@co-engram/core 0.1.3 → 0.1.5

package/dist/storage/index-cleanup.d.ts

@@ -0,0 +1,45 @@
+/**
+ * 派生索引 dangling reference 自愈(post-doctor cleanup)。
+ *
+ * 触发场景:
+ *   - 用户外部删除 .md 文件(git rm / rm / IDE 删除)
+ *   - runDoctor 清理 engram-index.json(去除 missing_file entry)
+ *   - **但**派生索引(observation-windows.jsonl / digest.jsonl / graph.json)
+ *     仍保留被删 engram 的 id → engram_search 返回 stale 结果 / viewer 显示重影
+ *
+ * 本模块在 runDoctor 完成后运行,基于 canonicalIds 清除这些悬空引用。
+ *
+ * 设计:
+ *   - 纯函数,失败不抛(返回空 issues),让上层 doctor 主流程继续
+ *   - 幂等(过滤逻辑重复运行结果一致)
+ *   - 廉价:observation-windows 直接过滤;digest/graph 检测到悬空才 fullRebuild
+ *
+ * 检查范围:
+ *   1. observation-windows.jsonl  — filter in-place by engramId
+ *   2. digest.jsonl + graph.json  — 检测到悬空则触发 IndexOrchestrator.fullRebuild
+ *
+ * 不检查(无 engram id 引用):
+ *   - topic-clusters.jsonl — 引用 cluster.id(短 hash),与 engram 无关
+ *   - proposals.jsonl      — entityId = cluster.id 或外部 .md path,非 engram id
+ *   - prompt-signals.json  — 字段是 tag 字符串
+ *   - audit.jsonl          — append-only 历史日志,不应清理
+ *
+ * @module @co-engram/core/storage
+ */
+import type { EngramRepository } from "./repository.js";
+import type { DoctorIssue } from "../types/repository-types.js";
+export interface IndexCleanupResult {
+    readonly fixes: readonly DoctorIssue[];
+}
+/**
+ * 清除派生索引中对已不存在 engram 的引用。
+ *
+ * 在 runDoctor 完成后调用 —— 此时 engram-index.json 已被刷新,
+ * canonicalIds 应来自 readEngramIndex(dataRoot).entries 或等价途径。
+ */
+export declare function cleanupDanglingIndexReferences(params: {
+    readonly repo: EngramRepository;
+    readonly dataRoot: string;
+    readonly canonicalIds: ReadonlySet<string>;
+}): IndexCleanupResult;
+//# sourceMappingURL=index-cleanup.d.ts.map

package/dist/storage/index-cleanup.d.ts.map

@@ -0,0 +1 @@
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package/dist/storage/index-cleanup.js

