@mison/ling 1.0.2 → 1.1.1

package/bin/{ag-kit.js → ling-cli.js}

@@ -5,19 +5,17 @@ const os = require("os");
 const path = require("path");
 
 const pkg = require("../package.json");
-const { readGlobalNpmDependencies, cloneBranchAgentDir } = require("./utils");
+const { readGlobalNpmDependencies, cloneBranchAgentDir, cloneBranchSpecDir } = require("./utils");
 const ManifestManager = require("./utils/manifest");
 const AtomicWriter = require("./utils/atomic-writer");
 const CodexBuilder = require("./core/builder");
 const GeminiAdapter = require("./adapters/gemini");
 const CodexAdapter = require("./adapters/codex");
-const { selectTargets } = require("./interactive");
+const { selectTargets, createConflictPrompter } = require("./interactive");
 
 const BUNDLED_AGENT_DIR = path.resolve(__dirname, "../.agents");
 const BUNDLED_SPEC_DIR = path.resolve(__dirname, "../.spec");
 const PRIMARY_CLI_NAME = "ling";
-const LEGACY_CLI_NAME = "ag-kit";
-const CURRENT_CLI_BASENAME = path.basename(process.argv[1] || "", path.extname(process.argv[1] || "")) || PRIMARY_CLI_NAME;
 const WORKSPACE_INDEX_VERSION = 2;
 const UPSTREAM_GLOBAL_PACKAGE = "@vudovn/ag-kit";
 const TOOLKIT_PACKAGE_NAMES = new Set(["@mison/ling", "@mison/ag-kit-cn", "antigravity-kit-cn", "antigravity-kit"]);
@@ -57,6 +55,9 @@ const QUIET_STATUS_EXIT_CODES = {
 const SPEC_STATE_VERSION = 1;
 const SPEC_SKILL_NAMES = ["harness-engineering", "cybernetic-systems-engineering"];
 const VERSION_TAG_PREFIX = "ling-";
+const SPEC_TEMPLATE_REQUIRED_FILES = ["issues.template.csv", "driver-prompt.md", "review-report.md", "phase-acceptance.md", "handoff.md"];
+const SPEC_REFERENCE_REQUIRED_FILES = ["README.md", "harness-engineering-digest.md", "gda-framework.md", "cse-quickstart.md"];
+const SPEC_PROFILE_REQUIRED_FILES = ["codex/AGENTS.spec.md", "codex/ling.spec.rules.md", "gemini/GEMINI.spec.md"];
 
 function nowISO() {
     return new Date().toISOString();
@@ -67,36 +68,11 @@ function getVersionTag() {
 }
 
 function getControlHomeDir() {
-    const preferred = path.join(os.homedir(), ".ling");
-    const legacy = path.join(os.homedir(), ".ag-kit");
-
-    if (fs.existsSync(preferred)) {
-        return preferred;
-    }
-    if (fs.existsSync(legacy)) {
-        return legacy;
-    }
-    return preferred;
-}
-
-function migrateLegacyControlHomeDir() {
-    if (process.env.LING_INDEX_PATH || process.env.AG_KIT_INDEX_PATH) {
-        return null;
-    }
-
-    const preferred = path.join(os.homedir(), ".ling");
-    const legacy = path.join(os.homedir(), ".ag-kit");
-
-    if (fs.existsSync(preferred) || !fs.existsSync(legacy)) {
-        return null;
-    }
-
-    copyDirRecursive(legacy, preferred);
-    return { from: legacy, to: preferred };
+    return path.join(os.homedir(), ".ling");
 }
 
 function getWorkspaceIndexPath() {
-    const customPath = process.env.LING_INDEX_PATH || process.env.AG_KIT_INDEX_PATH;
+    const customPath = process.env.LING_INDEX_PATH;
     if (customPath) {
         return path.resolve(process.cwd(), customPath);
     }
@@ -113,7 +89,7 @@ function createEmptyWorkspaceIndex() {
 }
 
 function resolveGlobalRootDir() {
-    const customRoot = process.env.LING_GLOBAL_ROOT || process.env.AG_KIT_GLOBAL_ROOT;
+    const customRoot = process.env.LING_GLOBAL_ROOT;
     if (typeof customRoot === "string" && customRoot.trim()) {
         return path.resolve(process.cwd(), customRoot);
     }
@@ -156,6 +132,22 @@ function copyDirRecursive(src, dest) {
     }
 }
 
+function backupWorkspaceDir(workspaceRoot, sourceDir, backupRootName, timestamp, options, label) {
+    if (!fs.existsSync(sourceDir)) {
+        return "";
+    }
+    const assetName = path.basename(sourceDir) || "asset";
+    const backupDir = path.join(workspaceRoot, backupRootName, timestamp, "preflight", assetName);
+    if (options.dryRun) {
+        log(options, `[dry-run] 将备份 ${label}: ${sourceDir} -> ${backupDir}`);
+        return backupDir;
+    }
+    fs.mkdirSync(path.dirname(backupDir), { recursive: true });
+    copyDirRecursive(sourceDir, backupDir);
+    log(options, `[backup] 已备份 ${label}: ${sourceDir} -> ${backupDir}`);
+    return backupDir;
+}
+
 function areDirectoriesEqual(leftDir, rightDir) {
     const left = ManifestManager.generateFromDir(leftDir);
     const right = ManifestManager.generateFromDir(rightDir);
@@ -183,6 +175,8 @@ function printUsage() {
     console.log(`  ${PRIMARY_CLI_NAME} spec enable [--target <name>|--targets <a,b>] [--quiet] [--dry-run]`);
     console.log(`  ${PRIMARY_CLI_NAME} spec disable [--target <name>|--targets <a,b>] [--quiet] [--dry-run]`);
     console.log(`  ${PRIMARY_CLI_NAME} spec status [--quiet]`);
+    console.log(`  ${PRIMARY_CLI_NAME} spec init [--path <dir>] [--target <name>|--targets <a,b>] [--branch <name>] [--force] [--non-interactive] [--no-index] [--quiet] [--dry-run]`);
+    console.log(`  ${PRIMARY_CLI_NAME} spec doctor [--path <dir>] [--quiet]`);
     console.log(`  ${PRIMARY_CLI_NAME} exclude list [--quiet]`);
     console.log(`  ${PRIMARY_CLI_NAME} exclude add --path <dir> [--dry-run] [--quiet]`);
     console.log(`  ${PRIMARY_CLI_NAME} exclude remove --path <dir> [--dry-run] [--quiet]`);
@@ -301,6 +295,8 @@ const COMMAND_ALLOWED_FLAGS = {
     "spec:enable": ["--target", "--targets", "--quiet", "--dry-run"],
     "spec:disable": ["--target", "--targets", "--quiet", "--dry-run"],
     "spec:status": ["--quiet"],
+    "spec:init": ["--force", "--path", "--branch", "--target", "--targets", "--non-interactive", "--no-index", "--quiet", "--dry-run"],
+    "spec:doctor": ["--path", "--quiet"],
     "exclude:list": ["--quiet"],
     "exclude:add": ["--path", "--dry-run", "--quiet"],
     "exclude:remove": ["--path", "--dry-run", "--quiet"],
@@ -428,10 +424,10 @@ function isPathExcludedByList(excludedPaths, workspacePath) {
 
 function isToolkitSourceDirectory(workspacePath) {
     const packageJsonPath = path.join(workspacePath, "package.json");
-    const legacyCliPath = path.join(workspacePath, "bin", "ag-kit.js");
+    const cliPath = path.join(workspacePath, "bin", "ling-cli.js");
     const primaryCliPath = path.join(workspacePath, "bin", "ling.js");
 
-    if (!fs.existsSync(packageJsonPath) || (!fs.existsSync(legacyCliPath) && !fs.existsSync(primaryCliPath))) {
+    if (!fs.existsSync(packageJsonPath) || (!fs.existsSync(cliPath) && !fs.existsSync(primaryCliPath))) {
         return false;
     }
 
