@oomkapwn/enquire-mcp 3.8.8 → 3.9.0-rc.2

package/dist/watcher.d.ts

@@ -1,7 +1,23 @@
 import type { EmbedDb } from "./embed-db.js";
 import type { loadEmbedder } from "./embeddings.js";
 import type { FtsIndex } from "./fts5.js";
+import type { HnswIndex } from "./hnsw.js";
 import type { Vault } from "./vault.js";
+/**
+ * v3.9.0-rc.2 — shape of the row-metadata entries the HNSW index keeps
+ * alongside each label. Mirrors `HnswPersistedMeta["rowsByLabel"][k]`
+ * but defined here so the watcher's TypeScript surface stays
+ * self-contained (no circular imports between watcher.ts and hnsw.ts's
+ * persistence types).
+ */
+export interface HnswRowMeta {
+    rel_path: string;
+    chunk_index: number;
+    line_start: number;
+    line_end: number;
+    text_preview: string;
+    kind: "md" | "pdf";
+}
 export interface WatcherOptions {
     /** Vault to watch — must already be ensureExists()'d. */
     vault: Vault;
@@ -51,6 +67,37 @@ export interface WatcherOptions {
      * vector space and search recall would drift over the session.
      */
     lateChunkContext?: number;
+    /**
+     * v3.9.0-rc.1 — when true, the watcher runs Tesseract OCR on
+     * image-only / scanned PDFs that pdfjs can't extract text from, then
+     * pipes the OCR-derived text through the standard embed pipeline so
+     * the embed-db keeps OCR'd PDFs in sync with edits during a long
+     * serve session. Off by default (OCR is slow: ~1-2s per page on M1
+     * CPU; a 100-page paper takes minutes and blocks the event loop).
+     *
+     * Requires `tesseract.js` + `@napi-rs/canvas` optional dependencies
+     * + the requested language trained-data files pre-installed via
+     * `enquire-mcp install-ocr-lang <code>` (see v3.7.16 P1-1 offline
+     * enforcement). If those aren't available, OCR fails-soft — the
+     * watcher still updates FTS5 + clears any stale embed-db rows.
+     *
+     * Recommended pairing: `--ocr-pdfs` + `--watch` + `--include-pdfs`
+     * for users with scanned-document vaults that change during sessions.
+     */
+    ocrPdfs?: boolean;
+    /**
+     * v3.9.0-rc.1 — language pack(s) passed to `extractPdfWithOcr`.
+     * Default `'eng'`. Multi-lang via `'+'`, e.g. `'eng+rus'`. See
+     * `src/ocr.ts` for the full language model.
+     */
+    ocrLangs?: string;
+    /**
+     * v3.9.0-rc.1 — page cap for OCR runs. Mirrors `DEFAULT_OCR_MAX_PAGES`
+     * (200) — image-only PDFs that exceed this won't be embed-sync'd
+     * (the watcher logs the skip + still updates FTS5). Operators can
+     * lift the cap when they trust their PDF set.
+     */
+    ocrMaxPages?: number;
 }
 export declare class VaultWatcher {
     private watcher;
@@ -61,8 +108,28 @@ export declare class VaultWatcher {
     private embedDb;
     private embedder;
     private lateChunkContext;
+    private ocrPdfs;
+    private ocrLangs;
+    private ocrMaxPages;
+    private hnsw;
+    private hnswRowsByLabel;
     private closed;
     constructor(opts: WatcherOptions);
+    /**
+     * v3.9.0-rc.1 — enable / configure OCR-on-watch after construction.
+     * Called by server.ts after attachEmbed() runs (since OCR fallback
+     * only makes sense once embed-db is wired). Fails loud if includePdfs
+     * is off — without it, PDF events are filtered before the OCR
+     * codepath runs.
+     *
+     * @param enabled - When true, image-only PDFs that pdfjs can't read
+     *   trigger a Tesseract OCR pass; the OCR-derived text feeds the
+     *   normal embed pipeline via embedSinglePdf's preExtractedPages path.
+     * @param langs - Tesseract language pack (default "eng"). Multi-lang
+     *   via `+`, e.g. "eng+rus".
+     * @param maxPages - Page cap for OCR runs. Default 200 (DEFAULT_OCR_MAX_PAGES).
+     */
+    setOcrPdfs(enabled: boolean, langs?: string, maxPages?: number): void;
     /**
      * v3.8.0-rc.2 R-7 — attach an embed-db handle + embedder after the
      * watcher has started. Used by `prepareServerDeps` when HNSW context
@@ -75,6 +142,34 @@ export declare class VaultWatcher {
      * detach (the FTS5-only sync continues).
      */
     attachEmbed(embedDb: EmbedDb | null, embedder: Awaited<ReturnType<typeof loadEmbedder>> | null, lateChunkContext?: number): void;
+    /**
+     * v3.9.0-rc.2 — wire an in-memory HNSW index for live updates. After
+     * this call, every md/pdf event that mutates embed-db ALSO updates
+     * the HNSW graph via `hnsw.applyDiff(oldIds, newPoints)` so search
+     * results reflect the change immediately. Pre-3.9.0, the HNSW index
+     * was rebuilt from embed-db only at serve startup; vault edits during
+     * the session left the HNSW stale until restart, and `--use-hnsw`
+     * users saw new content omitted from semantic-search results.
+     *
+     * Must be called AFTER `attachEmbed` (the HNSW + embed-db handles
+     * share a lifecycle — server.ts opens both during HNSW init).
+     *
+     * @param hnsw - the in-memory HNSW index built by server.ts.
+     * @param rowsByLabel - the mutable label→row map shared with
+     *   `searchHybrid` (the live update writes into it so subsequent
+     *   searches see the new chunks).
+     */
+    attachHnsw(hnsw: HnswIndex, rowsByLabel: Map<number, HnswRowMeta>): void;
+    /**
+     * v3.9.0-rc.2 — internal helper. Apply an embed-db {oldIds, newIds}
+     * diff to the wired HNSW index + rowsByLabel map. Called by both the
+     * md and pdf event handlers after upsertNote / deleteNote returns.
+     * Fail-soft: on any error, logs to stderr and returns — the embed-db
+     * is already updated, so the next serve restart will rebuild HNSW
+     * from the correct state. (Same posture as the watcher's existing
+     * embed-db fail-soft.)
+     */
+    private syncHnswForFile;
     /** Start watching. Resolves once the watcher has reported `ready`. */
     start(): Promise<void>;
     private handle;

