@indigoai-us/hq-cli 5.260.0 → 5.262.0

package/CHANGELOG.md

@@ -2,6 +2,26 @@
 
 ## [Unreleased]
 
+## [5.262.0] — 2026-09-28
+
+### Added
+
+- The `checkpoint.ontology.concept-project-link` flag (off by default) lets
+  checkpoint ontology link a knowledge concept whose alias is ambiguous to the
+  one project with the same canonical name, such as HQ. It writes nothing.
+
+### Fixed
+
+- `hq doctor --live-runtimes` uses a Windows `.cmd` shim only when the sibling file exists.
+
+## [5.261.0] — 2026-09-28
+
+### Fixed
+
+- Standing keep-alive leads now resume stories that remain open. Completed
+  stories resume only on standing leads with queued work, and reconcile reports
+  why other completed lanes stay idle.
+
 ## [5.260.0] — 2026-09-28
 
 ### Added

package/dist/commands/lanes.js

@@ -50,7 +50,7 @@ import { effectiveAccountHome } from "../lib/lanes/account-home.js";
 import { AccountResolutionError, compareLaneQueueOrder, LANE_PROVIDERS, LANE_STATES, QUESTION_STATUSES, SENIOR_KINDS, accountStatus, appendCappedHistory, canonicalizeHome, createLane, decideAdmission, defaultLivenessDeps, defaultSystemdUserDir, defaultThrottleDeps, installReconcileTimer, providerPathEnv, probeDrainHookRegistration, isLanesError, isLaneVersionConflict, isTerminalLaneState, aliveDirectChildren, assignedChildHireGrants, hireGrantCapacityError, planHireGrantBackfill, terminalChildResumeHireGrantError, withHireGrantAdmission, laneStoryLedgerEnabled, validateProjectStories, buildLaneStatusSnapshot, formatLaneStatusHuman, listLaneIds, listQuestionIds, loadLanesConfig, laneRunsHere, MAX_LANE_DEPTH, MONITOR_ERROR_EXIT_CODE, readLiveMonitorEvidence, resolveMachineIdentity as lookupMachineIdentity, loadLivenessIndex, parseLaneProvider, parseLaneRecord, parseLaneState, parseQuestionRecord, parseSeniorKind, readLane, retryUpdateLane, syncLaneRecordFromOwner, readQuestion, resolveAccount, resolveLaneWorker, ignoredWorkerProfileFields, loadWorkerProfile, loadWorkerProfileWithRegistry, registryWorkerRecord, runReconcilePass, sessionLiveness, tryReadLane, uninstallReconcileTimer, updateLane, updateQuestion, dropboxDir, laneDeliveryMechanism, hasActiveAdmissionReservation, hasActivePendingResume, hasRecordedSessionId, hasEarlierEligibleQueuedLane, laneAdmissionCapReason, providerSupportsSessionResume, providerSessionPortable, sessionNotPortableMessage, withLaneAdmissionLock, withAllLaneAdmissionLocks, withLaneHireLocks, raiseLaneQuestion, sha256Text, } from "../lib/lanes/index.js";
 import { activeLaneStories, laneStories, laneStory, storyWarning, } from "../lib/lanes/stories.js";
 import { resolveLaneKeepAlive } from "../lib/lanes/profile.js";
-import { keepAliveExclusion, LANE_SUPERSESSION_LINEAGE_AWARE_FLAG, loadRetiredLaneIds, } from "../lib/lanes/keep-alive.js";
+import { doneKeepAliveVerdict, hasPendingKeepAliveWork, keepAliveExclusion, LANE_SUPERSESSION_LINEAGE_AWARE_FLAG, loadRetiredLaneIds, } from "../lib/lanes/keep-alive.js";
 import { questionBodyAbsPath, resolveQuestionCompanyWithFallback, resolveProjectQuestionCompany, } from "../lib/lanes/questions.js";
 import { assertQuestionBodySecretSafe } from "../lib/lanes/questions.js";
 import { compactionAfterUsage, } from "../lib/lanes/compaction.js";
@@ -4524,6 +4524,9 @@ async function runShow(ctx, laneId) {
         : storedLane;
     const askDeliveryFailed = readJsonFile(askDeliveryFailedPath(hqRoot, laneId));
     const keepAliveState = resolveLaneKeepAlive(hqRoot, storedLane);
+    const doneStateVerdict = storedLane.state === "done" && storedLane.keep_alive === true
+        ? doneKeepAliveVerdict(storedLane, { decision: storedLane.last_envelope?.decision, story_complete: storedLane.story_complete }, storedLane.keep_alive_standing === true && hasPendingKeepAliveWork(hqRoot, storedLane))
+        : null;
     const managerStatusGate = await resolveManagerStatusGateForLane(hqRoot, storedLane, { env: ctx.env });
     const managerStatusTarget = managerStatusGate.target;
     const blockerFreshness = await resolveBlockerFreshnessForLane(hqRoot, storedLane, {
@@ -4560,6 +4563,7 @@ async function runShow(ctx, laneId) {
             enabled: keepAliveState.enabled,
             source: keepAliveState.source,
             standing: storedLane.keep_alive_standing === true,
+            done_state_verdict: doneStateVerdict,
             opted_in_at: storedLane.keep_alive_opted_in_at ?? null,
             blocked_reason: storedLane.keep_alive_blocked_reason ??
                 (storedLane.keep_alive === true ? null : "not_opted_in"),

