@cleocode/core 2026.9.23 → 2026.9.25

package/dist/memory/mental-model-queue.js

@@ -7,10 +7,20 @@
  * decouples the hot path (agent execution) from I/O latency.
  *
  * The queue is drained to brain.db either:
- *   1. Periodically — every {@link FLUSH_INTERVAL_MS} milliseconds via a timer.
- *   2. On high watermark — when the queue exceeds {@link FLUSH_WATERMARK} entries.
- *   3. On process exit — SIGINT, SIGTERM, and 'exit' hooks perform a best-effort
- *      synchronous flush so no observations are lost.
+ *   1. Promptly — every `enqueue` schedules a drain on the next macrotask
+ *      (`setImmediate`, NOT unref'd), so observations enqueued in the same tick
+ *      are written as one batch and the caller's promise always settles (T12817).
+ *   2. Periodically — every {@link FLUSH_INTERVAL_MS} milliseconds via a timer
+ *      (backstop; unref'd).
+ *   3. On high watermark — when the queue exceeds {@link FLUSH_WATERMARK} entries.
+ *   4. On process exit — SIGINT, SIGTERM, and 'exit' hooks perform a best-effort
+ *      flush.
+ *
+ * T12817: before the prompt drain existed, the ONLY drain a one-shot process
+ * could reach was the unref'd 5 s timer. `enqueue()` returned a promise that
+ * only that timer could settle, so an awaited `cleo memory observe --agent X`
+ * left the event loop empty: Node exited 0 with zero bytes on stdout and the
+ * `'exit'` hook's async drain never ran — the observation was silently lost.
  *
  * Observations without an `agent` field continue to use the existing synchronous
  * path in observeBrain() and are never routed here.
@@ -45,12 +55,18 @@ const MENTAL_MODEL_TYPES = new Set([
 // ---------------------------------------------------------------------------
 /** In-memory queue of pending mental-model observations. */
 const _queue = [];
-/** Whether a flush is currently in progress (prevents re-entrant flushes). */
-let _flushing = false;
 /** Whether process-exit hooks have been registered. */
 let _hooksRegistered = false;
 /** Handle for the periodic flush timer (undefined = no active timer). */
 let _timer;
+/** Handle for the pending prompt drain (undefined = none scheduled). T12817 */
+let _immediate;
+/**
+ * Tail of the serialized drain chain. Every drain runs after the previous one
+ * settles, so entries enqueued while a drain is in flight are picked up by the
+ * next link instead of waiting for the unref'd timer. T12817
+ */
+let _drainTail = Promise.resolve();
 /**
  * Drain the queue synchronously where possible, or fall back to async writes.
  * Returns when all observations in the current batch have been persisted.
@@ -76,6 +92,33 @@ async function drainQueue() {
     }
     return count;
 }
+/**
+ * Run {@link drainQueue} after every earlier drain has settled.
+ *
+ * @returns The number of observations this drain persisted.
+ */
+function serialDrain() {
+    const next = _drainTail.then(() => drainQueue());
+    _drainTail = next.catch(() => undefined);
+    return next;
+}
+/**
+ * Schedule a prompt drain on the next macrotask (T12817).
+ *
+ * The handle is deliberately NOT unref'd: an enqueued observation is pending
+ * I/O the process owes its caller, so it must keep the event loop alive until
+ * written. Entries enqueued in the same tick share one drain.
+ */
+function schedulePromptDrain() {
+    if (_immediate !== undefined)
+        return;
+    _immediate = setImmediate(() => {
+        _immediate = undefined;
+        serialDrain().catch(() => {
+            /* per-entry errors already rejected their callers */
+        });
+    });
+}
 /**
  * Best-effort synchronous exit flush.
  * Used in 'exit' event handler where async I/O is not guaranteed.
