@oomkapwn/enquire-mcp 3.9.0-rc.2 → 3.9.0-rc.21

package/dist/watcher.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"watcher.d.ts","sourceRoot":"","sources":["../src/watcher.ts"],"names":[],"mappings":"AAoBA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAC7C,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,WAAW,CAAC;AAC3C,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AAExC;;;;;;GAMG;AACH,MAAM,WAAW,WAAW;IAC1B,QAAQ,EAAE,MAAM,CAAC;IACjB,WAAW,EAAE,MAAM,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,IAAI,EAAE,IAAI,GAAG,KAAK,CAAC;CACpB;AAID,MAAM,WAAW,cAAc;IAC7B,yDAAyD;IACzD,KAAK,EAAE,KAAK,CAAC;IACb,yDAAyD;IACzD,QAAQ,CAAC,EAAE,QAAQ,GAAG,IAAI,CAAC;IAC3B,gEAAgE;IAChE,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB;;;;;;;;;;;;OAYG;IACH,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;;;;;;;;;;;;;OAaG;IACH,OAAO,CAAC,EAAE,OAAO,GAAG,IAAI,CAAC;IACzB;;;;OAIG;IACH,QAAQ,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,OAAO,YAAY,CAAC,CAAC,GAAG,IAAI,CAAC;IAC3D;;;;;OAKG;IACH,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B;;;;;;;;;;;;;;;;OAgBG;IACH,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB;;;;OAIG;IACH,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB;;;;;OAKG;IACH,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,wEAAwE;AACxE,UAAU,YAAY;IACpB,MAAM,EAAE,YAAY,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,WAAW,EAAE,MAAM,CAAC;CACrB;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,gBAAgB,CAC9B,IAAI,EAAE,aAAa,CAAC,YAAY,CAAC,EACjC,MAAM,EAAE,aAAa,CAAC,MAAM,CAAC,GAC5B,KAAK,CAAC,YAAY,GAAG;IAAE,EAAE,EAAE,MAAM,CAAA;CAAE,CAAC,CAuBtC;AAED,qBAAa,YAAY;IACvB,OAAO,CAAC,OAAO,CAA0B;IACzC,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAQ;IAC9B,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAkB;IAC3C,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAU;IACjC,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAU;IAKtC,OAAO,CAAC,OAAO,CAAiB;IAChC,OAAO,CAAC,QAAQ,CAAkD;IAClE,OAAO,CAAC,gBAAgB,CAAS;IAKjC,OAAO,CAAC,OAAO,CAAU;IACzB,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,WAAW,CAAqB;IAQxC,OAAO,CAAC,IAAI,CAA0B;IACtC,OAAO,CAAC,eAAe,CAAyC;IAchE,OAAO,CAAC,eAAe,CAAuB;IAC9C,OAAO,CAAC,SAAS,CAAS;IAC1B,OAAO,CAAC,MAAM,CAAS;IASvB,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAoC;gBAEnD,IAAI,EAAE,cAAc;IAwBhC;;;;;;;;;;;;;OAaG;IACH,UAAU,CAAC,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAE,MAAM,GAAG,IAAI;IAYrE;;;;;;;;;;OAUG;IACH,WAAW,CACT,OAAO,EAAE,OAAO,GAAG,IAAI,EACvB,QAAQ,EAAE,OAAO,CAAC,UAAU,CAAC,OAAO,YAAY,CAAC,CAAC,GAAG,IAAI,EACzD,gBAAgB,SAAI,GACnB,IAAI;IASP;;;;;;;;;;;;;;;;;;;;;;OAsBG;IACH,UAAU,CAAC,IAAI,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,WAAW,CAAC,EAAE,WAAW,CAAC,EAAE,MAAM,GAAG,IAAI;IAW9F;;;;;;;;;;;OAWG;IACG,eAAe,IAAI,OAAO,CAAC,OAAO,CAAC;IAwBzC;;;;;;;;OAQG;IACH,OAAO,CAAC,eAAe;IA+CvB,sEAAsE;IAChE,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;YAsEd,MAAM;IAyOd,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;CAiB7B"}

