sillyspec 3.27.6 → 3.27.9

package/src/index.js

@@ -182,7 +182,7 @@ async function main() {
   }
 
   // E22：重路径统一加载（轻路径 --version/help 已早退，未付此税）。
-  const { ProgressManager, resolvePlatformSpecDir } = await import('./progress.js');
+  const { ProgressManager, resolvePlatformSpecDir, resolvePlatformOpts } = await import('./progress.js');
   const { didYouMean, assertSafeChangeName, resolveSpecDir, detectWorktreeSpecDrift } = await import('./run/shared.js');
 
   // 解析全局选项
@@ -456,7 +456,7 @@ async function main() {
       // 自然报「跨仓 commit 找不到」等错误进入 check.errors，gate 结论仍如实反映问题（D-002@v1 只读契约不破）。
       try {
         const { getOrCreateMultiRepoContext } = await import('./run/shared.js');
-        const _ctx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: gateChange, platformOpts: specDir ? { specRoot: specDir } : {} });
+        const _ctx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: gateChange, platformOpts: { specRoot: gateSpecBase } });
         if (_ctx) gateOpts.ctx = _ctx;
       } catch (e) {
         console.warn(`⚠️ gate ctx 构造失败，降级单仓核验（${e.message}）`);
@@ -509,7 +509,7 @@ async function main() {
       // W3 task-09：derive 同 gate，best-effort 构造 ctx 透传给 verify-test/task-reviews facet（D-013）。
       try {
         const { getOrCreateMultiRepoContext } = await import('./run/shared.js');
-        const _ctx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: deriveChange, platformOpts: specDir ? { specRoot: specDir } : {} });
+        const _ctx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: deriveChange, platformOpts: { specRoot: deriveSpecBase } });
         if (_ctx) deriveOpts.ctx = _ctx;
       } catch (e) {
         console.warn(`⚠️ derive ctx 构造失败，降级单仓核验（${e.message}）`);
@@ -548,9 +548,14 @@ async function main() {
       // 与 run 入口同源消毒（防路径穿越；backfill 下游拼 marker/changes/review 路径）
       assertSafeChangeName(brChange, '--change 变更名');
       const { generateTaskReviewDrafts } = await import('./task-review.js');
-      // --spec-dir 透传 platformOpts.specRoot（与 gate/derive 对称）；不传走默认 join(cwd,'.sillyspec')。
+      // --spec-dir / 平台指针二合一解析（A4 同族，与 register-stage-review case 对称）：此前
+      // 只认显式 --spec-dir，平台模式下 specRoot 缺失 → 草稿/adopt 落本地 join(cwd,'.sillyspec')。
       const brPlatformOpts = {};
-      if (specDir) brPlatformOpts.specRoot = specDir;
+      const brResolved = resolvePlatformOpts(dir, specDir);
+      if (brResolved) {
+        brPlatformOpts.specRoot = brResolved.specRoot;
+        if (brResolved.runtimeRoot) brPlatformOpts.runtimeRoot = brResolved.runtimeRoot;
+      }
       // W3 task-09：best-effort 构造 ctx 透传（D-013），让 task-04 generateTaskReviewDrafts 跨仓 task
       // 用跨仓 gitDir 取 base..head diff。失败降级 null（与 gate/derive 同语义，辅助修复命令不阻断）。
       let _brCtx = null;
@@ -1052,8 +1057,17 @@ async function main() {
       // 与 run 入口同源消毒（防路径穿越；register 下游写 marker、拼 changes/review 路径）
       assertSafeChangeName(rsrChange, '--change 变更名');
       const { registerStageReview } = await import('./stage-review.js');
+      // A4 同族修复（2026-08-26 实证）：此前只认显式 --spec-dir 拼 platformOpts，平台模式
+      // （cwd/.sillyspec-platform.json 指针存在）下 specRoot 缺失 → registerStageReview 落
+      // join(cwd,'.sillyspec')/changes/... 找主审查文档 → 「主审查文档不存在，无法算 docHash」
+      // → 逼 agent 手算 sha256 兜底。改走 resolvePlatformOpts（--spec-dir > 指针 specRoot+
+      // runtimeRoot > 纯本地 null），指针失效 fail-closed 由顶层 catch 优雅引导。
       const rsrPlatformOpts = {};
-      if (specDir) rsrPlatformOpts.specRoot = specDir;
+      const rsrResolved = resolvePlatformOpts(dir, specDir);
+      if (rsrResolved) {
+        rsrPlatformOpts.specRoot = rsrResolved.specRoot;
+        if (rsrResolved.runtimeRoot) rsrPlatformOpts.runtimeRoot = rsrResolved.runtimeRoot;
+      }
       const rsrStages = rsrAll ? ['brainstorm', 'plan', 'execute'] : [rsrStage];
       const rsrResults = [];
       let rsrFailed = 0;
@@ -1260,9 +1274,9 @@ async function main() {
           }
         }
         const { runDocsGate } = await import('./docs-gate.js');
-        // specBase：平台模式（specDir 指针）优先，本地回退 <repo>/.sillyspec——基线文件锚定
+        // specBase：平台指针 / 显式 --spec-dir / 本地 fallback 三合一（A4 同族）——基线文件锚定
         // 进度库根（与 .runtime 同级），跨命令稳定。
-        const gateSpecBase = specDir || join(dir, '.sillyspec');
+        const gateSpecBase = resolvePlatformSpecDir(dir, specDir) || join(dir, '.sillyspec');
         const g = await runDocsGate(
           { projectRoot: dir, specBase: gateSpecBase, initBaseline },
           cliGatePaths ? { paths: cliGatePaths } : undefined
@@ -1459,11 +1473,12 @@ async function main() {
         const { runScanDiff } = await import('./scan-diff.js')
         const diffBaseIdx = filteredArgs.indexOf('--base')
         const diffBase = diffBaseIdx >= 0 && filteredArgs[diffBaseIdx + 1] ? filteredArgs[diffBaseIdx + 1] : null
-        // specBase/projectName 与 scan 主流程同口径（scan-profile.js：specBase=进度库根，projectName=仓库根 basename）