@@ -137,15 +180,8 @@ function ensureTimer() {
     _timer = setInterval(() => {
         if (_queue.length === 0)
             return;
-        if (_flushing)
-            return;
-        _flushing = true;
-        drainQueue()
-            .catch(() => {
+        serialDrain().catch(() => {
             /* best-effort */
-        })
-            .finally(() => {
-            _flushing = false;
         });
     }, FLUSH_INTERVAL_MS);
     // Unref so the timer doesn't prevent process exit when queue is idle
@@ -168,31 +204,20 @@ export const mentalModelQueue = {
         ensureTimer();
         return new Promise((resolve, reject) => {
             _queue.push({ projectRoot, params, resolve, reject });
-            // High-watermark flush
-            if (_queue.length >= FLUSH_WATERMARK && !_flushing) {
-                _flushing = true;
-                drainQueue()
-                    .catch(() => {
+            if (_queue.length >= FLUSH_WATERMARK) {
+                // High-watermark flush
+                serialDrain().catch(() => {
                     /* best-effort */
-                })
-                    .finally(() => {
-                    _flushing = false;
                 });
             }
+            else {
+                // T12817: guarantee the caller's promise settles in a one-shot process.
+                schedulePromptDrain();
+            }
         });
     },
-    async flush() {
-        if (_flushing) {
-            // Wait for the current flush to settle then flush again
-            await new Promise((r) => setTimeout(r, 50));
-        }
-        _flushing = true;
-        try {
-            return await drainQueue();
-        }
-        finally {
-            _flushing = false;
-        }
+    flush() {
+        return serialDrain();
     },
     size() {
         return _queue.length;
@@ -216,13 +241,17 @@ export function _resetMentalModelQueueForTests() {
         clearInterval(_timer);
         _timer = undefined;
     }
+    if (_immediate !== undefined) {
+        clearImmediate(_immediate);
+        _immediate = undefined;
+    }
+    _drainTail = Promise.resolve();
     // Reject all pending observations so test assertions can proceed.
     const pending = _queue.splice(0, _queue.length);
     const cancelErr = new Error('[test teardown] mental-model queue reset');
     for (const entry of pending) {
         entry.reject(cancelErr);
     }
-    _flushing = false;
     _hooksRegistered = false;
 }
 /**

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package/dist/memory/patterns.d.ts

@@ -66,7 +66,7 @@ export declare function storePattern(projectRoot: string, params: StorePatternPa
     id: string;
     qualityScore: number | null;
     updatedAt: string | null;
-    memoryTier: "short" | "long" | "medium" | null;
+    memoryTier: "medium" | "short" | "long" | null;
     memoryType: "semantic" | "episodic" | "procedural" | null;
     verified: boolean;
     validAt: string;
@@ -85,7 +85,7 @@ export declare function storePattern(projectRoot: string, params: StorePatternPa
     context: string;
     frequency: number;
     successRate: number | null;
-    impact: "high" | "medium" | "low" | null;
+    impact: "low" | "medium" | "high" | null;
     antiPattern: string | null;
     mitigation: string | null;
     examplesJson: string | null;
@@ -130,7 +130,7 @@ export declare function searchPatterns(projectRoot: string, params?: SearchPatte
     id: string;
     qualityScore: number | null;
     updatedAt: string | null;
-    memoryTier: "short" | "long" | "medium" | null;
+    memoryTier: "medium" | "short" | "long" | null;
     memoryType: "semantic" | "episodic" | "procedural" | null;
     verified: boolean;
     validAt: string;
@@ -149,7 +149,7 @@ export declare function searchPatterns(projectRoot: string, params?: SearchPatte
     context: string;
     frequency: number;
     successRate: number | null;
-    impact: "high" | "medium" | "low" | null;
+    impact: "low" | "medium" | "high" | null;
     antiPattern: string | null;
     mitigation: string | null;
     examplesJson: string | null;

package/dist/memory/pipeline-manifest-sqlite.d.ts

