@cleocode/core 2026.10.12 → 2026.10.13-rc.ci.682

package/dist/resources/run-governed.js

@@ -116,6 +116,7 @@ function defaultDeps() {
             };
         },
         jobsDir: runJobsDir(),
+        ppid: process.ppid,
         ledger: () => readLedger(),
         pid: process.pid,
         groupOf: processGroupOf,
@@ -191,86 +192,115 @@ export async function runGoverned(opts) {
         notice(`${describeAdmissionIoError(io)}: running ungoverned`, 'warn');
     };
     const deadline = t0 + (opts.timeoutMs ?? 30 * 60_000);
+    // T13681: a signal while queued leaves the queue and reports it, never a
+    // silent death with no envelope.
+    const queueAbort = new AbortController();
+    let queuedSignal = null;
+    const uninstallQueue = opts.wait
+        ? d.onRunnerSignal((signal) => {
+            queuedSignal ??= signal;
+            queueAbort.abort();
+        })
+        : () => { };
     let admission;
-    if (isLedgerClass(opts.cls)) {
-        // T13133: one budget and one FIFO queue for every heavy run. Nested in an
-        // admitted run's process tree (any class), it rides that admission; a
-        // memory-pressure wait and, after a minute, the holders are warnings, so
-        // --passthrough shows them.
-        const out = await d.admit({
-            label: `run:${opts.cls}`,
-            footprintBytes: opts.footprintBytes ?? footprintForClass(opts.cls),
-            ...(opts.footprintReason !== undefined ? { footprintReason: opts.footprintReason } : {}),
-            ...(opts.scope !== undefined ? { scope: opts.scope } : {}),
-            // T13237: one full-build machine-wide, whatever its footprint.
-            ...(opts.cls === 'full-build' ? { exclusive: true } : {}),
-            command,
-            cwd: opts.cwd,
-        }, {
-            wait: opts.wait === true,
-            timeoutMs: Math.max(1, deadline - d.now()),
-            ...(opts.queuePollMs !== undefined ? { pollMs: opts.queuePollMs } : {}),
-            memoryPressure: memoryGateReporter((line) => notice(line, 'warn'), `${opts.cls} job`, {
+    let queued = false;
+    try {
+        if (isLedgerClass(opts.cls)) {
+            // T13133: one budget and one FIFO queue for every heavy run. Nested in an
+            // admitted run's process tree (any class), it rides that admission; a
+            // memory-pressure wait and, after a minute, the holders are warnings, so
+            // --passthrough shows them.
+            const out = await d.admit({
+                label: `run:${opts.cls}`,
+                footprintBytes: opts.footprintBytes ?? footprintForClass(opts.cls),
+                ...(opts.footprintReason !== undefined ? { footprintReason: opts.footprintReason } : {}),
+                ...(opts.scope !== undefined ? { scope: opts.scope } : {}),
+                // T13237: one full-build machine-wide, whatever its footprint.
+                ...(opts.cls === 'full-build' ? { exclusive: true } : {}),
+                command,
+                cwd: opts.cwd,
+            }, {
+                wait: opts.wait === true,
+                timeoutMs: Math.max(1, deadline - d.now()),
+                ...(opts.queuePollMs !== undefined ? { pollMs: opts.queuePollMs } : {}),
+                memoryPressure: memoryGateReporter((line) => notice(line, 'warn'), `${opts.cls} job`, {
+                    now: d.now,
+                }),
+                notice: (line) => notice(line, 'warn'),
                 now: d.now,
-            }),
-            notice: (line) => notice(line, 'warn'),
-            now: d.now,
-            sleep: (ms) => d.sleep(ms),
-        });
-        if (!out.admitted) {
-            const { refusal } = out;
-            return deferral(opts, d, opts.wait
-                ? `timed out after ${Math.round((d.now() - t0) / 1000)}s waiting for the machine budget (position ${refusal.ahead + 1}): ${refusal.reason}`
-                : refusal.reason, refusal.retryAfterMs, sample, opts.wait ? refusal.ahead + 1 : null, refusal.memoryPressure);
-        }
-        const { grant } = out;
-        if (grant.ungoverned)
-            sayUngoverned(grant.ungoverned);
-        if (grant.nested) {
-            notice('nested in an admitted run: riding its admission, inside its process tree', 'info');
-        }
-        else if (grant.waitedMs >= 1_000 && opts.wait) {
-            notice(`admitted after ${Math.round(grant.waitedMs / 1000)}s in the queue`, 'info');
-        }
-        admission = {
-            release: () => grant.release(),
-            slot: grant.id === null ? -1 : 0,
-            token: grant.token,
-            holdsShare: grant.id !== null,
-        };
-    }
-    else {
-        // Classes outside the ledger (db-heavy) keep their governor slots. A run
-        // nested in a job of the SAME class rides its slot (#1777 round 3, M-2).
-        const parent = enclosing !== null && enclosing.class === opts.cls ? enclosing : null;
-        if (parent) {
-            notice(`nested in a running ${parent.class} job (${parent.command}): running on its slot`, 'info');
-            admission = { release: async () => { }, slot: -1, token: '', holdsShare: false };
-        }
-        else {
-            const tryAcquire = async (s) => {
-                const r = await admitFailOpen(opts.cls, () => d.tryAcquire(opts.cls, s));
-                if (r.ungoverned !== null)
-                    sayUngoverned(r.ungoverned);
-                return r.admission;
-            };
-            let result = await tryAcquire(sample);
-            while (result.deferred && opts.wait && d.now() < deadline) {
-                await d.sleep(opts.queuePollMs ?? 1000);
