@cleocode/core 2026.6.14 → 2026.6.17

package/dist/selfimprove/probe-helper.d.ts

@@ -0,0 +1,61 @@
+/**
+ * Self-improvement probe helper — selfimprove.probe op (T11988).
+ *
+ * This tiny module exists to give the seeded-code-regression scenario a
+ * **real, patchable code bug** for end-to-end fix-gen proof. The function
+ * {@link probeVersion} is supposed to return `1` (the canonical probe API
+ * version), but ships with an intentional off-by-one (`return 2`) so that a
+ * live replay of the `seeded-code-regression` scenario diverges from the
+ * golden (`version: 1`) and the LLM can produce a correct one-line unified
+ * diff to fix it.
+ *
+ * ### Why a dedicated file?
+ *
+ * The seeded bug must be:
+ *   1. **In a repo-relative path** the op-source-map can register under
+ *      `selfimprove.probe` so the fix-gen context loader includes it in the
+ *      LLM prompt.
+ *   2. **Minimal** — the simplest possible off-by-one so the model cannot
+ *      rationally refuse (`NO_PATCH`).
+ *   3. **Self-contained** — no live DB, no side effects; the probe op
+ *      never mutates.
+ *
+ * ### Fixing the bug
+ *
+ * Change `return 2` → `return 1` in {@link probeVersion}. This is the EXACT
+ * one-line fix the self-improvement loop's LLM fix-gen stage should propose
+ * when replaying the seeded scenario.
+ *
+ * @module @cleocode/core/selfimprove/probe-helper
+ * @task T11988
+ */
+/**
+ * Return the canonical probe API version.
+ *
+ * Expected value: `1`.
+ *
+ * @returns The probe version number.
+ *
+ * @example
+ * ```ts
+ * probeVersion(); // => 1 (expected)
+ * ```
+ *
+ * @bug SEEDED — currently returns `2` instead of `1` (T11988 intentional).
+ *   The seeded-code-regression scenario golden asserts `version: 1`; the
+ *   mismatch is the regression the fix-gen LLM prompt targets.
+ */
+export declare function probeVersion(): number;
+/**
+ * Build the `selfimprove.probe` response payload.
+ *
+ * Returns `{ probe: 'ok', version: <probeVersion()> }` — the envelope `data`
+ * block the `selfimprove.probe` query op emits.
+ *
+ * @returns The probe response payload.
+ */
+export declare function buildProbePayload(): {
+    probe: 'ok';
+    version: number;
+};
+//# sourceMappingURL=probe-helper.d.ts.map

package/dist/selfimprove/probe-helper.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"probe-helper.d.ts","sourceRoot":"","sources":["../../src/selfimprove/probe-helper.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8BG;AAEH;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,YAAY,IAAI,MAAM,CAIrC;AAED;;;;;;;GAOG;AACH,wBAAgB,iBAAiB,IAAI;IAAE,KAAK,EAAE,IAAI,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAEpE"}