@@ -16,6 +16,7 @@ import { docsPipelineManifest as pipelineManifest } from '../store/schema/cleo-p
 declare function getBinding(cwd?: string): Promise<import("../db/index.js").DomainBinding<import("drizzle-orm/node-sqlite/driver").NodeSQLiteDatabase<import("drizzle-orm").EmptyRelations>, import("../store/dual-scope-db.js").ProjectStore>>;
 import type { ContradictionDetail, ExtendedManifestEntry, ResearchFilter, SupersededDetail } from './index.js';
 import { filterManifestEntries } from './manifest-filter.js';
+import { type ManifestIdentityIssue } from './manifest-identity.js';
 export type ManifestEntry = ExtendedManifestEntry;
 export type { ContradictionDetail, ResearchFilter, SupersededDetail };
 export { filterManifestEntries };
@@ -84,6 +85,26 @@ export declare function readManifestEntriesSkippingMalformed(projectRoot?: strin
  * @task T12686
  */
 export declare function listMalformedManifestRows(projectRoot?: string): Promise<MalformedManifestRow[]>;
+/** A stored manifest row whose id, linked task ids or file reference fails T12829 validation. */
+export interface ManifestIdentityProblemRow {
+    /** Manifest entry id, truncated to 120 characters for display. */
+    entryId: string;
+    /** Tables holding the row (`docs_pipeline_manifest`, legacy `pipeline_manifest`). */
+    tables: string[];
+    /** The problems: `E_VALIDATION` (malformed or unsafe) or `E_NOT_FOUND` (linked task missing). */
+    issues: ManifestIdentityIssue[];
+}
+/**
+ * List every stored manifest row (archived included) whose entry id, linked
+ * task ids or file reference would be rejected by append today, and every
+ * well-formed linked task id that names no task. Read-only: the rows predate
+ * T12829 validation and are reported, never rewritten.
+ *
+ * @param projectRoot - Project root.
+ * @returns The offending rows, each with its problems.
+ * @task T12829
+ */
+export declare function listManifestIdentityProblems(projectRoot?: string): Promise<ManifestIdentityProblemRow[]>;
 /** One row a repair rewrote: its metadata before and after. */
 export interface ManifestRepairChange {
     entryId: string;
@@ -182,8 +203,22 @@ export declare function pipelineManifestPending(epicId?: string, projectRoot?: s
 export declare function pipelineManifestStats(epicId?: string, projectRoot?: string): Promise<EngineResult>;
 /** pipeline.manifest.read - Read manifest entries with optional filter */
 export declare function pipelineManifestRead(filter?: ResearchFilter, projectRoot?: string): Promise<EngineResult>;
-/** Append to canonical manifest storage after checking both histories for unresolved identities. */
-export declare function pipelineManifestAppend(entry: ExtendedManifestEntry, projectRoot?: string): Promise<EngineResult>;
+/** Options for {@link pipelineManifestAppend}. */
+export interface PipelineManifestAppendOptions {
+    /**
+     * Reject an entry whose linked task ids name no task in the project store
+     * (`E_NOT_FOUND`). The CLI/dispatch path sets it; direct SDK callers that
+     * record manifests for tasks held elsewhere may leave it off. Format checks
+     * on the id, linked task ids and file reference always run (T12829).
+     */
+    requireExistingTasks?: boolean;
+}
+/**
+ * Append to canonical manifest storage after checking both histories for
+ * unresolved identities. The entry id, linked task ids and file reference are
+ * validated first (T12829): no input can name a path outside the project.
+ */
+export declare function pipelineManifestAppend(entry: ExtendedManifestEntry, projectRoot?: string, options?: PipelineManifestAppendOptions): Promise<EngineResult>;
 /** pipeline.manifest.archive - Archive old manifest entries by date */
 export declare function pipelineManifestArchive(beforeDate: string, projectRoot?: string): Promise<EngineResult>;
 /** pipeline.manifest.compact - Dedup by contentHash (keep newest by createdAt) */
@@ -245,13 +280,20 @@ export declare function filterEntries(entries: ExtendedManifestEntry[], filter:
 export declare function distillManifestEntry(_entryId: string, _projectRoot?: string): Promise<EngineResult>;
 /**
  * Migrate existing .cleo/MANIFEST.jsonl entries into the pipeline_manifest table.
