@cleocode/core 2026.9.19 → 2026.9.21

package/dist/validation/doctor/utils.js

@@ -7,6 +7,7 @@
  * @task T4525
  * @epic T4454
  */
+import { isEphemeralPath } from '../../nexus/registry-hygiene.js';
 // ============================================================================
 // Temp Project Detection
 // ============================================================================
@@ -16,8 +17,12 @@ const TEMP_PATTERNS = ['/.temp/', '/tmp/', '/bats-run-', '/.tmp/', '/tmp.', '/ba
  * @task T4525
  */
 export function isTempProject(path) {
-    return (TEMP_PATTERNS.some((pattern) => path.includes(pattern)) ||
-        (path.includes('/test/') && (path.includes('bats-run-') || path.includes('test-'))));
+    // Patterns are '/'-form; fold Windows separators so they match there too,
+    // and defer real temp-dir containment to the shared check (T12606).
+    const p = path.replace(/\\/g, '/');
+    return (isEphemeralPath(path) ||
+        TEMP_PATTERNS.some((pattern) => p.includes(pattern)) ||
+        (p.includes('/test/') && (p.includes('bats-run-') || p.includes('test-'))));
 }
 // ============================================================================
 // Project Categorization

package/dist/validation/doctor/utils.js.map

@@ -1 +1 @@
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package/dist/validation/engine-ops.d.ts

@@ -72,6 +72,21 @@ export interface GateVerifyParams {
      * triggers a warning (or a hard reject in strict mode).
      */
     sharedEvidence?: boolean;
+    /**
+     * `--no-run` (T12621): serve every process-executing typed gate from the
+     * ADR-061 result cache and execute none. A gate without a fresh cached pass
+     * refuses the write, before anything is recorded, with `E_GATE_NOT_CACHED`.
+     */
+    noRun?: boolean;
+    /**
+     * Per-gate evidence for ONE write (T12625 · `cleo done`): each gate's own
+     * atom string goes through the same parse → `validateAtom` → gate minimum →
+     * `checkTaskEvidenceContext` path as `--gate … --evidence …`, and every gate
+     * is persisted in the same transaction. Exclusive with `gate`/`all`/
+     * `evidence`, and refuses `CLEO_OWNER_OVERRIDE` (the override stays a
+     * single-gate, audited `cleo verify` path).
+     */
+    gateEvidence?: Partial<Record<VerificationGate, string | readonly string[]>>;
 }
 export interface GateVerifyResult {
     /** Coverage assessed when evidence is recorded, independent of gate success. */

package/dist/validation/engine-ops.d.ts.map

@@ -1 +1 @@
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package/dist/validation/engine-ops.js

@@ -23,11 +23,12 @@ import { captureProjectScope, readProjectInfoAtDirectorySync, worktreeScope, } f
 import { checkAndIncrementOverrideCap } from '../security/override-cap.js';
 import { enforceSharedEvidence } from '../security/shared-evidence-tracker.js';
 import { warnIfNoActiveSession } from '../sessions/session-enforcement.js';
-import { createOperationExecutionContext } from '../store/background-ops.js';
+import { createOperationExecutionContext, OperationExecutionError, } from '../store/background-ops.js';
 import { getTaskAccessor } from '../store/data-accessor.js';
 import { checkCallsiteCoverageAtom, checkEngineMigrationLocDrop, checkGateEvidenceMinimumDetailed, checkTaskEvidenceContext, composeGateEvidence, DECISION_ONLY_INAPPLICABLE_GATES, isDecisionOnlyImplementation, isHardAtom, parseEvidence, validateAtom, } from '../tasks/evidence.js';
 import { appendForceBypassLine, appendGateAuditLine } from '../tasks/gate-audit.js';
-import { createTaskGateReceipt, revalidateTaskGateResults, runTaskGates, } from '../tasks/gate-runner.js';
+import { readAllowCachedGates } from '../tasks/gate-result-cache.js';
+import { createTaskGateReceipt, GATE_CACHE_INVALID_PREFIX, GATE_NOT_CACHED_PREFIX, revalidateTaskGateResults, runTaskGates, typedGateAdmissionMs, } from '../tasks/gate-runner.js';
 import { hasCallsiteCoverageLabel, hasEngineMigrationLabel, } from '../verification/evidence-atoms.js';
 import { checkArchitectureDecisionManifest, validateArchitectureDecisionTask, } from './protocols/architecture-decision.js';
 import { checkArtifactPublishManifest, validateArtifactPublishTask, } from './protocols/artifact-publish.js';
@@ -192,10 +193,10 @@ function protocolCatch(err) {
  * @adr ADR-051
  */
 export async function validateGateVerify(projectRoot, params) {
-    const admittedAt = Date.now();
     projectRoot = resolve(projectRoot);
     const inheritedExecution = worktreeScope.getStore()?.execution;
     let ownedVerificationExecution;
+    let typedPhase = 'task and evidence validation';
     try {
         const { taskId, gate, value = true, agent, all, reset } = params;
         const agentId = agent ?? 'unknown';
@@ -221,26 +222,44 @@ export async function validateGateVerify(projectRoot, params) {
         const originalUpdatedAt = task.updatedAt;
         const typedWrite = !reset &&
             value !== false &&
-            Boolean(gate || all) &&
+            Boolean(gate || all || params.gateEvidence) &&
             originalAcceptance.some((item) => typeof item !== 'string');
+        // T12621: `evidence.allowCachedGates: false` disables reuse, so `--no-run`
+        // has nothing it may record from.