@@ -856,7 +852,7 @@ function maybeWarnUpstreamGlobalConflict(command, options) {
     if (options.quiet) {
         return;
     }
-    if (process.env.LING_SKIP_UPSTREAM_CHECK === "1" || process.env.AG_KIT_SKIP_UPSTREAM_CHECK === "1") {
+    if (process.env.LING_SKIP_UPSTREAM_CHECK === "1") {
         return;
     }
     const shouldWarn =
@@ -879,20 +875,8 @@ function maybeWarnUpstreamGlobalConflict(command, options) {
     }
 
     log(options, `[warn] 检测到全局已安装上游英文版 ${UPSTREAM_GLOBAL_PACKAGE}。`);
-    log(options, `[warn] 上游英文版与当前版本共用 \`${LEGACY_CLI_NAME}\` 兼容命令名，后安装者会覆盖该入口。`);
-    log(options, `[hint] 建议执行: npm uninstall -g ${UPSTREAM_GLOBAL_PACKAGE}`);
-    log(options, `[info] 正式命令已切换为 \`${PRIMARY_CLI_NAME}\`。若你通过 bun install -g 安装，Bun 默认会阻止本包 postinstall；因此这里会在首次执行 CLI 时再次提醒。`);
-}
-
-function maybeWarnLegacyCliAlias(options) {
-    if (options.quiet) {
-        return;
-    }
-    if (CURRENT_CLI_BASENAME !== LEGACY_CLI_NAME) {
-        return;
-    }
-
-    console.log(`[warn] \`${LEGACY_CLI_NAME}\` 已进入兼容模式，请改用 \`${PRIMARY_CLI_NAME}\`.`);
+    log(options, `[hint] 如需仅保留一个来源，请执行: npm uninstall -g ${UPSTREAM_GLOBAL_PACKAGE}`);
+    log(options, `[info] 当前项目的正式命令为 \`${PRIMARY_CLI_NAME}\`。`);
 }
 
 function normalizeTargets(rawTargets) {
@@ -1219,9 +1203,106 @@ function syncGlobalSkillsFromRoot(targetName, skillsRoot, timestamp, options) {
     };
 }
 
+function planGlobalSyncTasks(targetName, agentDir) {
+    const destinations = getGlobalDestinations(targetName);
+
+    if (targetName === "codex") {
+        const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "ling-global-codex-"));
+        const mockRoot = path.join(tempRoot, "source");
+        const mockAgent = path.join(mockRoot, ".agents");
+        const outputDir = path.join(tempRoot, "out");
+
+        copyDirRecursive(agentDir, mockAgent);
+        CodexBuilder.build(mockRoot, outputDir);
+        const skillsRoot = path.join(outputDir, "skills");
+        const skillNames = listSkillDirectories(skillsRoot);
+
+        const tasks = [];
+        for (const destination of destinations) {
+            for (const skillName of skillNames) {
+                tasks.push({
+                    destination,
+                    skillName,
+                    srcDir: path.join(skillsRoot, skillName),
+                    destDir: path.join(destination.skillsRoot, skillName),
+                });
+            }
+        }
+
+        return {
+            tasks,
+            cleanup: () => fs.rmSync(tempRoot, { recursive: true, force: true }),
+        };
+    }
+
+    if (targetName === "gemini") {
+        const skillsRoot = path.join(agentDir, "skills");
+        const skillNames = listSkillDirectories(skillsRoot);
+        const tasks = [];
+        for (const destination of destinations) {
+            for (const skillName of skillNames) {
+                tasks.push({
+                    destination,
+                    skillName,
+                    srcDir: path.join(skillsRoot, skillName),
+                    destDir: path.join(destination.skillsRoot, skillName),
+                });
+            }
+        }
+        return { tasks, cleanup: null };
+    }
+
+    throw new Error(`未知目标: ${targetName}`);
+}
+
+function summarizeGlobalSync(tasks) {
+    const perDestination = new Map();
+    let synced = 0;
+    let skipped = 0;
+    let backedUp = 0;
+
+    for (const task of tasks) {
+        const id = task.destination.id;
+        if (!perDestination.has(id)) {
+            perDestination.set(id, {
+                targetName: id,
+                family: task.destination.targetName,
+                destRoot: task.destination.skillsRoot,
+                total: 0,
+                synced: 0,
+                skipped: 0,
+                backedUp: 0,
+            });
+        }
+        const entry = perDestination.get(id);
+        entry.total += 1;
+        if (task.result === "skipped") {
+            skipped += 1;
+            entry.skipped += 1;
+            continue;
+        }
+        if (task.result === "synced") {
+            synced += 1;
+            entry.synced += 1;
+        }
+        if (task.backedUp) {
+            backedUp += 1;
+            entry.backedUp += 1;
+        }
+    }
+
+    return {
+        total: tasks.length,
+        synced,
+        skipped,
+        backedUp,
+        destinations: Array.from(perDestination.values()),
+    };
+}
+
 function applyGlobalSync(targetName, agentDir, timestamp, options) {
     if (targetName === "codex") {
-        const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "ag-kit-global-codex-"));
+        const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "ling-global-codex-"));
         const mockRoot = path.join(tempRoot, "source");
         const mockAgent = path.join(mockRoot, ".agents");
         const outputDir = path.join(tempRoot, "out");
@@ -1248,21 +1329,70 @@ async function commandGlobalSync(options) {
     const targets = await resolveTargetsForGlobalSync(options);
     const { agentDir, cleanup, sourceLabel } = resolveAgentInstallSource(options);
     const timestamp = nowISO().replace(/[:.]/g, "-");
+    const prompter = createConflictPrompter(options);
 
     try {
         log(options, `[global] 全局同步源: ${sourceLabel}`);
         for (const target of targets) {
             log(options, `[sync] 正在同步全局目标 [${target}] ...`);
-            const result = applyGlobalSync(target, agentDir, timestamp, options);
-            if (!options.dryRun) {
-                log(options, `[summary] 全局同步完成 [${target}]：总计 ${result.total}，新增/覆盖 ${result.synced}，跳过 ${result.skipped}，备份 ${result.backedUp}`);
-                for (const item of result.destinations) {
-                    log(options, `   - ${item.targetName}: ${item.destRoot}（每目标 ${item.total} 个 Skills）`);
+            const plan = planGlobalSyncTasks(target, agentDir);
+            try {
+                for (const task of plan.tasks) {
+                    const exists = fs.existsSync(task.destDir);
+                    const equal = exists ? areDirectoriesEqual(task.srcDir, task.destDir) : false;
+                    if (exists && equal) {
+                        task.result = "skipped";
+                        continue;
+                    }
+
+                    if (exists && !equal && prompter) {
+                        const action = await prompter.resolveConflict({
+                            category: `global:${task.destination.id}`,
+                            label: `全局 Skill ${task.destination.id}/${task.skillName}`,
+                            path: task.destDir,
+                        });
+                        task.action = action;
+                    } else if (exists && !equal && !prompter && (options.nonInteractive || !process.stdin.isTTY)) {
+                        // 非交互环境保持原有行为：备份后覆盖
+                        task.action = "backup";
+                    }
+
+                    if (task.action === "keep") {
+                        task.result = "skipped";
+                        continue;
+                    }
+
+                    if (options.dryRun) {
+                        log(options, `[dry-run] 将同步全局 Skill: ${task.destination.id}/${task.skillName}`);
+                        task.result = "skipped";
+                        continue;
+                    }
+
+                    if (exists && task.action !== "remove") {
+                        backupSkillDirectory(task.destination.id, task.skillName, task.destDir, timestamp, options);
+                        task.backedUp = true;
+                    }
+
+                    const logger = options.quiet ? (() => {}) : log.bind(null, options);
+                    AtomicWriter.atomicCopyDir(task.srcDir, task.destDir, { logger });
+                    log(options, `[ok] 已同步全局 Skill: ${task.destination.id}/${task.skillName}`);
+                    task.result = "synced";
+                }
+
+                const summary = summarizeGlobalSync(plan.tasks);
+                if (!options.dryRun) {
+                    log(options, `[summary] 全局同步完成 [${target}]：总计 ${summary.total}，新增/覆盖 ${summary.synced}，跳过 ${summary.skipped}，备份 ${summary.backedUp}`);
+                    for (const item of summary.destinations) {
+                        log(options, `   - ${item.targetName}: ${item.destRoot}（每目标 ${item.total} 个 Skills）`);
+                    }
                 }
+            } finally {
+                if (plan.cleanup) plan.cleanup();
             }
         }
     } finally {
         if (cleanup) cleanup();
+        if (prompter) prompter.close();
     }
 }
 