package/dist/lib/checkpoint-ontology/apply.js

@@ -370,6 +370,21 @@ export function applyOntologyRun(options) {
             }
             continue;
         }
+        if (resolved.tier === "ambiguous_alias") {
+            // checkpoint.ontology.concept-project-link: a knowledge concept whose name is the
+            // canonical name of exactly one project links to that project. Nothing is written.
+            // Like the tier 1 and 2 links above, it runs before the stopword guard,
+            // which only stops new entities.
+            const projects = plan.concept_project_link === true && input.kind === "knowledge" && candidate.type === "concept"
+                ? [...(index.canonical.get(entityKey("project", normalizeEntityName(canonical, "project"))) ?? [])]
+                : [];
+            if (projects.length === 1) {
+                const linked = index.byRel.get(projects[0]);
+                report.matched += 1;
+                report.links.push({ input: candidate.input, action: "link", type: linked.type, canonical_name: linked.canonical_name, path: projects[0] });
+                continue;
+            }
+        }
         // A generic word never becomes a new entity, whatever else it collides with.
         if (isRejectedName(normalizeEntityName(canonical, candidate.type))) {
             note(report.rejected, "stopword");

package/dist/lib/checkpoint-ontology/plan.d.ts

@@ -78,6 +78,17 @@ export declare const FIRST_NAME_PEOPLE_FLAG = "checkpoint.ontology.first-name-pe
  * to 0.803 and cost recall 0.023 on a replay of six runs.
  */
 export declare const SKIP_AMBIGUOUS_CONCEPT_LINKS_FLAG = "checkpoint.ontology.skip-ambiguous-concept-links";
+/**
+ * A knowledge concept candidate whose name is an alias of more than one
+ * entity, and which apply would defer as `ambiguous_alias`, links instead to
+ * the one project whose canonical name it is (`HQ` typed as a concept beside
+ * `project/HQ` and several concepts aliased `HQ`). The plan carries
+ * `concept_project_link: true`. CO-51: over six runs of the shipping config
+ * the model typed HQ as a concept in some runs and not others, and the
+ * deferral lost 61 gold links; a replay of this rule raised recall from 0.639
+ * to 0.709 at precision 0.747 to 0.731 (61 of the 63 added links are HQ).
+ */
+export declare const CONCEPT_PROJECT_LINK_FLAG = "checkpoint.ontology.concept-project-link";
 export declare const PLAN_FILE = "ontology-plan.json";
 export declare const CANDIDATES_FILE = "ontology-candidates.json";
 export declare const REPORT_FILE = "ontology-report.json";
@@ -150,6 +161,8 @@ export interface OntologyPlan {
     first_name_people?: true;
     /** Set by checkpoint.ontology.skip-ambiguous-concept-links: apply rejects a knowledge link to a concept whose name another type also holds. */
     skip_ambiguous_concept_links?: true;
+    /** Set by checkpoint.ontology.concept-project-link: apply links a knowledge concept with an ambiguous alias to the one project of that canonical name. */
+    concept_project_link?: true;
     inputs: PlanInput[];
     /** The session's summary, decisions and learnings, for the `session` input. */
     session_text: string | null;