+        // specBase/projectName 与 scan 主流程同口径（scan-profile.js：specBase=进度库根，projectName=仓库根 basename）。
+        // A4 同族：平台指针 / 显式 --spec-dir / 本地 fallback 三合一，平台模式下 diff 不落本地孤儿库。
         const diffEffectiveDir = specDir ? dir : resolveEffectiveDir(dir)
         process.exitCode = runScanDiff({
           projectRoot: diffEffectiveDir,
-          specBase: specDir || join(diffEffectiveDir, '.sillyspec'),
+          specBase: resolvePlatformSpecDir(dir, specDir) || join(diffEffectiveDir, '.sillyspec'),
           projectName: basename(diffEffectiveDir),
           base: diffBase,
           full: filteredArgs.includes('--full'),
@@ -1629,7 +1644,7 @@ SillySpec worktree — git worktree 隔离管理
           let _applyCtx = null;
           try {
             const { getOrCreateMultiRepoContext } = await import('./run/shared.js');
-            _applyCtx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: wtName, platformOpts: specDir ? { specRoot: specDir } : {} });
+            _applyCtx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: wtName, platformOpts: { specRoot: resolvePlatformSpecDir(dir, specDir) } });
           } catch (e) {
             console.error(`❌ apply 失败：跨仓 MultiRepoContext 构造失败（${e.message}）`);
             process.exit(1);
@@ -1677,6 +1692,19 @@ SillySpec worktree — git worktree 隔离管理
             for (const f of result.changedFiles) {
               console.log(`   ${f}`);
             }
+            // 跨仓 worktree 回落报告（坑 cross-repo-no-worktree-isolation）：跨仓文件不进主仓
+            // changedFiles（在其所属仓的 diff 里），单独列出防漏看
+            if (Array.isArray(result.crossRepoApplied) && result.crossRepoApplied.length > 0) {
+              for (const c of result.crossRepoApplied) {
+                if (c.changedFiles.length > 0) {
+                  console.log(`✅ 跨仓 repo ${c.repoKey} 已回落 ${c.changedFiles.length} 个文件变更（worktree 已清理，分支保留作 review 锚点）:`);
+                  for (const f of c.changedFiles.slice(0, 20)) console.log(`   ${f}`);
+                  if (c.changedFiles.length > 20) console.log(`   … 共 ${c.changedFiles.length} 个`);
+                } else {
+                  console.log(`ℹ️ 跨仓 repo ${c.repoKey} 无交付变更（worktree 已清理）`);
+                }
+              }
+            }
             // filterDeliverableFiles 精细化排除（保留 .sillyspec/docs/，排 changes/+.runtime/+quicklog/ + meta.json）：
             // 模块文档（.sillyspec/docs/）= 交付物，会 auto-apply 到主工作区；变更文档/运行时/quicklog 不 apply。
             // 须告知 agent 哪些未落地，否则它期望这些文件落地却找不到（memory: worktree-apply-excludes-module-docs）。
@@ -1713,7 +1741,7 @@ SillySpec worktree — git worktree 隔离管理
           let _assessCtx = null;
           try {
             const { getOrCreateMultiRepoContext } = await import('./run/shared.js');
-            _assessCtx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: wtName, platformOpts: specDir ? { specRoot: specDir } : {} });
+            _assessCtx = await getOrCreateMultiRepoContext({ cwd: dir, changeName: wtName, platformOpts: { specRoot: resolvePlatformSpecDir(dir, specDir) } });
           } catch (e) {
             if (assessment.decision === 'SAFE' || assessment.decision === 'WARNING') {
               console.error(`❌ assess 自动 apply 失败：跨仓 MultiRepoContext 构造失败（${e.message}）`);
@@ -1863,6 +1891,18 @@ SillySpec worktree — git worktree 隔离管理
             // 与并行会话的 apply/cleanup 互踩会互相清——与其他写主仓操作共用一把 main-repo.lock
             const { withMainRepoLock } = await import('./worktree-apply.js');
             const result = await withMainRepoLock(dir, wtName, 'worktree-cleanup', () => wm.cleanup(wtName, { force: forceFlag }));
+            // 跨仓 worktree（坑 cross-repo-no-worktree-isolation）：与主仓同锁清理——跨仓 worktree
+            // 注册在各跨仓仓 .git 内，但目录/meta 在主仓 .sillyspec 运行时区，同样怕并发互踩
+            const { cleanupCrossWorktrees } = await import('./worktree-cross.js');
+            const crossResult = cleanupCrossWorktrees({ cwd: dir, changeName: wtName, specBase: resolvePlatformSpecDir(dir, specDir), force: forceFlag });
+            for (const cr of crossResult.results) {
+              if (cr.result === 'cleaned') {
+                console.log(`✅ 跨仓 worktree 已清理: repo=${cr.repoKey}（${(cr.details || []).filter(d => d.startsWith('分支')).join('；') || '详情见上'}）`);
+              } else if (cr.result === 'partial') {
+                console.error(`🚫 跨仓 repo=${cr.repoKey} 清理受阻：${(cr.details || []).join('; ')}`);
+                for (const r of cr.residual || []) console.error(`   残留: ${r}`);
+              }
+            }
             if (result.result === 'cleaned' || result.result === 'force-cleaned') {
               console.log(`✅ worktree 已清理: ${wtName} (mode: ${result.mode})`);
               if (result.details?.length > 0) {

package/src/module-impact.js

@@ -94,7 +94,7 @@ export function generateModuleImpactSkeleton({ cwd, changeName, specDir = null }
 