- * Skips entries that already exist (by id). Renames MANIFEST.jsonl to
- * MANIFEST.jsonl.migrated when done.
+ * Skips entries that already exist (by id). Entries whose id, linked task ids
+ * or file reference fail the T12829 identity checks are skipped, not inserted,
+ * and listed in `invalid`. Renames MANIFEST.jsonl to MANIFEST.jsonl.migrated
+ * when done.
  *
- * @returns Count of migrated and skipped entries.
+ * @returns Count of migrated and skipped entries (skipped includes invalid ones),
+ *   and every entry refused for an identity problem.
  */
 export declare function migrateManifestJsonlToSqlite(projectRoot?: string): Promise<{
     migrated: number;
     skipped: number;
+    invalid: Array<{
+        entryId: string;
+        issues: ManifestIdentityIssue[];
+    }>;
 }>;
 //# sourceMappingURL=pipeline-manifest-sqlite.d.ts.map

package/dist/memory/pipeline-manifest-sqlite.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"pipeline-manifest-sqlite.d.ts","sourceRoot":"","sources":["../../src/memory/pipeline-manifest-sqlite.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAMH,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAC;AAItF,OAAO,EAAsB,KAAK,YAAY,EAAqB,MAAM,qBAAqB,CAAC;AAE/F,OAAO,EAAE,oBAAoB,IAAI,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAOhG,iBAAe,UAAU,CAAC,GAAG,CAAC,EAAE,MAAM,wMAIrC;AAID,OAAO,KAAK,EACV,mBAAmB,EACnB,qBAAqB,EACrB,cAAc,EACd,gBAAgB,EACjB,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,qBAAqB,EAAE,MAAM,sBAAsB,CAAC;AAC7D,OAAO,EAEL,KAAK,qBAAqB,EAI3B,MAAM,wBAAwB,CAAC;AAGhC,MAAM,MAAM,aAAa,GAAG,qBAAqB,CAAC;AAClD,YAAY,EAAE,mBAAmB,EAAE,cAAc,EAAE,gBAAgB,EAAE,CAAC;AACtE,OAAO,EAAE,qBAAqB,EAAE,CAAC;AAEjC,UAAU,0BAA2B,SAAQ,cAAc;IACzD,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AA0HD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,aAAa,CAAC,OAAO,gBAAgB,CAAC,YAAY,CAAC,EACzD,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,OAAO,CAAC,UAAU,CAAC,OAAO,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC,GACvD,OAAO,CAAC,MAAM,CAAC,CA2CjB;AAiED,8DAA8D;AAC9D,MAAM,WAAW,oBAAoB;IACnC,yBAAyB;IACzB,OAAO,EAAE,MAAM,CAAC;IAChB,qFAAqF;IACrF,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,kGAAkG;IAClG,MAAM,EAAE,cAAc,GAAG,gBAAgB,CAAC;IAC1C,2EAA2E;IAC3E,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,gCAAgC;IAChC,OAAO,EAAE,MAAM,CAAC;IAChB,2CAA2C;IAC3C,cAAc,EAAE,MAAM,CAAC;CACxB;AAED,qFAAqF;AACrF,eAAO,MAAM,2BAA2B,uCAAuC,CAAC;AAEhF,+EAA+E;AAC/E,eAAO,MAAM,0BAA0B,+CAA+C,CAAC;AA4CvF;;;;;;;;;;GAUG;AACH,wBAAsB,oCAAoC,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC;IACxF,OAAO,EAAE,KAAK,CAAC,sBAAsB,CAAC,qBAAqB,CAAC,CAAC,CAAC;IAC9D,SAAS,EAAE,oBAAoB,EAAE,CAAC;CACnC,CAAC,CASD;AAED;;;;;;;GAOG;AACH,wBAAsB,yBAAyB,CAC7C,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,oBAAoB,EAAE,CAAC,CAEjC;AAED,iGAAiG;AACjG,MAAM,WAAW,0BAA0B;IACzC,kEAAkE;IAClE,OAAO,EAAE,MAAM,CAAC;IAChB,qFAAqF;IACrF,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,iGAAiG;IACjG,MAAM,EAAE,qBAAqB,EAAE,CAAC;CACjC;AAED;;;;;;;;;GASG;AACH,wBAAsB,4BAA4B,CAChD,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,0BAA0B,EAAE,CAAC,CA+CvC;AAED,+DAA+D;AAC/D,MAAM,WAAW,oBAAoB;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,MAAM,EAAE,oBAAoB,CAAC,QAAQ,CAAC,CAAC;IACvC,MAAM,EAAE,MAAM,EAAE,CAAC;IACjB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,KAAK,EAAE,MAAM,CAAC;CACf;AAED,8EAA8E;AAC9E,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,0BAA0B,CAAC;IACjC,IAAI,EAAE,QAAQ,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,MAAM,EAAE,OAAO,CAAC;IAChB;;;OAGG;IACH,OAAO,EAAE,oBAAoB,EAAE,CAAC;IAChC;;;;OAIG;IACH,OAAO,EAAE,kBAAkB,GAAG,IAAI,CAAC;CACpC;AAED,wEAAwE;AACxE,MAAM,WAAW,kBAAkB;IACjC,0DAA0D;IAC1D,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,+EAA+E;IAC/E,OAAO,EAAE,MAAM,EAAE,CAAC;CACnB;AAyBD;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAsB,2BAA2B,CAC/C,WAAW,CAAC,EAAE,MAAM,EACpB,IAAI,GAAE;IAAE,MAAM,CAAC,EAAE,OAAO,CAAA;CAAO,GAC9B,OAAO,CAAC,qBAAqB,CAAC,CA8ChC;AAED;;;;;;;;;GASG;AACH,wBAAsB,sBAAsB,CAC1C,WAAW,EAAE,MAAM,EACnB,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,kBAAkB,CAAC,CAU7B;AAiID;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,oBAAoB,CACxC,UAAU,EAAE,MAAM,EAClB,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAmHvB;AAED,kEAAkE;AAClE,wBAAsB,oBAAoB,CACxC,MAAM,EAAE,0BAA0B,EAClC,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CA4BvB;AAED,6FAA6F;AAC7F,wBAAsB,oBAAoB,CACxC,KAAK,EAAE,MAAM,EACb,OAAO,CAAC,EAAE;IAAE,UAAU,CAAC,EAAE,MAAM,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,EACjD,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAwEvB;AAED,6DAA6D;AAC7D,wBAAsB,uBAAuB,CAC3C,MAAM,CAAC,EAAE,MAAM,EACf,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAoCvB;AAED,oDAAoD;AACpD,wBAAsB,qBAAqB,CACzC,MAAM,CAAC,EAAE,MAAM,EACf,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CA2CvB;AAED,0EAA0E;AAC1E,wBAAsB,oBAAoB,CACxC,MAAM,CAAC,EAAE,cAAc,EACvB,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAiBvB;AAED,kDAAkD;AAClD,MAAM,WAAW,6BAA6B;IAC5C;;;;;OAKG;IACH,oBAAoB,CAAC,EAAE,OAAO,CAAC;CAChC;AAmBD;;;;GAIG;AACH,wBAAsB,sBAAsB,CAC1C,KAAK,EAAE,qBAAqB,EAC5B,WAAW,CAAC,EAAE,MAAM,EACpB,OAAO,GAAE,6BAAkC,GAC1C,OAAO,CAAC,YAAY,CAAC,CA4EvB;AAED,uEAAuE;AACvE,wBAAsB,uBAAuB,CAC3C,UAAU,EAAE,MAAM,EAClB,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAuCvB;AAED