package/dist/lib/checkpoint-ontology/plan.js

@@ -82,6 +82,17 @@ export const FIRST_NAME_PEOPLE_FLAG = "checkpoint.ontology.first-name-people";
  * to 0.803 and cost recall 0.023 on a replay of six runs.
  */
 export const SKIP_AMBIGUOUS_CONCEPT_LINKS_FLAG = "checkpoint.ontology.skip-ambiguous-concept-links";
+/**
+ * A knowledge concept candidate whose name is an alias of more than one
+ * entity, and which apply would defer as `ambiguous_alias`, links instead to
+ * the one project whose canonical name it is (`HQ` typed as a concept beside
+ * `project/HQ` and several concepts aliased `HQ`). The plan carries
+ * `concept_project_link: true`. CO-51: over six runs of the shipping config
+ * the model typed HQ as a concept in some runs and not others, and the
+ * deferral lost 61 gold links; a replay of this rule raised recall from 0.639
+ * to 0.709 at precision 0.747 to 0.731 (61 of the 63 added links are HQ).
+ */
+export const CONCEPT_PROJECT_LINK_FLAG = "checkpoint.ontology.concept-project-link";
 export const PLAN_FILE = "ontology-plan.json";
 export const CANDIDATES_FILE = "ontology-candidates.json";
 export const REPORT_FILE = "ontology-report.json";
@@ -265,6 +276,7 @@ export async function planOntologyRun(options) {
     const noLinkAliases = await options.readFlag(NO_LINK_ALIASES_FLAG, company);
     const firstNamePeople = await options.readFlag(FIRST_NAME_PEOPLE_FLAG, company);
     const skipAmbiguousConceptLinks = await options.readFlag(SKIP_AMBIGUOUS_CONCEPT_LINKS_FLAG, company);
+    const conceptProjectLink = await options.readFlag(CONCEPT_PROJECT_LINK_FLAG, company);
     const touched = sessionTouched(hqRoot, company, payload.files);
     // A first run takes its boundary from the entity tree, so the ledger is
     // refreshed before merge-back moves any `last_updated` forward.
@@ -380,6 +392,7 @@ export async function planOntologyRun(options) {
         ...(noLinkAliases ? { link_aliases: false } : {}),
         ...(firstNamePeople ? { first_name_people: true } : {}),
         ...(skipAmbiguousConceptLinks ? { skip_ambiguous_concept_links: true } : {}),
+        ...(conceptProjectLink ? { concept_project_link: true } : {}),
         inputs,
         session_text: sessionText,
         pending_after_run: remaining,

package/dist/lib/doctor/checks/runtime-health.d.ts

@@ -76,6 +76,8 @@ export interface ProbeOutcome {
 export interface RuntimeHealthDeps {
     /** Resolve an executable against PATH; null when not found. */
     resolveBinary?: (binary: string) => string | null;
+    /** Check whether a Windows command shim exists next to its resolved binary. */
+    fileExists?: (file: string) => boolean;
     /** Execute one probe. The default spawns from the OS temp dir. */
     execProbe?: (file: string, args: string[], timeoutMs: number) => Promise<ProbeOutcome>;
     /** Per-probe timeout. Default {@link DEFAULT_PROBE_TIMEOUT_MS}. */

package/dist/lib/doctor/checks/runtime-health.js

@@ -103,7 +103,7 @@ async function runRuntimeChecks(context, deps) {
     const resolved = {
         resolveBinary: deps.resolveBinary ?? resolveOnPath,
         execProbe: deps.execProbe ??
-            ((file, args, timeoutMs) => defaultExecProbe(file, args, timeoutMs, deps.platform ?? process.platform)),
+            ((file, args, timeoutMs) => defaultExecProbe(file, args, timeoutMs, deps.platform ?? process.platform, deps.fileExists ?? fs.existsSync)),
         timeoutMs: deps.probeTimeoutMs ?? DEFAULT_PROBE_TIMEOUT_MS,
         live: context.liveRuntimes === true,
     };
@@ -270,10 +270,13 @@ export function resolveOnPath(binary) {
  * CLI that reads piped stdin in non-TTY mode — blocks forever on a pipe that
  * never reaches EOF, which turns every probe into a timeout.
  */
-function defaultExecProbe(file, args, timeoutMs, platform) {
+function defaultExecProbe(file, args, timeoutMs, platform, fileExists) {
     return new Promise((resolve) => {
-        const command = platform === "win32" && !/\.(?:cmd|bat|exe|com)$/i.test(file)
-            ? `${file}.cmd`
+        const cmdSibling = `${file}.cmd`;
+        const command = platform === "win32" &&
+            !/\.(?:cmd|bat|exe|com)$/i.test(file) &&
+            fileExists(cmdSibling)
+            ? cmdSibling
             : file;
         const plan = planCommandSpawn(command, args, platform);
         const child = spawn(plan.cmd, plan.args, {