   // includeWorkingTree 同 verify module 子集（坑 module-subset-zero-hit-uncommitted）：
   // worktree 未提交改动也计入模块影响面（module-impact 按实际 diff 归属模块）
-  const diffFiles = resolveVerifyChangedFiles(cwd, changeName, null, { includeWorkingTree: true }) || []
+  const diffFiles = resolveVerifyChangedFiles(cwd, changeName, null, { includeWorkingTree: true, specBase }) || []
   const sourceFiles = diffFiles.map(f => f.split('\\').join('/')).filter(f => !f.startsWith('.sillyspec/'))
   if (sourceFiles.length === 0) return null
 

package/src/modules.js

@@ -78,29 +78,27 @@ export async function rebuildModuleMap(cwd, { force = false } = {}) {
   if (existsSync(modulesDir)) {
     const files = readdirSync(modulesDir).filter(f => f.endsWith('.md') && f !== '_module-map.yaml');
     for (const f of files) {
-      const content = readFileSync(join(modulesDir, f), 'utf8');
+      // CRLF 归一：Windows 卡片 \r 会使 parseModuleCardFrontmatter 的 ^---\n 与
+      // extractSection 的 ## <名>\n 失配 → module_id 回退文件名、role 提取恒空
+      const content = readFileSync(join(modulesDir, f), 'utf8').replace(/\r\n/g, '\n');
       const fm = parseModuleCardFrontmatter(content);
       const moduleId = fm.module_id || parseModuleIdFromFilename(f);
       cards.push({ filename: f, moduleId, content });
     }
   }
 
-  // 解析现有 _module-map.yaml 保留已有字段
+  // 解析现有 _module-map.yaml 保留已有字段（复用 parseModuleMapSimple：原内置解析只收模块名、
+  // 从不收集列表项 → existingPaths 恒空 → --force 重建后 core_files 全丢，scan-diff scope 退化
+  // 为全量、module-impact classifyFile 全 unmatched——注释声称的「从已有 map 保留」名存实亡）
   let existingModules = {};
   if (existingMap) {
-    // 简单解析：提取 modules: 下的条目
-    const lines = existingMap.split('\n');
-    let currentModule = null;
-    let inModules = false;
-    for (const line of lines) {
-      if (line.startsWith('modules:')) { inModules = true; continue; }
-      if (!inModules) continue;
-      if (line.startsWith('  ') === false && line.trim() !== '') break;
-      const moduleMatch = line.match(/^  ([a-zA-Z0-9_-]+):/);
-      if (moduleMatch) {
-        currentModule = moduleMatch[1];
-        existingModules[currentModule] = existingModules[currentModule] || { paths: [] };
-      }
+    const parsed = parseModuleMapSimple(existingMap);
+    for (const [id, fields] of Object.entries(parsed || {})) {
+      existingModules[id] = {
+        core_files: Array.isArray(fields.core_files) ? fields.core_files : [],
+        test_files: Array.isArray(fields.test_files) ? fields.test_files : [],
+        entrypoints: Array.isArray(fields.entrypoints) ? fields.entrypoints : [],
+      };
     }
   }
 
@@ -152,11 +150,13 @@ export async function rebuildModuleMap(cwd, { force = false } = {}) {
     yaml += `    review_reasons: []\n`;
     // context index 字段（v2）
     if (role) yaml += `    role: "${escapeYamlString(role)}"\n`;
-    // core_files / test_files / entrypoints 从已有 _module-map 保留，或从卡片文件名推导
-    const existingPaths = existingModules[moduleId]?.paths || [];
-    if (existingPaths.length > 0) {
-      yaml += `    core_files:\n`;
-      for (const p of existingPaths) yaml += `      - ${p}\n`;
+    // core_files / test_files / entrypoints 从已有 _module-map.yaml 全量保留（列表项级保真）
+    const existing = existingModules[moduleId] || {};
+    for (const [field, items] of [['core_files', existing.core_files], ['test_files', existing.test_files], ['entrypoints', existing.entrypoints]]) {
+      if (Array.isArray(items) && items.length > 0) {
+        yaml += `    ${field}:\n`;
+        for (const p of items) yaml += `      - ${p}\n`;
+      }
     }
     if (card) yaml += `    verify_commands: []\n`;
     yaml += `    risk_level: low\n`;
@@ -383,7 +383,9 @@ export function parseModuleMapSimple(content) {
   let currentArray = null;
 
   for (const line of content.split('\n')) {
-    const moduleMatch = line.match(/^  ([a-zA-Z0-9_-]+):$/);
+    // 模块 id 字符集含点（db.engine 等，与 module-impact.js classifyFile 同口径）：
+    // 不含点时带点 id 的条目被静默丢弃，上下文注入/scan-diff 侧与 module-impact 侧给相反结论
+    const moduleMatch = line.match(/^  ([a-zA-Z0-9_.\-]+):$/);
     if (moduleMatch) {
       if (currentArray && currentModule && currentKey) {
         modules[currentModule][currentKey] = currentArray;

package/src/progress/stage-machine.js

@@ -9,6 +9,20 @@ import { writeAtomicSync } from '../fs-atomic.js';
 import { runValidators } from '../stage-contract.js';
 import { VALID_STAGES, STAGE_LABELS, STAGE_ORDER, MAIN_FLOW_ORDER, SPEC_DIR_NAME, CURRENT_VERSION, emptyStage } from './shared.js';
 
