@cleocode/core 2026.9.24 → 2026.9.26

package/dist/skills/orchestrator/validator.js

@@ -5,10 +5,11 @@
  * @task T12282
  */
 import { readFileSync } from 'node:fs';
-import { join, resolve } from 'node:path';
+import { resolve } from 'node:path';
 import { MANIFEST_STATUSES } from '@cleocode/contracts';
 import { z } from 'zod';
 import { EngineResultError } from '../../engine-result.js';
+import { readContainedFile } from '../../memory/manifest-identity.js';
 import { pipelineManifestShow, readManifestEntries, } from '../../memory/pipeline-manifest-sqlite.js';
 import { getAgentOutputsAbsolute, getProjectRoot, resolveOrCwd } from '../../paths.js';
 import { captureProjectScope, worktreeScope } from '../../project-scope.js';
@@ -112,7 +113,13 @@ function historicalOutputIssue(entry, cwd) {
     try {
         const scope = captureProjectScope(cwd ?? getProjectRoot(), worktreeScope.getStore());
         const outputRoot = worktreeScope.run(scope, () => getAgentOutputsAbsolute(scope.worktreeRoot));
-        readFileSync(join(outputRoot, entry.file));
+        // T12829: read only a reference whose real path stays inside the output
+        // root, so a `../` or symlinked reference cannot probe other files.
+        const read = readContainedFile(outputRoot, entry.file);
+        if (read.status === 'unsafe')
+            return `OUTPUT_FILE_UNSAFE: ${entry.file}: ${read.reason}`;
+        if (read.status === 'not-found')
+            return `OUTPUT_FILE_READ_FAILED: ${entry.file}: ENOENT (not found)`;
         return null;
     }
     catch (error) {

package/dist/skills/orchestrator/validator.js.map

@@ -1 +1 @@
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package/dist/skills/validation.d.ts

@@ -36,8 +36,11 @@ export declare function validateSkill(skillDir: string): SkillValidationResult;
  */
 export declare function validateSkills(skillDirs: string[]): SkillValidationResult[];
 /**
- * Validate a return message against protocol-compliant patterns.
+ * Validate a return message against protocol-compliant patterns: the
+ * compressed contract (`<Type> <status>. manifest:<entryId>` plus optional
+ * `commits:`, `gates:`, `blocker:` lines — T12521) or a legacy one-liner.
  * @task T4517
+ * @task T12521
  */
 export declare function validateReturnMessage(message: string): {
     valid: boolean;

package/dist/skills/validation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"validation.d.ts","sourceRoot":"","sources":["../../src/skills/validation.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAWH,iCAAiC;AACjC,MAAM,MAAM,aAAa,GAAG,OAAO,GAAG,SAAS,GAAG,MAAM,CAAC;AAEzD,+BAA+B;AAC/B,MAAM,WAAW,eAAe;IAC9B,QAAQ,EAAE,aAAa,CAAC;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,qCAAqC;AACrC,MAAM,WAAW,qBAAqB;IACpC,KAAK,EAAE,OAAO,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;CACtB;AAmBD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,qBAAqB,CAwDrE;AAyDD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,qBAAqB,EAAE,CAE3E;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CA4BzF"}
+{"version":3,"file":"validation.d.ts","sourceRoot":"","sources":["../../src/skills/validation.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAYH,iCAAiC;AACjC,MAAM,MAAM,aAAa,GAAG,OAAO,GAAG,SAAS,GAAG,MAAM,CAAC;AAEzD,+BAA+B;AAC/B,MAAM,WAAW,eAAe;IAC9B,QAAQ,EAAE,aAAa,CAAC;IACxB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,qCAAqC;AACrC,MAAM,WAAW,qBAAqB;IACpC,KAAK,EAAE,OAAO,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,eAAe,EAAE,CAAC;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;CACtB;AAmBD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,qBAAqB,CAwDrE;AAyDD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,qBAAqB,EAAE,CAE3E;AAED;;;;;;GAMG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,EAAE,MAAM,GAAG;IAAE,KAAK,EAAE,OAAO,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CAiCzF"}