+        const allowCachedGates = readAllowCachedGates(projectRoot);
+        if (typedWrite && params.noRun && !allowCachedGates)
+            return engineError('E_GATE_CACHE_DISABLED', `--no-run: this project sets evidence.allowCachedGates to false, so typed gates must execute; drop --no-run to verify ${taskId}`);
         const initialAcRows = typedWrite ? await accessor.getAcRows(taskId) : [];
         let typedExecution;
+        // T12516: an owned typed lifetime is admitted only when the typed gates are
+        // about to run, and it is sized from their ADR-061 tool deadlines plus the
+        // shared bookkeeping budget. It used to be a fixed two seconds from admission,
+        // created here, so the lifetime was spent by evidence tools (`tool:test`) and
+        // by the gates themselves: any suite over two seconds ended in
+        // E_OPERATION_DEADLINE. A caller-owned (inherited) lifetime is kept as is.
+        let admitOwnedTypedExecution;
         if (typedWrite) {
             typedExecution = inheritedExecution;
             if (!typedExecution) {
                 const identity = readProjectInfoAtDirectorySync(projectRoot, join(projectRoot, '.cleo'));
-                if (!identity.projectId)
+                const projectId = identity.projectId;
+                if (!projectId)
                     throw new Error('Typed verification requires a stable project identity');
-                ownedVerificationExecution = createOperationExecutionContext({
-                    projectId: identity.projectId,
-                    projectRoot,
-                    actor: agentId,
-                    operation: 'check.gate.verify',
-                    idempotencyKey: `${taskId}:${randomUUID()}`,
-                }, { deadlineAt: admittedAt + 2000 });
-                typedExecution = ownedVerificationExecution;
+                const typedGates = originalAcceptance.filter((item) => typeof item !== 'string');
+                admitOwnedTypedExecution = () => {
+                    ownedVerificationExecution = createOperationExecutionContext({
+                        projectId,
+                        projectRoot,
+                        actor: agentId,
+                        operation: 'check.gate.verify',
+                        idempotencyKey: `${taskId}:${randomUUID()}`,
+                    }, { budgetMs: typedGateAdmissionMs(typedGates) });
+                    return ownedVerificationExecution;
+                };
+            }
+            else {
+                typedExecution.assertActive();
             }
-            typedExecution.assertActive();
         }
         const validateEvidenceAtom = (...args) => typedExecution
             ? worktreeScope.run(captureProjectScope(projectRoot, {
@@ -249,8 +268,24 @@ export async function validateGateVerify(projectRoot, params) {
             }), () => validateAtom(...args))
             : validateAtom(...args);
         const configGates = await loadRequiredGates(projectRoot);
+        // T12625: a multi-gate write names its gates by the keys of gateEvidence.