package/dist/watcher.js

@@ -18,6 +18,45 @@
 import * as path from "node:path";
 import chokidar from "chokidar";
 const SKIP_DIRS = [".git", ".obsidian", ".trash", "node_modules", ".DS_Store"];
+/**
+ * v3.9.0-rc.11 (audit) — zip embed-db rows with their freshly-assigned row ids
+ * for an HNSW add-diff. `EmbedDb.upsertNote` returns exactly one id per row in
+ * the same order, so a length mismatch is a bug. The pre-rc.11 code used
+ * `newIds[i] ?? -1`, which silently inserted a vector under SENTINEL label
+ * `-1` on any mismatch — corrupting the in-memory index, the shared
+ * `rowsByLabel` map, AND the persisted `.hnsw.bin` sidecar (a later
+ * `markDelete(-1)` or a real row colliding on `-1` then scrambles results).
+ * This throws (fail-closed) instead: the watcher's per-event try/catch logs it
+ * and skips the HNSW update for that file, and the signature guard rebuilds a
+ * correct index on the next serve. A corrupt sentinel label is never inserted.
+ *
+ * @param rows - The embed rows (vector + chunk metadata), in insertion order.
+ * @param newIds - The row ids `upsertNote` assigned, parallel to `rows`.
+ * @returns Add-points for `syncHnswForFile`, each id guaranteed defined.
+ * @throws {Error} If `newIds.length !== rows.length`.
+ */
+export function zipHnswAddPoints(rows, newIds) {
+    if (newIds.length !== rows.length) {
+        throw new Error(`HNSW sync: embed-db returned ${newIds.length} ids for ${rows.length} rows — refusing to insert a sentinel label (would corrupt the index).`);
+    }
+    const points = [];
+    for (let i = 0; i < rows.length; i++) {
+        const r = rows[i];
+        const id = newIds[i];
+        if (r === undefined || id === undefined) {
+            throw new Error("HNSW sync: unexpected undefined row/id during zip.");
+        }
+        points.push({
+            id,
+            vector: r.vector,
+            chunkIndex: r.chunkIndex,
+            lineStart: r.lineStart,
+            lineEnd: r.lineEnd,
+            textPreview: r.textPreview
+        });
+    }
+    return points;
+}
 export class VaultWatcher {
     watcher = null;
     vault;
@@ -47,7 +86,31 @@ export class VaultWatcher {
     // next serve restart rebuilt from the freshly-upserted embed-db).
     hnsw = null;
     hnswRowsByLabel = null;
+    // v3.9.0-rc.6 — HNSW disk persistence on live update. The in-memory
+    // HNSW index diverges from the persisted `.hnsw.bin` after every
+    // applyDiff. Correctness is already guaranteed by the signature guard
+    // (a stale `.hnsw.bin` is ignored on next serve because
+    // loadHnswFromDisk recomputes the embed-db signature and rebuilds on
+    // mismatch). The ONLY benefit of re-persisting is restart SPEED:
+    // keeping the sidecar current avoids the ~25s rebuild on next serve.
+    // We persist at watcher CLOSE time (not on a debounced during-serve
+    // timer): the close-time flush delivers the restart-speed benefit
+    // without timer-lifecycle complexity or mid-serve disk I/O. An
+    // ungraceful SIGKILL skips the flush, but the signature guard makes
+    // that safe (falls back to rebuild). `hnswPersistFile` is null when
+    // `--no-hnsw-persist` was passed (no sidecar to keep current).
+    hnswPersistFile = null;
+    hnswDirty = false;
     closed = false;
+    // v3.9.0-rc.11 (audit H1) — per-file serialization. chokidar dispatches file
+    // events concurrently; without this, two rapid saves to the SAME file
+    // interleave their embed-db upsert + HNSW applyDiff + shared-`rowsByLabel`
+    // mutation → silent index drift (ghost labels live in HNSW but absent from
+    // the embed-db → stale search hits). Each event chains on the file's prior
+    // handle so same-file events run strictly sequentially while different files
+    // keep independent chains and stay parallel. Keyed by absolute path; entries
+    // self-evict when a file's chain drains (bounded memory over a long serve).
+    fileQueues = new Map();
     constructor(opts) {
         this.vault = opts.vault;
         this.ftsIndex = opts.ftsIndex ?? null;
@@ -133,13 +196,52 @@ export class VaultWatcher {
      * @param rowsByLabel - the mutable label→row map shared with
      *   `searchHybrid` (the live update writes into it so subsequent
      *   searches see the new chunks).
+     * @param persistFile - v3.9.0-rc.6: optional sidecar base path
+     *   (`<embed-db-without-suffix>.hnsw`). When provided AND HNSW live
+     *   updates occurred, the watcher re-persists the index at close time
+     *   so the next serve loads the up-to-date sidecar instead of
+     *   rebuilding. Omit (or pass when `--no-hnsw-persist`) to skip
+     *   persistence — correctness is unaffected (signature guard).
      */
-    attachHnsw(hnsw, rowsByLabel) {
+    attachHnsw(hnsw, rowsByLabel, persistFile) {
         if (!this.embedDb) {
             throw new Error("VaultWatcher.attachHnsw: embedDb not attached — call attachEmbed first (HNSW live update requires it)");
         }
         this.hnsw = hnsw;
         this.hnswRowsByLabel = rowsByLabel;
+        this.hnswPersistFile = persistFile ?? null;
+    }
+    /**
+     * v3.9.0-rc.6 — flush the live-updated HNSW index to its disk sidecar.
+     * No-op unless ALL of: the index is dirty (had ≥1 applyDiff since the
+     * last flush), an index + rowsByLabel + persistFile + embedDb are all
+     * wired. Recomputes the embed-db signature so the persisted
+     * `.meta.json` matches what `loadHnswFromDisk` will expect on the next
+     * serve (any external embed-db change since then → signature mismatch
+     * → safe rebuild). Fail-soft: a save error is logged + swallowed (the
+     * signature guard means a stale/missing sidecar just triggers rebuild).
+     *
+     * @returns true if a flush was performed, false if it was a no-op.
+     */
+    async flushHnswToDisk() {
+        if (!this.hnswDirty || !this.hnsw || !this.hnswRowsByLabel || !this.hnswPersistFile || !this.embedDb) {
+            return false;
+        }
+        try {
+            const signature = this.embedDb.computeSignature();
+            await this.hnsw.saveTo(this.hnswPersistFile, this.hnswRowsByLabel, signature);
+            this.hnswDirty = false;
+            if (!this.silent) {
+                process.stderr.write(`enquire: watcher persisted live-updated HNSW index to ${this.hnswPersistFile}.bin (+ .meta.json)\n`);
+            }
+            return true;
+        }
+        catch (err) {
+            if (!this.silent) {
+                process.stderr.write(`enquire: watcher HNSW persist failed — ${err instanceof Error ? err.message : String(err)} (next serve will rebuild from embed-db; correctness unaffected)\n`);
+            }
+            return false;
+        }
     }
     /**
      * v3.9.0-rc.2 — internal helper. Apply an embed-db {oldIds, newIds}
@@ -155,6 +257,10 @@ export class VaultWatcher {
             return null;
         try {
             const result = this.hnsw.applyDiff(oldIds, newRows.map((r) => ({ label: r.id, vector: r.vector })));
+            // v3.9.0-rc.6 — mark the index dirty so close-time flushHnswToDisk
+            // re-persists it. Set only after applyDiff succeeds (a thrown diff
+            // leaves the on-disk sidecar as the last-known-good state).
+            this.hnswDirty = true;
             // Update the rowsByLabel map: drop old, add new. The map is shared
             // with searchHybrid via reference; mutations are visible immediately.
             for (const oldId of oldIds)
@@ -219,12 +325,25 @@ export class VaultWatcher {
             ignoreInitial: true
         });
         const onChange = (absPath, kind) => {
-            // Fire-and-forget; failures are logged, not propagated.
-            this.handle(absPath, kind).catch((err) => {
+            // v3.9.0-rc.11 (H1) — serialize per file. Chain this event on the file's
+            // prior handle (which always resolves — it catches its own errors) so
+            // same-file events run sequentially and never interleave their embed-db
+            // + HNSW mutations; different files keep independent chains → parallel.
+            const prev = this.fileQueues.get(absPath) ?? Promise.resolve();
+            const tail = prev
+                .then(() => this.handle(absPath, kind))
+                .catch((err) => {
                 if (!this.silent) {
                     process.stderr.write(`enquire: watcher error on ${path.relative(root, absPath)} (${kind}) — ${err instanceof Error ? err.message : String(err)}\n`);
                 }
             });
+            this.fileQueues.set(absPath, tail);
+            // Self-evict once this is the last queued event for the file so the map
+            // stays bounded. If a newer event chained after us it owns the entry.
+            void tail.finally(() => {
+                if (this.fileQueues.get(absPath) === tail)
+                    this.fileQueues.delete(absPath);
+            });
         };
         this.watcher.on("add", (p) => onChange(p, "add"));
         this.watcher.on("change", (p) => onChange(p, "change"));
@@ -269,7 +388,11 @@ export class VaultWatcher {
                 try {
                     const deletedIds = this.embedDb.deleteNote(relPath);
                     if (deletedIds.length > 0 && this.hnsw) {
-                        const result = this.syncHnswForFile(relPath, "md", deletedIds, []);
+                        // v3.9.0-rc.11 (L2) — pass the correct kind for PDF unlinks (was
+                        // hardcoded "md"). Cosmetic on a pure-delete diff today since no
+                        // new rows are set, but correct + future-proof if the delete path
+                        // ever records kind.
+                        const result = this.syncHnswForFile(relPath, isPdf ? "pdf" : "md", deletedIds, []);
                         if (result)
                             unlinkHnswNote = ` + hnsw -${result.removed}`;
                     }
@@ -374,14 +497,7 @@ export class VaultWatcher {
                             // The newIds array runs parallel to pdfResult.rows (same order)
                             // so we can zip them into HNSW add-points by index.
                             if (this.hnsw) {
-                                const hnswResult = this.syncHnswForFile(relPath, "pdf", oldIds, pdfResult.rows.map((r, i) => ({
-                                    id: newIds[i] ?? -1,
-                                    vector: r.vector,
-                                    chunkIndex: r.chunkIndex,
-                                    lineStart: r.lineStart,
-                                    lineEnd: r.lineEnd,
-                                    textPreview: r.textPreview
-                                })));
+                                const hnswResult = this.syncHnswForFile(relPath, "pdf", oldIds, zipHnswAddPoints(pdfResult.rows, newIds));
                                 if (hnswResult)
                                     pdfEmbedNote += ` + hnsw -${hnswResult.removed}/+${hnswResult.added}`;
                             }
@@ -427,14 +543,7 @@ export class VaultWatcher {
                         // v3.9.0-rc.2 — keep HNSW in sync. newIds and result.rows run
                         // parallel (same order), so we zip them into HNSW add-points.
                         if (this.hnsw) {
-                            const hnswResult = this.syncHnswForFile(relPath, "md", oldIds, result.rows.map((r, i) => ({
-                                id: newIds[i] ?? -1,
-                                vector: r.vector,
-                                chunkIndex: r.chunkIndex,
-                                lineStart: r.lineStart,
-                                lineEnd: r.lineEnd,
-                                textPreview: r.textPreview
-                            })));
+                            const hnswResult = this.syncHnswForFile(relPath, "md", oldIds, zipHnswAddPoints(result.rows, newIds));
                             if (hnswResult)
                                 embedNote += ` + hnsw -${hnswResult.removed}/+${hnswResult.added}`;
                         }
@@ -462,6 +571,15 @@ export class VaultWatcher {
         if (this.closed)
             return;
         this.closed = true;
+        // v3.9.0-rc.11 (H1) — drain in-flight per-file handlers first so a pending
+        // upsert + applyDiff completes and the flushed sidecar reflects it (rather
+        // than racing close vs. an in-progress live update). allSettled: a failed
+        // handler shouldn't block shutdown.
+        await Promise.allSettled([...this.fileQueues.values()]);
+        // v3.9.0-rc.6 — flush the live-updated HNSW index before shutting
+        // down so the next serve loads the up-to-date sidecar. No-op if no
+        // live updates occurred or persistence is disabled. Fail-soft.
+        await this.flushHnswToDisk();
         if (this.watcher) {
             await this.watcher.close();
             this.watcher = null;