package/dist/selfimprove/probe-helper.js

@@ -0,0 +1,64 @@
+/**
+ * Self-improvement probe helper — selfimprove.probe op (T11988).
+ *
+ * This tiny module exists to give the seeded-code-regression scenario a
+ * **real, patchable code bug** for end-to-end fix-gen proof. The function
+ * {@link probeVersion} is supposed to return `1` (the canonical probe API
+ * version), but ships with an intentional off-by-one (`return 2`) so that a
+ * live replay of the `seeded-code-regression` scenario diverges from the
+ * golden (`version: 1`) and the LLM can produce a correct one-line unified
+ * diff to fix it.
+ *
+ * ### Why a dedicated file?
+ *
+ * The seeded bug must be:
+ *   1. **In a repo-relative path** the op-source-map can register under
+ *      `selfimprove.probe` so the fix-gen context loader includes it in the
+ *      LLM prompt.
+ *   2. **Minimal** — the simplest possible off-by-one so the model cannot
+ *      rationally refuse (`NO_PATCH`).
+ *   3. **Self-contained** — no live DB, no side effects; the probe op
+ *      never mutates.
+ *
+ * ### Fixing the bug
+ *
+ * Change `return 2` → `return 1` in {@link probeVersion}. This is the EXACT
+ * one-line fix the self-improvement loop's LLM fix-gen stage should propose
+ * when replaying the seeded scenario.
+ *
+ * @module @cleocode/core/selfimprove/probe-helper
+ * @task T11988
+ */
+/**
+ * Return the canonical probe API version.
+ *
+ * Expected value: `1`.
+ *
+ * @returns The probe version number.
+ *
+ * @example
+ * ```ts
+ * probeVersion(); // => 1 (expected)
+ * ```
+ *
+ * @bug SEEDED — currently returns `2` instead of `1` (T11988 intentional).
+ *   The seeded-code-regression scenario golden asserts `version: 1`; the
+ *   mismatch is the regression the fix-gen LLM prompt targets.
+ */
+export function probeVersion() {
+    // SEEDED BUG (T11988): should be `return 1` — intentional off-by-one for
+    // the seeded-code-regression end-to-end fix-gen scenario.
+    return 2;
+}
+/**
+ * Build the `selfimprove.probe` response payload.
+ *
+ * Returns `{ probe: 'ok', version: <probeVersion()> }` — the envelope `data`
+ * block the `selfimprove.probe` query op emits.
+ *
+ * @returns The probe response payload.
+ */
+export function buildProbePayload() {
+    return { probe: 'ok', version: probeVersion() };
+}
+//# sourceMappingURL=probe-helper.js.map

package/dist/selfimprove/probe-helper.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"probe-helper.js","sourceRoot":"","sources":["../../src/selfimprove/probe-helper.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8BG;AAEH;;;;;;;;;;;;;;;GAeG;AACH,MAAM,UAAU,YAAY;IAC1B,yEAAyE;IACzE,0DAA0D;IAC1D,OAAO,CAAC,CAAC;AACX,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,iBAAiB;IAC/B,OAAO,EAAE,KAAK,EAAE,IAAI,EAAE,OAAO,EAAE,YAAY,EAAE,EAAE,CAAC;AAClD,CAAC"}