+        const multiTargets = params.gateEvidence
+            ? VALID_GATES.filter((g) => params.gateEvidence?.[g] !== undefined)
+            : null;
+        if (multiTargets) {
+            const unknown = Object.keys(params.gateEvidence ?? {}).filter((g) => !VALID_GATES.includes(g));
+            if (unknown.length > 0 ||
+                multiTargets.length === 0 ||
+                gate ||
+                all ||
+                reset ||
+                params.evidence)
+                return engineError('E_INVALID_INPUT', unknown.length > 0
+                    ? `Invalid gate(s) in gateEvidence: ${unknown.join(', ')}. Valid: ${VALID_GATES.join(', ')}`
+                    : 'gateEvidence needs at least one gate and excludes gate, all, reset and evidence');
+        }
         // View mode (no modifications)
-        if (!gate && !all && !reset) {
+        if (!gate && !all && !reset && !multiTargets) {
             const verification = task.verification ?? initVerification();
             const missing = getMissingGates(verification, configGates);
             return engineSuccess({
@@ -269,7 +304,9 @@ export async function validateGateVerify(projectRoot, params) {
         }
         // T9231 / ADR-070: FISE-2 — Lead authorship bypass prevention.
         // Reject implemented gate write from a Lead session without upstream delegation.
-        if (gate === 'implemented' && value !== false && !reset) {
+        if ((gate === 'implemented' || multiTargets?.includes('implemented')) &&
+            value !== false &&
+            !reset) {
             const { validateSpawnRequest } = await import('../lifecycle/ivtr-loop.js');
             const spawnCheck = await validateSpawnRequest(taskId, 'implemented', sessionId);
             if (!spawnCheck.allowed) {
@@ -278,8 +315,11 @@ export async function validateGateVerify(projectRoot, params) {
         }
         // Check if evidence-based requirement applies.  gate failures
         // (value=false) and resets do NOT require evidence.
-        const isWriteRequiringEvidence = (all || (gate && value !== false)) && !reset;
+        const isWriteRequiringEvidence = (all || multiTargets !== null || (gate && value !== false)) && !reset;
         const override = readOverrideState();
+        if (multiTargets && override.override)
+            return engineError('E_OVERRIDE_NOT_ACCEPTED', 'CLEO_OWNER_OVERRIDE is not accepted by a derived multi-gate write (cleo done / verify --auto). ' +
+                'Unset it, or record the gate with `cleo verify <id> --gate <gate> --evidence …`, which keeps the audited override path.');
         // T1501 / P0-5 — per-session CLEO_OWNER_OVERRIDE cap.
         // Enforce before the write proceeds so the error surfaces early.
         let sessionOverrideOrdinal;
@@ -303,8 +343,10 @@ export async function validateGateVerify(projectRoot, params) {
             else {
                 // Attempt to resolve the active session from the DB as a better key.
                 try {
-                    const activeSession = await accessor.getActiveSession();
-                    capSessionId = activeSession?.id ?? 'global';
+                    // T12500: the caller's BOUND session only — never charge an
+                    // override to whichever agent's session is newest.
+                    const { resolveBoundSessionId } = await import('../store/session-store.js');
+                    capSessionId = (await resolveBoundSessionId(projectRoot)) ?? 'global';
                 }
                 catch {
                     capSessionId = 'global';
@@ -320,13 +362,20 @@ export async function validateGateVerify(projectRoot, params) {
         // T1502 / P0-6 — shared-evidence detection.
         let sharedEvidenceAcknowledged = false;
         let sharedAtomWarned = false;
-        if (isWriteRequiringEvidence && !override.override && params.evidence && sessionId) {
-            const seResult = enforceSharedEvidence(projectRoot, sessionId, taskId, params.evidence, params.sharedEvidence === true);
+        const evidenceStrings = multiTargets
+            ? multiTargets.flatMap((g) => evidenceAttempts(params.gateEvidence?.[g]))
+            : params.evidence
+                ? [params.evidence]
+                : [];
+        for (const evidenceString of evidenceStrings) {
+            if (!isWriteRequiringEvidence || override.override || !sessionId)
+                break;
+            const seResult = enforceSharedEvidence(projectRoot, sessionId, taskId, evidenceString, params.sharedEvidence === true);
             if (!seResult.allowed) {
                 return engineError(seResult.errorCode ?? 'E_SHARED_EVIDENCE_FLAG_REQUIRED', seResult.errorMessage ?? 'Shared evidence flag required.');
             }
-            sharedEvidenceAcknowledged = seResult.acknowledged === true;
-            sharedAtomWarned = seResult.warned === true;
+            sharedEvidenceAcknowledged ||= seResult.acknowledged === true;
+            sharedAtomWarned ||= seResult.warned === true;
         }
         // Modification mode
         let verification = task.verification ?? initVerification();
@@ -336,21 +385,97 @@ export async function validateGateVerify(projectRoot, params) {
         const now = new Date().toISOString();
         let action = 'view';
         const evidenceStored = [];
+        const perGateAtoms = new Map();
         if (reset) {
             verification = initVerification();
             action = 'reset';
         }
         else if (isWriteRequiringEvidence) {
             // Determine target gates.