@@ -0,0 +1,186 @@
+/**
+ * 派生索引 dangling reference 自愈(post-doctor cleanup)。
+ *
+ * 触发场景:
+ *   - 用户外部删除 .md 文件(git rm / rm / IDE 删除)
+ *   - runDoctor 清理 engram-index.json(去除 missing_file entry)
+ *   - **但**派生索引(observation-windows.jsonl / digest.jsonl / graph.json)
+ *     仍保留被删 engram 的 id → engram_search 返回 stale 结果 / viewer 显示重影
+ *
+ * 本模块在 runDoctor 完成后运行,基于 canonicalIds 清除这些悬空引用。
+ *
+ * 设计:
+ *   - 纯函数,失败不抛(返回空 issues),让上层 doctor 主流程继续
+ *   - 幂等(过滤逻辑重复运行结果一致)
+ *   - 廉价:observation-windows 直接过滤;digest/graph 检测到悬空才 fullRebuild
+ *
+ * 检查范围:
+ *   1. observation-windows.jsonl  — filter in-place by engramId
+ *   2. digest.jsonl + graph.json  — 检测到悬空则触发 IndexOrchestrator.fullRebuild
+ *
+ * 不检查(无 engram id 引用):
+ *   - topic-clusters.jsonl — 引用 cluster.id(短 hash),与 engram 无关
+ *   - proposals.jsonl      — entityId = cluster.id 或外部 .md path,非 engram id
+ *   - prompt-signals.json  — 字段是 tag 字符串
+ *   - audit.jsonl          — append-only 历史日志,不应清理
+ *
+ * @module @co-engram/core/storage
+ */
+import { existsSync, readFileSync, writeFileSync, mkdirSync } from "node:fs";
+import { dirname, join } from "node:path";
+import { IndexOrchestrator, defaultCachePath } from "../index/orchestrator.js";
+/**
+ * 清除派生索引中对已不存在 engram 的引用。
+ *
+ * 在 runDoctor 完成后调用 —— 此时 engram-index.json 已被刷新,
+ * canonicalIds 应来自 readEngramIndex(dataRoot).entries 或等价途径。
+ */
+export function cleanupDanglingIndexReferences(params) {
+    const { repo, dataRoot, canonicalIds } = params;
+    const fixes = [];
+    const cachePath = defaultCachePath(dataRoot);
+    const windowsFix = cleanupObservationWindows(cachePath, canonicalIds);
+    if (windowsFix)
+        fixes.push(windowsFix);
+    const digestGraphFix = rebuildDigestGraphIfStale(repo, cachePath, canonicalIds);
+    if (digestGraphFix)
+        fixes.push(digestGraphFix);
+    return { fixes };
+}
+/**
+ * 过滤 observation-windows.jsonl,删除 engramId 不在 canonicalIds 中的行。
+ *
+ * 文件格式:JSONL,每行 { id, engramId, query, score, hitAt, deadline, kind, status }。
+ * 直接 in-place 重写(append-mostly 日志,过滤是正确语义)。
+ */
+function cleanupObservationWindows(cachePath, canonicalIds) {
+    const filePath = join(cachePath, "observation-windows.jsonl");
+    if (!existsSync(filePath))
+        return null;
+    let raw;
+    try {
+        raw = readFileSync(filePath, "utf8");
+    }
+    catch {
+        return null;
+    }
+    const lines = raw.split("\n");
+    let removed = 0;
+    const kept = [];
+    for (const line of lines) {
+        const trimmed = line.trim();
+        if (!trimmed)
+            continue;
+        let isDangling = false;
+        try {
+            const parsed = JSON.parse(trimmed);
+            if (typeof parsed.engramId === "string" &&
+                !canonicalIds.has(parsed.engramId)) {
+                isDangling = true;
+            }
+        }
+        catch {
+            // 保留无法解析的行(让 audit / 人工检查)
+        }
+        if (isDangling) {
+            removed++;
+            continue;
+        }
+        kept.push(trimmed);
+    }
+    if (removed === 0)
+        return null;
+    try {
+        mkdirSync(dirname(filePath), { recursive: true });
+        writeFileSync(filePath, kept.length > 0 ? kept.join("\n") + "\n" : "", "utf8");
+    }
+    catch {
+        return null;
+    }
+    return {
+        kind: "dangling_index_reference",
+        path: filePath,
+        message: `Removed ${removed} dangling observation window(s) whose engramId no longer exists`,
+        autoFixed: true,
+    };
+}
+/**
+ * 检测 digest.jsonl 与 graph.json 中的 dangling engram id。
+ *
+ * 若发现任何悬空,触发 IndexOrchestrator.fullRebuild
+ * (fullRebuild 一次性重建 digest + graph,保证二者一致)。
+ *
+ * 检测代价:O(digest 行数 + graph 节点数 + graph 边数)。
+ * 重建代价:仅在检测到悬空时才发生,常见路径(doctored 之后的稳态)开销为 0。
+ */
+function rebuildDigestGraphIfStale(repo, cachePath, canonicalIds) {
+    const digestPath = join(cachePath, "digest.jsonl");
+    const graphPath = join(cachePath, "graph.json");
+    let digestDangling = 0;
+    let graphDangling = 0;
+    if (existsSync(digestPath)) {
+        try {
+            const raw = readFileSync(digestPath, "utf8");
+            for (const line of raw.split("\n")) {
+                const trimmed = line.trim();
+                if (!trimmed)
+                    continue;
+                try {
+                    const parsed = JSON.parse(trimmed);
+                    if (typeof parsed.id === "string" && !canonicalIds.has(parsed.id)) {
+                        digestDangling++;
+                    }
+                }
+                catch {
+                    // 跳过无效行(不是 dangling,只是损坏 — 让别处报)
+                }
+            }
+        }
+        catch {
+            // 读失败:当作无 dangling,跳过
+        }
+    }
+    if (existsSync(graphPath)) {
+        try {
+            const raw = readFileSync(graphPath, "utf8");
+            const parsed = JSON.parse(raw);
+            for (const node of parsed.nodes ?? []) {
+                if (typeof node.id === "string" && !canonicalIds.has(node.id)) {
+                    graphDangling++;
+                }
+            }
+            for (const edge of parsed.edges ?? []) {
+                if (typeof edge.from === "string" && !canonicalIds.has(edge.from)) {
+                    graphDangling++;
+                }
+                if (typeof edge.to === "string" && !canonicalIds.has(edge.to)) {
+                    graphDangling++;
+                }
+            }
+        }
+        catch {
+            // 读失败:当作无 dangling,跳过
+        }
+    }
+    if (digestDangling === 0 && graphDangling === 0)
+        return null;
+    try {
+        const orchestrator = new IndexOrchestrator(repo, cachePath);
+        const result = orchestrator.fullRebuild();
+        return {
+            kind: "dangling_index_reference",
+            path: cachePath,
+            message: `Rebuilt stale derived indexes (digest had ${digestDangling} dangling entr${digestDangling === 1 ? "y" : "ies"}, graph had ${graphDangling} dangling ref${graphDangling === 1 ? "" : "s"}; rebuild produced digest=${result.digest.total}, graph nodes=${result.graph.nodes}, edges=${result.graph.edges})`,
+            autoFixed: true,
+        };
+    }
+    catch {
+        return {
+            kind: "dangling_index_reference",
+            path: cachePath,
+            message: `Detected ${digestDangling} dangling digest entry/${graphDangling} dangling graph ref but fullRebuild failed (check logs)`,
+            autoFixed: false,
+        };
+    }
+}
+//# sourceMappingURL=index-cleanup.js.map