-                sample = await d.sample();
-                result = await tryAcquire(sample);
+                sleep: (ms) => d.sleep(ms, queueAbort.signal),
+                signal: queueAbort.signal,
+            });
+            if (queuedSignal !== null) {
+                if (out.admitted)
+                    await out.grant.release();
+                return interrupted(queuedSignal);
+            }
+            if (!out.admitted) {
+                const { refusal } = out;
+                return deferral(opts, d, opts.wait
+                    ? `timed out after ${Math.round((d.now() - t0) / 1000)}s waiting for the machine budget (position ${refusal.ahead + 1}): ${refusal.reason}`
+                    : refusal.reason, refusal.retryAfterMs, sample, opts.wait ? refusal.ahead + 1 : null, refusal.memoryPressure);
             }
-            if (result.deferred) {
-                return deferral(opts, d, result.reason, result.retryAfterMs, sample, null, result.memoryPressure ?? null);
+            const { grant } = out;
+            if (grant.ungoverned)
+                sayUngoverned(grant.ungoverned);
+            if (grant.nested) {
+                notice('nested in an admitted run: riding its admission, inside its process tree', 'info');
+            }
+            else if (grant.waitedMs >= 1_000 && opts.wait) {
+                queued = true;
+                notice(`admitted after ${Math.round(grant.waitedMs / 1000)}s in the queue`, 'warn');
             }
-            const granted = result;
             admission = {
-                release: () => granted.release(),
-                slot: granted.slot,
-                token: '',
-                holdsShare: true,
+                release: () => grant.release(),
+                slot: grant.id === null ? -1 : 0,
+                token: grant.token,
+                holdsShare: grant.id !== null,
             };
         }
+        else {
+            // Classes outside the ledger (db-heavy) keep their governor slots. A run
+            // nested in a job of the SAME class rides its slot (#1777 round 3, M-2).
+            const parent = enclosing !== null && enclosing.class === opts.cls ? enclosing : null;
+            if (parent) {
+                notice(`nested in a running ${parent.class} job (${parent.command}): running on its slot`, 'info');
+                admission = { release: async () => { }, slot: -1, token: '', holdsShare: false };
+            }
+            else {
+                const tryAcquire = async (s) => {
+                    const r = await admitFailOpen(opts.cls, () => d.tryAcquire(opts.cls, s));
+                    if (r.ungoverned !== null)
+                        sayUngoverned(r.ungoverned);
+                    return r.admission;
+                };
+                let result = await tryAcquire(sample);
+                while (result.deferred && opts.wait && d.now() < deadline && queuedSignal === null) {
+                    await d.sleep(opts.queuePollMs ?? 1000, queueAbort.signal);
+                    sample = await d.sample();
+                    result = await tryAcquire(sample);
+                }
+                if (queuedSignal !== null) {
+                    if (!result.deferred)
+                        await result.release();
+                    return interrupted(queuedSignal);
+                }
+                if (result.deferred) {
+                    return deferral(opts, d, result.reason, result.retryAfterMs, sample, null, result.memoryPressure ?? null);
+                }
+                const granted = result;
+                admission = {
+                    release: () => granted.release(),
+                    slot: granted.slot,
+                    token: '',
+                    holdsShare: true,
+                };
+            }
+        }
+    }
+    finally {
+        // Every admission path, a throw or a nested ride included, drops the queue handler.
+        uninstallQueue();
     }
     const grant = admission;
     const waitedMs = d.now() - t0;
@@ -311,6 +341,8 @@ export async function runGoverned(opts) {
     };
     writeRunJob(job, d.jobsDir);
     let exited = false;
+    // Declared before the spawn: a spawn failure reports it too (null).
+    let runnerSignal = null;
     let pausedAtMs = null;
     let capResumedAtMs = null;
     let pausedTotalMs = 0;
@@ -353,6 +385,7 @@ export async function runGoverned(opts) {
     // 4, L-A).
     const forwardTo = leadsGroup ? d.signal : d.signalPid;
     const uninstall = d.onRunnerSignal((signal) => {
+        runnerSignal ??= { signal, atMs: d.now(), ppid: d.ppid };
         if (childPid === undefined || exited)
             return;
         // A terminal's Ctrl-C already reached its whole foreground group, child
@@ -360,6 +393,7 @@ export async function runGoverned(opts) {
         // runners treat as force-quit (#1777 R8). SIGTERM and SIGHUP still go.
         if (opts.foreground === true && signal === 'SIGINT')
             return;
+        notice(`runner received ${signal} (its parent pid ${d.ppid}); forwarding it to pid ${childPid}`, 'warn');
         forwardTo(childPid, 'SIGCONT');
         forwardTo(childPid, signal);
     });
@@ -476,7 +510,13 @@ export async function runGoverned(opts) {
             pauses,
             slot: grant.slot,
             ungoverned,
+            runnerSignal,
+            queued,
         };
     }
+    function interrupted(signal) {
+        notice(`${signal} while waiting in the queue: left the queue, nothing started`, 'warn');
+        return { kind: 'interrupted', signal, waitedMs: d.now() - t0, class: opts.cls, command };
+    }
 }
 //# sourceMappingURL=run-governed.js.map