-            const targets = all ? configGates : [gate];
+            const targets = multiTargets ?? (all ? configGates : [gate]);
             const evidenceContext = {
                 task,
                 gates: targets,
                 criteria: await accessor.getAcRows(taskId),
             };
-            if (!all && !VALID_GATES.includes(gate)) {
+            if (!all && !multiTargets && !VALID_GATES.includes(gate)) {
                 return engineError('E_INVALID_INPUT', `Invalid gate: ${gate}. Valid: ${VALID_GATES.join(', ')}`);
             }
+            // One evidence string, validated for `gates` through the ADR-051 path:
+            // parse → validateAtom → per-gate minimum → label gates. Shared by the
+            // single-gate write and the T12625 multi-gate write, so there is one
+            // validation path, not two.
+            const validateEvidenceFor = async (evidence, gates) => {
+                const atoms = [];
+                let parsed;
+                try {
+                    parsed = parseEvidence(evidence);
+                }
+                catch (err) {
+                    const message = err instanceof Error ? err.message : String(err);
+                    return engineError('E_EVIDENCE_INVALID', message);
+                }
+                // T12107 (gh#1195): a sibling `commit:` atom anchors `files:` paths —
+                // thread its sha so files are resolved against that commit's tree first.
+                const siblingCommitSha = parsed.atoms.find((a) => a.kind === 'commit')?.sha;
+                for (const atom of parsed.atoms.toSorted((a, b) => Number(b.kind === 'pr') - Number(a.kind === 'pr'))) {
+                    // T9178: pass taskId for branch-scope commit validation
+                    const check = await validateEvidenceAtom(atom, projectRoot, taskId, siblingCommitSha, {
+                        ...evidenceContext,
+                        artifactCommitSha: atoms.find((atom) => atom.kind === 'pr')?.mergeCommitSha,
+                    });
+                    if (!check.ok) {
+                        return engineError(check.codeName, check.reason);
+                    }
+                    atoms.push(check.atom);
+                }
+                // Check each target gate satisfies its minimum.
+                // T9949: surface the rich example-bearing remediation hint via
+                // `engineError({fix:})` so `note:`-only callers see exactly which
+                // alternative atom kind the gate requires (commit/files/decision/pr).
+                // gh#1215: a task whose `implemented` gate was satisfied by a DECISION
+                // with no commit/pr changed no code, so `testsPassed` / `qaPassed` have
+                // nothing to measure. Demanding them made correctly-evidenced audit and
+                // review tasks uncompletable: tool:test is meaningless when nothing
+                // changed, and the owner override is session-capped and rejected on
+                // critical gates. Satisfied by absence, as with the T12083
+                // `notApplicable` tool atom.
+                const decisionOnly = isDecisionOnlyImplementation(verification.evidence?.implemented);
+                for (const targetGate of gates) {
+                    if (decisionOnly && DECISION_ONLY_INAPPLICABLE_GATES.includes(targetGate))
+                        continue;
+                    const missing = checkGateEvidenceMinimumDetailed(targetGate, atoms);
+                    if (missing) {
+                        return engineError('E_EVIDENCE_INSUFFICIENT', missing.message, {
+                            fix: missing.hint,
+                        });
+                    }
+                }
+                // T1604 — engine-migration label gate.
+                // If the task carries the `engine-migration` label and the `implemented`
+                // gate is among the targets, require a `loc-drop` evidence atom proving
+                // the migrated engine shed ≥ the configured minimum percentage of LOC.
+                const isImplementedTarget = gates.includes('implemented');
+                if (isImplementedTarget && hasEngineMigrationLabel(task.labels ?? [])) {
+                    const locDropError = checkEngineMigrationLocDrop(atoms);
+                    if (locDropError) {
+                        return engineError('E_EVIDENCE_INSUFFICIENT', locDropError);
+                    }
+                }
+                // T1605 — callsite-coverage label gate.