package/dist/storage/index-cleanup.js.map

@@ -0,0 +1 @@
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package/dist/storage/index.d.ts

@@ -12,4 +12,5 @@ export * from "./git-stage.js";
 export * from "./engram-index.js";
 export * from "./repository.js";
 export * from "./infra-doctor.js";
+export * from "./index-cleanup.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/storage/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/storage/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,cAAc,WAAW,CAAC;AAC1B,cAAc,WAAW,CAAC;AAC1B,cAAc,mBAAmB,CAAC;AAClC,cAAc,oBAAoB,CAAC;AACnC,cAAc,UAAU,CAAC;AACzB,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAClC,cAAc,iBAAiB,CAAC;AAChC,cAAc,mBAAmB,CAAC;AAClC,cAAc,oBAAoB,CAAC"}

package/dist/storage/index.js

@@ -12,4 +12,5 @@ export * from "./git-stage.js";
 export * from "./engram-index.js";
 export * from "./repository.js";
 export * from "./infra-doctor.js";
+export * from "./index-cleanup.js";
 //# sourceMappingURL=index.js.map

package/dist/storage/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/storage/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,cAAc,WAAW,CAAC;AAC1B,cAAc,WAAW,CAAC;AAC1B,cAAc,mBAAmB,CAAC;AAClC,cAAc,oBAAoB,CAAC;AACnC,cAAc,UAAU,CAAC;AACzB,cAAc,gBAAgB,CAAC;AAC/B,cAAc,mBAAmB,CAAC;AAClC,cAAc,iBAAiB,CAAC;AAChC,cAAc,mBAAmB,CAAC;AAClC,cAAc,oBAAoB,CAAC"}