package/dist/resources/run-governed.js.map

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package/dist/sentient/worktree-dispatch.d.ts

@@ -20,7 +20,7 @@
  * @task T1161
  * @adr ADR-055
  */
-import type { CreateWorktreeOptions, CreateWorktreeResult, DestroyWorktreeOptions, DestroyWorktreeResult, ListWorktreesOptions, PruneWorktreesResult, WorktreeListEntry } from '@cleocode/contracts';
+import type { CreateWorktreeOptions, CreateWorktreeResult, DestroyWorktreeOptions, DestroyWorktreeResult, ListWorktreesOptions, PruneWorktreesResult, WorktreeDisposalBlockers, WorktreeListEntry } from '@cleocode/contracts';
 /**
  * Admit one worktree dependency install as a `scoped-build` run, without
  * waiting: the release on a grant, `null` when the budget is busy.
@@ -52,6 +52,17 @@ export declare function spawnWorktree(projectRoot: string, options: CreateWorktr
  * @task T1161
  */
 export declare function teardownWorktree(projectRoot: string, options: DestroyWorktreeOptions): Promise<DestroyWorktreeResult>;
+/**
+ * Surface a kept worktree as a `W_WORKTREE_KEPT` envelope warning, so
+ * `cleo complete` and `cleo cancel` never keep one silently (T13701).
+ *
+ * @param taskId - The task whose worktree was kept.
+ * @param kept - What still needs the worktree's files.
+ * @param message - The disposal's explanation (names the path and blockers).
+ *
+ * @task T13701
+ */
+export declare function warnWorktreeKept(taskId: string, kept: WorktreeDisposalBlockers, message: string | undefined): Promise<void>;
 /**
  * List worktrees scoped to a project via the native backend.
  *