+                // If the task carries the `callsite-coverage` label and the `implemented`
+                // gate is among the targets, require a `callsite-coverage` evidence atom
+                // proving the exported symbol has ≥1 production callsite outside its
+                // own source file, test files, and dist directories.  Catches the T1601
+                // pattern where a function is shipped but never wired to production.
+                if (isImplementedTarget && hasCallsiteCoverageLabel(task.labels ?? [])) {
+                    const callsiteError = checkCallsiteCoverageAtom(atoms);
+                    if (callsiteError) {
+                        return engineError('E_EVIDENCE_INSUFFICIENT', callsiteError);
+                    }
+                }
+                return atoms;
+            };
             // Parse evidence if provided.
             let validatedAtoms = [];
             if (override.override) {
@@ -433,81 +558,48 @@ export async function validateGateVerify(projectRoot, params) {
                 validatedAtoms = [{ kind: 'override', reason: override.reason }, ...overrideAtoms];
             }
             else {
-                if (!params.evidence) {
-                    return engineError('E_EVIDENCE_MISSING', `Evidence is required. See ADR-051.\n` +
-                        `Example: cleo verify ${taskId} --gate implemented --evidence commit:<sha>;files:<path>\n` +
-                        `Or set CLEO_OWNER_OVERRIDE=1 with CLEO_OWNER_OVERRIDE_REASON=<reason> for emergency bypass (audited).`);
-                }
-                let parsed;
-                try {
-                    parsed = parseEvidence(params.evidence);
-                }
-                catch (err) {
-                    const message = err instanceof Error ? err.message : String(err);
-                    return engineError('E_EVIDENCE_INVALID', message);
-                }
-                // T12107 (gh#1195): a sibling `commit:` atom anchors `files:` paths —
-                // thread its sha so files are resolved against that commit's tree first.
-                const siblingCommitSha = parsed.atoms.find((a) => a.kind === 'commit')?.sha;
-                for (const atom of parsed.atoms.toSorted((a, b) => Number(b.kind === 'pr') - Number(a.kind === 'pr'))) {
-                    // T9178: pass taskId for branch-scope commit validation
-                    const check = await validateEvidenceAtom(atom, projectRoot, taskId, siblingCommitSha, {
-                        ...evidenceContext,
-                        artifactCommitSha: validatedAtoms.find((atom) => atom.kind === 'pr')?.mergeCommitSha,
-                    });
-                    if (!check.ok) {
-                        return engineError(check.codeName, check.reason);
+                if (!multiTargets) {
+                    if (!params.evidence) {
+                        return engineError('E_EVIDENCE_MISSING', `Evidence is required. See ADR-051.\n` +
+                            `Example: cleo verify ${taskId} --gate implemented --evidence commit:<sha>;files:<path>\n` +
+                            `Or set CLEO_OWNER_OVERRIDE=1 with CLEO_OWNER_OVERRIDE_REASON=<reason> for emergency bypass (audited).`);
                     }
-                    validatedAtoms.push(check.atom);
+                    const checked = await validateEvidenceFor(params.evidence, targets);
+                    if (!Array.isArray(checked))
+                        return checked;
+                    validatedAtoms = checked;
                 }
-                // Check each target gate satisfies its minimum.
-                // T9949: surface the rich example-bearing remediation hint via
-                // `engineError({fix:})` so `note:`-only callers see exactly which
-                // alternative atom kind the gate requires (commit/files/decision/pr).
-                // gh#1215: a task whose `implemented` gate was satisfied by a DECISION
-                // with no commit/pr changed no code, so `testsPassed` / `qaPassed` have
-                // nothing to measure. Demanding them made correctly-evidenced audit and
-                // review tasks uncompletable: tool:test is meaningless when nothing
-                // changed, and the owner override is session-capped and rejected on
-                // critical gates. Satisfied by absence, as with the T12083
-                // `notApplicable` tool atom.
-                const decisionOnly = isDecisionOnlyImplementation(verification.evidence?.implemented);
-                for (const targetGate of targets) {
-                    if (decisionOnly && DECISION_ONLY_INAPPLICABLE_GATES.includes(targetGate))
-                        continue;
-                    const missing = checkGateEvidenceMinimumDetailed(targetGate, validatedAtoms);
-                    if (missing) {
-                        return engineError('E_EVIDENCE_INSUFFICIENT', missing.message, {
-                            fix: missing.hint,
-                        });
-                    }
-                }
-                // T1604 — engine-migration label gate.