package/dist/watcher.js.map

@@ -1 +1 @@
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package/docs/COMPARISON.md

@@ -42,8 +42,8 @@ The four axes the external audit (#3, 2026-05) called out as decisive — **REST
 | Invoke Obsidian palette commands / hotkeys    | **No**              | **Yes**          | Limited          | No               | No               |
 | Read open editor state, active note, etc.     | **No**              | **Yes**          | Limited          | No               | No               |
 | Zero outbound network calls in serve mode     | **Yes** (default)   | Local-only (REST)| Local-only (REST)| Yes              | Yes              |
-| SLSA-3 build provenance on releases           | **Yes**             | No               | No               | No               | No               |
-| Test count (public)                           | **911**             | (varies)         | (varies)         | (varies)         | (varies)         |
+| Signed build provenance on releases (SLSA L2) | **Yes**             | No               | No               | No               | No               |
+| Test count (public)                           | **995**             | (varies)         | (varies)         | (varies)         | (varies)         |
 | Tool count                                    | 44                  | ~25              | ~8               | ~10              | 3–5              |
 | MCP prompt count                              | 19                  | 0                | 0                | 0                | 0                |
 | License                                       | MIT                 | Apache-2.0       | MIT              | MIT              | (varies)         |
@@ -146,7 +146,7 @@ Conversely, the scenarios where the trade-offs land in enquire-mcp's favor:
 
 **Symptom:** you ask the agent a conceptual question, and it gets a note that happens to contain one of your keywords but isn't actually the right note.
 
