@indigoai-us/hq-cloud 6.13.2 → 6.13.4

package/dist/qmd-reindex.js

@@ -37,6 +37,7 @@ const defaultExec = (args) => {
     });
     return { status: res.status, stdout: res.stdout ?? "" };
 };
+const DEFAULT_CHANGED_PATH_DEBOUNCE_MS = 60_000;
 /**
  * Reindex qmd for an HQ tree after a sync. Never throws — all failures are
  * swallowed so a reindex problem can never mask or fail the sync result.
@@ -46,11 +47,29 @@ const defaultExec = (args) => {
 export function reindexAfterSync(hqRoot, opts = {}) {
     const exec = opts.exec ?? defaultExec;
     const existsSync = opts.existsSync ?? fs.existsSync;
-    const result = { qmdAvailable: false, collectionsAdded: [], updated: false, embedded: false };
+    const result = {
+        qmdAvailable: false,
+        collectionsAdded: [],
+        updated: false,
+        embedded: false,
+        pendingDirty: false,
+    };
     try {
         // Guard: only operate on a real HQ tree.
         if (!existsSync(path.join(hqRoot, "core", "core.yaml")))
             return result;
+        const statePath = opts.statePath ?? path.join(hqRoot, ".hq", "qmd-reindex-state.json");
+        const state = readState(statePath);
+        const changedPaths = opts.changedPaths;
+        const dirtyFromChanges = changedPaths === undefined ||
+            changedPaths.some(isKnowledgeMarkdownPath);
+        const registrationMayBeStale = opts.forceCollectionRefresh === true ||
+            changedPaths === undefined ||
+            dirtyFromChanges;
+        const pendingDirty = state.pendingDirty === true;
+        if (!dirtyFromChanges && !registrationMayBeStale && !pendingDirty) {
+            return result;
+        }
         // Guard: qmd must be installed. `qmd collection list` doubles as the
         // availability probe AND the source for which collections already exist.
         const list = exec(["collection", "list"]);
@@ -59,27 +78,61 @@ export function reindexAfterSync(hqRoot, opts = {}) {
         result.qmdAvailable = true;
         const existingCollections = list.stdout;
         // 1. Auto-register missing company knowledge collections.
-        const companiesDir = path.join(hqRoot, "companies");
-        const slugs = (opts.readCompanies ?? defaultReadCompanies)(companiesDir);
-        for (const slug of slugs) {
-            const knowledgeDir = path.join(companiesDir, slug, "knowledge");
-            if (!existsSync(knowledgeDir))
-                continue;
-            const hasMd = (opts.hasIndexableMarkdown ?? defaultHasIndexableMarkdown)(knowledgeDir);
-            if (!hasMd)
-                continue;
-            // Already registered? qmd collection URIs look like `qmd://<slug>/`.
-            if (existingCollections.includes(`qmd://${slug}/`))
-                continue;
-            const add = exec(["collection", "add", knowledgeDir, "--name", slug, "--mask", "**/*.md"]);
-            if (add.status === 0) {
-                exec(["context", "add", `qmd://${slug}`, `Knowledge base for ${slug}.`]);
-                result.collectionsAdded.push(slug);
+        if (registrationMayBeStale) {
+            const companiesDir = path.join(hqRoot, "companies");
+            const slugs = (opts.readCompanies ?? defaultReadCompanies)(companiesDir);
+            for (const slug of slugs) {
+                const knowledgeDir = path.join(companiesDir, slug, "knowledge");
+                if (!existsSync(knowledgeDir))
+                    continue;
+                const hasMd = (opts.hasIndexableMarkdown ?? defaultHasIndexableMarkdown)(knowledgeDir);
+                if (!hasMd)
+                    continue;
+                // Already registered? qmd collection URIs look like `qmd://<slug>/`.
+                if (existingCollections.includes(`qmd://${slug}/`))
+                    continue;
+                const add = exec(["collection", "add", knowledgeDir, "--name", slug, "--mask", "**/*.md"]);
+                if (add.status === 0) {
+                    exec(["context", "add", `qmd://${slug}`, `Knowledge base for ${slug}.`]);
+                    result.collectionsAdded.push(slug);
+                }
             }
         }
         // 2. Incremental lexical reindex.
-        const update = exec(["update"]);
-        result.updated = update.status === 0;
+        const shouldUpdate = dirtyFromChanges || pendingDirty;
+        if (shouldUpdate) {
+            const nowMs = opts.nowMs ?? Date.now();
+            const debounceMs = opts.debounceMs ??
+                (changedPaths === undefined ? 0 : DEFAULT_CHANGED_PATH_DEBOUNCE_MS);
+            const pendingSinceMs = pendingDirty && typeof state.pendingSinceMs === "number"
+                ? state.pendingSinceMs
+                : nowMs;
+            if (debounceMs > 0 && nowMs - pendingSinceMs < debounceMs) {
+                writeState(statePath, {
+                    ...state,
+                    pendingDirty: true,
+                    pendingSinceMs,
+                });
+                result.pendingDirty = true;
+                return result;
+            }
+            const update = exec(["update"]);
+            result.updated = update.status === 0;
+            if (result.updated) {
+                writeState(statePath, {
+                    pendingDirty: false,
+                    lastSuccessMs: nowMs,
+                });
+            }
+            else {
+                writeState(statePath, {
+                    ...state,
+                    pendingDirty: true,
+                    pendingSinceMs,
+                });
+                result.pendingDirty = true;
+            }
+        }
         // 3. Embeddings only on explicit request.
         if (opts.embed) {
             const embed = exec(["embed"]);
@@ -102,6 +155,27 @@ export function reindexAfterSync(hqRoot, opts = {}) {
     }
     return result;
 }
+function readState(statePath) {
+    try {
+        return JSON.parse(fs.readFileSync(statePath, "utf8"));
+    }
+    catch {
+        return {};
+    }
+}
+function writeState(statePath, state) {
+    try {
+        fs.mkdirSync(path.dirname(statePath), { recursive: true });
+        fs.writeFileSync(statePath, JSON.stringify(state, null, 2) + "\n");
+    }
+    catch {
+        // State is an optimization/guarantee aid; QMD failures must not fail sync.
+    }
+}
+function isKnowledgeMarkdownPath(relPath) {
+    const normalized = relPath.split(path.sep).join("/");
+    return /^companies\/[^/]+\/knowledge\/.+\.md$/i.test(normalized);
+}
 function defaultReadCompanies(companiesDir) {
     try {
         return fs