package/dist/lib/lanes/keep-alive.d.ts

@@ -27,11 +27,9 @@ export interface KeepAliveDoneEnvelope {
     decision?: string;
     story_complete?: boolean;
 }
-/**
- * Shared done-state policy: ordinary opted-in lanes resume open stories;
- * standing leads wait for queued work, even when each turn marks the story
- * complete. Watch and reconcile both use this decision.
- */
+export type DoneKeepAliveVerdict = "eligible" | "standing_idle" | "story_complete";
+/** Shared done-state policy used by watch, reconcile, and the show command. */
+export declare function doneKeepAliveVerdict(lane: Pick<LaneRecord, "keep_alive_standing">, envelope: KeepAliveDoneEnvelope, hasQueuedWork: boolean): DoneKeepAliveVerdict | null;
 export declare function canResumeDoneKeepAliveLane(lane: Pick<LaneRecord, "keep_alive_standing">, envelope: KeepAliveDoneEnvelope, hasQueuedWork: boolean): boolean;
 /** Work signals already persisted for a lane that ended its turn. */
 export declare function hasPendingKeepAliveWork(hqRoot: string, lane: Pick<LaneRecord, "lane_id" | "company" | "pending_resume">, questionRecords?: readonly QuestionRecord[]): boolean;

package/dist/lib/lanes/keep-alive.js

@@ -89,17 +89,18 @@ export function queueManagerStatusGateResume(hqRoot, laneId, entry, resumeText)
 }
 export const LEAD_LANE_KEEP_ALIVE_RESUME_TEXT = "Automatic keep-alive resume: your last turn ended with decision done and story_complete false. Continue the open work from where you stopped. End with done only when story_complete is true; if you are waiting, use hq lanes ask or stay in the loop.";
 export const LEAD_LANE_KEEP_ALIVE_INTERRUPTED_RESUME_TEXT = "Automatic keep-alive resume: your previous turn was interrupted by a provider process exit. Check your last state before continuing. Continue the open work from where you stopped. End with done only when story_complete is true; if you are waiting, use hq lanes ask or stay in the loop.";
-/**
- * Shared done-state policy: ordinary opted-in lanes resume open stories;
- * standing leads wait for queued work, even when each turn marks the story
- * complete. Watch and reconcile both use this decision.
- */
-export function canResumeDoneKeepAliveLane(lane, envelope, hasQueuedWork) {
+/** Shared done-state policy used by watch, reconcile, and the show command. */
+export function doneKeepAliveVerdict(lane, envelope, hasQueuedWork) {
     if (envelope.decision !== "done")
-        return false;
-    return lane.keep_alive_standing === true
-        ? hasQueuedWork
-        : envelope.story_complete !== true;
+        return null;
+    if (envelope.story_complete !== true)
+        return "eligible";
+    if (lane.keep_alive_standing !== true)
+        return "story_complete";
+    return hasQueuedWork ? "eligible" : "standing_idle";
+}
+export function canResumeDoneKeepAliveLane(lane, envelope, hasQueuedWork) {
+    return doneKeepAliveVerdict(lane, envelope, hasQueuedWork) === "eligible";
 }
 /** Work signals already persisted for a lane that ended its turn. */
 export function hasPendingKeepAliveWork(hqRoot, lane, questionRecords) {