package/dist/selfimprove/run-loop.d.ts

@@ -17,8 +17,15 @@
  *   4. on a regression, **emit ONE DHQ** row via the leased
  *      {@link "./dhq-adapter.js".DhqAdapter} (UPSERT under
  *      `withWriterLease('project','bulk',…)`) — ONLY when `execute` is set;
+ *   4b. **generate a fix** ({@link "./fix-gen.js".generateFixPatch}, T11975) — ONLY
+ *      when `execute` AND `CLEO_PI_RUNNER_ENABLED=1`. Drives the LLM strictly via
+ *      the E9 chokepoint to produce a unified-diff patch at the path the egress
+ *      expects (`<cwd>/selfimprove-<scenario>.patch`). Degrades gracefully (no
+ *      patch ⇒ the egress guard skips the PR); the outcome is recorded back onto
+ *      the DHQ row. NEVER throws a rogue mutation, NEVER auto-merges;
  *   5. **open ONE DRAFT PR** ({@link "./draft-pr.js".openDraftPr}, dry-run unless
- *      `execute`) and record its URL back on the DHQ row.
+ *      `execute`) and record its URL back on the DHQ row — fires only when the
+ *      fix-gen stage wrote a patch file (the existing `existsSync` egress guard).
  *
  * Self-dogfooding guardrails (NON-NEGOTIABLE, P5 spec §B.7):
  *   - **Default OFF.** Mutation + egress require `opts.execute === true`. Without
@@ -30,8 +37,12 @@
  *   - **Budget caps** (in-code): `maxTokens` / `maxUsd` / `maxPrs = 1` /
  *     `maxWorktrees = 1`, checked PRE-FLIGHT before each costed step. `MemoryMax=32G`
  *     is an operational launch-wrapper, not an in-code cap.
- *   - **NO autonomous fix-gen, NO auto-merge, NO end-user mode in v1.** The loop
- *     surfaces regressions as DHQs + draft PRs; a human drives the fix.
+ *   - **Fix-gen is GATED + DRAFT-PR-ONLY (T11975).** The autonomous fix-generation
+ *     stage runs ONLY behind BOTH `execute` AND `CLEO_PI_RUNNER_ENABLED=1` (the
+ *     same gates guarding the rest of the loop). It produces a candidate patch via
+ *     the E9 LLM chokepoint and lets the EXISTING egress open a DRAFT PR — NEVER
+ *     an auto-merge, NEVER an end-user mode, NEVER a `main` push. A failed or empty
+ *     fix-gen degrades to "no patch" and the egress simply skips the PR.
  *
  * CORE-first: this engine lives in `core` and owns the `ReplayDispatch` port TYPE;
  * the cleo dispatch handler supplies the concrete adapter (dependency inversion —
@@ -45,8 +56,9 @@ import { type ExecutionEnvBackend } from '../llm/pi/resolve-execution-env.js';
 import { type ToolGuard } from '../tools/guard.js';
 import { type CircuitBreakerState, DEFAULT_BUDGET, type SelfImproveBudget } from './budget.js';
 import { type DhqAdapter } from './dhq-adapter.js';
-import { type DraftPrResult } from './draft-pr.js';
+import { type CommandRunner, type DraftPrResult } from './draft-pr.js';
 import { type DiffEntry } from './envelope-diff.js';
+import { type FixGenerator, type FixGenResult } from './fix-gen.js';
 import { type ReplayDispatch } from './replay.js';
 /** Options for {@link runSelfImprove}. */
 export interface RunSelfImproveOptions {
@@ -87,6 +99,27 @@ export interface RunSelfImproveOptions {
     readonly gateRedCheck?: () => Promise<boolean>;
     /** Test seam: inject a DHQ adapter (defaults to the real leased adapter). */
     readonly adapter?: DhqAdapter;
+    /**
+     * Test seam: inject the fix generator (the LLM dependency). Defaults to the real
+     * {@link "./fix-gen.js".createLlmFixGenerator} backed by the E9 chokepoint — unit
+     * tests inject a deterministic fake returning a canned patch so NO real LLM is
+     * reached. The fix-gen stage only runs when BOTH `execute` is set AND the
+     * Pi-runner gate (`CLEO_PI_RUNNER_ENABLED=1`) is on, unless `piRunnerEnabled` is
+     * supplied (test seam) to override the env read.
+     */
+    readonly fixGenerator?: FixGenerator;
+    /**
+     * Test seam: override the `CLEO_PI_RUNNER_ENABLED` env gate that arms fix-gen.
+     * Defaults to `process.env.CLEO_PI_RUNNER_ENABLED === '1'`. Supplied explicitly
+     * by tests so the deterministic fake runs without mutating process env.
+     */
+    readonly piRunnerEnabled?: boolean;
+    /**
+     * Test seam: inject the draft-PR egress command runner (captures the git/gh
+     * shell-out). Defaults to the real `execFileSync`-backed runner. Supplied by
+     * tests so the capstone proves the egress WITHOUT a real `gh`/`git` invocation.
+     */
+    readonly draftPrRun?: CommandRunner;
     /** Test seam: inject the guard backing the in-process fallback env. */
     readonly guard?: ToolGuard;
     /** Test seam: inject the run id (defaults to a timestamped id). */
@@ -120,6 +153,13 @@ export interface SelfImproveResult {
     readonly questionHash: string | null;
     /** The draft-PR egress result, or `null` when none fired (green / dry-run-no-egress). */
     readonly draftPr: DraftPrResult | null;
+    /**
+     * The fix-generation outcome (T11975), or `null` when the stage did not run
+     * (green run, dry-run, gate off, or breaker tripped before persist). `'written'`
+     * means a candidate patch was produced and the egress was armed; `'skipped'`
+     * means fix-gen degraded gracefully (no patch ⇒ no PR).
+     */
+    readonly fixGen: FixGenResult | null;
     /** The final circuit-breaker state. */
     readonly breaker: CircuitBreakerState;
 }

package/dist/selfimprove/run-loop.d.ts.map

@@ -1 +1 @@
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package/dist/selfimprove/run-loop.js