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,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,MAAM,CAAS;gBAEX,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;;;;;;;;;;;;;;;;OAgBG;IACH,UAAU,CAAC,IAAI,EAAE,SAAS,EAAE,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,WAAW,CAAC,GAAG,IAAI;IAUxE;;;;;;;;OAQG;IACH,OAAO,CAAC,eAAe;IA2CvB,sEAAsE;IAChE,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;YA0Dd,MAAM;IAwPd,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;CAQ7B"}

package/dist/watcher.js

@@ -31,6 +31,22 @@ export class VaultWatcher {
     embedDb;
     embedder;
     lateChunkContext;
+    // v3.9.0-rc.1 — OCR-on-watch options. Mutable so server.ts can wire
+    // them via setOcrPdfs() AFTER attachEmbed() runs — the embed-db opens
+    // late, but the watcher boots early so file events from boot-time
+    // edits are captured.
+    ocrPdfs;
+    ocrLangs;
+    ocrMaxPages;
+    // v3.9.0-rc.2 — HNSW in-memory live update wiring. The watcher
+    // boots before HNSW initializes (similar pattern to embedDb above),
+    // so attachHnsw() is the late-binding entry point. When wired, every
+    // md/pdf event that mutates embed-db also calls
+    // `hnsw.applyDiff(oldIds, newPoints)` so search reflects the change
+    // immediately (pre-3.9.0 the in-memory HNSW went stale until the
+    // next serve restart rebuilt from the freshly-upserted embed-db).
+    hnsw = null;
+    hnswRowsByLabel = null;
     closed = false;
     constructor(opts) {
         this.vault = opts.vault;
@@ -40,12 +56,48 @@ export class VaultWatcher {
         this.embedDb = opts.embedDb ?? null;
         this.embedder = opts.embedder ?? null;
         this.lateChunkContext = opts.lateChunkContext ?? 0;
+        // v3.9.0-rc.1 — OCR-on-watch wiring. Constructor accepts the flags
+        // but defers validation: when the watcher is built BEFORE attachEmbed
+        // runs (the normal startup order in server.ts), ocrPdfs would fail
+        // the embedDb-required check. Instead, the PDF event handler checks
+        // `ocrPdfs && embedDb && includePdfs` at runtime and skips the OCR
+        // codepath silently if any leg is missing.
+        this.ocrPdfs = opts.ocrPdfs ?? false;
+        this.ocrLangs = opts.ocrLangs ?? "eng";
+        this.ocrMaxPages = opts.ocrMaxPages;
         // v3.8.0-rc.2 R-7 — fail loud if embedDb is wired without embedder.
         // Pre-flight check vs silently no-op'ing the embed sync.
         if (this.embedDb && !this.embedder) {
             throw new Error("VaultWatcher: embedDb wired without embedder — both must be set together");
         }
     }
+    /**
+     * v3.9.0-rc.1 — enable / configure OCR-on-watch after construction.
+     * Called by server.ts after attachEmbed() runs (since OCR fallback
+     * only makes sense once embed-db is wired). Fails loud if includePdfs
+     * is off — without it, PDF events are filtered before the OCR
+     * codepath runs.
+     *
+     * @param enabled - When true, image-only PDFs that pdfjs can't read
+     *   trigger a Tesseract OCR pass; the OCR-derived text feeds the
+     *   normal embed pipeline via embedSinglePdf's preExtractedPages path.
+     * @param langs - Tesseract language pack (default "eng"). Multi-lang
+     *   via `+`, e.g. "eng+rus".
+     * @param maxPages - Page cap for OCR runs. Default 200 (DEFAULT_OCR_MAX_PAGES).
+     */
+    setOcrPdfs(enabled, langs, maxPages) {
+        if (enabled && !this.includePdfs) {
+            throw new Error("VaultWatcher.setOcrPdfs: enabling OCR requires includePdfs=true at construction time");
+        }
+        if (enabled && !this.embedDb) {
+            throw new Error("VaultWatcher.setOcrPdfs: enabling OCR requires embedDb (call attachEmbed first)");
+        }
+        this.ocrPdfs = enabled;
+        if (langs !== undefined)
+            this.ocrLangs = langs;
+        if (maxPages !== undefined)
+            this.ocrMaxPages = maxPages;
+    }
     /**
      * v3.8.0-rc.2 R-7 — attach an embed-db handle + embedder after the
      * watcher has started. Used by `prepareServerDeps` when HNSW context
@@ -65,6 +117,67 @@ export class VaultWatcher {
         this.embedder = embedder;
         this.lateChunkContext = lateChunkContext;
     }
+    /**
+     * v3.9.0-rc.2 — wire an in-memory HNSW index for live updates. After
+     * this call, every md/pdf event that mutates embed-db ALSO updates