package/dist/qmd-reindex.js.map

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+{"version":3,"file":"qmd-reindex.js","sourceRoot":"","sources":["../src/qmd-reindex.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AAEH,OAAO,KAAK,EAAE,MAAM,IAAI,CAAC;AACzB,OAAO,KAAK,IAAI,MAAM,MAAM,CAAC;AAC7B,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAO1C,MAAM,WAAW,GAAY,CAAC,IAAI,EAAE,EAAE;IACpC,MAAM,GAAG,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE;QACjC,QAAQ,EAAE,MAAM;QAChB,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,EAAE,OAAO;KACjB,CAAC,CAAC;IACH,OAAO,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,IAAI,EAAE,EAAE,CAAC;AAC1D,CAAC,CAAC;AAEF,MAAM,gCAAgC,GAAG,MAAM,CAAC;AAmChD;;;;;GAKG;AACH,MAAM,UAAU,gBAAgB,CAC9B,MAAc,EACd,OAAuB,EAAE;IAQzB,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,IAAI,WAAW,CAAC;IACtC,MAAM,UAAU,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAC,UAAU,CAAC;IACpD,MAAM,MAAM,GAAG;QACb,YAAY,EAAE,KAAK;QACnB,gBAAgB,EAAE,EAAc;QAChC,OAAO,EAAE,KAAK;QACd,QAAQ,EAAE,KAAK;QACf,YAAY,EAAE,KAAK;KACpB,CAAC;IAEF,IAAI,CAAC;QACH,yCAAyC;QACzC,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,WAAW,CAAC,CAAC;YAAE,OAAO,MAAM,CAAC;QAEvE,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,KAAK,EAAE,wBAAwB,CAAC,CAAC;QACvF,MAAM,KAAK,GAAG,SAAS,CAAC,SAAS,CAAC,CAAC;QACnC,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAC;QACvC,MAAM,gBAAgB,GACpB,YAAY,KAAK,SAAS;YAC1B,YAAY,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QAC7C,MAAM,sBAAsB,GAC1B,IAAI,CAAC,sBAAsB,KAAK,IAAI;YACpC,YAAY,KAAK,SAAS;YAC1B,gBAAgB,CAAC;QACnB,MAAM,YAAY,GAAG,KAAK,CAAC,YAAY,KAAK,IAAI,CAAC;QACjD,IAAI,CAAC,gBAAgB,IAAI,CAAC,sBAAsB,IAAI,CAAC,YAAY,EAAE,CAAC;YAClE,OAAO,MAAM,CAAC;QAChB,CAAC;QAED,qEAAqE;QACrE,yEAAyE;QACzE,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC,CAAC;QAC1C,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,MAAM,CAAC,CAAC,gCAAgC;QACtE,MAAM,CAAC,YAAY,GAAG,IAAI,CAAC;QAC3B,MAAM,mBAAmB,GAAG,IAAI,CAAC,MAAM,CAAC;QAExC,0DAA0D;QAC1D,IAAI,sBAAsB,EAAE,CAAC;YAC3B,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,WAAW,CAAC,CAAC;YACpD,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,aAAa,IAAI,oBAAoB,CAAC,CAAC,YAAY,CAAC,CAAC;YACzE,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;gBACzB,MAAM,YAAY,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,EAAE,IAAI,EAAE,WAAW,CAAC,CAAC;gBAChE,IAAI,CAAC,UAAU,CAAC,YAAY,CAAC;oBAAE,SAAS;gBACxC,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,oBAAoB,IAAI,2BAA2B,CAAC,CAAC,YAAY,CAAC,CAAC;gBACvF,IAAI,CAAC,KAAK;oBAAE,SAAS;gBACrB,qEAAqE;gBACrE,IAAI,mBAAmB,CAAC,QAAQ,CAAC,SAAS,IAAI,GAAG,CAAC;oBAAE,SAAS;gBAE7D,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,YAAY,EAAE,KAAK,EAAE,YAAY,EAAE,QAAQ,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC,CAAC;gBAC3F,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