@@ -17,8 +17,15 @@
  *   4. on a regression, **emit ONE DHQ** row via the leased
  *      {@link "./dhq-adapter.js".DhqAdapter} (UPSERT under
  *      `withWriterLease('project','bulk',…)`) — ONLY when `execute` is set;
+ *   4b. **generate a fix** ({@link "./fix-gen.js".generateFixPatch}, T11975) — ONLY
+ *      when `execute` AND `CLEO_PI_RUNNER_ENABLED=1`. Drives the LLM strictly via
+ *      the E9 chokepoint to produce a unified-diff patch at the path the egress
+ *      expects (`<cwd>/selfimprove-<scenario>.patch`). Degrades gracefully (no
+ *      patch ⇒ the egress guard skips the PR); the outcome is recorded back onto
+ *      the DHQ row. NEVER throws a rogue mutation, NEVER auto-merges;
  *   5. **open ONE DRAFT PR** ({@link "./draft-pr.js".openDraftPr}, dry-run unless
- *      `execute`) and record its URL back on the DHQ row.
+ *      `execute`) and record its URL back on the DHQ row — fires only when the
+ *      fix-gen stage wrote a patch file (the existing `existsSync` egress guard).
  *
  * Self-dogfooding guardrails (NON-NEGOTIABLE, P5 spec §B.7):
  *   - **Default OFF.** Mutation + egress require `opts.execute === true`. Without
@@ -30,8 +37,12 @@
  *   - **Budget caps** (in-code): `maxTokens` / `maxUsd` / `maxPrs = 1` /
  *     `maxWorktrees = 1`, checked PRE-FLIGHT before each costed step. `MemoryMax=32G`
  *     is an operational launch-wrapper, not an in-code cap.
- *   - **NO autonomous fix-gen, NO auto-merge, NO end-user mode in v1.** The loop
- *     surfaces regressions as DHQs + draft PRs; a human drives the fix.
+ *   - **Fix-gen is GATED + DRAFT-PR-ONLY (T11975).** The autonomous fix-generation
+ *     stage runs ONLY behind BOTH `execute` AND `CLEO_PI_RUNNER_ENABLED=1` (the
+ *     same gates guarding the rest of the loop). It produces a candidate patch via
+ *     the E9 LLM chokepoint and lets the EXISTING egress open a DRAFT PR — NEVER
+ *     an auto-merge, NEVER an end-user mode, NEVER a `main` push. A failed or empty
+ *     fix-gen degrades to "no patch" and the egress simply skips the PR.
  *
  * CORE-first: this engine lives in `core` and owns the `ReplayDispatch` port TYPE;
  * the cleo dispatch handler supplies the concrete adapter (dependency inversion —
@@ -49,6 +60,7 @@ import { CircuitBreaker, DEFAULT_BUDGET, resolveBudget, } from './budget.js';
 import { createDhqAdapter } from './dhq-adapter.js';
 import { openDraftPr } from './draft-pr.js';
 import { computeQuestionHash, diffEnvelopes } from './envelope-diff.js';
+import { createLlmFixGenerator, fixPatchPath, generateFixPatch, } from './fix-gen.js';
 import { replayScenario } from './replay.js';
 import { loadScenario } from './scenario.js';
 /**
@@ -99,6 +111,7 @@ export async function runSelfImprove(opts) {
         regressions,
         questionHash,
         draftPr: null,
+        fixGen: null,
         breaker: breaker.state,
     });
     // ── 1. boot ONE sandbox (counts against maxWorktrees=1) ─────────────────────
@@ -133,6 +146,7 @@ export async function runSelfImprove(opts) {
                 regressions: [],
                 questionHash: null,
                 draftPr: null,
+                fixGen: null,
                 breaker: breaker.state,
             };
         }
@@ -154,16 +168,19 @@ export async function runSelfImprove(opts) {
                 regressions: diff.regressions,
                 questionHash,
                 draftPr: null,
+                fixGen: null,
                 breaker: breaker.state,
             };
         }
         // ── 4. emit ONE leased DHQ (require-mode lease throw ⇒ breaker trip) ────────
+        const dhqId = `DHQ-${questionHash.slice(0, 8)}`;
+        const dhqTitle = `selfimprove regression in '${opts.scenario}' (${diff.regressions.length} path(s))`;
         try {
             await adapter.upsertOpenDhq({
-                dhqId: `DHQ-${questionHash.slice(0, 8)}`,
+                dhqId,
                 scenario: opts.scenario,
                 questionHash,
-                title: `selfimprove regression in '${opts.scenario}' (${diff.regressions.length} path(s))`,
+                title: dhqTitle,