-                // If the task carries the `engine-migration` label and the `implemented`
-                // gate is among the targets, require a `loc-drop` evidence atom proving
-                // the migrated engine shed ≥ the configured minimum percentage of LOC.
-                const isImplementedTarget = targets.includes('implemented');
-                if (isImplementedTarget && hasEngineMigrationLabel(task.labels ?? [])) {
-                    const locDropError = checkEngineMigrationLocDrop(validatedAtoms);
-                    if (locDropError) {
-                        return engineError('E_EVIDENCE_INSUFFICIENT', locDropError);
-                    }
-                }
-                // T1605 — callsite-coverage label gate.
-                // If the task carries the `callsite-coverage` label and the `implemented`
-                // gate is among the targets, require a `callsite-coverage` evidence atom
-                // proving the exported symbol has ≥1 production callsite outside its
-                // own source file, test files, and dist directories.  Catches the T1601
-                // pattern where a function is shipped but never wired to production.
-                if (isImplementedTarget && hasCallsiteCoverageLabel(task.labels ?? [])) {
-                    const callsiteError = checkCallsiteCoverageAtom(validatedAtoms);
-                    if (callsiteError) {
-                        return engineError('E_EVIDENCE_INSUFFICIENT', callsiteError);
-                    }
+            }
+            // T12625: each gate validates and composes its OWN atoms, in gate order,
+            // so `implemented` is on the record before the decision-only rule for
+            // testsPassed/qaPassed reads it.
+            //
+            // T12628 (D11151): a gate may carry ORDERED attempts (one per PR a task
+            // shipped in). Every attempt is validated before anything is persisted,
+            // each gets its own audit line, and the gate's stored evidence is the
+            // last attempt — so the whole set is recorded in this one write or not
+            // at all.
+            for (const targetGate of multiTargets ?? []) {
+                const attempts = [];
+                for (const attempt of evidenceAttempts(params.gateEvidence?.[targetGate])) {
+                    const atoms = await validateEvidenceFor(attempt, [targetGate]);
+                    if (!Array.isArray(atoms))
+                        return atoms;
+                    const contextualFailure = checkTaskEvidenceContext(evidenceContext, targetGate, atoms);
+                    if (contextualFailure)
+                        return engineError('E_EVIDENCE_CONTENT_MISMATCH', contextualFailure);
+                    evidenceStored.push(...atoms);
+                    attempts.push(atoms);
                 }
+                const last = attempts[attempts.length - 1];
+                if (!last)
+                    return engineError('E_INVALID_INPUT', `gateEvidence.${targetGate} is empty`);
+                perGateAtoms.set(targetGate, attempts);
+                verification.gates[targetGate] = true;
+                verification.evidence[targetGate] = composeGateEvidence(last, agentId, undefined, undefined, evidenceContext, targetGate);
             }
             evidenceStored.push(...validatedAtoms);
-            for (const targetGate of targets) {
+            for (const targetGate of multiTargets ? [] : targets) {
                 const contextualFailure = override.override && targetGate !== 'implemented' && targetGate !== 'testsPassed'
                     ? null
                     : checkTaskEvidenceContext(evidenceContext, targetGate, validatedAtoms);
@@ -518,7 +610,7 @@ export async function validateGateVerify(projectRoot, params) {
             }
             verification.lastAgent = agent;
             verification.lastUpdated = now;
-            action = all ? 'set_all' : 'set_gate';
+            action = all || multiTargets ? 'set_all' : 'set_gate';
         }
         else if (gate) {
             // Gate failure — no evidence required (failures do not need proof).
@@ -539,11 +631,32 @@ export async function validateGateVerify(projectRoot, params) {
             });
             action = 'set_gate';
         }
+        if (admitOwnedTypedExecution)
+            typedExecution = admitOwnedTypedExecution();
         if (typedExecution) {
+            typedPhase = 'typed gate execution';
+            typedExecution.assertActive();
             verification.gateResults = await runTaskGates(task, initialAcRows, {
                 projectRoot,
                 execution: typedExecution,
+                // T12621: reuse a pass cached by `cleo verify --run` or an earlier
+                // attempt; `--no-run` executes nothing.