package/dist/lib/lanes/reconcile.js

@@ -22,7 +22,7 @@ import { ANSWERED_QUESTIONS_FILE, armLaneWatcher, envelopeRepairMode, isPidRecor
 import { appendCappedHistory, lanesStoreRoot, parseLaneRecord, parseQuestionRecord, readLane, readQuestion, updateLane, updateQuestion, } from "./store.js";
 import { applyThrottleDecision, decideAdmission, defaultThrottleDeps, emptyThrottleState, evaluateThrottle, isCpuCheckEnabled, readAvailableMemMb, readThrottleState, resolveCpuBusyFraction, throttleStatePath, writeThrottleState, } from "./throttle.js";
 import { readLanesRegistryFlag } from "./registry-flag.js";
-import { LEAD_LANE_KEEP_ALIVE_FLAG, LEAD_LANE_KEEP_ALIVE_INTERRUPTED_RESUME_TEXT, LEAD_LANE_KEEP_ALIVE_MAX_RESUMES, LEAD_LANE_KEEP_ALIVE_RESUME_TEXT, LANE_SUPERSESSION_LINEAGE_AWARE_FLAG, canResumeDoneKeepAliveLane, hasPendingKeepAliveWork, keepAliveExclusion, loadRetiredLaneIds, leadLaneKeepAliveBackoffMs, undeliveredAnsweredQuestions, } from "./keep-alive.js";
+import { LEAD_LANE_KEEP_ALIVE_FLAG, LEAD_LANE_KEEP_ALIVE_INTERRUPTED_RESUME_TEXT, LEAD_LANE_KEEP_ALIVE_MAX_RESUMES, LEAD_LANE_KEEP_ALIVE_RESUME_TEXT, LANE_SUPERSESSION_LINEAGE_AWARE_FLAG, doneKeepAliveVerdict, hasPendingKeepAliveWork, keepAliveExclusion, loadRetiredLaneIds, leadLaneKeepAliveBackoffMs, undeliveredAnsweredQuestions, } from "./keep-alive.js";
 import { providerSupportsSessionResume } from "./delivery.js";
 import { applyDefaultQuotaHold, readQuotaSignal, recordAccountQuota } from "./quota.js";
 import { answeredQuestionEntries, questionRecordRefusalCode, raiseEnvelopeQuestions, resolveQuestionCompanyWithFallback, } from "./questions.js";
@@ -848,7 +848,7 @@ export async function runPassBody(hqRoot, deps) {
             if (!envelope || envelope.decision !== "done")
                 continue;
             const hasQueuedWork = lane.keep_alive_standing === true && hasPendingKeepAliveWork(hqRoot, lane, questions);
-            if (!canResumeDoneKeepAliveLane(lane, envelope, hasQueuedWork))
+            if (doneKeepAliveVerdict(lane, envelope, hasQueuedWork) !== "eligible")
                 continue;
         }
         const key = keepAliveCompanyKey(lane.company);
@@ -1137,10 +1137,8 @@ async function heartbeatAndDeadHosts(hqRoot, lanes, summary, deps, now) {
                     if (terminalEnvelope && latest) {
                         const envelope = terminalEnvelope;
                         next.story_status = envelope.story_status;
-                        if (envelope.story_complete !== undefined) {
-                            next.story_complete = envelope.story_complete;
-                            next.story_complete_reason = envelope.story_complete_reason;
-                        }
+                        next.story_complete = envelope.story_complete;
+                        next.story_complete_reason = envelope.story_complete_reason;
                         const storyStatus = envelope.decision === "blocked"
                             ? "blocked"
                             : envelope.decision === "done"
@@ -1550,6 +1548,13 @@ function recordKeepAliveSkip(hqRoot, lane, reason, summary, deps, detail) {
         });
     }
 }
+function recordDoneKeepAlivePolicySkip(summary, lane, verdict) {
+    summary.skipped.push({
+        kind: "lane",
+        id: lane.lane_id,
+        why: `keep_alive_${verdict}`,
+    });
+}
 function readLatestInterruptedClassificationAt(hqRoot, lane) {
     const logPath = watcherOutLogPath(hqRoot, lane.lane_id);
     let body;
@@ -1624,7 +1629,10 @@ function resumeKeepAlive(hqRoot, lanes, questions, summary, deps, now, flagByCom
             if (!envelope || envelope.decision !== "done")
                 continue;
             const hasQueuedWork = lane.keep_alive_standing === true && hasPendingKeepAliveWork(hqRoot, lane, questions);
-            if (!canResumeDoneKeepAliveLane(lane, envelope, hasQueuedWork)) {
+            const verdict = doneKeepAliveVerdict(lane, envelope, hasQueuedWork);
+            if (verdict !== "eligible") {
+                if (verdict !== null)
+                    recordDoneKeepAlivePolicySkip(summary, lane, verdict);
                 if (envelope.story_complete === true && lane.keep_alive_standing !== true && hasKeepAliveProgress(lane)) {
                     casLaneIf(hqRoot, lane.lane_id, (current) => current.version === lane.version &&
                         current.state === "done" &&
@@ -1713,8 +1721,15 @@ function resumeKeepAlive(hqRoot, lanes, questions, summary, deps, now, flagByCom
             if (!latest || latest.envelope.decision !== "done")
                 continue;
             const hasQueuedWork = lane.keep_alive_standing === true && hasPendingKeepAliveWork(hqRoot, lane, questions);
-            if (!canResumeDoneKeepAliveLane(lane, latest.envelope, hasQueuedWork))
+            const verdict = doneKeepAliveVerdict(lane, latest.envelope, hasQueuedWork);
+            if (verdict !== "eligible") {
+                if (verdict !== null)
+                    recordDoneKeepAlivePolicySkip(summary, lane, verdict);
+                if (latest.envelope.story_complete === true && lane.keep_alive_standing !== true && hasKeepAliveProgress(lane)) {
+                    casLaneIf(hqRoot, lane.lane_id, (current) => current.version === lane.version && current.state === "done", (current) => ({ ...clearedKeepAliveProgress(current), keep_alive_blocked_reason: undefined }), deps.dryRun);
+                }
                 continue;
+            }
             try {
                 eligibilityAtMs = latestEnvelopeMtimeMs(hqRoot, lane, latest.ref);
             }
@@ -1788,7 +1803,10 @@ function resumeKeepAlive(hqRoot, lanes, questions, summary, deps, now, flagByCom
             if (!currentEnvelope || currentEnvelope.envelope.decision !== "done")
                 continue;
             const hasQueuedWork = current.keep_alive_standing === true && hasPendingKeepAliveWork(hqRoot, current, questions);
-            if (!canResumeDoneKeepAliveLane(current, currentEnvelope.envelope, hasQueuedWork)) {
+            const verdict = doneKeepAliveVerdict(current, currentEnvelope.envelope, hasQueuedWork);
+            if (verdict !== "eligible") {
+                if (verdict !== null)
+                    recordDoneKeepAlivePolicySkip(summary, current, verdict);
                 if (currentEnvelope.envelope.story_complete === true && current.keep_alive_standing !== true && hasKeepAliveProgress(current)) {
                     casLaneIf(hqRoot, current.lane_id, (latestLane) => latestLane.version === current.version &&
                         latestLane.state === "done" &&