+     * the HNSW graph via `hnsw.applyDiff(oldIds, newPoints)` so search
+     * results reflect the change immediately. Pre-3.9.0, the HNSW index
+     * was rebuilt from embed-db only at serve startup; vault edits during
+     * the session left the HNSW stale until restart, and `--use-hnsw`
+     * users saw new content omitted from semantic-search results.
+     *
+     * Must be called AFTER `attachEmbed` (the HNSW + embed-db handles
+     * share a lifecycle — server.ts opens both during HNSW init).
+     *
+     * @param hnsw - the in-memory HNSW index built by server.ts.
+     * @param rowsByLabel - the mutable label→row map shared with
+     *   `searchHybrid` (the live update writes into it so subsequent
+     *   searches see the new chunks).
+     */
+    attachHnsw(hnsw, rowsByLabel) {
+        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;
+    }
+    /**
+     * v3.9.0-rc.2 — internal helper. Apply an embed-db {oldIds, newIds}
+     * diff to the wired HNSW index + rowsByLabel map. Called by both the
+     * md and pdf event handlers after upsertNote / deleteNote returns.
+     * Fail-soft: on any error, logs to stderr and returns — the embed-db
+     * is already updated, so the next serve restart will rebuild HNSW
+     * from the correct state. (Same posture as the watcher's existing
+     * embed-db fail-soft.)
+     */
+    syncHnswForFile(relPath, kind, oldIds, newRows) {
+        if (!this.hnsw || !this.hnswRowsByLabel)
+            return null;
+        try {
+            const result = this.hnsw.applyDiff(oldIds, newRows.map((r) => ({ label: r.id, vector: r.vector })));
+            // 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)
+                this.hnswRowsByLabel.delete(oldId);
+            for (const r of newRows) {
+                this.hnswRowsByLabel.set(r.id, {
+                    rel_path: relPath,
+                    chunk_index: r.chunkIndex,
+                    line_start: r.lineStart,
+                    line_end: r.lineEnd,
+                    text_preview: r.textPreview,
+                    kind
+                });
+            }
+            return result;
+        }
+        catch (err) {
+            if (!this.silent) {
+                process.stderr.write(`enquire: watcher HNSW live-update failed for ${relPath} — ${err instanceof Error ? err.message : String(err)} (search results may be stale until next serve restart)\n`);
+            }
+            return null;
+        }
+    }
     /** Start watching. Resolves once the watcher has reported `ready`. */
     async start() {
         const root = this.vault.root;
@@ -146,9 +259,20 @@ export class VaultWatcher {
             // v3.8.0-rc.2 R-7 — also drop embed-db rows so search results
             // don't surface vectors for deleted notes.
             // v3.8.0-rc.3 R-7 — extended to PDFs (rc.2 was md-only).
+            // v3.9.0-rc.2 — propagate the deletion to the in-memory HNSW
+            // index too via syncHnswForFile (with empty newRows = pure-delete
+            // diff). Pre-3.9.0 HNSW retained deleted-file labels until next
+            // serve restart; semantic-search results would surface vectors
+            // for files no longer in the vault.
+            let unlinkHnswNote = "";
             if (this.embedDb) {
                 try {
-                    this.embedDb.deleteNote(relPath);
+                    const deletedIds = this.embedDb.deleteNote(relPath);
+                    if (deletedIds.length > 0 && this.hnsw) {
+                        const result = this.syncHnswForFile(relPath, "md", deletedIds, []);
+                        if (result)
+                            unlinkHnswNote = ` + hnsw -${result.removed}`;
+                    }
                 }
                 catch (err) {
                     if (!this.silent) {
@@ -158,7 +282,7 @@ export class VaultWatcher {
             }
             if (!this.silent) {
                 const embedNote = this.embedDb ? " + embed-db dropped" : "";
-                process.stderr.write(`enquire: watcher unlink ${relPath} (fts5 dropped${embedNote})\n`);
+                process.stderr.write(`enquire: watcher unlink ${relPath} (fts5 dropped${embedNote}${unlinkHnswNote})\n`);
             }
             return;
         }
@@ -180,19 +304,87 @@ export class VaultWatcher {
                 // because they have no useful embedding content (same v3.7.6 H-4