package/dist/sentient/worktree-dispatch.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"worktree-dispatch.d.ts","sourceRoot":"","sources":["../../src/sentient/worktree-dispatch.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAEH,OAAO,KAAK,EACV,qBAAqB,EACrB,oBAAoB,EACpB,sBAAsB,EACtB,qBAAqB,EACrB,oBAAoB,EACpB,oBAAoB,EACpB,wBAAwB,EACxB,iBAAiB,EAClB,MAAM,qBAAqB,CAAC;AAoB7B;;;;;GAKG;AACH,wBAAsB,oBAAoB,IAAI,OAAO,CAAC,CAAC,MAAM,OAAO,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,CAUlF;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,aAAa,CACjC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,qBAAqB,GAC7B,OAAO,CAAC,oBAAoB,CAAC,CAsB/B;AAED;;;;;;;;GAQG;AACH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,sBAAsB,GAC9B,OAAO,CAAC,qBAAqB,CAAC,CAGhC;AAED;;;;;;;;;GASG;AACH,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,IAAI,EAAE,wBAAwB,EAC9B,OAAO,EAAE,MAAM,GAAG,SAAS,GAC1B,OAAO,CAAC,IAAI,CAAC,CAQf;AAED;;;;;;;GAOG;AACH,wBAAgB,oBAAoB,CAAC,OAAO,GAAE,oBAAyB,GAAG,iBAAiB,EAAE,CAE5F;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,wBAAwB,CACtC,WAAW,EAAE,MAAM,EACnB,aAAa,EAAE,GAAG,CAAC,MAAM,CAAC,GACzB,oBAAoB,CAEtB;AA6CD;;;;;;;;GAQG;AACH,wBAAsB,qBAAqB,IAAI,OAAO,CAAC,IAAI,CAAC,CAO3D"}

package/dist/sentient/worktree-dispatch.js

@@ -101,6 +101,25 @@ export async function teardownWorktree(projectRoot, options) {
     const mod = await backend();
     return mod.destroyWorktree(projectRoot, options);
 }
+/**
+ * Surface a kept worktree as a `W_WORKTREE_KEPT` envelope warning, so
+ * `cleo complete` and `cleo cancel` never keep one silently (T13701).
+ *
+ * @param taskId - The task whose worktree was kept.
+ * @param kept - What still needs the worktree's files.
+ * @param message - The disposal's explanation (names the path and blockers).
+ *
+ * @task T13701
+ */
+export async function warnWorktreeKept(taskId, kept, message) {
+    const { pushWarning } = await import('../output.js');
+    pushWarning({
+        // @sync-invariant none:local-only a warning about a worktree on this machine's disk; never replicated
+        code: 'W_WORKTREE_KEPT',
+        message: message ?? `Worktree for ${taskId} kept: something still needs its files.`,
+        context: { taskId, dependents: kept.dependents, evidence: kept.evidence },
+    });
+}
 /**
  * List worktrees scoped to a project via the native backend.
  *

package/dist/sentient/worktree-dispatch.js.map

@@ -1 +1 @@
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package/dist/spawn/branch-lock.d.ts