-If you have 5k+ notes and you've already noticed that simple grep / BM25 search returns wrong-but-keyword-matching results, the **BM25 + TF-IDF + dense-embeddings → RRF → cross-encoder reranker** stack is exactly what closes that gap. Typical +5–10 NDCG@10 over single-ranker baselines (BGE reranker, v2.9+). None of the other four servers in the matrix does multi-signal fusion or reranking.
+If you have 5k+ notes and you've already noticed that simple grep / BM25 search returns wrong-but-keyword-matching results, the **BM25 + TF-IDF + dense-embeddings → RRF → cross-encoder reranker** stack is exactly what closes that gap. Measured +15.5 NDCG@10 / +24.7 MRR over single-ranker baselines (BGE reranker, 60-query ablation). None of the other four servers in the matrix does multi-signal fusion or reranking.
 
 What enquire-mcp gives you, specifically:
 
@@ -193,7 +193,7 @@ The alternatives expose tools but not curated agent-facing prompts. If your clie
 
 ### 6. Supply-chain hygiene matters
 
-enquire-mcp publishes **SLSA-3 build provenance** with every release — npm artifacts are signed and verifiable against the GitHub Actions build. If your org's MCP install path requires verifying that the binary you got from npm was built from the commit it claims, that's available out of the box.
+enquire-mcp publishes **signed build provenance** with every release — npm artifacts carry a Sigstore-signed provenance attestation (via `npm publish --provenance` + GitHub OIDC), verifiable with `npm audit signatures` against the GitHub Actions build. This is **SLSA Build Level 2** (hosted builder + signed, non-forgeable-by-author provenance). Isolated-builder **Level 3** (via the `slsa-github-generator` reusable workflow) is on the roadmap. If your org's MCP install path requires verifying that the binary you got from npm was built from the commit it claims, that's available out of the box.
 
 None of the four alternatives currently ships SLSA provenance. For some users this is a hard "no" on installing anything else; for most it's a "nice to have".
 