                 // staleness fix as bulk sync). Fail-soft: embed-db errors don't
                 // fail the watcher event.
+                //
+                // v3.9.0-rc.1 — when `ocrPdfs` is on AND the cheap pdfjs path
+                // returns hasText=false, fall back to Tesseract OCR + feed
+                // OCR-derived pages through embedSinglePdf's new preExtractedPages
+                // mode. Without this, scanned PDFs that change during a serve
+                // session lose their embed rows + slowly degrade hybrid recall
+                // until the next manual `enquire-mcp build-embeddings` run.
                 let pdfEmbedNote = "";
                 if (this.embedDb && this.embedder) {
                     try {
+                        let preExtractedPages;
+                        // OCR fallback path. The cheap pdfjs result already lives in
+                        // `result` (from the FTS5 reindex above); if it's image-only,
+                        // we run Tesseract + use the OCR pages directly.
+                        if (this.ocrPdfs && !result.hasText) {
+                            try {
+                                const { extractPdfWithOcr } = await import("./ocr.js");
+                                const ocrResult = await extractPdfWithOcr(buf, {
+                                    langs: this.ocrLangs,
+                                    ...(this.ocrMaxPages !== undefined ? { maxPages: this.ocrMaxPages } : {})
+                                });
+                                // Filter empty pages so we don't emit `[page: N]\n` blocks
+                                // that the chunker would otherwise group with surrounding
+                                // text. (Tesseract returns isEmpty=true for blank pages.)
+                                preExtractedPages = ocrResult.pages
+                                    .filter((p) => !p.isEmpty)
+                                    .map((p) => ({ pageNumber: p.pageNumber, text: p.text }));
+                                if (preExtractedPages.length === 0) {
+                                    // OCR returned zero pages with text — treat as image-only
+                                    // (drop rows). Don't pass empty preExtractedPages; that
+                                    // would short-circuit to null on the embed-pipeline side.
+                                    preExtractedPages = undefined;
+                                }
+                            }
+                            catch (ocrErr) {
+                                // OCR fails-soft. Log, then fall through to the default
+                                // path (which will treat the PDF as image-only and drop
+                                // stale rows). Common failure: tesseract.js / canvas not
+                                // installed, or language file missing.
+                                if (!this.silent) {
+                                    process.stderr.write(`enquire: watcher PDF OCR failed for ${relPath} — ${ocrErr instanceof Error ? ocrErr.message : String(ocrErr)}\n`);
+                                }
+                            }
+                        }
                         const { embedSinglePdf } = await import("./embed-pipeline.js");
-                        const pdfResult = await embedSinglePdf(this.vault, this.embedder, { relPath, absPath, mtimeMs: stat.mtimeMs }, { lateChunkContext: this.lateChunkContext });
+                        const pdfResult = await embedSinglePdf(this.vault, this.embedder, { relPath, absPath, mtimeMs: stat.mtimeMs }, {
+                            lateChunkContext: this.lateChunkContext,
+                            ...(preExtractedPages ? { preExtractedPages } : {})
+                        });
                         if (pdfResult === null) {
                             // Image-only or zero chunks — drop any stale embed-db rows.
-                            this.embedDb.deleteNote(relPath);
-                            pdfEmbedNote = " + embed-db cleared (image-only or empty)";
+                            const deletedIds = this.embedDb.deleteNote(relPath);
+                            pdfEmbedNote = preExtractedPages
+                                ? " + embed-db cleared (OCR also empty)"
+                                : " + embed-db cleared (image-only or empty)";