,kFAAkF;AAClF,wBAAsB,uBAAuB,CAAC,WAAW,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC,CAqCzF;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,wBAAwB,CAC5C,MAAM,EAAE,MAAM,EACd,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAgHvB;AAED,2GAA2G;AAC3G,wBAAsB,8BAA8B,CAClD,WAAW,CAAC,EAAE,MAAM,EACpB,MAAM,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,GAC1B,OAAO,CAAC,YAAY,CAAC;IAAE,cAAc,EAAE,mBAAmB,EAAE,CAAA;CAAE,CAAC,CAAC,CA2ElE;AAED,2FAA2F;AAC3F,wBAAsB,0BAA0B,CAC9C,WAAW,CAAC,EAAE,MAAM,EACpB,MAAM,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,GAC1B,OAAO,CAAC,YAAY,CAAC;IAAE,UAAU,EAAE,gBAAgB,EAAE,CAAA;CAAE,CAAC,CAAC,CAyC3D;AAED,6DAA6D;AAC7D,wBAAsB,oBAAoB,CACxC,MAAM,EAAE,MAAM,EACd,UAAU,EAAE,MAAM,EAClB,KAAK,CAAC,EAAE,MAAM,EACd,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,YAAY,CAAC,CAkDvB;AAMD;;;;;;;;;;;;;GAaG;AACH,wBAAsB,mBAAmB,CACvC,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,KAAK,CAAC,sBAAsB,CAAC,qBAAqB,CAAC,CAAC,CAAC,CAE/D;AAED;;GAEG;AACH,wBAAgB,aAAa,CAC3B,OAAO,EAAE,qBAAqB,EAAE,EAChC,MAAM,EAAE,cAAc,G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package/dist/memory/pipeline-manifest-sqlite.js

@@ -32,6 +32,7 @@ async function getBinding(cwd) {
 import { createPage } from '../pagination.js';
 import { getProjectRoot, resolveCleoDir } from '../paths.js';
 import { filterManifestEntries } from './manifest-filter.js';
+import { findMissingLinkedTasks, manifestEntryIdProblem, manifestIdentityIssues, readContainedFile, } from './manifest-identity.js';
 export { filterManifestEntries };
 function normalizeLimit(limit) {
     return typeof limit === 'number' && limit > 0 ? limit : undefined;
@@ -324,6 +325,54 @@ export async function readManifestEntriesSkippingMalformed(projectRoot) {
 export async function listMalformedManifestRows(projectRoot) {
     return (await readRows(projectRoot, true)).flatMap((row) => metadataProblem(row) ?? []);
 }
+/**
+ * List every stored manifest row (archived included) whose entry id, linked
+ * task ids or file reference would be rejected by append today, and every
+ * well-formed linked task id that names no task. Read-only: the rows predate
+ * T12829 validation and are reported, never rewritten.
+ *
+ * @param projectRoot - Project root.
+ * @returns The offending rows, each with its problems.
+ * @task T12829
+ */
+export async function listManifestIdentityProblems(projectRoot) {
+    const scope = manifestScope(projectRoot);
+    const checked = (await readRows(scope.worktreeRoot, true)).map((row) => {
+        // A row with unreadable metadata is `listMalformedManifestRows`' finding;
+        // here it falls back to the columns.