package/dist/skills/validation.js

@@ -9,6 +9,7 @@
  */
 import { existsSync, readFileSync } from 'node:fs';
 import { basename, join } from 'node:path';
+import { parseReturnMessage } from '../validation/protocol-common.js';
 import { parseFrontmatter } from './discovery.js';
 // ============================================================================
 // Structural Validation
@@ -137,12 +138,16 @@ export function validateSkills(skillDirs) {
     return skillDirs.map(validateSkill);
 }
 /**
- * Validate a return message against protocol-compliant patterns.
+ * Validate a return message against protocol-compliant patterns: the
+ * compressed contract (`<Type> <status>. manifest:<entryId>` plus optional
+ * `commits:`, `gates:`, `blocker:` lines — T12521) or a legacy one-liner.
  * @task T4517
+ * @task T12521
  */
 export function validateReturnMessage(message) {
-    // ADR-027: manifest is pipeline_manifest (SQLite). Return messages no longer
-    // reference the flat-file — they say "Manifest appended to pipeline_manifest."
+    // ADR-027: manifest is pipeline_manifest (SQLite). Legacy return messages say
+    // "Manifest appended to pipeline_manifest."; T12521 compressed messages name
+    // the verified entry id instead (`manifest:<entryId>`).
     const validPatterns = [
         /^Research complete\. Manifest appended to pipeline_manifest\.$/,
         /^Epic created\. Manifest appended to pipeline_manifest\.$/,
@@ -156,6 +161,9 @@ export function validateReturnMessage(message) {
     if (!trimmed) {
         return { valid: false, error: 'Return message is empty' };
     }
+    if (parseReturnMessage(trimmed) !== null) {
+        return { valid: true };
+    }
     for (const pattern of validPatterns) {
         if (pattern.test(trimmed)) {
             return { valid: true };

package/dist/skills/validation.js.map

@@ -1 +1 @@
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package/dist/snapshot/index.d.ts

@@ -35,6 +35,10 @@ export interface SnapshotTask {
     createdAt: string;
     updatedAt?: string | null;
     completedAt?: string;
+    /** Row uid (T12341), when the exporting store had one: a restore carries it (T12806). */
+    uid?: string;
+    /** Birth fingerprint that goes with `uid`. */
+    birthFp?: string;
 }
 /** Complete snapshot package. */
 export interface Snapshot {

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

@@ -1 +1 @@
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package/dist/snapshot/index.js

@@ -13,9 +13,12 @@ import { mkdir, readFile, writeFile } from 'node:fs/promises';
 import { dirname, join } from 'node:path';
 import { resolveCleoDir } from '../paths.js';
 import { getTaskAccessor } from '../store/data-accessor.js';
+import { SameRowPresentError } from '../store/db-helpers.js';
 import { queryTasksIncludingArchived } from '../store/import-remap.js';
+import { rowUidFillEnabled } from '../store/row-identity-flag.js';
 /** Snapshot format version. */
-const SNAPSHOT_FORMAT_VERSION = '1.0.0';
+/** 1.1.0 (T12806): tasks may carry `uid` / `birthFp` (row uids on). */
+const SNAPSHOT_FORMAT_VERSION = '1.1.0';
 /**
  * Strip a Task down to its portable snapshot representation.
  * Removes local-only fields: position, positionVersion, verification,
@@ -59,7 +62,22 @@ export async function exportSnapshot(cwd) {
     const { tasks } = await accessor.queryTasks({});
     const projectMeta = await accessor.getMetaValue('project');
     const version = await accessor.getMetaValue('version');
-    const snapshotTasks = tasks.map(toSnapshotTask);
+    // T12806: carry each task's row identity, so a restore re-creates the same
+    // row rather than a new one. Row uids off: the snapshot is unchanged.
+    const identities = new Map((rowUidFillEnabled()
+        ? ((await accessor.getTaskIdentities?.(tasks.map((t) => t.id))) ?? [])
+        : []).map((r) => [r.id, r]));
+    const snapshotTasks = tasks.map((task) => {
+        const row = toSnapshotTask(task);
+        const identity = identities.get(task.id);
+        if (!identity?.uid)
+            return row;
+        return {
+            ...row,
+            uid: identity.uid,
+            ...(identity.birthFp ? { birthFp: identity.birthFp } : {}),
+        };
+    });
     const checksum = computeChecksum(snapshotTasks);
     return {
         $schema: 'https://lafs.dev/schemas/v1/cleo-snapshot.schema.json',
@@ -136,6 +154,10 @@ export async function importSnapshot(snapshot, cwd) {
         conflicts: [],
     };
     const localTaskMap = new Map(localTasks.map((t) => [t.id, t]));
+    // T12806: the row identity of the local tasks the snapshot names (uids on).
+    const localUids = new Map((rowUidFillEnabled()
+        ? ((await accessor.getTaskIdentities?.(snapshot.tasks.map((t) => t.id))) ?? [])
+        : []).map((r) => [r.id, r.uid]));
     // One transaction: a collision on any task leaves nothing half-imported (T12724).
     await accessor.transaction(async (tx) => {
         for (const snapshotTask of snapshot.tasks) {
@@ -159,10 +181,35 @@ export async function importSnapshot(snapshot, cwd) {
                     completedAt: snapshotTask.completedAt,
                 };
                 // Missing locally: insert, never overwrite a task stored since (T12724).
-                await tx.insertNewTask(newTask);
+                // A restore re-creates an existing row: it carries the snapshot's uid,
+                // or leaves it to the deterministic recipe, never a new one (T12806).
+                try {
+                    await tx.insertNewTask(newTask, {
+                        origin: 'imported',
+                        uid: snapshotTask.uid ?? null,
+                        birthFp: snapshotTask.birthFp ?? null,
+                    });
+                }
+                catch (error) {
+                    // The same row (uid + fingerprint) is here already, under another id
+                    // or held for sync: writing it again would duplicate the work.
+                    if (!(error instanceof SameRowPresentError))
+                        throw error;
+                    result.skipped++;
+                    result.conflicts.push(`${snapshotTask.id}: already present ${error.presentAs === 'held' ? '(held for sync)' : `as ${error.presentAs}`} (same uid and birth fingerprint); not restored`);
+                    continue;
+                }
                 result.added++;
                 continue;
             }
+            // The same id names DIFFERENT rows here and in the snapshot (row uids
+            // on): never overwrite one with the other; report it (T12806 review).
+            const localUid = localUids.get(snapshotTask.id);
+            if (snapshotTask.uid && localUid && localUid !== snapshotTask.uid) {
+                result.skipped++;
+                result.conflicts.push(`${snapshotTask.id}: the snapshot's task (uid ${snapshotTask.uid}) is a different row from the local one (uid ${localUid}); not overwritten`);
+                continue;
+            }
             // Task exists locally -- compare timestamps
             const localUpdated = localTask.updatedAt ?? localTask.createdAt;
             const snapshotUpdated = snapshotTask.updatedAt ?? snapshotTask.createdAt;