package/dist/storage/repository.d.ts

@@ -15,6 +15,7 @@
 import type { Engram, EngramCatalogEntry, EngramCreateInput, EngramDigest, EngramFreshness, EngramStatus, EngramUpdateInput, ImportanceVector, VerificationStatus, Synapse, SynapseCreateInput, SynapseEvidence, SynapseKind, SynapseResolutionState, SynapseUpdateInput } from "../types/index.js";
 import type { EngramIndexEntry, DoctorReport, PathTreeNode } from "../types/repository-types.js";
 import { type Language } from "../i18n/index.js";
+import { type EngramFile } from "./engram-store.js";
 import { type EngramIndexMap } from "./engram-index.js";
 /** Repository 配置 */
 export interface RepositoryConfig {
@@ -31,6 +32,29 @@ export interface RepositoryConfig {
      */
     readonly language?: Language;
 }
+/**
+ * 外部 .md 检测钩子参数:watcher 发现 dataRoot 下未追踪的 .md 文件时构造。
+ *
+ * - `absPath`:文件绝对路径,host 可读取内容做进一步处理
+ * - `relPath`:相对 rootPath 的路径(用于提案展示与去重命名空间)
+ * - `raw`:文件原始内容(避免 hook 反复读盘)
+ * - `parsed`:尝试解析 frontmatter 的结果;`null` 表示文件不是合法 engram
+ *   格式(无 frontmatter 或解析失败)—— host 通常应当跳过此类文件
+ */
+export interface ExternalMarkdownHookParams {
+    readonly absPath: string;
+    readonly relPath: string;
+    readonly raw: string;
+    readonly parsed: EngramFile | null;
+}
+/**
+ * 外部 .md 检测钩子签名。
+ *
+ * 由 host 适配层(claude-code-mcp / openclaw-plugin)实现,绑定到
+ * ProposalEngine.proposeExternalMarkdown,把"未授权来源"的 .md 转成
+ * 待审批提案而非直接落库。
+ */
+export type ExternalMarkdownHook = (params: ExternalMarkdownHookParams) => void;
 /**
  * EngramRepository — per-edge synapse + ULID stable id + 单文件 engram
  *
@@ -57,6 +81,32 @@ export declare class EngramRepository {
      * 会立即触发缓存失效,无需等下次 getIndex 的 mtime 兜底检查。
      */
     private indexWatcher;
+    /**
+     * 递归 fs.watch 句柄,监听 dataRoot 下所有 .md 文件变化(可选)。
+     *
+     * 触发场景(关键):git pull / git checkout / 手动编辑 / rsync / 用户拷贝文件
+     * 等任何外部写入 .md 的途径,startWatching() 单独监听 index.json 看不到这些变化。
+     *
+     * 信任边界设计(关键安全语义):
+     *   - git pull 来的 .md → 由 post-merge hook 调 runDoctor 自动接受(团队可信)
+     *   - 其他来源的 .md(用户拷贝、IDE 写入等)→ **不**自动接受,通过
+     *     externalMarkdownHook 通知 host 适配层形成 proposal,等用户审批
+     *   - watcher 自身只做"扫描 + diff + 通知 hook",不写 index.json
+     *   - 安全动机:防止恶意/误植的 .md 通过文件系统投毒直接进入团队记忆库
+     */
+    private dataWatcher;
+    /** dataWatcher debounce 定时器。git pull 一次性触发大量事件,合并为一次扫描。 */
+    private dataRebuildTimer;
+    /**
+     * 外部 .md 检测钩子(由 host 适配层设置)。
+     *
+     * watcher 扫描发现"dataRoot 下存在但 index 中没有"的 .md 文件时调用。
+     * host 适配层通常把回调绑到 ProposalEngine.proposeExternalMarkdown,
+     * 让用户审批后再决定是否纳入团队记忆。
+     *
+     * 未设置时 → watcher 发现新 .md 仅记录 orphan,不自动接受(noop)。
+     */
+    private externalMarkdownHook;
     private readonly language;
     constructor(config: RepositoryConfig);
     /** 当前写入语言(读取时自动兼容任意语言格式) */
@@ -103,20 +153,71 @@ export declare class EngramRepository {
      */
     private purgeStaleIndexEntriesForPath;
     /**
-     * 启动对 engram-index.json 的 fs.watch 监听。