+        const meta = metadataProblem(row) === null ? readRowMetadata(row) : undefined;
+        const linkedTasks = meta?.linked_tasks ?? (row.taskId ? [row.taskId] : []);
+        const file = meta?.file ?? row.sourceFile ?? undefined;
+        return {
+            row,
+            linkedTasks,
+            issues: manifestIdentityIssues({ id: row.id, linked_tasks: linkedTasks, file }, scope.worktreeRoot),
+        };
+    });
+    const missing = new Set(await worktreeScope.run(scope, () => findMissingLinkedTasks(checked.flatMap((c) => c.linkedTasks), scope.worktreeRoot)));
+    return checked.flatMap(({ row, linkedTasks, issues }) => {
+        const all = [
+            ...issues,
+            ...linkedTasks
+                .filter((id) => missing.has(id))
+                .map((id) => ({
+                field: 'linked_tasks',
+                code: 'E_NOT_FOUND',
+                value: id,
+                message: 'no such task in this project',
+            })),
+        ];
+        if (all.length === 0)
+            return [];
+        return [
+            {
+                entryId: row.id.length <= 120 ? row.id : `${row.id.slice(0, 120)}… (${row.id.length} chars)`,
+                tables: [...row.provenance.tables],
+                issues: all,
+            },
+        ];
+    });
+}
 /**
  * Rewrite one malformed metadata document so it conforms, keeping every byte:
  * an offending field moves under `_malformed.<field>`; an unparseable or
@@ -561,6 +610,19 @@ export async function pipelineManifestShow(researchId, projectRoot) {
             error: { code: 'E_INVALID_INPUT', message: 'researchId is required' },
         };
     }
+    // T12829: a malformed id can never have been stored by append; refuse it
+    // before it reaches the store or any path.
+    const idProblem = manifestEntryIdProblem(researchId);
+    if (idProblem) {
+        return {
+            success: false,
+            error: {
+                code: 'E_VALIDATION',
+                message: `Invalid manifest entry id: ${idProblem}`,
+                details: { field: 'id', length: researchId.length },
+            },
+        };
+    }
     try {
         const scope = manifestScope(projectRoot);
         const rows = await readRows(scope.worktreeRoot, true, researchId);
@@ -625,13 +687,20 @@ export async function pipelineManifestShow(researchId, projectRoot) {
             });
         }
         else if (entry.file) {
-            try {
-                fileContent = readFileSync(join(scope.worktreeRoot, entry.file), 'utf-8');
-            }
-            catch (error) {
-                if (!(error instanceof Error && 'code' in error && error.code === 'ENOENT'))
-                    throw error;
+            // T12829: never read a file reference that escapes the project (or
+            // whose name the filesystem cannot hold) — rows stored before append
+            // validated `file` may carry one. The read resolves real paths, so an
+            // in-project symlink pointing outside the project is refused too.
+            const read = readContainedFile(scope.worktreeRoot, entry.file);
+            if (read.status === 'unsafe') {
+                throw new EngineResultError({
+                    code: 'E_MANIFEST_FILE_UNSAFE',
+                    message: `Manifest '${researchId}' has an unsafe file reference (${read.reason}); it was not read. Run \`cleo doctor manifest-rows\` to list such rows.`,
+                    details: { entryId: researchId, field: 'file' },
+                });
             }
+            if (read.status === 'ok')
+                fileContent = read.content;
         }
         return {
             success: true,
@@ -812,8 +881,28 @@ export async function pipelineManifestRead(filter, projectRoot) {
         return manifestFailure('E_MANIFEST_READ', error instanceof Error ? error : new Error(String(error)));
     }
 }
-/** Append to canonical manifest storage after checking both histories for unresolved identities. */
-export async function pipelineManifestAppend(entry, projectRoot) {
+/**
+ * Build the failure for identity problems, preferring `E_VALIDATION` over
+ * `E_NOT_FOUND` so a malformed value is reported before a missing task.
+ */
+function identityFailure(issues) {
+    const code = issues.some((i) => i.code === 'E_VALIDATION') ? 'E_VALIDATION' : 'E_NOT_FOUND';
+    const shown = issues.filter((i) => i.code === code);
+    return {
+        success: false,
+        error: {
+            code,
+            message: `Invalid manifest entry: ${shown.map((i) => `${i.field} '${i.value}': ${i.message}`).join('; ')}`,
+            details: { field: shown[0]?.field, issues },
+        },
+    };
+}
+/**
+ * Append to canonical manifest storage after checking both histories for
+ * unresolved identities. The entry id, linked task ids and file reference are
+ * validated first (T12829): no input can name a path outside the project.