+                            // v3.9.0-rc.2 — propagate cleared rows to HNSW live update.
+                            if (deletedIds.length > 0 && this.hnsw) {
+                                const hnswResult = this.syncHnswForFile(relPath, "pdf", deletedIds, []);
+                                if (hnswResult)
+                                    pdfEmbedNote += ` + hnsw -${hnswResult.removed}`;
+                            }
                         }
                         else {
-                            this.embedDb.upsertNote(relPath, stat.mtimeMs, pdfResult.rows, "pdf");
-                            pdfEmbedNote = ` + embed-db upserted (${pdfResult.chunks} chunks, kind=pdf)`;
+                            const { oldIds, newIds } = this.embedDb.upsertNote(relPath, stat.mtimeMs, pdfResult.rows, "pdf");
+                            const sourceLabel = preExtractedPages ? "OCR" : "pdfjs";
+                            pdfEmbedNote = ` + embed-db upserted (${pdfResult.chunks} chunks, kind=pdf, src=${sourceLabel})`;
+                            // v3.9.0-rc.2 — keep HNSW in sync with the embed-db change.
+                            // The newIds array runs parallel to pdfResult.rows (same order)
+                            // so we can zip them into HNSW add-points by index.
+                            if (this.hnsw) {
+                                const hnswResult = this.syncHnswForFile(relPath, "pdf", oldIds, pdfResult.rows.map((r, i) => ({
+                                    id: newIds[i] ?? -1,
+                                    vector: r.vector,
+                                    chunkIndex: r.chunkIndex,
+                                    lineStart: r.lineStart,
+                                    lineEnd: r.lineEnd,
+                                    textPreview: r.textPreview
+                                })));
+                                if (hnswResult)
+                                    pdfEmbedNote += ` + hnsw -${hnswResult.removed}/+${hnswResult.added}`;
+                            }
                         }
                     }
                     catch (err) {
@@ -220,12 +412,32 @@ export class VaultWatcher {
                     const { embedSingleNote } = await import("./embed-pipeline.js");
                     const result = await embedSingleNote(this.vault, this.embedder, { relPath, absPath, mtimeMs: stat.mtimeMs }, { lateChunkContext: this.lateChunkContext });
                     if (result === null) {
-                        this.embedDb.deleteNote(relPath);
+                        const deletedIds = this.embedDb.deleteNote(relPath);
                         embedNote = " + embed-db cleared (empty note)";
+                        // v3.9.0-rc.2 — propagate cleared rows to HNSW live update.
+                        if (deletedIds.length > 0 && this.hnsw) {
+                            const hnswResult = this.syncHnswForFile(relPath, "md", deletedIds, []);
+                            if (hnswResult)
+                                embedNote += ` + hnsw -${hnswResult.removed}`;
+                        }
                     }
                     else {
-                        this.embedDb.upsertNote(relPath, stat.mtimeMs, result.rows);
+                        const { oldIds, newIds } = this.embedDb.upsertNote(relPath, stat.mtimeMs, result.rows);
                         embedNote = ` + embed-db upserted (${result.chunks} chunks)`;
+                        // v3.9.0-rc.2 — keep HNSW in sync. newIds and result.rows run
+                        // parallel (same order), so we zip them into HNSW add-points.
+                        if (this.hnsw) {
+                            const hnswResult = this.syncHnswForFile(relPath, "md", oldIds, result.rows.map((r, i) => ({
+                                id: newIds[i] ?? -1,
+                                vector: r.vector,
+                                chunkIndex: r.chunkIndex,
+                                lineStart: r.lineStart,
+                                lineEnd: r.lineEnd,
+                                textPreview: r.textPreview
+                            })));
+                            if (hnswResult)
+                                embedNote += ` + hnsw -${hnswResult.removed}/+${hnswResult.added}`;
+                        }
                     }
                 }
                 catch (err) {