+                cache: allowCachedGates ? (params.noRun ? 'only' : 'use') : 'off',
             });
+            // `--no-run` refuses the whole write rather than recording a gate it
+            // declined to execute as an `error` result.
+            const results = verification.gateResults;
+            const refusedFrom = (prefix) => results
+                .filter((result) => result.errorMessage?.startsWith(prefix))
+                .map((result) => result.errorMessage.replace('<taskId>', taskId));
+            const invalid = refusedFrom(GATE_CACHE_INVALID_PREFIX);
+            if (invalid.length > 0)
+                return engineError('E_GATE_CACHE_INVALID', invalid.join('\n'));
+            const notCached = refusedFrom(GATE_NOT_CACHED_PREFIX);
+            if (notCached.length > 0)
+                return engineError('E_GATE_NOT_CACHED', notCached.join('\n'));
+            typedExecution.assertActive();
+            typedPhase = 'persisting the verification';
         }
         verification.passed =
             computePassed(verification, configGates) &&
@@ -636,7 +749,22 @@ export async function validateGateVerify(projectRoot, params) {
                 override: override.override,
             };
             try {
-                await appendGateAuditLine(projectRoot, auditRecord);
+                // T12625: a multi-gate write logs one line per gate with that gate's
+                // own atoms, the shape every single-gate write already has.
+                if (multiTargets) {
+                    for (const g of multiTargets) {
+                        for (const attempt of perGateAtoms.get(g) ?? []) {
+                            await appendGateAuditLine(projectRoot, {
+                                ...auditRecord,
+                                gate: g,
+                                action: 'set',
+                                evidence: composeGateEvidence(attempt, agentId),
+                            });
+                        }
+                    }
+                }
+                else
+                    await appendGateAuditLine(projectRoot, auditRecord);
                 if (override.override && action !== 'reset') {
                     // T1501: include sessionOverrideOrdinal in the force-bypass record.
                     // T1504: include workTreeContext when the override was exempt from the cap counter.
@@ -684,7 +812,7 @@ export async function validateGateVerify(projectRoot, params) {
             result.gateSet = gate;
         }
         else if (action === 'set_all') {
-            result.gatesSet = configGates;
+            result.gatesSet = multiTargets ?? configGates;
         }
         if (evidenceStored.length > 0) {
             result.evidenceStored = evidenceStored;
@@ -717,6 +845,10 @@ export async function validateGateVerify(projectRoot, params) {
         return engineSuccess(result);
     }
     catch (err) {
+        // T12621: a bare "Shared operation deadline reached" named neither the
+        // phase that ran out nor the remedy, so agents grepped the dist bundle.
+        if (err instanceof OperationExecutionError && err.code === 'E_OPERATION_DEADLINE')
+            return engineError('E_OPERATION_DEADLINE', typedDeadlineMessage(params.taskId, typedPhase));
         const message = err instanceof Error
             ? [err.message, err.cause instanceof Error ? err.cause.message : undefined]
                 .filter(Boolean)
@@ -728,6 +860,25 @@ export async function validateGateVerify(projectRoot, params) {
         ownedVerificationExecution?.close();
     }
 }
+/** A gate's evidence as ordered attempts (a single string is one attempt). */
+function evidenceAttempts(value) {
+    if (value === undefined)
+        return [];
+    return typeof value === 'string' ? [value] : [...value];
+}
+/**
+ * Deadline diagnostic for a typed verification write: the phase that ran out
+ * and the remedies, in one self-contained message (the CLI envelope carries
+ * only `code` and `message`).
+ */
+function typedDeadlineMessage(taskId, phase) {
+    return (`Typed verification of ${taskId} reached its operation deadline during ${phase}. ` +
+        'Each typed gate is bounded by its own timeout (gate `timeoutMs`, else CLEO_GATE_TIMEOUT_MS, ' +
+        'else CLEO_TOOL_TIMEOUT_<KIND>, else 1800000 ms for test and 300000 ms otherwise). ' +
+        'Fix: raise that timeout for a slow gate, or run `cleo verify ' +
+        taskId +
+        ' --run` first so passing results are cached and the write reuses them (add --no-run to forbid execution).');
+}
 // ---------------------------------------------------------------------------
 // Protocol validation operations (T5327 + T260)
 // ---------------------------------------------------------------------------