package/dist/snapshot/index.js.map

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package/dist/spawn/branch-lock.d.ts

@@ -167,6 +167,100 @@ export declare function pruneWorktree(taskId: string, projectRoot: string, opts?
  * @adr ADR-062
  */
 export declare function getDefaultBranch(projectRoot: string): string;
+/**
+ * Verdict of {@link assessUpstreamIntegration}.
+ *
+ * - `landed` — the task branch is already on the upstream default branch
+ *   (ancestor of it, or its changes are fully contained in it). No local
+ *   merge may run.
+ * - `nothing` — the task branch has no commits beyond the local default
+ *   branch (e.g. a worktree that was never committed to). There is nothing to
+ *   integrate, and it is NOT reported as landed upstream.
+ * - `stale-target` — the local default branch is behind the upstream default
+ *   branch (possibly also ahead of it — diverged); a merge there would fork it
+ *   from upstream. No local merge may run.
+ * - `proceed` — no upstream to compare against, or the local default branch is
+ *   current; the ADR-062 local `--no-ff` integration may run.
+ *
+ * @task T12773
+ */
+export type UpstreamIntegrationKind = 'landed' | 'nothing' | 'stale-target' | 'proceed';
+/**
+ * Result of {@link assessUpstreamIntegration}.
+ *
+ * @task T12773
+ */
+export interface UpstreamIntegrationAssessment {
+    /** What the caller may do next. */
+    kind: UpstreamIntegrationKind;
+    /** Remote-tracking ref compared against (e.g. `refs/remotes/origin/main`), or null. */
+    upstreamRef: string | null;
+    /**
+     * True when this assessment ran `git fetch <remote> <targetBranch>` (whether
+     * or not it succeeded), so a later integration step need not fetch again.
+     */
+    fetched: boolean;
+    /** Commits on the upstream ref missing from the local default branch. */
+    behind: number;
+    /** Commits on the local default branch missing from the upstream ref. */
+    ahead: number;
+    /**
+     * Exact shell command that syncs the local default branch with upstream,
+     * or empty when no sync is needed. NEVER run by CLEO — the operator's
+     * checkout is never moved (hint-only policy).
+     */
+    syncCommand: string;
+    /** Operator-facing explanation / next step (empty for `proceed`). */
+    hint: string;
+}
+/**
+ * Default timeout for the upstream `git fetch` in
+ * {@link assessUpstreamIntegration}. Short on purpose: the fetch is
+ * best-effort, and a hung network or credential prompt must never stall
+ * `cleo done` for the 180s generic git timeout.
+ *
+ * @task T12773
+ */
+export declare const UPSTREAM_FETCH_TIMEOUT_MS = 20000;
+/**
+ * Decide whether a local ADR-062 `--no-ff` integration of `branch` into
+ * `targetBranch` is safe, by comparing against the upstream default branch
+ * (`<remote>/<targetBranch>`).
+ *
+ * T12773: `cleo done --pr <n>` for a task whose PR had already merged on
+ * origin ran `git merge --no-ff task/<id>` into a local `main` that was 199
+ * commits behind origin, creating a local merge commit that forked `main`
+ * from `origin/main`. This check runs BEFORE any checkout or merge:
+ *
+ * - branch has no commits beyond the local default branch → `nothing`.
+ * - branch already on upstream → `landed`; when the local default branch is
+ *   behind, the hint names the exact sync command. The checkout is never
+ *   moved (hint-only).
+ * - local default branch behind upstream → `stale-target`; a distinct hint
+ *   when it is also ahead (diverged: unpushed local commits).
+ * - otherwise (no remote, no upstream ref, current target) → `proceed`.
+ *
+ * The fetch is best-effort, non-interactive (`GIT_TERMINAL_PROMPT=0`, ssh