@@ -18,7 +18,7 @@
  * @adr ADR-055
  * @adr ADR-062
  */
-import type { AgentWorktreeState, FsHardenCapabilities, FsHardenState, WorktreeCleanupResult, WorktreeMergeResult, WorktreeSpawnResult } from '@cleocode/contracts';
+import type { AgentWorktreeState, EvidenceAtom, FsHardenCapabilities, FsHardenState, WorktreeCleanupResult, WorktreeDisposalBlockers, WorktreeMergeResult, WorktreeSpawnResult } from '@cleocode/contracts';
 import { getGitRoot } from '@cleocode/worktree';
 export { getGitRoot };
 /**
@@ -118,6 +118,8 @@ export interface PruneWorktreeResult {
     wasDirty: boolean;
     /** Error message if any step failed. */
     error?: string;
+    /** Set (with `status: 'skipped'`) when the worktree was kept because something still needs its files (T13696). */
+    kept?: WorktreeDisposalBlockers;
 }
 /**
  * Prune the worktree for a single completed or cancelled task.
@@ -138,11 +140,14 @@ export interface PruneWorktreeResult {
  *   the result — callers should use `completeAgentWorktreeViaMerge` first.
  * - Always writes a `--force` remove with an audit log entry (`.cleo/audit/worktree-prune.jsonl`)
  *   when the worktree is detected as dirty.
+ * - Keeps the worktree (`{ status: 'skipped', kept }`) while another checkout
+ *   symlinks into it or it holds evidence found nowhere else (T13696).
  * - Never throws — failures are returned in `{ status: 'error', error }`.
  *
  * @param taskId     - The CLEO task ID (e.g. "T1462").
  * @param projectRoot - Absolute path to the project root.
  * @param opts.auditLogPath - Override path for the audit JSONL (testing).
+ * @param opts.evidence - The task's recorded evidence atoms (T13696).
  * @returns Prune outcome.
  *
  * @task T1462
@@ -150,6 +155,7 @@ export interface PruneWorktreeResult {
  */
 export declare function pruneWorktree(taskId: string, projectRoot: string, opts?: {
     auditLogPath?: string;
+    evidence?: readonly EvidenceAtom[];
 }): PruneWorktreeResult;
 /**
  * Resolve the project's default integration branch in a project-agnostic way.
@@ -299,6 +305,7 @@ export declare function assessUpstreamIntegration(gitRoot: string, branch: strin
  * @param opts.targetBranch - Override the resolved default branch.
  * @param opts.taskTitle - Task title used in the merge commit message subject.
  * @param opts.skipFetch - Skip every `git fetch` (test fixtures).
+ * @param opts.evidence - The task's evidence atoms; the prune keeps a worktree holding the only copy (T13696).
  * @param opts.fetchTimeoutMs - Timeout for the upstream fetch (default
  *   {@link UPSTREAM_FETCH_TIMEOUT_MS}).
  * @returns Merge integration result.
@@ -311,6 +318,7 @@ export declare function completeAgentWorktreeViaMerge(taskId: string, projectRoo
     taskTitle?: string;
     skipFetch?: boolean;
     fetchTimeoutMs?: number;
+    evidence?: readonly EvidenceAtom[];
 }): WorktreeMergeResult;
 /**
  * Result of a complete post-merge worktree integration.
@@ -343,6 +351,7 @@ export interface WorktreeIntegrationResult extends WorktreeMergeResult {
  * @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.auditLogPath - Override the audit JSONL path (testing).
+ * @param opts.evidence - The task's evidence atoms; the prune keeps a worktree holding the only copy (T13696).
  * @returns Integration result including audit log path.
  *
  * @task T9043
@@ -353,6 +362,7 @@ export declare function completeAgentWorktreeIntegration(taskId: string, project
     taskTitle?: string;
     skipFetch?: boolean;
     auditLogPath?: string;
+    evidence?: readonly EvidenceAtom[];
 }): WorktreeIntegrationResult;
 /** Result of {@link ensureGitShimDir}. */
 export interface GitShimInstall {