;oBACrB,IAAI,CAAC,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,IAAI,EAAE,EAAE,sBAAsB,IAAI,GAAG,CAAC,CAAC,CAAC;oBACzE,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBACrC,CAAC;YACH,CAAC;QACH,CAAC;QAED,kCAAkC;QAClC,MAAM,YAAY,GAAG,gBAAgB,IAAI,YAAY,CAAC;QACtD,IAAI,YAAY,EAAE,CAAC;YACjB,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,GAAG,EAAE,CAAC;YACvC,MAAM,UAAU,GACd,IAAI,CAAC,UAAU;gBACf,CAAC,YAAY,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,gCAAgC,CAAC,CAAC;YACtE,MAAM,cAAc,GAClB,YAAY,IAAI,OAAO,KAAK,CAAC,cAAc,KAAK,QAAQ;gBACtD,CAAC,CAAC,KAAK,CAAC,cAAc;gBACtB,CAAC,CAAC,KAAK,CAAC;YACZ,IAAI,UAAU,GAAG,CAAC,IAAI,KAAK,GAAG,cAAc,GAAG,UAAU,EAAE,CAAC;gBAC1D,UAAU,CAAC,SAAS,EAAE;oBACpB,GAAG,KAAK;oBACR,YAAY,EAAE,IAAI;oBAClB,cAAc;iBACf,CAAC,CAAC;gBACH,MAAM,CAAC,YAAY,GAAG,IAAI,CAAC;gBAC3B,OAAO,MAAM,CAAC;YAChB,CAAC;YAED,MAAM,MAAM,GAAG,IAAI,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC;YAChC,MAAM,CAAC,OAAO,GAAG,MAAM,CAAC,MAAM,KAAK,CAAC,CAAC;YACrC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACnB,UAAU,CAAC,SAAS,EAAE;oBACpB,YAAY,EAAE,KAAK;oBACnB,aAAa,EAAE,KAAK;iBACrB,CAAC,CAAC;YACL,CAAC;iBAAM,CAAC;gBACN,UAAU,CAAC,SAAS,EAAE;oBACpB,GAAG,KAAK;oBACR,YAAY,EAAE,IAAI;oBAClB,cAAc;iBACf,CAAC,CAAC;gBACH,MAAM,CAAC,YAAY,GAAG,IAAI,CAAC;YAC7B,CAAC;QACH,CAAC;QAED,0CAA0C;QAC1C,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC;YACf,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC;YAC9B,MAAM,CAAC,QAAQ,GAAG,KAAK,CAAC,MAAM,KAAK,CAAC,CAAC;QACvC,CAAC;IACH,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,IAAI,CAAC;YACH,IAAI,CAAC,GAAG,EAAE,CAAC;gBACT,KAAK,EAAE,oCAAoC;gBAC3C,OAAO,EAAE,8BAA8B;gBACvC,GAAG;gBACH,OAAO,EAAE,EAAE,MAAM,EAAE;aACpB,CAAC,CAAC;QACL,CAAC;QAAC,MAAM,CAAC;YACP,wCAAwC;QAC1C,CAAC;QACD,qEAAqE;IACvE,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAQD,SAAS,SAAS,CAAC,SAAiB;IAClC,IAAI,CAAC;QACH,OAAO,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,YAAY,CAAC,SAAS,EAAE,MAAM,CAAC,CAAoB,CAAC;IAC3E,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,EAAE,CAAC;IACZ,CAAC;AACH,CAAC;AAED,SAAS,UAAU,CAAC,SAAiB,EAAE,KAAsB;IAC3D,IAAI,CAAC;QACH,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QAC3D,EAAE,CAAC,aAAa,CAAC,SAAS,EAAE,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;IACrE,CAAC;IAAC,MAAM,CAAC;QACP,2EAA2E;IAC7E,CAAC;AACH,CAAC;AAED,SAAS,uBAAuB,CAAC,OAAe;IAC9C,MAAM,UAAU,GAAG,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACrD,OAAO,wCAAwC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;AACnE,CAAC;AAED,SAAS,oBAAoB,CAAC,YAAoB;IAChD,IAAI,CAAC;QACH,OAAO,EAAE;aACN,WAAW,CAAC,YAAY,EAAE,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC;aAClD,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,IAAI,CAAC,CAAC,CAAC,IAAI,CA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package/dist/qmd-reindex.test.js