+/**
+ * 归一化步骤的已记录等待回答（show 渲染用，跨会话恢复数据源）。
+ * waitAnswers 走 pm.read 时已 JSON.parse，但容错字符串/损坏；单值列 wait_answer（旧路径）并入第 1 轮。
+ */
+function _stepWaitRounds(step) {
+  let arr = step.waitAnswers;
+  if (typeof arr === 'string') { try { arr = JSON.parse(arr); } catch { arr = null; } }
+  const rounds = Array.isArray(arr) ? arr.filter(r => r && typeof r.answer === 'string' && r.answer.trim() !== '') : [];
+  if (rounds.length === 0 && typeof step.waitAnswer === 'string' && step.waitAnswer.trim() !== '') {
+    return [{ round: 1, answer: step.waitAnswer }];
+  }
+  return rounds.map((r, i) => ({ round: typeof r.round === 'number' ? r.round : i + 1, answer: r.answer }));
+}
+
 export class StageMachine {
   constructor(pm) {
     this.pm = pm;
@@ -245,6 +259,15 @@ export class StageMachine {
             if (step.waitOptions) console.log(`       选项：${(() => { try { const p = JSON.parse(step.waitOptions); return Array.isArray(p) ? p.join(', ') : step.waitOptions; } catch { return step.waitOptions; }})()}`);
             if (step.waitedAt) console.log(`       等待时间：${step.waitedAt}`);
           }
+          // 已记录的历史回答（等待中/已完成步骤都可能累积多轮；续跑时由 outputStep 自动回放，
+          // 此处摘要供人工排查「中断后哪些用户回答还在」）。每轮截断 120 字，全文在进度库 wait_answers。
+          const rounds = _stepWaitRounds(step);
+          if (rounds.length > 0) {
+            console.log(`       历史回答（${rounds.length} 轮，续跑自动回放）：`);
+            for (const r of rounds) {
+              console.log(`         第${r.round}轮: ${r.answer.length > 120 ? r.answer.slice(0, 120) + '…' : r.answer}`);
+            }
+          }
         }
       }
 
@@ -326,7 +349,9 @@ export class StageMachine {
             command: `sillyspec run ${s} --continue --answer "用户回答"${cc}`,
           };
         }
-        const hasPending = sd.steps.some(st => ['pending', 'waiting', 'failed'].includes(st.status));
+        // blocked（deps/review.json 门控阻断标记）也计入待办（坑 deps-gate-blocked-invisible）：
+        // 漏计会让全局「下一步」建议跳过被阻断的阶段/步骤，误导 agent 去跑更后面的阶段。
+        const hasPending = sd.steps.some(st => ['pending', 'waiting', 'failed', 'blocked'].includes(st.status));
         if (hasPending) {
           return {
             text: `${STAGE_LABELS[s] || s} 进行中，继续执行下一步。`,

package/src/progress.js

@@ -25,8 +25,7 @@ import { STAGE_ORDER, MAIN_FLOW_ORDER, VALID_STAGES, STAGE_LABELS, SPEC_DIR_NAME
 // resolveSpecDir 单一真相源在 src/run/shared.js（含 home 拒绝守卫，坑 cwd-correction-home-collision
 // 根治：home 下 .sillyspec 恒不命中，防 smoke/临时目录污染自我延续）。此处 re-export 保持
 // 既有 import 路径兼容；run/shared.js 对 progress.js 只有动态 import，无静态循环。
-import { resolveSpecDir } from './run/shared.js';
-import { checkPlatformManaged, PLATFORM_MANAGED_FILENAME } from './run/shared.js';
+import { resolveSpecDir, checkPlatformManaged, PLATFORM_MANAGED_FILENAME, isSelfReferentialSpecRoot } from './run/shared.js';
 export { resolveSpecDir };
 
 // 默认规范目录名（相对于 cwd）
@@ -145,6 +144,43 @@ export function resolvePlatformSpecDir(cwd, explicitSpecDir = null) {
   return ptr.specRoot;
 }
 