                 regressionJson: JSON.stringify(diff),
                 severity: null,
                 runId,
@@ -172,17 +189,65 @@ export async function runSelfImprove(opts) {
         catch (err) {
             return tripFromError(breaker, err, logger, opts.scenario, runId, execute, diff.regressions, questionHash);
         }
+        // ── 4b. AUTONOMOUS FIX-GENERATION (T11975) — gated, DRAFT-PR-ONLY ───────────
+        // Runs ONLY behind BOTH `execute` AND the Pi-runner gate. Produces a candidate
+        // unified-diff patch via the E9 LLM chokepoint at the exact path the egress
+        // below `existsSync`-checks. Degrades gracefully (no patch ⇒ the egress guard
+        // skips the PR) and NEVER throws a rogue mutation. The outcome is folded back
+        // onto the DHQ row (refresh-UPSERT — same leased, idempotent path).
+        const piRunnerEnabled = opts.piRunnerEnabled ?? process.env.CLEO_PI_RUNNER_ENABLED === '1';
+        let fixGen = null;
+        if (piRunnerEnabled) {
+            const generator = opts.fixGenerator ?? createLlmFixGenerator({ projectRoot: workspaceRoot });
+            fixGen = await generateFixPatch({
+                request: {
+                    dhqId,
+                    scenario: opts.scenario,
+                    questionHash,
+                    regressions: diff.regressions,
+                    repoContext: {
+                        projectRoot: workspaceRoot,
+                        summary: loaded.scenario.description,
+                    },
+                },
+                generator,
+                ...(opts.cwd !== undefined ? { cwd: opts.cwd } : {}),
+                logger,
+            });
+            // Record the fix-gen outcome back onto the open DHQ row (leased, idempotent).
+            // A throw here trips the breaker exactly like the initial emit (lease-denial).
+            try {
+                await adapter.upsertOpenDhq({
+                    dhqId,
+                    scenario: opts.scenario,
+                    questionHash,
+                    title: dhqTitle,
+                    regressionJson: JSON.stringify({ diff, fixGen }),
+                    severity: null,
+                    runId,
+                });
+            }
+            catch (err) {
+                return tripFromError(breaker, err, logger, opts.scenario, runId, execute, diff.regressions, questionHash);
+            }
+        }
+        else {
+            logger.info({ scenario: opts.scenario, runId }, 'self-improve fix-gen SKIPPED (CLEO_PI_RUNNER_ENABLED!=1) — DHQ emitted, no patch generated');
+        }
         // ── 5. open ONE DRAFT PR (counts against maxPrs=1) + record url back ────────
         let draftPr = null;
         try {
             breaker.chargeOrTrip({ prs: 1 });
             draftPr = await openDraftPr({
                 scenario: opts.scenario,
-                diffPath: `selfimprove-${opts.scenario}.patch`,
+                // SAME path fix-gen writes to (sanitized, resolved against cwd) so the
+                // egress `existsSync` guard finds exactly the file 4b produced.
+                diffPath: fixPatchPath(opts.scenario, opts.cwd),
                 title: `fix(selfimprove): ${opts.scenario} regression`,
                 body: `Auto-detected regression in the \`${opts.scenario}\` dogfood scenario (run ${runId}).`,
                 execute,
                 ...(opts.cwd !== undefined ? { cwd: opts.cwd } : {}),
+                ...(opts.draftPrRun !== undefined ? { run: opts.draftPrRun } : {}),
             });
             if (draftPr.kind === 'ok') {
                 await adapter.recordPrUrl(questionHash, draftPr.prUrl);
@@ -199,6 +264,7 @@ export async function runSelfImprove(opts) {
             regressions: diff.regressions,
             questionHash,
             draftPr,
+            fixGen,
             breaker: breaker.state,
         };
     }
@@ -233,6 +299,7 @@ function tripFromError(breaker, err, logger, scenario, runId, executed, regressi
         regressions,
         questionHash,
         draftPr: null,
+        fixGen: null,
         breaker: breaker.state,
     };
 }