@@ -89,6 +89,53 @@ describe("reindexAfterSync", () => {
         expect(r.collectionsAdded).toEqual([]);
         expect(calls).toEqual([["collection", "list"], ["update"]]);
     });
+    it("skips qmd entirely when provided changed paths do not touch knowledge markdown", () => {
+        const { exec, calls } = fakeExec({ listStdout: "" });
+        const r = reindexAfterSync("/hq", {
+            exec,
+            existsSync: () => true,
+            changedPaths: ["companies/acme/docs/readme.txt"],
+        });
+        expect(r.qmdAvailable).toBe(false);
+        expect(r.updated).toBe(false);
+        expect(calls).toEqual([]);
+    });
+    it("debounces dirty updates with a pending marker and flushes the final update later", () => {
+        const dir = fs.mkdtempSync(path.join(os.tmpdir(), "hq-qmd-debounce-"));
+        try {
+            const statePath = path.join(dir, "qmd-state.json");
+            const { exec, calls } = fakeExec({ listStdout: "acme (qmd://acme/)\n" });
+            const first = reindexAfterSync("/hq", {
+                exec,
+                existsSync: () => true,
+                changedPaths: ["companies/acme/knowledge/note.md"],
+                debounceMs: 60_000,
+                nowMs: 100_000,
+                statePath,
+            });
+            expect(first.updated).toBe(false);
+            expect(first.pendingDirty).toBe(true);
+            expect(calls).toEqual([["collection", "list"]]);
+            const second = reindexAfterSync("/hq", {
+                exec,
+                existsSync: () => true,
+                changedPaths: [],
+                debounceMs: 60_000,
+                nowMs: 161_000,
+                statePath,
+            });
+            expect(second.updated).toBe(true);
+            expect(second.pendingDirty).toBe(false);
+            expect(calls).toEqual([
+                ["collection", "list"],
+                ["collection", "list"],
+                ["update"],
+            ]);
+        }
+        finally {
+            fs.rmSync(dir, { recursive: true, force: true });
+        }
+    });
     it("runs embed only when embed:true", () => {
         const { exec, calls } = fakeExec({ listStdout: "" });
         const r = reindexAfterSync("/hq", {