@@ -1324,6 +1454,10 @@ function getSpecHomeDir() {
     return path.join(resolveGlobalRootDir(), ".ling", "spec");
 }
 
+function getSpecWorkspaceDir() {
+    return path.join(resolveGlobalRootDir(), ".ling", "spec-workspace");
+}
+
 function getSpecStatePath() {
     return path.join(getSpecHomeDir(), "state.json");
 }
@@ -1401,6 +1535,46 @@ function ensureBundledSpecResources() {
     }
 }
 
+function listMissingFiles(rootDir, requiredRelPaths) {
+    if (!fs.existsSync(rootDir)) {
+        return requiredRelPaths.map((rel) => rel);
+    }
+    return requiredRelPaths.filter((rel) => !fs.existsSync(path.join(rootDir, ...rel.split("/"))));
+}
+
+function collectSpecOrphanIssues(specHome, hasStateFile) {
+    const issues = [];
+    const templatesDir = path.join(specHome, "templates");
+    const referencesDir = path.join(specHome, "references");
+    const profilesDir = path.join(specHome, "profiles");
+
+    if (fs.existsSync(templatesDir)) issues.push("Detected spec templates directory");
+    if (fs.existsSync(referencesDir)) issues.push("Detected spec references directory");
+    if (fs.existsSync(profilesDir)) issues.push("Detected spec profiles directory");
+
+    for (const targetName of SUPPORTED_TARGETS) {
+        for (const destination of getGlobalDestinations(targetName)) {
+            for (const skillName of SPEC_SKILL_NAMES) {
+                if (fs.existsSync(path.join(destination.skillsRoot, skillName, "SKILL.md"))) {
+                    issues.push(`Detected spec skill: ${destination.id}/${skillName}`);
+                }
+            }
+        }
+    }
+
+    if (issues.length === 0) {
+        return [];
+    }
+
+    if (!hasStateFile) {
+        issues.unshift("Spec artifacts detected but state.json missing (run: ling spec enable to repair)");
+    } else {
+        issues.unshift("Spec artifacts detected but no targets enabled (run: ling spec enable to reconcile or clean manually)");
+    }
+
+    return issues;
+}
+
 function backupDirSnapshot(sourceDir, backupDir, options, label) {
     if (!fs.existsSync(sourceDir)) {
         return "";
@@ -1437,7 +1611,60 @@ function removeDirIfExists(targetDir, options, label) {
     log(options, `[clean] 已删除 ${label}: ${targetDir}`);
 }
 
-function ensureSpecAssetsInstalled(state, timestamp, options) {
+function atomicWriteFile(targetPath, content, options, label) {
+    const targetDir = path.dirname(targetPath);
+    if (options.dryRun) {
+        log(options, `[dry-run] 将写入 ${label}: ${targetPath}`);
+        return;
+    }
+    fs.mkdirSync(targetDir, { recursive: true });
+    const tempPath = `${targetPath}.tmp-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`;
+    fs.writeFileSync(tempPath, content, "utf8");
+    try {
+        if (fs.existsSync(targetPath)) {
+            const backupPath = `${targetPath}.bak-${Date.now()}-${Math.random().toString(36).slice(2, 5)}`;
+            fs.renameSync(targetPath, backupPath);
+            try {
+                fs.renameSync(tempPath, targetPath);
+            } catch (err) {
+                try {
+                    fs.renameSync(backupPath, targetPath);
+                } catch (restoreErr) {
+                    throw new Error(`临界失败: 无法将新版本写入目标且无法恢复旧版本。旧版本位于 ${backupPath}。错误: ${err.message}`);
+                }
+                throw err;
+            }
+            try {
+                fs.rmSync(backupPath, { force: true });
+            } catch (cleanupErr) {
+                log(options, `[warn] 无法清理备份文件 ${backupPath}: ${cleanupErr.message}`);
+            }
+            return;
+        }
+        fs.renameSync(tempPath, targetPath);
+    } catch (err) {
+        if (fs.existsSync(tempPath)) {
+            fs.rmSync(tempPath, { force: true });
+        }
+        throw new Error(`原子写入失败: ${err.message}`);
+    }
+}
+
+function backupFileSnapshot(sourcePath, backupPath, options, label) {
+    if (!fs.existsSync(sourcePath)) {
+        return "";
+    }
+    if (options.dryRun) {
+        log(options, `[dry-run] 将备份 ${label}: ${sourcePath} -> ${backupPath}`);
+        return backupPath;
+    }
+    fs.mkdirSync(path.dirname(backupPath), { recursive: true });
+    fs.copyFileSync(sourcePath, backupPath);
+    log(options, `[backup] 已备份 ${label}: ${sourcePath} -> ${backupPath}`);
+    return backupPath;
+}
+
+async function ensureSpecAssetsInstalled(state, timestamp, options, prompter) {
     const specHome = getSpecHomeDir();
     const assets = {
         templates: {
@@ -1448,32 +1675,102 @@ function ensureSpecAssetsInstalled(state, timestamp, options) {
             sourceDir: path.join(BUNDLED_SPEC_DIR, "references"),
             destDir: path.join(specHome, "references"),
         },
+        profiles: {
+            sourceDir: path.join(BUNDLED_SPEC_DIR, "profiles"),
+            destDir: path.join(specHome, "profiles"),
+        },
     };
 
     for (const [assetName, config] of Object.entries(assets)) {
-        if (state.assets[assetName] && state.assets[assetName].installedAt) {
+        const existingAssetState = state.assets[assetName];
+        const hasState = existingAssetState && existingAssetState.installedAt;
+        const exists = fs.existsSync(config.destDir);
+        const mode = normalizeSpecAssetMode(existingAssetState);
+
+        if (mode === "kept" && exists) {
+            continue;
+        }
+
+        const equal = exists ? areDirectoriesEqual(config.sourceDir, config.destDir) : false;
+
+        if (exists && equal) {
+            if (!hasState) {
+                log(options, `[skip] Spec ${assetName} 已存在且一致，视为已启用: ${config.destDir}`);
+                state.assets[assetName] = {
+                    destPath: config.destDir,
+                    backupPath: "",
+                    installedAt: nowISO(),
+                    mode: "kept",
+                };
+            }
+            continue;
+        }
+
+        let action = exists ? "backup" : "";
+        if (exists && prompter) {
+            action = await prompter.resolveConflict({
+                category: "spec:assets",
+                label: `Spec ${assetName}`,
+                path: config.destDir,
+            });
+        } else if (exists && !prompter && (options.nonInteractive || !process.stdin.isTTY)) {
+            action = "backup";
+        }
+
+        if (action === "keep") {
+            log(options, `[skip] 已保留 Spec ${assetName} 资产，不覆盖: ${config.destDir}`);
+            state.assets[assetName] = {
+                destPath: config.destDir,
+                backupPath: "",
+                installedAt: nowISO(),
+                mode: "kept",
+            };
             continue;
         }
 