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

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package/dist/spawn/branch-lock.js

@@ -28,7 +28,7 @@ import { computeProjectHash, findOnPath, pathEnvKey, prependPathEntry, resolveWo
 // ---------------------------------------------------------------------------
 // Re-exports from @cleocode/worktree
 // ---------------------------------------------------------------------------
-import { acquireWorktreeTaskLock, getGitRoot, gitSilent, gitSync, integrateWorktree, napiDestroyWorktree, pruneWorktrees, releaseWorktreeTaskLock, } from '@cleocode/worktree';
+import { acquireWorktreeTaskLock, describeDisposalBlockers, getGitRoot, gitSilent, gitSync, guardWorktreeDisposal, integrateWorktree, napiDestroyWorktree, pruneWorktrees, releaseWorktreeTaskLock, } from '@cleocode/worktree';
 import { resolveSpawnLockHolder } from './worktree-lock-holder.js';
 // Re-export getGitRoot for barrel consumers
 export { getGitRoot };
@@ -288,11 +288,14 @@ function leaveDirectoryBeforeRemoval(dir, to) {
  *   the result — callers should use `completeAgentWorktreeViaMerge` first.
  * - Always writes a `--force` remove with an audit log entry (`.cleo/audit/worktree-prune.jsonl`)
  *   when the worktree is detected as dirty.
+ * - Keeps the worktree (`{ status: 'skipped', kept }`) while another checkout
+ *   symlinks into it or it holds evidence found nowhere else (T13696).
  * - Never throws — failures are returned in `{ status: 'error', error }`.
  *
  * @param taskId     - The CLEO task ID (e.g. "T1462").
  * @param projectRoot - Absolute path to the project root.
  * @param opts.auditLogPath - Override path for the audit JSONL (testing).
+ * @param opts.evidence - The task's recorded evidence atoms (T13696).
  * @returns Prune outcome.
  *
  * @task T1462
@@ -335,6 +338,43 @@ export function pruneWorktree(taskId, projectRoot, opts = {}) {
         }
         return { taskId, status: 'skipped', worktreeRemoved: false, branchDeleted, wasDirty: false };
     }
+    // T13696: removal deletes the whole directory, so refuse while another
+    // checkout links into it or it holds the only copy of the task's evidence.
+    const kept = guardWorktreeDisposal(worktreePath, {
+        taskId,
+        reason: 'complete',
+        gitRoot,
+        projectRoot,
+        evidence: opts.evidence,
+    });
+    if (kept !== null) {
+        const error = describeDisposalBlockers(worktreePath, kept);
+        try {
+            const logPath = opts.auditLogPath ?? join(projectRoot, '.cleo', 'audit', 'worktree-prune.jsonl');
+            mkdirSync(dirname(logPath), { recursive: true });
+            const entry = JSON.stringify({
+                timestamp: new Date().toISOString(),
+                taskId,
+                worktreePath,
+                action: 'kept',
+                ...kept,
+                agent: process.env['CLEO_AGENT_ID'] ?? 'cleo',
+            });
+            appendFileSync(logPath, entry + '\n', 'utf-8');
+        }
+        catch {
+            /* audit is best-effort */
+        }
+        return {
+            taskId,
+            status: 'skipped',
+            worktreeRemoved: false,
+            branchDeleted: false,
+            wasDirty: false,
+            error,
+            kept,
+        };
+    }
     // Detect dirty state: uncommitted changes in the worktree.
     let wasDirty = false;
     try {
@@ -773,6 +813,7 @@ export function assessUpstreamIntegration(gitRoot, branch, targetBranch, opts =
  * @param opts.targetBranch - Override the resolved default branch.
  * @param opts.taskTitle - Task title used in the merge commit message subject.
  * @param opts.skipFetch - Skip every `git fetch` (test fixtures).
+ * @param opts.evidence - The task's evidence atoms; the prune keeps a worktree holding the only copy (T13696).