package/dist/qmd-reindex.test.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@indigoai-us/hq-cloud",
-  "version": "6.13.2",
+  "version": "6.13.4",
   "description": "HQ by Indigo cloud sync engine — bidirectional S3 sync for mobile access",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

package/src/bin/sync-runner-company.ts

@@ -168,6 +168,7 @@ export async function executeCompanyFanout(options: {
         filesOutOfScope: 0,
         scopeOrphansRemoved: 0,
         scopeOrphansBlocked: 0,
+        changedPaths: [],
       };
 
       // Local (non-cloud) companies always sync to the personal vault. The
@@ -255,6 +256,7 @@ export async function executeCompanyFanout(options: {
           ...(options.operationLockAlreadyHeld
             ? { operationLockAlreadyHeld: true }
             : {}),
+          skipReindex: true,
           onEvent: tagAndEmit,
         });
       }
@@ -273,6 +275,12 @@ export async function executeCompanyFanout(options: {
 
       state.filesDownloaded = pullResult.filesDownloaded;
       state.bytesDownloaded = pullResult.bytesDownloaded;
+      state.filesTombstoned = pullResult.filesTombstoned;
+      state.scopeOrphansRemoved = pullResult.scopeOrphansRemoved;
+      state.changedPaths = normalizePullChangedPaths(
+        target,
+        pullResult.changedPaths,
+      );
       state.filesUploaded = pushResult.filesUploaded;
       state.bytesUploaded = pushResult.bytesUploaded;
       state.status = companyHadTransferError
@@ -342,6 +350,7 @@ export async function executeCompanyFanout(options: {
         filesOutOfScope: 0,
         scopeOrphansRemoved: 0,
         scopeOrphansBlocked: 0,
+        changedPaths: [],
       });
       options.emit({
         type: "error",
@@ -354,3 +363,15 @@ export async function executeCompanyFanout(options: {
 
   return { stateByCompany, errors, allConflicts };
 }
+
+function normalizePullChangedPaths(
+  target: RunnerTarget,
+  changedPaths: string[] | undefined,
+): string[] {
+  const paths = changedPaths ?? [];
+  return paths.map((p) => {
+    const normalized = p.split(path.sep).join("/");
+    if (target.personalMode === true) return normalized;
+    return `companies/${target.slug}/${normalized}`;
+  });
+}