package/dist/selfimprove/run-loop.js.map

@@ -1 +1 @@
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package/dist/selfimprove/scenarios/seeded-code-regression/golden.json

@@ -0,0 +1,18 @@
+{
+  "name": "seeded-code-regression",
+  "envelopes": [
+    {
+      "success": true,
+      "meta": {
+        "gateway": "query",
+        "domain": "selfimprove",
+        "operation": "probe",
+        "source": "rpc"
+      },
+      "data": {
+        "probe": "ok",
+        "version": 1
+      }
+    }
+  ]
+}

package/dist/selfimprove/scenarios/seeded-code-regression/scenario.json

@@ -0,0 +1,12 @@
+{
+  "name": "seeded-code-regression",
+  "description": "Seeded code-regression scenario for end-to-end fix-gen proof (T11988). A deliberately broken selfimprove helper returns the wrong value; the regression is detectable from the replay envelope and fixable by a targeted one-line code patch.",
+  "ops": [
+    {
+      "gateway": "query",
+      "domain": "selfimprove",
+      "operation": "probe",
+      "params": { "scenario": "seeded-code-regression" }
+    }
+  ]
+}

package/dist/sentient/cross-project-hygiene.d.ts

@@ -183,8 +183,17 @@ export declare function runDuplicateEpicDetection(): Promise<DuplicateEpicResult
  * `packages/core/src/spawn/branch-lock.ts` so there is zero duplication
  * of the worktree-management logic (DRY).
  *
- * Active task IDs are resolved from each project's tasks.db before calling
- * pruneOrphanedWorktrees so in-flight worktrees are never removed.
+ * Preserve set (T11996 Amendment 1 — PREDICATE BLOCKER fix):
+ * Any task whose status is NOT terminal (i.e. not `done`, `cancelled`, or
+ * `archived`) must be preserved. Querying only `status: 'active'` was the
+ * original bug — it silently removed worktrees for `pending`, `blocked`, and
+ * `proposed` tasks. We now query all non-terminal statuses and build the
+ * preserve set from their union.
+ *
+ * Fail-closed (T11996 Amendment 2):
+ * If the task store is unreadable for a project, skip pruning for that
+ * project and write a structured audit warning. If ALL projects fail to
+ * load tasks, return with zero pruning.
  *
  * Never throws.
  */

package/dist/sentient/cross-project-hygiene.d.ts.map

@@ -1 +1 @@
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package/dist/sentient/cross-project-hygiene.js