-        const backupPath = backupDirSnapshot(
-            config.destDir,
-            path.join(resolveSpecBackupRoot(timestamp), "assets", assetName),
-            options,
-            `Spec ${assetName}`,
-        );
+        let backupPath = "";
+        if (exists && action !== "remove") {
+            backupPath = backupDirSnapshot(
+                config.destDir,
+                path.join(resolveSpecBackupRoot(timestamp), "assets", assetName),
+                options,
+                `Spec ${assetName}`,
+            );
+        } else if (exists && action === "remove") {
+            removeDirIfExists(config.destDir, options, `Spec ${assetName}`);
+        }
+
         applyDirSnapshot(config.sourceDir, config.destDir, options, `Spec ${assetName}`);
         state.assets[assetName] = {
             destPath: config.destDir,
             backupPath,
             installedAt: nowISO(),
+            mode: exists ? (action === "remove" ? "replaced" : "backup") : "created",
         };
     }
 }
 
+function normalizeSpecAssetMode(assetState) {
+    if (!assetState || typeof assetState !== "object") {
+        return "";
+    }
+    if (typeof assetState.mode === "string" && assetState.mode) {
+        return assetState.mode;
+    }
+    if (typeof assetState.backupPath === "string" && assetState.backupPath) {
+        return "backup";
+    }
+    return "created";
+}
+
 function restoreSpecAsset(assetState, options, label) {
     if (!assetState || typeof assetState.destPath !== "string") {
         return;
     }
+    const mode = normalizeSpecAssetMode(assetState);
+    if (mode === "kept") {
+        return;
+    }
     if (assetState.backupPath && fs.existsSync(assetState.backupPath)) {
         applyDirSnapshot(assetState.backupPath, assetState.destPath, options, label);
         return;
@@ -1481,37 +1778,100 @@ function restoreSpecAsset(assetState, options, label) {
     removeDirIfExists(assetState.destPath, options, label);
 }
 
-function enableSpecTarget(targetName, state, timestamp, options) {
-    if (state.targets[targetName]) {
-        log(options, `[skip] Spec 目标已启用: ${targetName}`);
-        return;
-    }
-
+async function enableSpecTarget(targetName, state, timestamp, options, prompter) {
     const destinations = getGlobalDestinations(targetName);
-    const targetState = {
+    const existingTargetState = state.targets[targetName];
+    if (existingTargetState) {
+        log(options, `[info] Spec 目标已启用，执行一致性修复: ${targetName}`);
+    }
+    const targetState = existingTargetState || {
         enabledAt: nowISO(),
         consumers: {},
     };
 
     for (const destination of destinations) {
+        const existingConsumerState =
+            targetState.consumers && targetState.consumers[destination.id] ? targetState.consumers[destination.id] : null;
         const consumerState = {
             skills: [],
         };
+        const existingSkills = new Map();
+        if (existingConsumerState && Array.isArray(existingConsumerState.skills)) {
+            for (const skill of existingConsumerState.skills) {
+                if (skill && typeof skill.name === "string") {
+                    existingSkills.set(skill.name, skill);
+                }
+            }
+        }
 
         for (const skillName of SPEC_SKILL_NAMES) {
             const srcDir = path.join(BUNDLED_SPEC_DIR, "skills", skillName);
             const destDir = path.join(destination.skillsRoot, skillName);
-            const backupPath = backupDirSnapshot(
-                destDir,
-                path.join(resolveSpecBackupRoot(timestamp), destination.id, "skills", skillName),
-                options,
-                `Spec Skill ${destination.id}/${skillName}`,
-            );
+            const existingSkillState = existingSkills.get(skillName);
+            const mode = normalizeSpecAssetMode(existingSkillState);
+            const exists = fs.existsSync(destDir);
+            const equal = exists ? areDirectoriesEqual(srcDir, destDir) : false;
+
+            if (mode === "kept" && exists) {
+                consumerState.skills.push({
+                    name: skillName,
+                    destPath: destDir,
+                    backupPath: existingSkillState && existingSkillState.backupPath ? existingSkillState.backupPath : "",
+                    mode: "kept",
+                });
+                continue;
+            }
+
+            if (exists && equal) {
+                consumerState.skills.push({
+                    name: skillName,
+                    destPath: destDir,
+                    backupPath: existingSkillState && existingSkillState.backupPath ? existingSkillState.backupPath : "",
+                    mode: existingSkillState && existingSkillState.mode ? existingSkillState.mode : "kept",
+                });
+                continue;
+            }
+
+            let action = exists ? "backup" : "";
+            if (exists && prompter) {
+                action = await prompter.resolveConflict({
+                    category: `spec:skills:${destination.id}`,
+                    label: `Spec Skill ${destination.id}/${skillName}`,
+                    path: destDir,
+                });
+            } else if (exists && !prompter && (options.nonInteractive || !process.stdin.isTTY)) {
+                action = "backup";
+            }
+
+            if (action === "keep") {
+                log(options, `[skip] 已保留 Spec Skill，不覆盖: ${destination.id}/${skillName}`);
+                consumerState.skills.push({
+                    name: skillName,
+                    destPath: destDir,
+                    backupPath: existingSkillState && existingSkillState.backupPath ? existingSkillState.backupPath : "",
+                    mode: "kept",
+                });
+                continue;
+            }
+
+            let backupPath = existingSkillState && existingSkillState.backupPath ? existingSkillState.backupPath : "";
+            if (exists && action !== "remove") {
+                backupPath = backupDirSnapshot(
+                    destDir,
+                    path.join(resolveSpecBackupRoot(timestamp), destination.id, "skills", skillName),
+                    options,
+                    `Spec Skill ${destination.id}/${skillName}`,
+                );
+            } else if (exists && action === "remove") {
+                removeDirIfExists(destDir, options, `Spec Skill ${destination.id}/${skillName}`);
+            }
+
             applyDirSnapshot(srcDir, destDir, options, `Spec Skill ${destination.id}/${skillName}`);
             consumerState.skills.push({
                 name: skillName,
                 destPath: destDir,
                 backupPath,
+                mode: exists ? (action === "remove" ? "replaced" : "backup") : "created",
             });
         }
 
@@ -1530,6 +1890,10 @@ function disableSpecTarget(targetName, state, options) {
 
     for (const [consumerId, consumerState] of Object.entries(targetState.consumers || {})) {
         for (const skill of consumerState.skills || []) {
+            const mode = normalizeSpecAssetMode(skill);
+            if (mode === "kept") {
+                continue;
+            }
             if (skill.backupPath && fs.existsSync(skill.backupPath)) {
                 applyDirSnapshot(skill.backupPath, skill.destPath, options, `恢复 Spec Skill ${consumerId}/${skill.name}`);
             } else {
@@ -1542,14 +1906,28 @@ function disableSpecTarget(targetName, state, options) {
 }
 
 function evaluateSpecState() {
+    const statePath = getSpecStatePath();
+    const hasStateFile = fs.existsSync(statePath);
     const { state } = readSpecState();
     const targetNames = Object.keys(state.targets || {});
     if (targetNames.length === 0) {
+        const specHome = getSpecHomeDir();
+        const orphanIssues = collectSpecOrphanIssues(specHome, hasStateFile);
+        if (orphanIssues.length > 0) {
+            return {
+                state: "broken",
+                targets: [],
+                assets: state.assets || {},
+                specHome,
+                issues: orphanIssues,
+            };
+        }
         return {
             state: "missing",
             targets: [],
             assets: state.assets || {},
-            specHome: getSpecHomeDir(),
+            specHome,
+            issues: [],
         };
     }
 
@@ -1565,10 +1943,23 @@ function evaluateSpecState() {
         }
     }
 
-    for (const assetName of ["templates", "references"]) {
+    const specHome = getSpecHomeDir();
+    const assetRequirements = {
+        templates: { dir: path.join(specHome, "templates"), files: SPEC_TEMPLATE_REQUIRED_FILES },
+        references: { dir: path.join(specHome, "references"), files: SPEC_REFERENCE_REQUIRED_FILES },
+        profiles: { dir: path.join(specHome, "profiles"), files: SPEC_PROFILE_REQUIRED_FILES },
+    };
+
+    for (const assetName of ["templates", "references", "profiles"]) {
         const asset = state.assets[assetName];
         if (!asset || !asset.destPath || !fs.existsSync(asset.destPath)) {
             issues.push(`Missing spec asset: ${assetName}`);
+            continue;
+        }
+        const requirement = assetRequirements[assetName];
+        const missing = listMissingFiles(requirement.dir, requirement.files);
+        for (const rel of missing) {
+            issues.push(`Missing spec asset file: ${assetName}/${rel}`);
         }
     }
 