package/src/bin/sync-runner-rollup.ts

@@ -8,6 +8,9 @@ export interface CompanyState {
   status: CompanyStatus;
   filesDownloaded: number;
   bytesDownloaded: number;
+  filesTombstoned: number;
+  scopeOrphansRemoved: number;
+  changedPaths: string[];
   filesUploaded: number;
   bytesUploaded: number;
 }
@@ -15,8 +18,12 @@ export interface CompanyState {
 export interface AllCompleteRollup {
   totalDownloaded: number;
   totalDownloadedBytes: number;
+  totalTombstoned: number;
+  totalScopeOrphansRemoved: number;
   totalUploaded: number;
   totalUploadedBytes: number;
+  changedPaths: string[];
+  needsReindex: boolean;
   partial: boolean;
   companies: Extract<RunnerEvent, { type: "all-complete" }>["companies"];
 }
@@ -27,6 +34,9 @@ export function createCompanyState(company: string): CompanyState {
     status: "errored",
     filesDownloaded: 0,
     bytesDownloaded: 0,
+    filesTombstoned: 0,
+    scopeOrphansRemoved: 0,
+    changedPaths: [],
     filesUploaded: 0,
     bytesUploaded: 0,
   };
@@ -38,8 +48,11 @@ export function rollupAllComplete(
 ): AllCompleteRollup {
   let totalDownloaded = 0;
   let totalDownloadedBytes = 0;
+  let totalTombstoned = 0;
+  let totalScopeOrphansRemoved = 0;
   let totalUploaded = 0;
   let totalUploadedBytes = 0;
+  const changedPaths: string[] = [];
   let partial = false;
   const companies: AllCompleteRollup["companies"] = [];
 
@@ -48,8 +61,11 @@ export function rollupAllComplete(
     if (!s) continue;
     totalDownloaded += s.filesDownloaded;
     totalDownloadedBytes += s.bytesDownloaded;
+    totalTombstoned += s.filesTombstoned;
+    totalScopeOrphansRemoved += s.scopeOrphansRemoved;
     totalUploaded += s.filesUploaded;
     totalUploadedBytes += s.bytesUploaded;
+    changedPaths.push(...s.changedPaths);
     if (s.status !== "complete") partial = true;
     companies.push({
       company: s.company,
@@ -64,8 +80,15 @@ export function rollupAllComplete(
   return {
     totalDownloaded,
     totalDownloadedBytes,
+    totalTombstoned,
+    totalScopeOrphansRemoved,
     totalUploaded,
     totalUploadedBytes,
+    changedPaths,
+    needsReindex:
+      totalDownloaded > 0 ||
+      totalTombstoned > 0 ||
+      totalScopeOrphansRemoved > 0,
     partial,
     companies,
   };

package/src/bin/sync-runner.test.ts

@@ -112,6 +112,7 @@ function defaultSyncResult(overrides: Partial<SyncResult> = {}): SyncResult {
     filesOutOfScope: 0,
     scopeOrphansRemoved: 0,
     scopeOrphansBlocked: 0,
+    changedPaths: [],
     ...overrides,
   };
 }
@@ -205,6 +206,14 @@ function makeDeps(overrides: Partial<RunnerDeps> = {}): TestDeps {
     getAccessToken: vi.fn().mockResolvedValue("test-access-token"),
     createVaultClient: vi.fn().mockImplementation(() => makeVaultStub()),
     sync: vi.fn().mockResolvedValue(defaultSyncResult()),
+    reindex: vi.fn(() => ({ status: 0 })),
+    qmdReindex: vi.fn(() => ({
+      qmdAvailable: true,
+      collectionsAdded: [],
+      updated: true,
+      embedded: false,
+      pendingDirty: false,
+    })),
     ...overrides,
     stdout,
     stderr,
@@ -1602,6 +1611,87 @@ describe("all-complete aggregate", () => {
     });
   });
 