+/**
+ * resolvePlatformSpecDir 的 platformOpts 版本：除 specRoot 外连 runtimeRoot 一起恢复。
+ *
+ * 供 register-stage-review / backfill-reviews 等需要拼 runtime 路径（marker、stage-reviews、
+ * execute-runs）的顶层子命令使用——此前这些 case 只认显式 --spec-dir，平台模式（指针存在）
+ * 下 specRoot 缺失 → 下游回退 join(cwd,'.sillyspec')，在项目本地找 design.md 报「主审查文档
+ * 不存在」，逼 agent 手算 docHash 兜底（2026-08-26 实证）。
+ *
+ * 语义（与 resolvePlatformSpecDir / runCommand 恢复链对齐）：
+ *   - 显式 --spec-dir：{ specRoot: resolve(显式), runtimeRoot: null }（runtimeRoot 走
+ *     resolveRuntimeRoot 默认 specRoot/.runtime）；
+ *   - 无指针：调一次 resolvePlatformSpecDir 保留接管声明 fail-closed（声明存在 →
+ *     PlatformManagedError 上抛），随后返回 null = 纯本地，调用方 platformOpts 保持空；
+ *   - 有指针：specRoot 经 resolvePlatformSpecDir 全量校验（损坏/缺字段/不可达 →
+ *     PointerUnreachableError 上抛），另读指针 runtimeRoot；自指回环（repo-native junction）
+ *     忽略指针返回 null（对齐 run/command.js:326 恢复链免疫）。
+ *
+ * @param {string} cwd 项目根
+ * @param {string|null} [explicitSpecDir] 显式 --spec-dir
+ * @returns {{ specRoot: string, runtimeRoot: string|null } | null} null = 纯本地（不设 specRoot）
+ */
+export function resolvePlatformOpts(cwd, explicitSpecDir = null) {
+  if (explicitSpecDir) return { specRoot: resolve(explicitSpecDir), runtimeRoot: null }
+  const pointerPath = join(resolve(cwd), '.sillyspec-platform.json')
+  const hasPointer = existsSync(pointerPath)
+  // 无指针也先过 resolvePlatformSpecDir：接管声明存在时它负责 fail-closed 上抛
+  const specRoot = resolvePlatformSpecDir(cwd, null)
+  if (!hasPointer) return null
+  if (isSelfReferentialSpecRoot(cwd, specRoot)) return null
+  let runtimeRoot = null
+  try {
+    runtimeRoot = JSON.parse(readFileSync(pointerPath, 'utf8')).runtimeRoot || null
+  } catch { /* specRoot 校验已在 resolvePlatformSpecDir 内做过，此处仅补读字段 */
+  }
+  return { specRoot, runtimeRoot }
+}
+
 const CHANGES_SUBDIR = 'changes';
 // CURRENT_VERSION → ./progress/shared.js（W6 Step9d）
 // VALID_STAGES → ./progress/shared.js（W6 Step9c）

package/src/quicklog.js

@@ -813,7 +813,7 @@ export async function cancelQuickSession({ specBase, gitUser, qlId, sessionId =
       const content = existsSync(p) ? readFileSync(p, 'utf8') : ''
       if (!content.includes(`## ${qlId} |`)) continue
       quicklogFile = p
-      const lines = content.split('\n')
+      const lines = content.split(/\r?\n/)
       const startIdx = lines.findIndex(l => l.startsWith(`## ${qlId} |`))
       let endIdx = lines.length
       for (let i = startIdx + 1; i < lines.length; i++) {
@@ -832,8 +832,10 @@ export async function cancelQuickSession({ specBase, gitUser, qlId, sessionId =
         }
       }
       if (flipped) {
+        // split(/\r?\n/) 吃掉行尾 \r 再按原 eol join：旧写法 split('\n') 保留 \r 又 join('\r\n')
+        // 会产出 \r\r\n 字节级污染（git diff 全文件红）；原子写防 agent/dashboard 轮询读半截
         const eol = content.includes('\r\n') ? '\r\n' : '\n'
-        writeFileSync(p, lines.join(eol === '\r\n' ? '\r\n' : '\n'))
+        await writeAtomic(p, lines.join(eol))
       }
       break
     }
@@ -849,10 +851,10 @@ export async function cancelQuickSession({ specBase, gitUser, qlId, sessionId =
       if (!c.isDirectory() || c.name === 'archive') continue
       const tp = tasksPath(specBase, c.name)
       if (!existsSync(tp)) continue
-      await withFileLock(tasksLockPath(tp), () => {
+      await withFileLock(tasksLockPath(tp), async () => {
         const content = readFileSync(tp, 'utf8')
         if (!content.includes(qlId)) return
-        const lines = content.split('\n')
+        const lines = content.split(/\r?\n/)
         const kept = lines.filter(l => {
           const m = l.match(/^[-*]\s*\[([ xX])\]\s*(\S+)/)
           if (m && m[2] === qlId) {
@@ -864,7 +866,7 @@ export async function cancelQuickSession({ specBase, gitUser, qlId, sessionId =
         })
         if (kept.length !== lines.length) {
           const eol = content.includes('\r\n') ? '\r\n' : '\n'
-          writeFileSync(tp, kept.join(eol === '\r\n' ? '\r\n' : '\n'))
+          await writeAtomic(tp, kept.join(eol))
         }
       })
     }