package/docs/QUICKSTART.md

@@ -29,7 +29,7 @@ Verify the install:
 enquire-mcp --version
 ```
 
-Expected output: the current version string (e.g. `3.7.12`).
+Expected output: the current version string (e.g. `3.9.0-rc.N` on `@rc` or `3.8.8` on `@latest`).
 
 ## Step 2 — Smoke test (30 seconds)
 
@@ -126,7 +126,7 @@ You now have working TF-IDF search. To unlock the full hybrid stack:
 
 - **One-command full setup** — `enquire-mcp setup --vault /absolute/path/to/your/vault` downloads the multilingual embedding model (~120 MB, one-time), builds the FTS5 BM25 index, and builds the embedding index. Idempotent.
 - **PDF search** — add `--include-pdfs` to your Claude Desktop args. PDFs get blended into `obsidian_search` results with `[page: N]` citation markers.
-- **Cross-encoder reranking** — add `--enable-reranker`. Typical +5-10 NDCG@10 retrieval-quality boost.
+- **Cross-encoder reranking** — add `--enable-reranker`. Measured +15.5 NDCG@10 / +24.7 MRR (60-query ablation).
 - **Sub-10ms top-K at scale** — add `--use-hnsw`. HNSW vector index, persisted to disk so cold starts stay ~50ms.
 - **Harder questions** — try `obsidian_hyde_search` (HyDE retrieval, Gao et al 2023) when the literal query phrasing doesn't match how the notes are written.
 - **Full 44-tool surface** — see [`docs/api.md`](./api.md) for every read/write tool, MCP resource, and prompt.

package/docs/api.md

@@ -1,8 +1,8 @@
 # enquire — API
 
-**enquire is the most advanced Obsidian MCP — a long-term memory layer for AI agents, built on your Obsidian vault.** Open-source, MCP-native, vendor-neutral persistence: agents (Claude Code / Claude Desktop / Cursor / ChatGPT / Codex / OpenClaw / any MCP client) get durable, queryable recall across sessions, models, and providers — your knowledge lives in plain markdown you own, not a vendor cloud. 44 MCP tools (33 always-on read + 4 opt-in read + 7 opt-in write); the 4 opt-ins are: 1 via `--persistent-index` + `--diagnostic-search-tools` (`obsidian_full_text_search` — needs BOTH flags: persistent-index for the FTS5 index, diagnostic-search-tools to surface it as a single-ranker tool alongside the hybrid default `obsidian_search`) + 3 via `--diagnostic-search-tools` (the single-ranker `obsidian_search_text` / `obsidian_semantic_search` / `obsidian_embeddings_search` — gated by default in v2.0+ since `obsidian_search` auto-detects + fuses signals). 2 + 1 opt-in MCP resources, 19 MCP prompts. **v3.1.0+ adds `obsidian_hyde_search`** (HyDE-augmented retrieval, Gao et al 2023; agent supplies a synthetic answer, server embeds it for retrieval) plus the `vault_research` (sub-question decomposition) and `vault_synthesis_page` (Karpathy LLM-Wiki synthesis loop) prompts. v2.6.0+ also speaks Streamable HTTP via `serve-http` (bearer auth + rate-limit + CORS). v2.7.0+ indexes PDFs as a separate read tool surface; **v2.8.0+ blends PDF chunks into `obsidian_search` hybrid retrieval** with `--include-pdfs` — every hit carries a `kind: "md" | "pdf"` flag and PDF snippets include `[page: N]` markers for citation. **v2.9.0+ adds BGE cross-encoder reranking** on top of RRF with `--enable-reranker` — typical +5-10 NDCG@10 retrieval-quality boost. **v2.10.0+ adds Tesseract OCR for image-only / scanned PDFs** via `obsidian_ocr_pdf` — completes the PDF retrieval story.
+**enquire is the most advanced Obsidian MCP — a long-term memory layer for AI agents, built on your Obsidian vault.** Open-source, MCP-native, vendor-neutral persistence: agents (Claude Code / Claude Desktop / Cursor / ChatGPT / Codex / OpenClaw / any MCP client) get durable, queryable recall across sessions, models, and providers — your knowledge lives in plain markdown you own, not a vendor cloud. 44 MCP tools (33 always-on read + 4 opt-in read + 7 opt-in write); the 4 opt-ins are: 1 via `--persistent-index` + `--diagnostic-search-tools` (`obsidian_full_text_search` — needs BOTH flags: persistent-index for the FTS5 index, diagnostic-search-tools to surface it as a single-ranker tool alongside the hybrid default `obsidian_search`) + 3 via `--diagnostic-search-tools` (the single-ranker `obsidian_search_text` / `obsidian_semantic_search` / `obsidian_embeddings_search` — gated by default in v2.0+ since `obsidian_search` auto-detects + fuses signals). 2 + 1 opt-in MCP resources, 19 MCP prompts. **v3.1.0+ adds `obsidian_hyde_search`** (HyDE-augmented retrieval, Gao et al 2023; agent supplies a synthetic answer, server embeds it for retrieval) plus the `vault_research` (sub-question decomposition) and `vault_synthesis_page` (Karpathy LLM-Wiki synthesis loop) prompts. v2.6.0+ also speaks Streamable HTTP via `serve-http` (bearer auth + rate-limit + CORS). v2.7.0+ indexes PDFs as a separate read tool surface; **v2.8.0+ blends PDF chunks into `obsidian_search` hybrid retrieval** with `--include-pdfs` — every hit carries a `kind: "md" | "pdf"` flag and PDF snippets include `[page: N]` markers for citation. **v2.9.0+ adds BGE cross-encoder reranking** on top of RRF with `--enable-reranker` — measured +15.5 NDCG@10 / +24.7 MRR (60-query ablation). **v2.10.0+ adds Tesseract OCR for image-only / scanned PDFs** via `obsidian_ocr_pdf` — completes the PDF retrieval story.
 
-> **Channels:** stable since v3.8.x (`@latest` on npm) ships 44 tools including `obsidian_search` (hybrid BM25 + TF-IDF + ML embeddings, RRF-fused) with optional BGE cross-encoder reranking, `obsidian_embeddings_search`, `obsidian_hyde_search`, plus the `install-model` / `build-embeddings` / `clear-embeddings` / `setup` / `doctor` / `eval` subcommands. The `@rc` dist-tag carries the most recent release candidate (currently v3.9.0-rc.1 — OCR'd PDF watcher embed-sync). Benchmarks live behind `npm run bench:retrieval` (not a CLI subcommand). This document covers the **stable v3.8.x** surface plus what the upcoming v3.9.0 will add — see [CHANGELOG.md](../CHANGELOG.md) for the v3.8.x release series and the in-flight v3.9.0-rc.1.
+> **Channels:** stable since v3.8.x (`@latest` on npm) ships 44 tools including `obsidian_search` (hybrid BM25 + TF-IDF + ML embeddings, RRF-fused) with optional BGE cross-encoder reranking, `obsidian_embeddings_search`, `obsidian_hyde_search`, plus the `install-model` / `build-embeddings` / `clear-embeddings` / `setup` / `doctor` / `eval` subcommands. The `@rc` dist-tag carries the most recent release candidate (see [CHANGELOG.md](../CHANGELOG.md) for the current RC and its features — recent RCs add OCR'd PDF watcher embed-sync, HNSW in-memory live update, adaptive HNSW refill, OCR offline enforcement, and watcher concurrency hardening). Benchmarks live behind `npm run bench:retrieval` (not a CLI subcommand). This document covers the **stable v3.8.x** surface plus the in-flight v3.9.0 RCs — see [CHANGELOG.md](../CHANGELOG.md) for full release history.
 
 > Versioned dynamically — see [`CHANGELOG.md`](../CHANGELOG.md) for the current release.
 
@@ -86,7 +86,19 @@ Canonical list of every registered MCP tool. The `Kind` column splits read/write
 | `--read-paths <pattern...>` | none | **Strict allowlist** — when set, ONLY paths matching one of these glob patterns are visible. Complement to `--exclude-glob`. If both are set: a path must match an allow-glob AND not match any exclude-glob. Same glob semantics. Repeatable. Example: `--read-paths '01_Projects/**' '99_Daily/**'`. |