+  it("skips per-target native reindex and runs one final reindex for tombstones or scope orphans", async () => {
+    const slugs: Record<string, string> = { cmp_a: "acme", cmp_b: "beta" };
+    const reindex = vi.fn(() => ({ status: 0 }));
+    const syncSpy = vi
+      .fn<(opts: SyncOptions) => Promise<SyncResult>>()
+      .mockResolvedValueOnce(defaultSyncResult({ filesTombstoned: 1 }))
+      .mockResolvedValueOnce(defaultSyncResult({ scopeOrphansRemoved: 1 }));
+    const deps = makeDeps({
+      operationLockAlreadyHeld: true,
+      createVaultClient: () =>
+        makeVaultStub({
+          memberships: [{ companyUid: "cmp_a" }, { companyUid: "cmp_b" }],
+          entityGet: (uid: string) =>
+            Promise.resolve({ uid, slug: slugs[uid] ?? uid } as unknown as EntityInfo),
+        }),
+      sync: syncSpy,
+      reindex,
+    } as Partial<RunnerDeps>);
+
+    const code = await runRunner(["--companies", "--hq-root", "/tmp/fake-hq"], deps);
+
+    expect(code).toBe(0);
+    expect(syncSpy).toHaveBeenCalledTimes(2);
+    expect(syncSpy.mock.calls.map(([opts]) => opts.skipReindex)).toEqual([
+      true,
+      true,
+    ]);
+    expect(reindex).toHaveBeenCalledTimes(1);
+    expect(reindex).toHaveBeenCalledWith({
+      repoRoot: "/tmp/fake-hq",
+      skipLock: true,
+    });
+  });
+
+  it("gates qmd to knowledge markdown changes and propagates hq-relative changed paths", async () => {
+    const slugs: Record<string, string> = { cmp_a: "acme", cmp_b: "beta" };
+    const qmdReindex = vi.fn(() => ({
+      qmdAvailable: true,
+      collectionsAdded: [],
+      updated: true,
+      embedded: false,
+      pendingDirty: false,
+    }));
+    const deps = makeDeps({
+      createVaultClient: () =>
+        makeVaultStub({
+          memberships: [{ companyUid: "cmp_a" }, { companyUid: "cmp_b" }],
+          entityGet: (uid: string) =>
+            Promise.resolve({ uid, slug: slugs[uid] ?? uid } as unknown as EntityInfo),
+        }),
+      sync: vi
+        .fn<(opts: SyncOptions) => Promise<SyncResult>>()
+        .mockResolvedValueOnce(
+          defaultSyncResult({
+            filesDownloaded: 1,
+            changedPaths: ["docs/readme.txt"],
+          } as Partial<SyncResult>),
+        )
+        .mockResolvedValueOnce(
+          defaultSyncResult({
+            filesTombstoned: 1,
+            changedPaths: ["knowledge/old.md"],
+          } as Partial<SyncResult>),
+        ),
+      reindex: vi.fn(() => ({ status: 0 })),
+      qmdReindex,
+    } as Partial<RunnerDeps>);
+
+    const code = await runRunner(["--companies", "--hq-root", "/tmp/fake-hq"], deps);
+
+    expect(code).toBe(0);
+    expect(qmdReindex).toHaveBeenCalledTimes(1);
+    expect(qmdReindex).toHaveBeenCalledWith(
+      "/tmp/fake-hq",
+      expect.objectContaining({
+        changedPaths: ["companies/beta/knowledge/old.md"],
+        forceCollectionRefresh: true,
+      }),
+    );
+  });
+
   it("collects company-level errors into the all-complete errors array", async () => {
     const slugs: Record<string, string> = { cmp_a: "acme", cmp_b: "beta" };
     const deps = makeDeps({