+ * `BatchMode`) and bounded by {@link UPSTREAM_FETCH_TIMEOUT_MS}; offline, the
+ * last-known remote-tracking ref is used. Never creates a commit and never
+ * moves any ref other than the remote-tracking one the fetch updates.
+ *
+ * @param gitRoot - Absolute git root of the project checkout.
+ * @param branch - Task branch (e.g. `task/T123`).
+ * @param targetBranch - Resolved default branch (e.g. `main`).
+ * @param opts.skipFetch - Skip `git fetch <remote> <targetBranch>` (fixtures).
+ * @param opts.remote - Remote name (default `origin`).
+ * @param opts.fetchTimeoutMs - Fetch timeout (default {@link UPSTREAM_FETCH_TIMEOUT_MS}).
+ * @returns The assessment.
+ *
+ * @task T12773
+ * @adr ADR-062
+ */
+export declare function assessUpstreamIntegration(gitRoot: string, branch: string, targetBranch: string, opts?: {
+    skipFetch?: boolean;
+    remote?: string;
+    fetchTimeoutMs?: number;
+}): UpstreamIntegrationAssessment;
 /**
  * Complete a worker task's worktree via `git merge --no-ff` (ADR-062).
  *
@@ -179,12 +273,19 @@ export declare function getDefaultBranch(projectRoot: string): string;
  *
  * 1. Resolve target branch via {@link getDefaultBranch} (or `opts.targetBranch`
  *    override). NEVER hardcodes "main".
- * 2. `git fetch origin` then `git rebase origin/<targetBranch>` inside the
- *    worktree. Conflicts cause an early non-fatal return — the agent must
- *    re-resolve before completion.
- * 3. From the project's git root on `<targetBranch>`, run
- *    `git merge --no-ff task/<taskId> -m "Merge T<id>: <title>"` so the
- *    merge commit subject is `git log --grep`-friendly.
+ * 1a. T12773: {@link assessUpstreamIntegration} — when `task/<id>` already
+ *    landed on `origin/<targetBranch>` the merge is skipped
+ *    (`landedUpstream: true`); when it has no commits beyond the local
+ *    target it is `nothingToIntegrate` without `landedUpstream`; when the
+ *    local target is behind (or diverged from) origin the merge is refused
+ *    (`staleTarget: true`) with a `hint`. None of these paths creates a
+ *    commit or moves the operator's checkout — syncing is hint-only.
+ * 2. Optionally `git fetch` (skipped when step 1a already fetched), then
+ *    `git checkout <targetBranch>` in the project's git root. The task
+ *    branch is NOT rebased — agent SHAs are preserved.
+ * 3. Run `git merge --no-ff task/<taskId> -m "<taskId>: <title> (worktree
+ *    merge)"`; a failed merge is aborted so the repo is left clean, and the
+ *    worktree is preserved.
  * 4. Capture the merge commit SHA and report it.
  * 5. Delegate worktree+branch removal to {@link pruneWorktree} (T1462).
  *
@@ -195,7 +296,9 @@ export declare function getDefaultBranch(projectRoot: string): string;
  * @param projectRoot - Absolute path to the project root.
  * @param opts.targetBranch - Override the resolved default branch.
  * @param opts.taskTitle - Task title used in the merge commit message subject.
- * @param opts.skipFetch - Skip the `git fetch origin` step (test fixtures).
+ * @param opts.skipFetch - Skip every `git fetch` (test fixtures).
+ * @param opts.fetchTimeoutMs - Timeout for the upstream fetch (default
+ *   {@link UPSTREAM_FETCH_TIMEOUT_MS}).
  * @returns Merge integration result.
  *
  * @task T1587
@@ -205,6 +308,7 @@ export declare function completeAgentWorktreeViaMerge(taskId: string, projectRoo
     targetBranch?: string;
     taskTitle?: string;
     skipFetch?: boolean;
+    fetchTimeoutMs?: number;
 }): WorktreeMergeResult;
 /**
  * Result of a complete post-merge worktree integration.

package/dist/spawn/branch-lock.d.ts.map

@@ -1 +1 @@
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