package/dist/watcher.js.map

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

@@ -43,7 +43,7 @@ The four axes the external audit (#3, 2026-05) called out as decisive — **REST
 | 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)                           | **893**             | (varies)         | (varies)         | (varies)         | (varies)         |
+| Test count (public)                           | **911**             | (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)         |

package/docs/api.md

@@ -2,7 +2,7 @@
 
 **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.
 
-> **Channels:** stable 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. Benchmarks live behind `npm run bench:retrieval` (not a CLI subcommand). This document covers the **v3.8.x stable** surface — see [CHANGELOG.md](../CHANGELOG.md) for the v3.8.0 minor (K-3 readOnlyHint invariant, R-7 watcher embed-db sync, Tier A/B AI/LLM discoverability, 8 new structural invariants) and v3.8.1 retraction (overclaim instance #11 — incorrectly-attributed external audit).
+> **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.
 
 > Versioned dynamically — see [`CHANGELOG.md`](../CHANGELOG.md) for the current release.
 

package/package.json

@@ -1,9 +1,9 @@
 {
   "$schema": "https://json.schemastore.org/package.json",
   "name": "@oomkapwn/enquire-mcp",
-  "version": "3.8.8",
+  "version": "3.9.0-rc.2",
   "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, 893 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, 911 tests, SLSA-3, semver-bound, MIT, zero cloud calls during serve.",
   "type": "module",
   "bin": {
     "enquire-mcp": "dist/index.js"