@indigoai-us/hq-cli 5.261.0 → 5.262.0

package/CHANGELOG.md

@@ -2,6 +2,18 @@
 
 ## [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

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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@indigoai-us/hq-cli",
-  "version": "5.261.0",
+  "version": "5.262.0",
   "description": "HQ by Indigo management CLI — modules and cloud sync",
   "main": "dist/index.js",
   "bin": {