@@ -1577,7 +1968,7 @@ function evaluateSpecState() {
         targets: targetNames,
         issues,
         assets: state.assets || {},
-        specHome: getSpecHomeDir(),
+        specHome,
     };
 }
 
@@ -1608,15 +1999,308 @@ function commandSpecStatus(options) {
     setQuietStatusExitCode(summary.state);
 }
 
-function commandSpecEnable(options) {
+function stripUtf8Bom(text) {
+    if (!text) return "";
+    return text.charCodeAt(0) === 0xFEFF ? text.slice(1) : text;
+}
+
+function parseCsvLine(line) {
+    const cells = [];
+    let current = "";
+    let inQuotes = false;
+
+    for (let i = 0; i < line.length; i++) {
+        const ch = line[i];
+        if (ch === "\"") {
+            if (inQuotes && line[i + 1] === "\"") {
+                current += "\"";
+                i += 1;
+                continue;
+            }
+            inQuotes = !inQuotes;
+            continue;
+        }
+        if (ch === "," && !inQuotes) {
+            cells.push(current);
+            current = "";
+            continue;
+        }
+        current += ch;
+    }
+    cells.push(current);
+    return cells;
+}
+
+function analyzeIssuesCsv(issuesPath) {
+    if (!fs.existsSync(issuesPath)) {
+        return { status: "missing", issues: ["Missing issues.csv"], stats: { total: 0, inProgress: 0 } };
+    }
+
+    const raw = stripUtf8Bom(fs.readFileSync(issuesPath, "utf8"));
+    const lines = raw.split(/\r?\n/).filter((line) => line.trim().length > 0);
+    if (lines.length === 0) {
+        return { status: "broken", issues: ["issues.csv is empty"], stats: { total: 0, inProgress: 0 } };
+    }
+
+    const header = parseCsvLine(lines[0]).map((cell) => cell.trim());
+    const statusIndex = header.findIndex((cell) => cell === "状态" || cell.includes("(状态)") || /状态/.test(cell));
+    if (statusIndex < 0) {
+        return { status: "broken", issues: ["issues.csv header missing 状态 column"], stats: { total: Math.max(0, lines.length - 1), inProgress: 0 } };
+    }
+
+    const allowedStates = new Set(["未开始", "进行中", "已完成"]);
+    let total = 0;
+    let inProgress = 0;
+    const issues = [];
+
+    for (let i = 1; i < lines.length; i++) {
+        const row = parseCsvLine(lines[i]);
+        const isEmpty = row.every((cell) => String(cell || "").trim() === "");
+        if (isEmpty) {
+            continue;
+        }
+        total += 1;
+        const state = String(row[statusIndex] || "").trim();
+        if (!allowedStates.has(state)) {
+            issues.push(`Invalid 状态 at row ${i + 1}: ${state || "(empty)"}`);
+            continue;
+        }
+        if (state === "进行中") {
+            inProgress += 1;
+        }
+    }
+
+    if (inProgress > 1) {
+        issues.push(`Multiple tasks in 进行中: ${inProgress}`);
+    }
+
+    return {
+        status: issues.length > 0 ? "broken" : "ok",
+        issues,
+        stats: { total, inProgress },
+    };
+}
+
+function checkSpecProjectIntegrity(workspaceRoot) {
+    const issues = [];
+    const issuesPath = path.join(workspaceRoot, "issues.csv");
+    const issuesResult = analyzeIssuesCsv(issuesPath);
+
+    const specDir = path.join(workspaceRoot, ".ling", "spec");
+    const templatesDir = path.join(specDir, "templates");
+    const referencesDir = path.join(specDir, "references");
+    const profilesDir = path.join(specDir, "profiles");
+
+    const hasSpecDir = fs.existsSync(specDir);
+    if (!hasSpecDir) {
+        if (issuesResult.status !== "missing") {
+            issues.push("Missing .ling/spec directory (run: ling spec init)");
+        }
+    } else {
+        if (issuesResult.status === "missing") {
+            issues.push("Missing issues.csv (run: ling spec init)");
+        }
+        for (const rel of SPEC_TEMPLATE_REQUIRED_FILES) {
+            const filePath = path.join(templatesDir, rel);
+            if (!fs.existsSync(filePath)) {
+                issues.push(`Missing spec template: .ling/spec/templates/${rel}`);
+            }
+        }
+        for (const rel of SPEC_REFERENCE_REQUIRED_FILES) {
+            const filePath = path.join(referencesDir, rel);
+            if (!fs.existsSync(filePath)) {
+                issues.push(`Missing spec reference: .ling/spec/references/${rel}`);
+            }
+        }
+        for (const rel of SPEC_PROFILE_REQUIRED_FILES) {
+            const filePath = path.join(profilesDir, ...rel.split("/"));
+            if (!fs.existsSync(filePath)) {
+                issues.push(`Missing spec profile: .ling/spec/profiles/${rel}`);
+            }
+        }
+    }
+
+    if (issuesResult.status === "broken") {
+        issues.push(...issuesResult.issues);
+    }
+
+    const hasAnySpecSignal = hasSpecDir || issuesResult.status !== "missing";
+    if (!hasAnySpecSignal) {
+        return { status: "missing", issues: [], stats: { total: 0, inProgress: 0 } };
+    }
+
+    return {
+        status: issues.length > 0 ? "broken" : "ok",
+        issues,
+        stats: issuesResult.stats,
+    };
+}
+
+function resolveWorkspaceSpecBackupRoot(workspaceRoot, timestamp) {
+    return path.join(workspaceRoot, ".ling", "backups", "spec", timestamp, "before");
+}
+
+async function commandSpecInit(options) {
+    const workspaceRoot = options.path ? resolveWorkspaceRoot(options.path) : getSpecWorkspaceDir();
+    const prompter = createConflictPrompter(options);
+    const timestamp = nowISO().replace(/[:.]/g, "-");
+    const backupRoot = resolveWorkspaceSpecBackupRoot(workspaceRoot, timestamp);
+
+    const specDir = path.join(workspaceRoot, ".ling", "spec");
+    let specSourceDir = BUNDLED_SPEC_DIR;
+    let cleanupSpec = null;
+    if (options.branch) {
+        const remote = cloneBranchSpecDir(options.branch, {
+            quiet: options.quiet,
+            logger: log.bind(null, options),
+        });
+        specSourceDir = remote.specDir;
+        cleanupSpec = remote.cleanup;
+    }
+    const assets = {
+        templates: {
+            sourceDir: path.join(specSourceDir, "templates"),
+            destDir: path.join(specDir, "templates"),
+        },
+        references: {
+            sourceDir: path.join(specSourceDir, "references"),
+            destDir: path.join(specDir, "references"),
+        },
+        profiles: {
+            sourceDir: path.join(specSourceDir, "profiles"),
+            destDir: path.join(specDir, "profiles"),
+        },
+    };
+
+    try {
+        fs.mkdirSync(workspaceRoot, { recursive: true });
+
+        for (const [assetName, config] of Object.entries(assets)) {
+            const exists = fs.existsSync(config.destDir);
+            if (exists && areDirectoriesEqual(config.sourceDir, config.destDir)) {
+                log(options, `[skip] Spec ${assetName} 已最新，无需覆盖: ${config.destDir}`);
+                continue;
+            }
+
+            let action = exists ? "backup" : "";
+            if (exists && prompter) {
+                action = await prompter.resolveConflict({
+                    category: "spec:project:assets",
+                    label: `Spec ${assetName}`,
+                    path: config.destDir,
+                });
+            } else if (exists && !prompter && (options.force || options.nonInteractive || !process.stdin.isTTY)) {
+                action = "backup";
+            }
+
+            if (action === "keep") {
+                log(options, `[skip] 已保留 Spec ${assetName} 资产，不覆盖: ${config.destDir}`);
+                continue;
+            }
+
+            if (exists && action !== "remove") {
+                backupDirSnapshot(config.destDir, path.join(backupRoot, "assets", assetName), options, `Spec ${assetName}`);
+            } else if (exists && action === "remove") {
+                removeDirIfExists(config.destDir, options, `Spec ${assetName}`);
+            }
+            applyDirSnapshot(config.sourceDir, config.destDir, options, `Spec ${assetName}`);
+        }
+
+        const issuesPath = path.join(workspaceRoot, "issues.csv");
+        const issuesTemplatePath = path.join(specSourceDir, "templates", "issues.template.csv");
+        const issuesTemplate = stripUtf8Bom(fs.readFileSync(issuesTemplatePath, "utf8"));
+        const hasIssues = fs.existsSync(issuesPath);
+        if (hasIssues) {
+            let action = "backup";
+            if (prompter) {
+                action = await prompter.resolveConflict({
+                    category: "spec:project:file",
+                    label: "issues.csv",
+                    path: issuesPath,
+                });
+            }
+            if (action === "keep") {
+                log(options, "[skip] 已保留现有 issues.csv，不覆盖");
+            } else {
+                if (action !== "remove") {
+                    backupFileSnapshot(issuesPath, path.join(backupRoot, "issues.csv"), options, "issues.csv");
+                } else if (!options.dryRun) {
+                    fs.rmSync(issuesPath, { force: true });
+                }
+                atomicWriteFile(issuesPath, `${issuesTemplate.trimEnd()}\n`, options, "issues.csv");
+                log(options, options.dryRun ? `[dry-run] 将写入任务跟踪文件: ${issuesPath}` : `[ok] 已写入任务跟踪文件: ${issuesPath}`);
+            }
+        } else {
+            atomicWriteFile(issuesPath, `${issuesTemplate.trimEnd()}\n`, options, "issues.csv");
+            log(options, options.dryRun ? `[dry-run] 将创建任务跟踪文件: ${issuesPath}` : `[ok] 已创建任务跟踪文件: ${issuesPath}`);
+        }
+
+        const docsReviewsDir = path.join(workspaceRoot, "docs", "reviews");
+        const docsHandoffDir = path.join(workspaceRoot, "docs", "handoff");
+        if (options.dryRun) {
+            log(options, `[dry-run] 将确保目录存在: ${docsReviewsDir}`);
+            log(options, `[dry-run] 将确保目录存在: ${docsHandoffDir}`);
+        } else {
+            fs.mkdirSync(docsReviewsDir, { recursive: true });
+            fs.mkdirSync(docsHandoffDir, { recursive: true });
+        }
+
+        const requestedTargets = normalizeTargets(options.targets);
+        const shouldInitTargets = options.path ? requestedTargets.length > 0 : true;
+        const targets = shouldInitTargets ? (requestedTargets.length > 0 ? requestedTargets : [...SUPPORTED_TARGETS]) : [];
+        if (targets.length > 0) {
+            await initTargets(workspaceRoot, targets, options, prompter);
+        }
+
+        log(options, `[ok] Spec 初始化完成: ${workspaceRoot}`);
+    } finally {
+        if (cleanupSpec) cleanupSpec();
+        if (prompter) prompter.close();
+    }
+}
+
+function commandSpecDoctor(options) {
+    const workspaceRoot = options.path ? resolveWorkspaceRoot(options.path) : getSpecWorkspaceDir();
+    const result = checkSpecProjectIntegrity(workspaceRoot);
+    const state = result.status === "ok" ? "installed" : result.status;
+
+    if (options.quiet) {
+        console.log(state);
+        setQuietStatusExitCode(state);
+        return;
+    }
+
+    if (state === "missing") {
+        console.log("[warn] 未检测到 Spec 项目资产");
+        console.log(`   工作区: ${workspaceRoot}`);
+        setQuietStatusExitCode("missing");
+        return;
+    }
+
+    console.log(state === "installed" ? "[ok] Spec 项目资产状态正常" : "[warn] Spec 项目资产存在问题");
+    console.log(`   工作区: ${workspaceRoot}`);
+    console.log(`   任务数: ${result.stats.total}`);
+    console.log(`   进行中: ${result.stats.inProgress}`);
+    for (const issue of result.issues || []) {
+        console.log(`   Issue: ${issue}`);
+    }
+    setQuietStatusExitCode(state);
+}
+
+async function commandSpecEnable(options) {
     ensureBundledSpecResources();
     const targets = resolveTargetsForSpec(options);
     const { statePath, state } = readSpecState();
     const timestamp = nowISO().replace(/[:.]/g, "-");
+    const prompter = createConflictPrompter(options);
 