 | `--disabled-tools <name...>` | none | Skip registration of specific tools by exact name (matches `tools/list`). Repeatable. Useful for narrow-surface agents. Example: `--disabled-tools obsidian_dataview_query obsidian_full_text_search`. |
 | `--enabled-tools <name...>` | none | **Strict allowlist** — when set, ONLY listed tools register. Complement to `--disabled-tools`. If both are set: a tool must be in allowlist AND not in denylist. Repeatable. Example: `--enabled-tools obsidian_search_text obsidian_read_note obsidian_get_recent_edits`. |
-| `--watch`              | off     | Watch the vault for `.md` add/change/unlink events (and `.pdf` if `--include-pdfs`). On change: invalidate the parsed-note cache for that file; if `--persistent-index` is also enabled, incrementally re-sync just that file's FTS5 chunks AND (since v3.8.0-rc.2 for `.md`, v3.8.0-rc.3 for `.pdf`) the embed-db rows when the embed-db file exists. Editor saves are debounced via chokidar's `awaitWriteFinish`. `--exclude-glob` patterns are honored — edits to excluded paths don't fire. Off by default; opt in for long-running servers. |
+| `--watch`              | off     | Watch the vault for `.md` add/change/unlink events (and `.pdf` if `--include-pdfs`). On change: invalidate the parsed-note cache for that file; if `--persistent-index` is also enabled, incrementally re-sync just that file's FTS5 chunks AND (since v3.8.0-rc.2 for `.md`, v3.8.0-rc.3 for `.pdf`) the embed-db rows when the embed-db file exists. **Since v3.9.0-rc.2 with `--use-hnsw`:** the in-memory HNSW index is updated in lockstep so semantic search reflects edits within ~250ms (pre-3.9.0 needed serve restart). Editor saves are debounced via chokidar's `awaitWriteFinish`. `--exclude-glob` patterns are honored — edits to excluded paths don't fire. Off by default; opt in for long-running servers. |
+| `--include-pdfs`       | off     | v2.8.0 — also index PDF files into FTS5 (and embeddings, if `build-embeddings --include-pdfs` ran). With `--persistent-index`, PDF chunks become first-class hits in `obsidian_search` results with `kind: "pdf"` flag. ~50–200ms per page on M1 cold. Requires the `pdfjs-dist` optionalDependency (default-installed). |
+| `--ocr-pdfs`           | off     | **v3.9.0-rc.1** — when paired with `--watch` + `--include-pdfs`, runs Tesseract OCR on image-only / scanned PDFs that pdfjs can't read text from. OCR-derived text feeds the embed-db so scanned PDFs stay in sync during long sessions. Requires `tesseract.js` + `@napi-rs/canvas` optional deps + the language pack pre-installed via `enquire-mcp install-ocr-lang <code>` (serve makes no runtime CDN download — a missing pack throws fail-closed, v3.9.0-rc.10; see [SECURITY.md "OCR network posture"](../SECURITY.md#ocr-network-posture)). |
+| `--ocr-langs <langs>`  | `eng`   | **v3.9.0-rc.1** — Tesseract language pack for `--ocr-pdfs`. Multi-lang via `+`, e.g. `eng+rus`. Each `<lang>.traineddata` (~10 MB) must be pre-installed. |
+| `--ocr-max-pages <n>`  | `200`   | **v3.9.0-rc.1** — page cap per OCR run. Image-only PDFs exceeding this skip the OCR pass (FTS5 still reindexes from empty pages). Lift the cap for trusted PDF sets; lower for shared deployments to bound per-event CPU. |
+| `--enable-reranker`    | off     | v2.9.0 — BGE cross-encoder reranking on top of RRF. ~30–50ms per query on M1; measured +15.5 NDCG@10 / +24.7 MRR (60-query ablation). Requires `@huggingface/transformers` optional dep. |
+| `--reranker-model <alias>` | `rerank-bge` | v2.9.0 — reranker alias from `RERANKER_MODELS`. Default verified-working in v3.6.1 (Xenova/bge-reranker-base, ~110 MB, English). |
+| `--reranker-top-n <n>` | `50`    | v2.9.0 — how many top RRF-fused candidates to rerank. Only effective with `--enable-reranker`. |
+| `--use-hnsw`           | off     | v2.13.0 — build an in-memory HNSW vector index on serve start (or reload from `.hnsw.bin` sidecar if `--hnsw-persist`). Sub-10ms top-K queries at any scale. Recall@10 ≥ 98% vs brute-force. **Since v3.9.0-rc.2 with `--watch`:** the index updates live on every md/pdf event (no serve restart needed). **Since v3.9.0-rc.3:** queries auto-refill when post-filter hits < limit (closes the >66% excluded under-return). Requires `hnswlib-node` optional dep. |
+| `--hnsw-ef <n>`        | `100`   | v2.13.0 — HNSW search-time beam width (must be ≥ k). Higher = more accurate, slightly slower. |
+| `--late-chunk-context <chars>` | `0` | v2.15.0 — late-chunking context windowing on embeddings. Typical +2–5 NDCG@10 boost. Only effective during `build-embeddings` or auto-rebuild. |
+| `--no-hnsw-persist`    | persist on | v2.16.0 — disable HNSW persistence sidecar. Default behavior: save `.hnsw.bin` + `.meta.json` next to `.embed.db`; reload on next serve when signature matches (~25s rebuild → ~50ms reload on 50K chunks). |
+| `--quantize-embeddings <mode>` | `f32` | v2.17.0 — vector storage mode. `f32` (default) or `int8` (~4× storage reduction at ~1–2% recall@10 cost). Switching modes triggers a full rebuild. |
 
 ## Subcommands
 
@@ -114,6 +126,7 @@ Canonical list of every registered MCP tool. The `Kind` column splits read/write
 | `install-model` (v2.0+) | `[alias]` (default `multilingual`) | Pre-download an embedding model so the first MCP call doesn't block on a ~120MB HuggingFace download. Aliases: `multilingual` (Xenova/paraphrase-multilingual-MiniLM-L12-v2, 384-dim, 50+ languages, ~120MB) or `bge` (Xenova/bge-small-en-v1.5, 384-dim, English-only, ~33MB). Models cached under `~/.cache/huggingface/transformers.js/` and reused across vaults. Idempotent. |
 | `build-embeddings` (v2.0+) | `--vault <path>` `[--embedding-model <alias>]` `[--embed-file <path>]` `[--exclude-glob <pattern...>]` `[--read-paths <pattern...>]` `[--late-chunk-context <chars>]` `[--quantize-embeddings <mode>]` | Cold-build (or refresh) the persistent embedding index for a vault. Required before `obsidian_embeddings_search` and `obsidian_search` (in hybrid mode) are useful. Same paragraph-level chunking as the FTS5 index — chunk identity matches across BM25 and embeddings. Incremental rebuilds via `source_state` mtime tracking. Reports `added`/`updated`/`deleted`/`unchanged` chunk counts. v2.15.0 `--late-chunk-context <chars>` prepends doc title + breadcrumb + neighbor-chunk tails of N chars before embedding (typical 100-200 for +2-5 NDCG@10). v2.17.0 `--quantize-embeddings <mode>` (`f32` default, `int8` for ~4× smaller BLOBs at ≈1-2% recall cost; mode change triggers a full rebuild). |
 | `clear-embeddings` (v2.0+) | `--vault <path>` `[--embed-file <path>]` | Delete the embedding-index files (`.embed.db` + WAL/SHM sidecar). Idempotent. |
+| `install-ocr-lang` (v3.9.0-rc.10) | `<code>` (e.g. `eng`, `rus`, `chi_sim`) | Download a Tesseract OCR language pack (`<code>.traineddata`, ~10 MB) into the local tessdata cache (`$ENQUIRE_TESSDATA_DIR` → `$XDG_CACHE_HOME/enquire-mcp/tessdata` → `~/.cache/enquire-mcp/tessdata`) so `--ocr-pdfs` works fully offline during serve. The ONLY OCR-related network call — explicit + opt-in, mirroring `install-model`. `serve` itself makes no runtime CDN fetch (a missing pack throws fail-closed). One code per invocation. Idempotent. |
 
 ## Read tools (always registered)
 
@@ -848,7 +861,7 @@ BM25-ranked full-text search over a SQLite FTS5 inverted index. Sub-100ms on mul
 }
 ```
 
