originalVersion}" in ${restored} file(s)` +
+        (stale > 0 ? `; ${stale} file(s) had already been replaced by a re-provision` : "") +
+        "; override record removed",
+    );
     return;
   }
 
@@ -155,7 +174,22 @@ function main() {
     console.log(`already ${version} — nothing to do`);
     return;
   }
-  if (active) throw new Error(`an override is already recorded (→ ${active.requestedVersion}); run --disable first`);
+  if (active) {
+    // Re-provisioning rea-agents replaces the tree, so a record can outlive the patch
+    // it describes. That stale record must not block the next --enable, and it must
+    // not be trusted by --disable either: judge it by the files on disk.
+    const stillApplied = active.files.every((entry) => {
+      const file = path.join(vendor, entry.file);
+      if (!existsSync(file)) return false;
+      const text = readFileSync(file, "utf8");
+      return new RegExp(`${CONSTANT}\\s*=\\s*"${entry.patched.replace(/\./g, "\\.")}"`).test(text);
+    });
+    if (stillApplied) {
+      throw new Error(`an override is already recorded (→ ${active.requestedVersion}); run --disable first`);
+    }
+    console.log(`previous record is stale (rea-agents was re-provisioned); replacing it`);
+    unlinkSync(record);
+  }
 
   const files = [];
   for (const entry of declarations) {