-    ensureSpecAssetsInstalled(state, timestamp, options);
-    for (const targetName of targets) {
-        enableSpecTarget(targetName, state, timestamp, options);
+    try {
+        await ensureSpecAssetsInstalled(state, timestamp, options, prompter);
+        for (const targetName of targets) {
+            await enableSpecTarget(targetName, state, timestamp, options, prompter);
+        }
+    } finally {
+        if (prompter) prompter.close();
     }
 
     state.updatedAt = nowISO();
@@ -1639,6 +2323,7 @@ function commandSpecDisable(options) {
     if (remainingTargets.length === 0) {
         restoreSpecAsset(state.assets.templates, options, "Spec templates");
         restoreSpecAsset(state.assets.references, options, "Spec references");
+        restoreSpecAsset(state.assets.profiles, options, "Spec profiles");
         state.assets = {};
     }
 
@@ -1646,6 +2331,14 @@ function commandSpecDisable(options) {
     if (!options.dryRun) {
         if (remainingTargets.length === 0) {
             removeSpecStateFile();
+            const specHome = getSpecHomeDir();
+            try {
+                if (fs.existsSync(specHome) && fs.readdirSync(specHome).length === 0) {
+                    fs.rmdirSync(specHome);
+                }
+            } catch (err) {
+                log(options, `[warn] 无法清理 Spec 根目录: ${err.message}`);
+            }
         } else {
             writeSpecState(statePath, state);
         }
@@ -1654,29 +2347,110 @@ function commandSpecDisable(options) {
     log(options, `[ok] Spec Profile 已停用 (Targets: ${targets.join(", ")})`);
 }
 
-function commandSpec(options) {
+async function commandSpec(options) {
     const subcommand = String(options.subcommand || "status").toLowerCase();
     if (subcommand === "status") {
         return commandSpecStatus(options);
     }
     if (subcommand === "enable") {
-        return commandSpecEnable(options);
+        return await commandSpecEnable(options);
     }
     if (subcommand === "disable") {
         return commandSpecDisable(options);
     }
+    if (subcommand === "init") {
+        return await commandSpecInit(options);
+    }
+    if (subcommand === "doctor") {
+        return commandSpecDoctor(options);
+    }
     throw new Error(`未知 spec 子命令: ${subcommand}`);
 }
 
