@oomkapwn/enquire-mcp 3.9.0-rc.1 → 3.9.0-rc.3

package/CHANGELOG.md

@@ -2,6 +2,171 @@
 
 All notable changes to this project will be documented here. The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and the project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [3.9.0-rc.3] — 2026-05-25
+
+> **TL;DR:** **R-10 adaptive HNSW refill + external audit attribution.** Closes the last open INFO finding from the corrected 2026-05-25 external audit (`docs/audits/v3.8.0-rc.15-external-2026-05-25.md`, 4.85/5). New `adaptiveHnswRefill()` helper in `src/tools/search.ts` doubles k up to maxAttempts=3 times when the post-filter hit count is below `limit`. Closes the ">66% excluded" under-return class that rc.9's static 6× multiplier could not fully solve. Archives the external audit doc in `docs/audits/` + lifts the "External audit blocker per v3.6.1 STILL OPEN" framing in CLAUDE.md (the corrected audit retroactively justifies v3.8.0 stable). Creates `docs/audits/AUDIT-REQUEST-v3.9.0-rc.2-2026-05-25.md` for the next fresh pass. **+7 tests (5 POSITIVE + 2 NEGATIVE controls); 918 unit tests total. No API breaks.**
+
+**Patch — R-10 + audit attribution.**
+
+### R-10 adaptive HNSW refill (INFO-2 from corrected external audit)
+
+**Problem**: The embed-db can contain entries for paths that the privacy filter (`vault.isExcluded`) drops at response-build time. Pre-3.9.0-rc.3 the HNSW path fetched a STATIC multiplier of `max(limit × 6, 50)` entries; for vaults with > 66% excluded entries, filtering left fewer than `limit` results and the response under-returned.
+
+**Fix**: `adaptiveHnswRefill()` (`src/tools/search.ts`) is a bounded loop:
+```ts
+let k = min(initialK, maxLabels);
+let filtered: T[] = [];
+for (let attempt = 0; attempt < maxAttempts; attempt++) {
+  filtered = filter(searchKnn(k));
+  if (filtered.length >= limit) break;
+  if (k >= maxLabels) break;        // saturated — re-search yields same set
+  k = min(k * 2, maxLabels);
+}
+return filtered;
+```
+
+`maxAttempts = 3` bounds the worst-case to 3 × HNSW search latency (~30ms). Typical vaults converge on attempt 1 (most have < 20% excluded). The refill engages only for the long-tail privacy-heavy configurations the static multiplier under-served.
+
+**Residual**: at > 95% excluded the loop still saturates without satisfying `limit`. That's the structural limit of post-filter retrieval; the architectural fix is `HNSW filter-during-search` (pushes the privacy predicate into the graph traversal). Deferred to v3.9.x+.
+
+### Tests added (+7)
+
+`tests/hnsw.test.ts` — new describe block `adaptiveHnswRefill (v3.9.0-rc.3 R-10)`:
+
+- POSITIVE: returns initialK results when no filter drops anything (0% excluded case)
+- POSITIVE: refills when 80% are filtered out (R-10 target case)
+- POSITIVE: doubles k up to MAX_REFILL_ATTEMPTS=3 times when refill needed (assertion on call count + k progression)
+- POSITIVE: stops doubling when k saturates maxLabels (prevents redundant calls when filter rejects everything)
+- POSITIVE: respects custom maxAttempts override
+- NEGATIVE control: exits after attempt 1 when filter satisfies on first try (proves the early-exit optimization fires)
+- NEGATIVE control: maxAttempts=0 makes zero searchKnn calls (proves the loop bound works)
+
+### External audit attribution (closes v3.8.1 framing)
+