+     * 启动对 engram-index.json 的 fs.watch 监听 + dataRoot .md 递归监听。
      *
-     * 启动后,外部进程修改 index(创建/更新/删除 engram)会触发 watcher,
-     * 主动失效 indexCache。下次 getIndex 调用时从磁盘重读。
+     * 启动后:
+     *   - index.json watcher:外部进程修改 index(创建/更新/删除 engram)→ 失效 cache
+     *   - dataRoot .md watcher:任何途径(git pull / checkout / 手动编辑 / 用户拷贝)
+     *     写入 .md → debounce 后扫描,diff 出"未在 index 中的 .md"并通过
+     *     externalMarkdownHook 通知 host 适配层。**watcher 自身不写 index**。
      *
-     * 幂等:多次调用安全,只创建一个 watcher。
+     * 信任边界(安全关键):
+     *   - git pull 来源由 post-merge hook 调 runDoctor 接受,不依赖 watcher
+     *   - 其他来源由 host 通过 hook 决策(典型:形成 proposal 等待用户审批)
+     *   - 防止"用户拷贝恶意 .md → 直接进团队记忆库"的攻击面
      *
-     * 适用场景:多个 host adapter(MCP server / OpenClaw plugin)共享同一
-     * dataRoot 时,确保各进程的缓存相互一致。
+     * 幂等:多次调用安全,只创建一个 watcher。
      *
      * 不需要显式停止 — 进程退出时 OS 自动回收 fd。stopWatching() 仅用于
      * 测试 / 显式资源管理场景。
      */
     startWatching(): void;
+    /**
+     * 注册外部 .md 检测钩子。host 适配层应在创建 repository + ProposalEngine
+     * 之后、调用 startWatching 之前设置钩子,以确保 watcher 触发时回调就绪。
+     *
+     * @returns 取消注册函数(测试隔离 / 资源释放用)
+     */
+    setExternalMarkdownHook(hook: ExternalMarkdownHook): () => void;
+    /**
+     * 启动 dataRoot 下 .md 文件的递归 fs.watch。
+     *
+     * Node 22+ 在 Linux/macOS/Windows 都支持 `recursive: true`(Linux 通过 inotify)。
+     * 不支持的平台(NFS / 老 Node)→ catch 后 noop,startWatching 的 index.json
+     * watcher + getIndex 的 mtime 兜底仍然有效。
+     *
+     * 触发后 debounce 调用 scanForExternalMarkdown(只读 + hook 通知),
+     * **不**调用 rebuildIndex(避免 untrusted .md 直接落库)。
+     */
+    private startDataRootWatcher;
+    /**
+     * Debounce 扫描,合并短时间内的多次 .md 变化事件。
+     *
+     * git pull / rsync 等批量操作会一次性产生几十~几百个事件,逐个扫描会卡死。
+     * 2000ms debounce 既合并事件,也给 post-merge hook(post-merge 在 git pull
+     * 完成后同步执行)足够时间完成可信路径的 index 写入,避免 watcher 与
+     * post-merge 同时处理同一批文件造成竞争。
+     */
+    private scheduleDataScan;
+    /**
+     * 扫描 dataRoot 下所有 .md,diff 出"未在 index 中的 .md",逐个调用
+     * externalMarkdownHook(若设置)。
+     *
+     * 关键不变量:
+     *   - **不**写 engram-index.json(防止 untrusted .md 直接进 index)
+     *   - **不**调用 getIndex() — getIndex 在 index.json 缺失时会触发 rebuildIndex
+     *     把所有合法 .md 灌入,这会让"未追踪"判定全部失效。这里直接读
+     *     index.json,不存在则视为空集合,所有 .md 都视为未追踪。
+     *   - 已在 index.json 中的 .md → noop(post-merge 或 engram_create 已处理)
+     *   - 未设置 hook → noop(等价于"未启用外部提案",安全默认)
+     *   - hook 自身负责去重(典型:ProposalEngine.proposeExternalMarkdown
+     *     检查 proposal 状态:pending/accepted/dismissed 都返回 no-change)
+     *
+     * 性能:全量扫盘读所有 .md,大仓库(>10k 文件)可能耗时数百毫秒。
+     * 可接受因为:(1) 2s debounce 已经限频;(2) post-merge hook 通常先完成,
+     * 大部分 .md 已在 index,scan 仅对增量做 hook 调用。
+     */
+    private scanForExternalMarkdown;
     /** 停止 watcher(主要用于测试隔离) */
     stopWatching(): void;
     /** 失效缓存 — 下次 getIndex 从磁盘重读。同时通知 invalidate listeners。 */

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