  * @param opts.fetchTimeoutMs - Timeout for the upstream fetch (default
  *   {@link UPSTREAM_FETCH_TIMEOUT_MS}).
  * @returns Merge integration result.
@@ -852,7 +893,9 @@ export function completeAgentWorktreeViaMerge(taskId, projectRoot, opts = {}) {
             // worktree unless it holds uncommitted work, which is left for the
             // operator. The checkout itself is never moved (hint-only).
             const dirty = existsSync(worktreePath) && isWorktreeDirty(worktreePath);
-            const pruneResult = dirty ? null : pruneWorktree(taskId, projectRoot);
+            const pruneResult = dirty
+                ? null
+                : pruneWorktree(taskId, projectRoot, { evidence: opts.evidence });
             let branchDeleted = pruneResult?.branchDeleted ?? false;
             // pruneWorktree only deletes a branch with zero commits ahead of the
             // checkout HEAD, so a stale local default branch, a squash merge, or a
@@ -873,13 +916,16 @@ export function completeAgentWorktreeViaMerge(taskId, projectRoot, opts = {}) {
                 commitCount: 0,
                 rebased: false,
                 worktreeRemoved: pruneResult?.worktreeRemoved ?? false,
+                ...(pruneResult?.kept ? { worktreeKept: pruneResult.kept } : {}),
                 branchDeleted,
                 nothingToIntegrate: true,
                 ...(upstream.kind === 'landed' ? { landedUpstream: true } : {}),
                 ...(upstream.syncCommand ? { syncCommand: upstream.syncCommand } : {}),
                 hint: dirty
                     ? `${upstream.hint} Worktree ${worktreePath} has uncommitted changes and was preserved.`
-                    : upstream.hint,
+                    : pruneResult?.kept
+                        ? `${upstream.hint} ${pruneResult.error}`
+                        : upstream.hint,
             };
         }
         if (upstream.kind === 'stale-target') {
@@ -923,7 +969,7 @@ export function completeAgentWorktreeViaMerge(taskId, projectRoot, opts = {}) {
             error: result.error,
         };
     }
-    const pruneResult = pruneWorktree(taskId, projectRoot);
+    const pruneResult = pruneWorktree(taskId, projectRoot, { evidence: opts.evidence });
     return {
         taskId,
         targetBranch,
@@ -932,6 +978,7 @@ export function completeAgentWorktreeViaMerge(taskId, projectRoot, opts = {}) {
         commitCount: result.commitCount,
         rebased: result.rebased,
         worktreeRemoved: pruneResult.worktreeRemoved,
+        ...(pruneResult.kept ? { worktreeKept: pruneResult.kept } : {}),
         branchDeleted: pruneResult.branchDeleted,
         error: pruneResult.error,
     };
@@ -955,6 +1002,7 @@ export function completeAgentWorktreeViaMerge(taskId, projectRoot, opts = {}) {
  * @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.auditLogPath - Override the audit JSONL path (testing).
+ * @param opts.evidence - The task's evidence atoms; the prune keeps a worktree holding the only copy (T13696).
  * @returns Integration result including audit log path.
  *
  * @task T9043
@@ -965,6 +1013,7 @@ export function completeAgentWorktreeIntegration(taskId, projectRoot, opts = {})
         targetBranch: opts.targetBranch,
         taskTitle: opts.taskTitle,
         skipFetch: opts.skipFetch,
+        evidence: opts.evidence,
     });
     // Write audit log entry.
     let auditLogEntry = null;
@@ -980,6 +1029,7 @@ export function completeAgentWorktreeIntegration(taskId, projectRoot, opts = {})
             mergeCommit: mergeResult.mergeCommit,
             merged: mergeResult.merged,
             worktreeRemoved: mergeResult.worktreeRemoved,
+            worktreeKept: mergeResult.worktreeKept ?? null,
             branchDeleted: mergeResult.branchDeleted,
             error: mergeResult.error ?? null,
             agent: process.env['CLEO_AGENT_ID'] ?? 'cleo',