@@ -33,7 +33,7 @@
  * @epic T1627
  */
 import { createHash, randomUUID } from 'node:crypto';
-import { existsSync } from 'node:fs';
+import { appendFileSync, existsSync, mkdirSync } from 'node:fs';
 import { appendFile, mkdir, readFile, rename, writeFile } from 'node:fs/promises';
 import { join } from 'node:path';
 import { getLogger } from '../logger.js';
@@ -426,8 +426,17 @@ export async function runDuplicateEpicDetection() {
  * `packages/core/src/spawn/branch-lock.ts` so there is zero duplication
  * of the worktree-management logic (DRY).
  *
- * Active task IDs are resolved from each project's tasks.db before calling
- * pruneOrphanedWorktrees so in-flight worktrees are never removed.
+ * Preserve set (T11996 Amendment 1 — PREDICATE BLOCKER fix):
+ * Any task whose status is NOT terminal (i.e. not `done`, `cancelled`, or
+ * `archived`) must be preserved. Querying only `status: 'active'` was the
+ * original bug — it silently removed worktrees for `pending`, `blocked`, and
+ * `proposed` tasks. We now query all non-terminal statuses and build the
+ * preserve set from their union.
+ *
+ * Fail-closed (T11996 Amendment 2):
+ * If the task store is unreadable for a project, skip pruning for that
+ * project and write a structured audit warning. If ALL projects fail to
+ * load tasks, return with zero pruning.
  *
  * Never throws.
  */
@@ -450,19 +459,73 @@ export async function runWorktreePrune() {
             continue;
         projectsScanned++;
         try {
-            // Resolve active task IDs so in-flight worktrees are preserved.
-            const activeTaskIds = new Set();
+            // T11996 Amendment 1: build preserve set from ALL non-terminal statuses.
+            // A task is non-terminal if its status is not in TERMINAL_TASK_STATUSES
+            // (done / cancelled / archived). Pending, active, blocked, and proposed
+            // tasks must NEVER have their worktrees auto-removed or quarantined.
+            const preserveTaskIds = new Set();
+            let taskStoreReadable = false;
             try {
                 const accessor = await getTaskAccessor(proj.path);
-                const { tasks } = await accessor.queryTasks({ status: 'active' });
-                for (const t of tasks)
-                    activeTaskIds.add(t.id);
+                // Query each non-terminal status and union the results.
+                const nonTerminalStatuses = ['pending', 'active', 'blocked', 'proposed'];
+                for (const status of nonTerminalStatuses) {
+                    const { tasks } = await accessor.queryTasks({ status });
+                    for (const t of tasks)
+                        preserveTaskIds.add(t.id);
+                }
+                taskStoreReadable = true;
             }
             catch {
-                // Cannot read tasks — skip pruning this project conservatively.
+                // T11996 Amendment 2: task store unreadable — skip this project.
+                // Write a structured audit warning (no desktop output, ZERO notifications).
+                try {
+                    const auditDir = join(proj.path, '.cleo', 'audit');
+                    mkdirSync(auditDir, { recursive: true });
+                    const auditPath = join(auditDir, 'worktree-lifecycle.jsonl');
+                    const entry = JSON.stringify({
+                        ts: new Date().toISOString(),
+                        action: 'prune-skip-fail-closed',
+                        projectPath: proj.path,
+                        reason: 'task store unreadable — skipping worktree prune to prevent data loss (T11996 fail-closed)',
+                        agentId: process.env['CLEO_AGENT_ID'] ?? 'cleo',
+                    });
+                    appendFileSync(auditPath, `${entry}\n`, { encoding: 'utf-8' });
+                }
+                catch {
+                    // audit is best-effort
+                }
+                log.warn({ projectPath: proj.path }, `${LOG}: step4 — task store unreadable, skipping project`);
+                continue;
+            }
+            if (!taskStoreReadable)
+                continue;
+            // T11996 Amendment 2: fail-closed — if the preserve set is empty while
+            // worktrees may exist, skip to prevent mass-deletion.
+            // NOTE: pruneOrphanedWorktrees (branch-lock.ts) calls pruneWorktrees
+            // (worktree-prune.ts) which has its own fail-closed guard; this is an
+            // additional layer at the hygiene-loop level so we can log the skip here.
+            if (preserveTaskIds.size === 0) {
+                log.warn({ projectPath: proj.path }, `${LOG}: step4 — preserve set empty, skipping project (fail-closed)`);
+                try {
+                    const auditDir = join(proj.path, '.cleo', 'audit');
+                    mkdirSync(auditDir, { recursive: true });
+                    const auditPath = join(auditDir, 'worktree-lifecycle.jsonl');
+                    const entry = JSON.stringify({
+                        ts: new Date().toISOString(),
+                        action: 'prune-skip-fail-closed',
+                        projectPath: proj.path,
+                        reason: 'preserve set empty — skipping worktree prune to prevent mass-deletion (T11996 fail-closed)',
+                        agentId: process.env['CLEO_AGENT_ID'] ?? 'cleo',
+                    });
+                    appendFileSync(auditPath, `${entry}\n`, { encoding: 'utf-8' });
+                }
+                catch {
+                    // audit is best-effort
+                }
                 continue;
             }
-            const pruneResult = pruneOrphanedWorktrees(proj.path, activeTaskIds);
+            const pruneResult = pruneOrphanedWorktrees(proj.path, preserveTaskIds);
             totalPruned += pruneResult.removed;
             for (const e of pruneResult.errors) {
                 errors.push({ projectPath: proj.path, reason: `${e.path}: ${e.reason}` });