package/dist/lib/lanes/types.d.ts

@@ -434,7 +434,7 @@ export interface LaneRecord {
     worker_profile?: string;
     /** Whether this lead lane should resume completed turns while its story is open. */
     keep_alive?: boolean;
-    /** Whether a keep-alive lead waits for queued work after every done turn. */
+    /** Whether completed keep-alive stories wait for queued work after a done turn. */
     keep_alive_standing?: boolean;
     /** Time this lane most recently explicitly opted into keep-alive. */
     keep_alive_opted_in_at?: string;

package/dist/lib/lanes/watcher.js

@@ -405,10 +405,8 @@ export function applyTerminalToLaneWithResult(hqRoot, laneId, classification, op
                 ...(envelope.blocked_reason !== undefined ? { blocked_reason: envelope.blocked_reason } : {}),
             };
             next.story_status = envelope.story_status;
-            if (envelope.story_complete !== undefined) {
-                next.story_complete = envelope.story_complete;
-                next.story_complete_reason = envelope.story_complete_reason;
-            }
+            next.story_complete = envelope.story_complete;
+            next.story_complete_reason = envelope.story_complete_reason;
             const currentProject = current.project_id;
             const currentStory = current.story_id;
             const storyStatus = envelope.decision === "blocked"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@indigoai-us/hq-cli",
-  "version": "5.260.0",
+  "version": "5.262.0",
   "description": "HQ by Indigo management CLI — modules and cloud sync",
   "main": "dist/index.js",
   "bin": {