+async function initTargets(workspaceRoot, targets, options, prompter) {
+    for (const target of targets) {
+        const runOptions = { ...options };
+        const conflicts = [];
+
+        if (target === "gemini") {
+            const agentDir = path.join(workspaceRoot, ".agent");
+            if (fs.existsSync(agentDir)) {
+                conflicts.push({
+                    category: "project:gemini",
+                    label: ".agent",
+                    path: agentDir,
+                    target,
+                });
+            }
+        }
+
+        if (target === "codex") {
+            const managedDir = path.join(workspaceRoot, ".agents");
+            const legacyDir = path.join(workspaceRoot, ".codex");
+            if (fs.existsSync(managedDir) || fs.existsSync(legacyDir)) {
+                if (fs.existsSync(managedDir)) {
+                    conflicts.push({
+                        category: "project:codex",
+                        label: ".agents",
+                        path: managedDir,
+                        target,
+                    });
+                }
+                if (fs.existsSync(legacyDir)) {
+                    conflicts.push({
+                        category: "project:codex",
+                        label: ".codex",
+                        path: legacyDir,
+                        target,
+                    });
+                }
+            }
+        }
+
+        if (conflicts.length > 0) {
+            if (!prompter && !runOptions.force) {
+                throw new Error("检测到已有资产且当前环境不可交互，请使用 --force 或在交互终端中重试。");
+            }
+
+            const timestamp = nowISO().replace(/[:.]/g, "-");
+            let shouldSkip = false;
+
+            for (const conflict of conflicts) {
+                const action = prompter ? await prompter.resolveConflict(conflict) : "backup";
+                if (action === "keep") {
+                    log(options, `[skip] 已保留现有资产，跳过初始化: ${conflict.label}`);
+                    shouldSkip = true;
+                    break;
+                }
+                if (action === "backup") {
+                    const backupRootName = conflict.label === ".agent" ? ".agent-backup" : ".agents-backup";
+                    backupWorkspaceDir(workspaceRoot, conflict.path, backupRootName, timestamp, options, `工作区资产 ${conflict.label}`);
+                }
+                // remove/backup 都需要强制覆盖才能继续
+                runOptions.force = true;
+            }
+
+            if (shouldSkip) {
+                continue;
+            }
+        }
+
+        const adapter = createAdapter(target, workspaceRoot, runOptions);
+        log(options, `[sync] 正在初始化目标 [${target}] ...`);
+        adapter.install(BUNDLED_AGENT_DIR);
+        registerWorkspaceTarget(workspaceRoot, target, runOptions);
+    }
+}
+
 async function commandInit(options) {
     const workspaceRoot = resolveWorkspaceRoot(options.path);
     const targets = await resolveTargetsForInit(options);
+    const prompter = createConflictPrompter(options);
 
-    for (const target of targets) {
-        const adapter = createAdapter(target, workspaceRoot, options);
-        log(options, `[sync] 正在初始化目标 [${target}] ...`);
-        adapter.install(BUNDLED_AGENT_DIR);
-        registerWorkspaceTarget(workspaceRoot, target, options);
+    try {
+        await initTargets(workspaceRoot, targets, options, prompter);
+    } finally {
+        if (prompter) prompter.close();
     }
 
     if (targets.length > 0) {
@@ -1684,9 +2458,62 @@ async function commandInit(options) {
     }
 }
 
+function evaluateCodexUpdateConflict(activeDir) {
+    const manifestPath = path.join(activeDir, "manifest.json");
+    const details = {
+        hasConflict: false,
+        manifestMissing: false,
+        modifiedCount: 0,
+        unknownCount: 0,
+    };
+
+    if (!fs.existsSync(manifestPath)) {
+        details.hasConflict = true;
+        details.manifestMissing = true;
+        return details;
+    }
+
+    try {
+        const manager = new ManifestManager(manifestPath, { target: "codex" });
+        manager.load();
+        const drift = manager.checkDrift(activeDir);
+        if (drift.modified.length > 0) {
+            details.hasConflict = true;
+            details.modifiedCount = drift.modified.length;
+        }
+
+        const manifestFiles = manager.manifest.files || {};
+        const stack = [activeDir];
+        while (stack.length > 0) {
+            const dir = stack.pop();
+            const entries = fs.readdirSync(dir, { withFileTypes: true });
+            for (const entry of entries) {
+                const fullPath = path.join(dir, entry.name);
+                if (entry.isDirectory()) {
+                    stack.push(fullPath);
+                    continue;
+                }
+                const relPath = path.relative(activeDir, fullPath).split(path.sep).join("/");
+                if (!manifestFiles[relPath]) {
+                    details.unknownCount += 1;
+                }
+            }
+        }
+        if (details.unknownCount > 0) {
+            details.hasConflict = true;
+        }
+    } catch (err) {
+        details.hasConflict = true;
+        details.manifestMissing = true;
+    }
+
+    return details;
+}
+
 async function commandUpdate(options) {
     const workspaceRoot = resolveWorkspaceRoot(options.path);
     const targets = resolveTargetsForUpdate(workspaceRoot, options);
+    const prompter = createConflictPrompter(options);
 
     if (targets.length === 0) {
         throw new Error(`此目录未检测到 ${PRIMARY_CLI_NAME} 安装，无法更新。请先执行 init。`);
@@ -1695,7 +2522,8 @@ async function commandUpdate(options) {
     log(options, `[update] 正在更新 Ling (Targets: ${targets.join(", ")})...`);
 
     let updatedAny = false;
-    for (const target of targets) {
+    try {
+        for (const target of targets) {
         if (!isTargetInstalled(workspaceRoot, target) && options.targets.length > 0) {
             throw new Error(`目标未安装: ${target}`);
         }
@@ -1705,15 +2533,69 @@ async function commandUpdate(options) {
         }
 
         const runOptions = { ...options, force: true };
+
+        const timestamp = nowISO().replace(/[:.]/g, "-");
+        if (target === "gemini") {
+            const agentDir = path.join(workspaceRoot, ".agent");
+            if (fs.existsSync(agentDir) && !areDirectoriesEqual(BUNDLED_AGENT_DIR, agentDir)) {
+                let action = "backup";
+                if (prompter) {
+                    action = await prompter.resolveConflict({
+                        category: "project:gemini",
+                        label: ".agent",
+                        path: agentDir,
+                        target,
+                    });
+                }
+                if (action === "keep") {
+                    log(options, "[skip] 已保留现有资产，跳过更新: .agent");
+                    continue;
+                }
+                if (action === "backup") {
+                    backupWorkspaceDir(workspaceRoot, agentDir, ".agent-backup", timestamp, options, "工作区资产 .agent");
+                }
+            }
+        }
+
+        if (target === "codex") {
+            const managedDir = path.join(workspaceRoot, ".agents");
+            const legacyDir = path.join(workspaceRoot, ".codex");
+            const activeDir = fs.existsSync(managedDir) ? managedDir : legacyDir;
+            const conflict = evaluateCodexUpdateConflict(activeDir);
+            if (conflict.hasConflict) {
+                let action = "backup";
+                if (prompter) {
+                    action = await prompter.resolveConflict({
+                        category: "project:codex",
+                        label: fs.existsSync(managedDir) ? ".agents" : ".codex",
+                        path: activeDir,
+                        target,
+                    });
+                }
+                if (action === "keep") {
+                    log(options, `[skip] 已保留现有资产，跳过更新: ${path.basename(activeDir)}`);
+                    continue;
+                }
+                if (action === "backup") {
+                    const backupRootName = ".agents-backup";
+                    backupWorkspaceDir(workspaceRoot, activeDir, backupRootName, timestamp, options, `工作区资产 ${path.basename(activeDir)}`);
+                }
+            }
+        }
+
         const adapter = createAdapter(target, workspaceRoot, runOptions);
         log(options, `[sync] 更新 [${target}] ...`);
         adapter.update(BUNDLED_AGENT_DIR);
         registerWorkspaceTarget(workspaceRoot, target, runOptions);
         updatedAny = true;
+        }
+    } finally {
+        if (prompter) prompter.close();
     }
 
     if (!updatedAny) {
-        throw new Error("未找到可更新的目标");
+        log(options, "[skip] 未执行更新（已保留现有资产）");
+        return;
     }
 }
 
@@ -1754,6 +2636,7 @@ async function commandUpdateAll(options) {
 
     log(options, `[update] 开始批量更新工作区（共 ${records.length} 个）...`);
     log(options, `[index] 索引文件: ${indexPath}`);
+    const prompter = createConflictPrompter(options);
 
     let updated = 0;
     let skipped = 0;
@@ -1764,7 +2647,8 @@ async function commandUpdateAll(options) {
     const nextRecords = [];
     const removedRecordKeys = new Set();
 