package/src/bin/sync-runner.ts

@@ -104,6 +104,9 @@ import { HQ_CLOUD_VERSION } from "../version.js";
 import { collectAndSendTelemetry } from "../telemetry.js";
 import { collectAndSendSkillTelemetry } from "../skill-telemetry.js";
 import { reindexAfterSync } from "../qmd-reindex.js";
+import type { ReindexOptions as QmdReindexOptions } from "../qmd-reindex.js";
+import { reindex as defaultReindex } from "../cli/reindex.js";
+import type { ReindexOptions, ReindexResult } from "../cli/reindex.js";
 import { pruneConflictIndex } from "../lib/conflict-index.js";
 import { materializeCodexAgents } from "../agent-codex-instructions.js";
 import { getOrCreateMachineId } from "../lib/machine-id.js";
@@ -577,6 +580,13 @@ export interface RunnerDeps {
   createVaultClient?: (config: VaultServiceConfig) => VaultClientSurface;
   /** Sync function. Defaults to `cli/sync.sync`. */
   sync?: (options: SyncOptions) => Promise<SyncResult>;
+  /** Native post-fanout reindex function. Defaults to `cli/reindex.reindex`. */
+  reindex?: (options: ReindexOptions) => ReindexResult;
+  /** QMD post-sync reindex function. Defaults to `qmd-reindex.reindexAfterSync`. */
+  qmdReindex?: (
+    hqRoot: string,
+    options: QmdReindexOptions,
+  ) => ReturnType<typeof reindexAfterSync>;
   /** Internal: set when runRunner is invoked under the per-root operation lock. */
   operationLockAlreadyHeld?: boolean;
   /** Share function (push phase). Defaults to `cli/share.share`. */
@@ -622,6 +632,11 @@ function defaultGetIdTokenClaims(): IdTokenClaims | null {
   return decodeJwtClaims(tokens.idToken);
 }
 
+function isKnowledgeMarkdownPath(relPath: string): boolean {
+  const normalized = relPath.split(path.sep).join("/");
+  return /^companies\/[^/]+\/knowledge\/.+\.md$/i.test(normalized);
+}
+
 /**
  * Best-effort: claim any email-keyed pending invites that were sent before
  * this user had a person entity. Mirrors the installer's vault-handoff flow.
@@ -1200,6 +1215,23 @@ export async function runRunner(
   const { errors, allConflicts } = fanout;
   const rollup = rollupAllComplete(plan, fanout.stateByCompany);
 
+  if (rollup.needsReindex) {
+    try {
+      (deps.reindex ?? defaultReindex)({
+        repoRoot: parsed.hqRoot,
+        ...(deps.operationLockAlreadyHeld === true ? { skipLock: true } : {}),
+      });
+    } catch (err) {
+      reportDiagnostic({
+        component: "native-reindex",
+        event: "runner.native_reindex.failed",
+        message: "post-fanout native reindex failed",
+        err,
+        context: { hqRoot: parsed.hqRoot },
+      });
+    }
+  }
+
   // Fire telemetry collector before the all-complete emit so the cursor at
   // `~/.hq/telemetry-cursor.json` is consistent with what the menubar sees.
   await awaitTelemetryWithTimeout(
@@ -1250,12 +1282,12 @@ export async function runRunner(
   // pulled in (nothing to reindex otherwise) and not explicitly disabled.
   // Self-contained: shells out to the global `qmd` binary, no dependency on
   // any (possibly stale) script inside the synced HQ tree. See qmd-reindex.ts.
-  if (
-    rollup.totalDownloaded > 0 &&
-    process.env.HQ_QMD_REINDEX_ON_SYNC !== "0"
-  ) {
+  const qmdChangedPaths = rollup.changedPaths.filter(isKnowledgeMarkdownPath);
+  if (qmdChangedPaths.length > 0 && process.env.HQ_QMD_REINDEX_ON_SYNC !== "0") {
     try {
-      reindexAfterSync(parsed.hqRoot, {
+      (deps.qmdReindex ?? reindexAfterSync)(parsed.hqRoot, {
+        changedPaths: qmdChangedPaths,
+        forceCollectionRefresh: true,
         log: ({ event, message, err, context }) =>
           reportDiagnostic({
             component: "qmd-reindex",