package/src/run/command.js

@@ -23,9 +23,9 @@ import { basename, join, resolve, dirname } from 'node:path'
 import { existsSync, readdirSync, mkdirSync, writeFileSync, readFileSync, rmSync } from 'node:fs'
 import { randomBytes, randomUUID } from 'node:crypto'
 import { writeAtomicSync } from '../fs-atomic.js'
-import { resolveSpecDir, countAncestorSpecDirs, resolveChangeDir, triggerSync, getStageSteps, formatWaitOptions, checkApproval, warnApprovalUnknown, didYouMean, assertSafeChangeName, detectQuickSessionDrift, detectWorktreeSpecDrift, resolveRuntimeRoot, writePlatformPointer, checkPlatformManaged, isSelfReferentialSpecRoot, PLATFORM_MANAGED_FILENAME } from './shared.js'
+import { resolveSpecDir, countAncestorSpecDirs, ancestorSpecDirs, resolveAncestorCeiling, resolveChangeDir, triggerSync, getStageSteps, formatWaitOptions, checkApproval, warnApprovalUnknown, didYouMean, assertSafeChangeName, detectQuickSessionDrift, detectWorktreeSpecDrift, resolveRuntimeRoot, writePlatformPointer, checkPlatformManaged, isSelfReferentialSpecRoot, PLATFORM_MANAGED_FILENAME } from './shared.js'
 import { resolveQuickLinkedChanges } from './quick-audit.js'
-import { outputStep } from './prompt.js'
+import { outputStep, collectStageWaitHistory } from './prompt.js'
 import { completeStep, skipStep, waitStep, continueStep } from './complete.js'
 import { runStage } from './stage.js'
 import { sanitizeDesc } from '../quicklog.js'
@@ -385,14 +385,26 @@ export async function runCommand(args, cwd, specDir = null, opts = {}) {
   // let：下方 worktree 副本漂移守卫命中时锚回 wt.mainSpecBase（task-05/D-03）
   let specBase = platformOpts.specRoot || join(cwd, '.sillyspec')
 
-  // 漂移提醒:cwd 祖先链 ≥2 个 .sillyspec = monorepo 多实例,当前命中的「最近」实例
+  // 漂移阻断:cwd 祖先链 ≥2 个 .sillyspec = monorepo 多实例,当前命中的「最近」实例
   // 可能不是用户意图的项目(如 cd 进被独立 scan 的子项目跑测试后忘回根)。
-  // 平台模式 / 显式 --spec-dir 跳过(已明确指定,无歧义)。仅提醒不阻断。
+  // 平台模式 / 显式 --spec-dir 跳过(已明确指定,无歧义)。
+  // 当前实例 ≠ git 顶层仓库实例 → 默认拒绝(坑 monorepo-cwd-wrong-spec-instance)。
   if (!platformOpts.specRoot && !specDir) {
-    const ancestorCount = countAncestorSpecDirs(cwd)
-    if (ancestorCount >= 2) {
-      console.warn(`⚠️  检测到祖先链有 ${ancestorCount} 个 .sillyspec 实例(monorepo 多实例),当前使用: ${specBase}`)
-      console.warn(`    若意图是另一个项目:cd 回该项目根,或用 --spec-dir <根>/.sillyspec 显式指定。`)
+    const ancestorSpecs = ancestorSpecDirs(cwd)
+    if (ancestorSpecs.length >= 2) {
+      // 判断当前命中的 .sillyspec 是否在 git 顶层仓库根下
+      const gitRoot = resolveAncestorCeiling(resolve(cwd))
+      const currentSpecParent = dirname(resolve(specBase))
+      const isAtGitRoot = gitRoot && resolve(currentSpecParent) === resolve(gitRoot)
+      if (!isAtGitRoot) {
+        console.error(`❌ 检测到祖先链有 ${ancestorSpecs.length} 个 .sillyspec 实例(monorepo 多实例)，当前使用: ${specBase}`)
+        console.error(`   当前 cwd 不在 git 顶层仓库根下，静默绑定到子项目实例会导致进度/QUICKLOG 分裂。`)
+        console.error(`   修复：cd 回项目根目录，或用 --spec-dir <根>/.sillyspec 显式指定。`)
+        process.exit(2)
+      }
+      // 在 git 根下但有多实例(子项目也有 .sillyspec)→ 仅警告(正确实例已命中)
+      console.warn(`⚠️  检测到祖先链有 ${ancestorSpecs.length} 个 .sillyspec 实例(monorepo 多实例)，当前使用: ${specBase}`)
+      console.warn(`    当前已绑定 git 顶层仓库实例。若意图是子项目:用 --spec-dir 显式指定。`)
     }
   }
 
@@ -896,9 +908,9 @@ export async function runCommand(args, cwd, specDir = null, opts = {}) {
     if (readonlySteps && readonlySteps.length > 0) {
       // 已有进度（历史 seed 过）则渲染当前待办步；无进度从首步开始
       const existingSteps = progress.stages?.[stageName]?.steps
-      const pendingIdx = existingSteps ? existingSteps.findIndex(s => s.status === 'pending' || s.status === 'in-progress') : -1
+      const pendingIdx = existingSteps ? existingSteps.findIndex(s => s.status === 'pending' || s.status === 'in-progress' || s.status === 'blocked') : -1
       const stepIdx = pendingIdx !== -1 ? pendingIdx : 0
-      await outputStep(stageName, stepIdx, readonlySteps, cwd, readOnlyChange, progress.project || null, platformOpts)
+      await outputStep(stageName, stepIdx, readonlySteps, cwd, readOnlyChange, progress.project || null, platformOpts, null, collectStageWaitHistory(progress, stageName))
     }
     return
   }
@@ -1295,7 +1307,7 @@ function showStatus(progress, stageName, nextSuggestion = null) {
 
   console.log('')
 