-    for (let i = 0; i < records.length; i++) {
+    try {
+        for (let i = 0; i < records.length; i++) {
         const item = normalizeWorkspaceRecordV2(records[i], normalizeAbsolutePath(records[i].path));
         const workspacePath = normalizeAbsolutePath(item.path);
         const exclusion = evaluateWorkspaceExclusion(index, workspacePath);
@@ -1825,6 +2709,54 @@ async function commandUpdateAll(options) {
                     path: workspacePath,
                     silentIndexLog: true,
                 };
+
+                const timestampForBackup = nowISO().replace(/[:.]/g, "-");
+
+                if (target === "gemini") {
+                    const agentDir = path.join(workspacePath, ".agent");
+                    if (fs.existsSync(agentDir) && !areDirectoriesEqual(BUNDLED_AGENT_DIR, agentDir)) {
+                        let action = "backup";
+                        if (prompter) {
+                            action = await prompter.resolveConflict({
+                                category: "update-all:project:gemini",
+                                label: `.agent (${workspacePath})`,
+                                path: agentDir,
+                            });
+                        }
+                        if (action === "keep") {
+                            log(options, `[skip] [${i + 1}/${records.length}] 已保留现有资产，跳过更新: ${workspacePath} [gemini]`);
+                            continue;
+                        }
+                        if (action === "backup") {
+                            backupWorkspaceDir(workspacePath, agentDir, ".agent-backup", timestampForBackup, options, `工作区资产 .agent (${workspacePath})`);
+                        }
+                    }
+                }
+
+                if (target === "codex") {
+                    const managedDir = path.join(workspacePath, ".agents");
+                    const legacyDir = path.join(workspacePath, ".codex");
+                    const activeDir = fs.existsSync(managedDir) ? managedDir : legacyDir;
+                    const conflict = evaluateCodexUpdateConflict(activeDir);
+                    if (conflict.hasConflict) {
+                        let action = "backup";
+                        if (prompter) {
+                            action = await prompter.resolveConflict({
+                                category: "update-all:project:codex",
+                                label: `${path.basename(activeDir)} (${workspacePath})`,
+                                path: activeDir,
+                            });
+                        }
+                        if (action === "keep") {
+                            log(options, `[skip] [${i + 1}/${records.length}] 已保留现有资产，跳过更新: ${workspacePath} [codex]`);
+                            continue;
+                        }
+                        if (action === "backup") {
+                            backupWorkspaceDir(workspacePath, activeDir, ".agents-backup", timestampForBackup, options, `工作区资产 ${path.basename(activeDir)} (${workspacePath})`);
+                        }
+                    }
+                }
+
                 const adapter = createAdapter(target, workspacePath, runOptions);
                 adapter.update(BUNDLED_AGENT_DIR);
                 updatedTargets.push(target);
@@ -1844,44 +2776,49 @@ async function commandUpdateAll(options) {
             skipped += 1;
             nextRecords.push(item);
         }
-    }
+        }
 
-    if (!options.dryRun) {
-        withWorkspaceIndexLock(indexPath, () => {
-            const { index: latestIndex } = readWorkspaceIndex();
-            const mergedMap = new Map();
+        if (!options.dryRun) {
+            withWorkspaceIndexLock(indexPath, () => {
+                const { index: latestIndex } = readWorkspaceIndex();
+                const mergedMap = new Map();
 
-            for (const item of latestIndex.workspaces || []) {
-                if (!item || typeof item.path !== "string") continue;
-                mergedMap.set(pathCompareKey(item.path), normalizeWorkspaceRecordV2(item, normalizeAbsolutePath(item.path)));
-            }
+                for (const item of latestIndex.workspaces || []) {
+                    if (!item || typeof item.path !== "string") continue;
+                    mergedMap.set(pathCompareKey(item.path), normalizeWorkspaceRecordV2(item, normalizeAbsolutePath(item.path)));
+                }
 
-            for (const removedKey of removedRecordKeys) {
-                mergedMap.delete(removedKey);
-            }
+                for (const removedKey of removedRecordKeys) {
+                    mergedMap.delete(removedKey);
+                }
 
-            for (const item of nextRecords) {
-                if (!item || typeof item.path !== "string") continue;
-                mergedMap.set(pathCompareKey(item.path), normalizeWorkspaceRecordV2(item, normalizeAbsolutePath(item.path)));
-            }
+                for (const item of nextRecords) {
+                    if (!item || typeof item.path !== "string") continue;
+                    mergedMap.set(pathCompareKey(item.path), normalizeWorkspaceRecordV2(item, normalizeAbsolutePath(item.path)));
+                }
 
-            latestIndex.workspaces = Array.from(mergedMap.values()).sort((a, b) => a.path.localeCompare(b.path));
-            latestIndex.updatedAt = timestamp;
-            writeWorkspaceIndex(indexPath, latestIndex);
-        });
-    }
+                latestIndex.workspaces = Array.from(mergedMap.values()).sort((a, b) => a.path.localeCompare(b.path));
+                latestIndex.updatedAt = timestamp;
+                writeWorkspaceIndex(indexPath, latestIndex);
+            });
+        }
 
-    log(options, "[summary] 批量更新完成");
-    log(options, `   成功: ${updated}`);
-    log(options, `   跳过: ${skipped}`);
-    log(options, `   失败: ${failed}`);
-    log(options, `   清理排除路径: ${removedExcluded}`);
-    if (options.pruneMissing) {
-        log(options, `   清理失效索引: ${removedMissing}`);
-    }
+        log(options, "[summary] 批量更新完成");
+        log(options, `   成功: ${updated}`);
+        log(options, `   跳过: ${skipped}`);
+        log(options, `   失败: ${failed}`);
+        log(options, `   清理排除路径: ${removedExcluded}`);
+        if (options.pruneMissing) {
+            log(options, `   清理失效索引: ${removedMissing}`);
+        }
 
-    if (failed > 0) {
-        process.exitCode = 1;
+        if (failed > 0) {
+            process.exitCode = 1;
+        }
+    } finally {
+        if (prompter) {
+            prompter.close();
+        }
     }
 }
 
@@ -1946,6 +2883,22 @@ async function commandDoctor(options) {
         }
     }
 
+    const specResult = checkSpecProjectIntegrity(workspaceRoot);
+    if (specResult.status !== "missing") {
+        out(`\n[SPEC] 检查 Spec 项目资产...`);
+        if (specResult.status === "ok") {
+            out("  [ok] 状态正常");
+            out(`     - 任务数: ${specResult.stats.total}, 进行中: ${specResult.stats.inProgress}`);
+        } else {
+            out(`  [error] 状态: ${specResult.status}`);
+            out(`     - 任务数: ${specResult.stats.total}, 进行中: ${specResult.stats.inProgress}`);
+            for (const issue of specResult.issues || []) {
+                out(`     - ${issue}`);
+            }
+            hasIssue = true;
+        }
+    }
+
     if (hasIssue) {
         process.exitCode = 1;
     }
@@ -2191,14 +3144,8 @@ function commandStatus(options) {
 
 async function main() {
     try {
-        const migration = migrateLegacyControlHomeDir();
         const { command, options, providedFlags } = parseArgs(process.argv.slice(2));
 
-        if (migration && !options.quiet) {
-            console.log(`[migrate] 已迁移控制目录: ${migration.from} -> ${migration.to}`);
-        }
-        maybeWarnLegacyCliAlias(options);
-
         if (!command || command === "--help" || command === "-h") {
             printUsage();
             if (!command || command === "--help" || command === "-h") {
@@ -2240,7 +3187,7 @@ async function main() {
         }
 
         if (command === "spec") {
-            commandSpec(options);
+            await commandSpec(options);
             return;
         }