+ */
+export async function pipelineManifestAppend(entry, projectRoot, options = {}) {
     if (!entry) {
         return { success: false, error: { code: 'E_INVALID_INPUT', message: 'entry is required' } };
     }
@@ -843,6 +932,21 @@ export async function pipelineManifestAppend(entry, projectRoot) {
             },
         };
     }
+    const scope = manifestScope(projectRoot);
+    const issues = manifestIdentityIssues(entry, scope.worktreeRoot);
+    if (issues.length > 0)
+        return identityFailure(issues);
+    if (options.requireExistingTasks === true && (entry.linked_tasks?.length ?? 0) > 0) {
+        const missing = await worktreeScope.run(scope, () => findMissingLinkedTasks(entry.linked_tasks ?? [], scope.worktreeRoot));
+        if (missing.length > 0) {
+            return identityFailure(missing.map((id) => ({
+                field: 'linked_tasks',
+                code: 'E_NOT_FOUND',
+                value: id,
+                message: 'no such task in this project',
+            })));
+        }
+    }
     try {
         const binding = await getBinding(projectRoot);
         const row = entryToRow(entry);
@@ -1247,16 +1351,19 @@ export async function distillManifestEntry(_entryId, _projectRoot) {
 // ============================================================================
 /**
  * Migrate existing .cleo/MANIFEST.jsonl entries into the pipeline_manifest table.
- * Skips entries that already exist (by id). Renames MANIFEST.jsonl to
- * MANIFEST.jsonl.migrated when done.
+ * Skips entries that already exist (by id). Entries whose id, linked task ids
+ * or file reference fail the T12829 identity checks are skipped, not inserted,
+ * and listed in `invalid`. Renames MANIFEST.jsonl to MANIFEST.jsonl.migrated
+ * when done.
  *
- * @returns Count of migrated and skipped entries.
+ * @returns Count of migrated and skipped entries (skipped includes invalid ones),
+ *   and every entry refused for an identity problem.
  */
 export async function migrateManifestJsonlToSqlite(projectRoot) {
     const root = manifestScope(projectRoot).worktreeRoot;
     const manifestPath = join(resolveCleoDir(root), 'MANIFEST.jsonl');
     if (!existsSync(manifestPath)) {
-        return { migrated: 0, skipped: 0 };
+        return { migrated: 0, skipped: 0, invalid: [] };
     }
     const content = readFileSync(manifestPath, 'utf-8');
     const lines = content.split('\n');
@@ -1273,17 +1380,26 @@ export async function migrateManifestJsonlToSqlite(projectRoot) {
         }
     }
     if (entries.length === 0) {
-        return { migrated: 0, skipped: 0 };
+        return { migrated: 0, skipped: 0, invalid: [] };
     }
     const binding = await getBinding(projectRoot);
     const db = binding.db;
     let migrated = 0;
     let skipped = 0;
+    const invalid = [];
     for (const entry of entries) {
         if (!entry.id) {
             skipped++;
             continue;
         }
+        // T12829: never import an identity append would refuse (bad id, bad
+        // linked task id, or a file reference that escapes the project).
+        const issues = manifestIdentityIssues(entry, root);
+        if (issues.length > 0) {
+            invalid.push({ entryId: String(entry.id).slice(0, 120), issues });
+            skipped++;
+            continue;
+        }
         const inserted = db.transaction(() => {
             const existing = readStoredRows(binding, true, entry.id);
             requireModernRows(existing);
@@ -1304,6 +1420,6 @@ export async function migrateManifestJsonlToSqlite(projectRoot) {
     catch {
         // Non-fatal — file may already be renamed or locked
     }
-    return { migrated, skipped };
+    return { migrated, skipped, invalid };
 }
 //# sourceMappingURL=pipeline-manifest-sqlite.js.map