-  const firstPending = steps.findIndex(s => s.status === 'pending' || s.status === 'in-progress')
+  const firstPending = steps.findIndex(s => s.status === 'pending' || s.status === 'in-progress' || s.status === 'blocked')
 
   if (progress.batchProgress) {
     const bp = progress.batchProgress
@@ -1314,10 +1326,13 @@ function showStatus(progress, stageName, nextSuggestion = null) {
   }
 
   steps.forEach((step, i) => {
-    const icon = step.status === 'completed' ? '✅' : step.status === 'skipped' ? '⏭️' : step.status === 'waiting' ? '⏸️' : '⬜'
-    const isCurrent = (step.status === 'pending' || step.status === 'in-progress') && i === firstPending
+    const icon = step.status === 'completed' ? '✅' : step.status === 'skipped' ? '⏭️' : step.status === 'waiting' ? '⏸️' : step.status === 'blocked' ? '🚫' : '⬜'
+    const isCurrent = (step.status === 'pending' || step.status === 'in-progress' || step.status === 'blocked') && i === firstPending
     const isWaiting = step.status === 'waiting'
-    console.log(`${icon} Step ${i + 1}: ${step.name}${isCurrent ? ' ← 当前' : ''}${isWaiting ? ' [WAITING]' : ''}`)
+    console.log(`${icon} Step ${i + 1}: ${step.name}${isCurrent ? ' ← 当前' : ''}${isWaiting ? ' [WAITING]' : ''}${step.status === 'blocked' ? ' [BLOCKED]' : ''}`)
+    if (step.status === 'blocked') {
+      console.log(`       此前被门控阻断——${step.blockReason || 'deps 未就绪 / review.json 不完整'}；修复后重跑 --done 即恢复，无需 --reset`)
+    }
     if (isWaiting) {
       if (step.waitReason) console.log(`       原因：${step.waitReason}`)
       if (step.waitOptions) console.log(`       选项：${formatWaitOptions(step.waitOptions)}`)
@@ -1355,6 +1370,22 @@ async function resetStage(pm, progress, stageName, cwd, changeName, platformOpts
     } catch (e) {
       console.warn(`⚠️  reset 清理 worktree 失败（不阻断 reset）: ${e.message}`)
     }
+    // 跨仓 worktree 一并清理（坑 cross-repo-no-worktree-isolation）：否则下次 execute 因 meta
+    // 存在复用带脏状态的旧跨仓 worktree
+    try {
+      const { cleanupCrossWorktrees } = await import('../worktree-cross.js')
+      const cross = cleanupCrossWorktrees({
+        cwd, changeName,
+        specBase: platformOpts?.specRoot || join(cwd, '.sillyspec'),
+        force: true,
+      })
+      for (const cr of cross.results) {
+        if (cr.result === 'cleaned') console.log(`🧹 已清理跨仓 worktree repo=${cr.repoKey}，下次 execute 将重建`)
+        else if (cr.result === 'partial') console.warn(`⚠️ 跨仓 repo=${cr.repoKey} 清理残留: ${(cr.details || []).join('; ')} ${(cr.residual || []).join('; ')}`)
+      }
+    } catch (e) {
+      console.warn(`⚠️  reset 清理跨仓 worktree 失败（不阻断 reset）: ${e.message}`)
+    }
   }
   const defSteps = await getStageSteps(stageName, cwd, progress, platformOpts?.specRoot || null)
   progress.stages[stageName] = {
@@ -1484,7 +1515,7 @@ async function runAutoMode(pm, progress, cwd, flags, changeName, platformOpts =
     console.log('')
 
     const defSteps = await getAutoSteps(currentStage)
-    const pendingIdx = progress.stages[currentStage]?.steps?.findIndex(step => step.status === 'pending' || step.status === 'in-progress') ?? -1
+    const pendingIdx = progress.stages[currentStage]?.steps?.findIndex(step => step.status === 'pending' || step.status === 'in-progress' || step.status === 'blocked') ?? -1
     if (pendingIdx === -1) {
       const wsIdx = progress.stages[currentStage]?.steps?.findIndex(step => step.status === 'waiting') ?? -1
       if (wsIdx !== -1) {
@@ -1517,7 +1548,7 @@ async function runAutoMode(pm, progress, cwd, flags, changeName, platformOpts =
         }
       }
     }
-    await outputStep(currentStage, pendingIdx, defSteps, cwd, changeName, progress.project || null, platformOpts)
+    await outputStep(currentStage, pendingIdx, defSteps, cwd, changeName, progress.project || null, platformOpts, null, collectStageWaitHistory(progress, currentStage))
     return
   }
 
@@ -1536,7 +1567,7 @@ async function runAutoMode(pm, progress, cwd, flags, changeName, platformOpts =
     return
   }
 
-  const nextPendingIdx = progress.stages[currentStage]?.steps?.findIndex(step => step.status === 'pending' || step.status === 'in-progress') ?? -1
+  const nextPendingIdx = progress.stages[currentStage]?.steps?.findIndex(step => step.status === 'pending' || step.status === 'in-progress' || step.status === 'blocked') ?? -1
   if (nextPendingIdx !== -1) {
     const defSteps = await getAutoSteps(currentStage)
     // execute 阶段启动前检查审批
@@ -1557,7 +1588,7 @@ async function runAutoMode(pm, progress, cwd, flags, changeName, platformOpts =
         }
       }
     }
-    await outputStep(currentStage, nextPendingIdx, defSteps, cwd, changeName, progress.project || null, platformOpts)
+    await outputStep(currentStage, nextPendingIdx, defSteps, cwd, changeName, progress.project || null, platformOpts, null, collectStageWaitHistory(progress, currentStage))
     return
   }
 