-**Implementation note:** see [issue #10](https://github.com/oomkapwn/enquire-mcp/issues/10) for the full architecture (production-verified by an external contributor at 1771 chunks / 368 files, 9.8 MB index, 50–100ms BM25 top-10). Local bench against synthetic vault sees 37–103x speedup over the linear-scan path on 100–1000 notes — see [`scripts/bench-search.mjs`](../scripts/bench-search.mjs).
+**Implementation note:** see [issue #10](https://github.com/oomkapwn/enquire-mcp/issues/10) for the full architecture (production-verified by an external contributor at 1771 chunks / 368 files, 9.8 MB index, 50–100ms BM25 top-10). Local bench against synthetic vault sees 37–103x speedup over the linear-scan path on 100–1000 notes — see [`scripts/bench-search.mjs`](https://github.com/oomkapwn/enquire-mcp/blob/main/scripts/bench-search.mjs).
 
 ## `obsidian://chunk/{chunkIndex}/{+notePath}` resource _(opt-in, requires `--persistent-index`)_
 

package/docs/benchmarks.md

@@ -1,6 +1,6 @@
 # Benchmarks — enquire-mcp retrieval quality
 
-**Last updated:** 2026-05-15 (latency numbers re-measured under v3.7.10 against `bench/benchmarks.json`; methodology table updated v3.7.13 M11 to drop the duplicate latency column; ratio claim recomputed v3.7.18 B-3 against current TL;DR figures). Quality metrics (MRR / NDCG@10 / Recall@10) are deterministic and stable across the v3.7.x cascade. · **Generated by:** `npm run bench:retrieval`
+**Last updated:** 2026-05-15 (latency numbers re-measured under v3.7.10 against `bench/benchmarks.json`; methodology table updated v3.7.13 M11 to drop the duplicate latency column; ratio claim recomputed v3.7.18 B-3 against current TL;DR figures). Quality metrics (MRR / NDCG@10 / Recall@10) are deterministic and stable across the v3.7.x → v3.9.0-rc cascade (still valid through the v3.9.0-rc cascade — retrieval pipeline unchanged; v3.8.x→v3.9.0 work was correctness/hardening + watcher live-update, not algorithmic). · **Generated by:** `npm run bench:retrieval`
 
 This page reports retrieval-quality numbers for every layer of the enquire-mcp
 hybrid stack against a deterministic synthetic vault. **Every metric below is
@@ -27,7 +27,7 @@ reproducible from this repository — there are no hand-edited numbers.** Run
 **Headline takeaways:**
 
 - The cross-encoder reranker is the single biggest top-K-precision win:
-  **+25 MRR points** and **+16 NDCG@10 points** vs. plain hybrid RRF — at a
+  **+24.7 MRR points** and **+15.5 NDCG@10 points** vs. plain hybrid RRF — at a
   ~290 ms latency cost per query on M-series CPU.
 - Hybrid retrieval maximizes **recall** (every relevant note is somewhere
   in the top-10 96 % of the time) but base RRF without a reranker has weak
@@ -61,7 +61,7 @@ so the FTS5/embed-db source_state hashes are bit-identical across runs.
 ### Ground-truth queries
 