@@ -1615,7 +1646,7 @@ async function runAutoMode(pm, progress, cwd, flags, changeName, platformOpts =
 
   console.log(`\n${currentStage} complete. Auto advanced to ${next}.`)
   const nextSteps = await getAutoSteps(next)
-  const firstPending = progress.stages[next]?.steps?.findIndex(step => step.status === 'pending' || step.status === 'in-progress') ?? -1
+  const firstPending = progress.stages[next]?.steps?.findIndex(step => step.status === 'pending' || step.status === 'in-progress' || step.status === 'blocked') ?? -1
   if (firstPending !== -1) {
     // execute 阶段启动前检查审批
     if (next === 'execute' && !skipApproval) {
@@ -1635,7 +1666,7 @@ async function runAutoMode(pm, progress, cwd, flags, changeName, platformOpts =
         }
       }
     }
-    await outputStep(next, firstPending, nextSteps, cwd, changeName, progress.project || null, platformOpts)
+    await outputStep(next, firstPending, nextSteps, cwd, changeName, progress.project || null, platformOpts, null, collectStageWaitHistory(progress, next))
   }
 }
 

package/src/run/complete-handlers.js

@@ -25,6 +25,7 @@
 import { basename, join, resolve, relative, isAbsolute } from 'node:path'
 import { existsSync, readdirSync, readFileSync, writeFileSync, mkdirSync, unlinkSync, rmSync } from 'node:fs'
 import { renameSyncRetry, writeAtomicSync } from '../fs-atomic.js'
+import { gitQuiet } from '../git-helper.js'
 import { resolveChangeDir, resolveQuickSessionsDir, safeGit, auditQuickCompletion, triggerSync, isQuickMetadata, resolveRuntimeRoot, collectOtherQuickSessionDeclarations } from './shared.js'
 import { detectConcurrentChanges, formatConcurrentWarning, resolveConcurrentAnchor } from './concurrent-detect.js'
 import { stageRegistry } from '../stages/index.js'
@@ -1213,7 +1214,7 @@ export async function closeQuickLinkedChanges({ pm, cwd, specBase, linkedChanges
  * ctx：stageName/steps/currentIdx/changeName/specBase/cwd。extractArtifactsForChange ← 动态 ../contract-matrix.js，
  * WorktreeManager ← 动态 ../worktree.js（真环依赖保留动态）。
  */
-export async function handleExecuteWaveArtifact({ stageName, steps, currentIdx, changeName, specBase, cwd }) {
+export async function handleExecuteWaveArtifact({ stageName, steps, currentIdx, changeName, specBase, cwd, platformOpts }) {
   if (stageName === 'execute' && /^Wave \d+ 执行$/.test(steps[currentIdx]?.name || '')) {
     try {
       const { extractArtifactsForChange } = await import('../contract-matrix.js')
@@ -1223,7 +1224,10 @@ export async function handleExecuteWaveArtifact({ stageName, steps, currentIdx,
         const meta = new WorktreeManager({ cwd }).getMeta(changeName)
         if (meta?.worktreePath && existsSync(meta.worktreePath)) worktreePath = meta.worktreePath
       } catch {}
-      const msg = extractArtifactsForChange({ changeDir: join(specBase, 'changes', changeName), specBase, changeName, worktreePath })
+      // 写侧与读侧（gates.js verify parity / prompt.js consumer 注入）同走 resolveRuntimeRoot：
+      // 平台模式 runtimeRoot ≠ specBase/.runtime，分裂时 artifact 写一处读另一处恒空
+      const runtimeRoot = resolveRuntimeRoot(platformOpts || {}, specBase)
+      const msg = extractArtifactsForChange({ changeDir: join(specBase, 'changes', changeName), specBase, changeName, worktreePath, runtimeRoot })
       if (msg) console.log(msg)
     } catch (e) { console.warn(`⚠️ 契约 artifact 提取跳过: ${e?.message || e}`) }
   }
@@ -1381,6 +1385,26 @@ export async function handleExecuteWorktreeCleanup({ stageName, changeName, cwd
     } catch (e) {
       console.warn(`🔗 Worktree: check failed — ${e.message}`);
     }
+    // 跨仓 worktree（坑 cross-repo-no-worktree-isolation）：execute 完成时不自动清——交付还在
+    // 跨仓 worktree 分支上未回落主工作副本，与主仓「pending apply」同语义，报状态 + 下一步指引
+    try {
+      const { listCrossWorktreeMetas } = await import('../worktree-cross.js')
+      const specBase = join(cwd, '.sillyspec')
+      for (const { repoKey, meta: cm } of listCrossWorktreeMetas(specBase, changeName)) {
+        let pending = 0
+        try {
+          const d = safeGit(cm.worktreePath, ['diff', '--name-only', cm.baseHash], { timeout: 30000 })
+          const u = safeGit(cm.worktreePath, ['ls-files', '--others', '--exclude-standard'], { timeout: 30000 })
+          pending = ((d.value || '') + '\n' + (u.value || '')).split('\n').filter(Boolean).length
+        } catch { /* 状态探测失败按未知处理 */ }
+        if (pending > 0) {
+          console.log(`🔗 跨仓 worktree repo=${repoKey}: pending apply (${pending} 个未回落变更)`)
+          console.log(`   下一步: sillyspec worktree apply ${changeName}（跨仓与主仓一并回落）`)
+        } else {
+          console.log(`🔗 跨仓 worktree repo=${repoKey}: 无未回落变更（apply 时将自动清理）`)
+        }
+      }
+    } catch { /* 跨仓状态报告 best-effort */ }
   }
   return null
 }