 The 60 queries live in
-[`tests/fixtures/benchmark-queries.jsonl`](../tests/fixtures/benchmark-queries.jsonl).
+[`tests/fixtures/benchmark-queries.jsonl`](https://github.com/oomkapwn/enquire-mcp/blob/main/tests/fixtures/benchmark-queries.jsonl).
 Each line is one JSON object:
 
 ```jsonl
@@ -99,7 +99,7 @@ We report three standard IR metrics from Manning, Raghavan & Schütze,
   many of the relevant docs did we surface at all?"*
 
 All three are computed by the existing
-[`src/eval.ts`](../src/eval.ts) implementations — the same code that powers
+[`src/eval.ts`](https://github.com/oomkapwn/enquire-mcp/blob/main/src/eval.ts) implementations — the same code that powers
 the `enquire-mcp eval` CLI subcommand.
 
 ### Stack configurations
@@ -443,6 +443,49 @@ which makes Recall@10 forgiving. On a 1,000-note vault Recall@10 captures
 reranker's Recall@10 cost (-5.2 points here) would likely be smaller in
 relative terms.
 
+## LongMemEval retrieval (external benchmark)
+
+[LongMemEval](https://github.com/xiaowu0162/LongMemEval) (Wu et al. 2024,
+[arXiv:2410.10813](https://arxiv.org/abs/2410.10813)) is the standard
+long-term-memory benchmark the AI-memory leaders (Mem0, Zep) publish against.
+No Obsidian-MCP has any LongMemEval-derived number — so a measured one is a
+clear differentiator.
+
+**What we measure — and what we don't.** enquire-mcp is a *retriever* over a
+vault, not an answer-generating chat assistant. So this harness reports
+**retrieval quality** — `recall@k` / `MRR` / `NDCG@k` of the *answer-bearing
+session(s)* per question, using the **same `src/eval.ts` metrics** as the rest
+of this document. It deliberately does **not** report LongMemEval's end-to-end
+QA accuracy: that requires an LLM to generate an answer from the retrieved
+context, which is the calling agent's job, not the memory layer's. Reporting a
+QA-accuracy number for a retriever would be an overclaim.
+
+**Harness.** [`scripts/bench-longmemeval.mjs`](https://github.com/oomkapwn/enquire-mcp/blob/main/scripts/bench-longmemeval.mjs)
+(shipped v3.9.0-rc.19) materializes each question's haystack sessions into a
+throwaway vault (one note per session), indexes it with FTS5, runs
+`searchHybrid`, and scores `recall@k` / `MRR` / `NDCG@k` of the answer
+session(s) — aggregated overall and per `question_type` (single-session,
+multi-session, temporal-reasoning, knowledge-update, …). Abstention questions
+(`*_abs`) are counted separately, not scored for recall.
+
+**Running it** (the dataset is **not** committed — size + licensing):
+
+```bash
+# 1. Download longmemeval_s / _m / _oracle from the LongMemEval repo
+# 2. Then:
+npm run bench:longmemeval -- --dataset path/to/longmemeval_s.json --k 10
+#   optional: --limit N (sample the first N questions) · --embeddings (add the
+#   dense arm — heavy: per-question embed-db build)
+```
+
+**Status:** the harness + its pure-function tests ship in v3.9.0-rc.19; the
+**headline numbers are intentionally not published here yet** — they will be
+added once the maintainer runs the full set on reference hardware and reviews
+the methodology (a published LongMemEval figure is the project's credibility
+centerpiece, so it goes through the same "measured, reproducible, reviewed"
+bar as every other number in this document — never a placeholder or an
+estimate).
+
 ## Future work
 
 - Reproduce on **public BEIR / TREC subsets** so numbers can be compared
@@ -462,12 +505,12 @@ relative terms.
 
 - [`docs/COMPARISON.md`](./COMPARISON.md) — feature matrix vs. other
   Obsidian-MCP servers.
-- [`docs/api-reference/`](./api-reference/) — TypeDoc-generated API
+- [`docs/api-reference/`](https://oomkapwn.github.io/enquire-mcp/) — TypeDoc-generated API
   reference (links into `searchHybrid`, `embeddingsSearch`,
   `semanticSearch`).
-- [`src/eval.ts`](../src/eval.ts) — the eval harness used by both this
+- [`src/eval.ts`](https://github.com/oomkapwn/enquire-mcp/blob/main/src/eval.ts) — the eval harness used by both this
   bench script and the `enquire-mcp eval` CLI subcommand.
-- [`tests/fixtures/benchmark-queries.jsonl`](../tests/fixtures/benchmark-queries.jsonl)
+- [`tests/fixtures/benchmark-queries.jsonl`](https://github.com/oomkapwn/enquire-mcp/blob/main/tests/fixtures/benchmark-queries.jsonl)
   — the ground-truth query set.
-- [`bench/benchmarks.json`](../bench/benchmarks.json) — machine-readable
+- [`bench/benchmarks.json`](https://github.com/oomkapwn/enquire-mcp/blob/main/bench/benchmarks.json) — machine-readable
   output (includes per-query scores and per-category breakdowns).

package/package.json

@@ -1,9 +1,9 @@
 {
   "$schema": "https://json.schemastore.org/package.json",
   "name": "@oomkapwn/enquire-mcp",
-  "version": "3.9.0-rc.2",
+  "version": "3.9.0-rc.21",
   "mcpName": "io.github.oomkapwn/enquire-mcp",
-  "description": "MCP server giving AI agents (Claude Code, Claude Desktop, Cursor, ChatGPT, Codex, OpenClaw) persistent long-term memory backed by your local Obsidian markdown vault. Hybrid retrieval (BM25 + ML embeddings + BGE reranker, RRF-fused), HNSW + int8 quantization, agentic RAG (HyDE + sub-question decomposition), GraphRAG-light (Louvain), standalone Obsidian Bases, PDFs + Tesseract OCR. Vendor-neutral memory layer for any MCP-compatible agent. 44 tools, 19 MCP prompts, 911 tests, SLSA-3, semver-bound, MIT, zero cloud calls during serve.",
+  "description": "MCP server giving AI agents (Claude Code, Claude Desktop, Cursor, ChatGPT, Codex, OpenClaw) persistent long-term memory backed by your local Obsidian markdown vault. Hybrid retrieval (BM25 + ML embeddings + BGE reranker, RRF-fused), HNSW + int8 quantization, agentic RAG (HyDE + sub-question decomposition), GraphRAG-light (Louvain), standalone Obsidian Bases, PDFs + Tesseract OCR. Vendor-neutral memory layer for any MCP-compatible agent. 44 tools, 19 MCP prompts, 995 tests, signed npm build provenance (SLSA L2), semver-bound, MIT, zero cloud calls during serve.",
   "type": "module",
   "bin": {
     "enquire-mcp": "dist/index.js"
@@ -82,6 +82,7 @@
     "bench:quick": "npm run build && node scripts/bench.mjs --quick",
     "bench:retrieval": "npm run build && node scripts/run-benchmarks.mjs",
     "bench:peek-cache": "npm run build && node scripts/bench-peek-cache.mjs",
+    "bench:longmemeval": "npm run build && node scripts/bench-longmemeval.mjs",
     "docs:api": "typedoc",
     "prepare": "tsc && chmod +x dist/index.js && (husky 2>/dev/null || true)",
     "prepublishOnly": "npm run lint && npm run build && npm test && node scripts/check-version-consistency.mjs && npm audit --audit-level=high && npm run test:coverage --silent && node scripts/check-changelog-coverage.mjs && node scripts/check-per-file-coverage.mjs",
@@ -160,7 +161,7 @@
     "tesseract",
     "streamable-http",
     "remote-mcp",
-    "slsa-3"
+    "build-provenance"
   ],
   "author": "Alex (@OomkaBear)",
   "license": "MIT",
@@ -183,7 +184,7 @@
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.15",
+    "@biomejs/biome": "^2.4.16",
     "@huggingface/transformers": "^4.2.0",
     "@types/better-sqlite3": "^7.6.13",
     "@types/node": "^25.6.2",