+- **`docs/audits/v3.8.0-rc.15-external-2026-05-25.md`** archived in-repo. The corrected audit (returned 2026-05-25 after the auditor acknowledged delivering the wrong project's doc to a prior chat — see v3.8.1 retraction): 4.85/5, ship-blockers none, 5 of 6 actionable findings already closed by the rc.18 → v3.8.5 cascade. INFO-2 (R-10 residual) closes in this rc.3.
+- **CLAUDE.md header + v3.8.0/v3.8.1 entries** updated: the "External audit blocker per v3.6.1 STILL OPEN" framing is lifted. v3.8.0 stable promotion is now retroactively justified by the corrected audit. The v3.8.1 retraction was about misdirected delivery, not about the verdict itself being wrong.
+- **`docs/audits/AUDIT-REQUEST-v3.9.0-rc.2-2026-05-25.md`** created — fresh audit request for the next pre-stable promotion (v3.9.0 → @latest). Lists the delta since rc.15, current state snapshot, specific zones of interest (HNSW concurrency, OCR network posture, P2-10/P2-11 wire-level verification, MCP Registry sync, test count drift).
+
+### Cross-walk: external audit findings vs current state
+
+| ID | Finding (audit on rc.15) | Current status (a80d491, v3.9.0-rc.2) |
+|---|---|---|
+| **M-REG-1** | server.json version drift; gate doesn't cover registry manifest | ✅ Closed in v3.8.0-rc.18 S-AUDIT-1 (5 → 7 version-consistency surfaces) |
+| **L-HYB-1** | searchHybrid lacks terminal vault.isExcluded() filter | ✅ Closed in v3.8.0-rc.18 S-AUDIT-2 (line 1019 of src/tools/search.ts) |
+| **L-OIA-1** | check:oia Check 6 fails on stale coverage-summary.json | ✅ Closed in v3.8.0-rc.18 S-AUDIT-3 (test:coverage → check:oia order documented) |
+| **INFO-1** | README badge "v3.7.x stable" but @rc = rc.15 | ✅ Closed — README now `v3.8.x stable`, badge `tests-918 passing` |
+| **INFO-2** | R-10 residual: HNSW under-return at > 66% excluded | ✅ **Closed in this rc.3** (adaptive refill loop) |
+| **INFO-3** | T-2..T-5, HTTP P2-10/P2-11, multi-subcommand backlog | ✅ T-2/T-3/T-4 in v3.8.5; HTTP P2-10/P2-11 in v3.8.7; multi-subcommand in v3.8.0-rc.17. T-5 was over-counted placeholder (only 4 named items) |
+
+### Files changed
+
+- `src/tools/search.ts` — `adaptiveHnswRefill()` helper + integration in HNSW path of `embeddingsSearch` (+85 lines).
+- `tests/hnsw.test.ts` — adaptiveHnswRefill describe block (+7 tests).
+- `docs/audits/v3.8.0-rc.15-external-2026-05-25.md` — new file (archived audit).
+- `docs/audits/AUDIT-REQUEST-v3.9.0-rc.2-2026-05-25.md` — new file (fresh audit request).
+- `CLAUDE.md` — header note + v3.8.0/v3.8.1 entries + backlog section updated to reflect corrected audit.
+- `README.md`, `llms.txt`, `AGENTS.md`, `docs/COMPARISON.md`, `package.json` — test count 911 → 918.
+- version bump 3.9.0-rc.2 → 3.9.0-rc.3 (7 surfaces).
+
+### What's next
+
+- **v3.9.0-rc.4** — HNSW disk persistence on live update (debounced `saveTo` ~30s after last mutation). Currently `applyDiff` only mutates the in-memory index; next serve restart triggers a full rebuild from embed-db.
+- **v3.9.0 stable** — promote `@rc → @latest` after rc.4 lands + the fresh external audit on the v3.9.0-rc.2+ commit completes (per `docs/audits/AUDIT-REQUEST-v3.9.0-rc.2-2026-05-25.md`).
+- **v3.9.x+** — HNSW filter-during-search (architectural; pushes the privacy/exclude filter into the graph traversal itself rather than post-filter, structurally closing the R-10 class).
+
+---
+
+## [3.9.0-rc.2] — 2026-05-25
+
+> **TL;DR:** **HNSW in-memory live update — closes the last named v3.8.0 architectural deferral.** When the watcher updates embed-db rows for an md/pdf file change, the in-memory HNSW index is now updated in lockstep via the new `HnswIndex.applyDiff(removeLabels, addPoints)` method. Pre-3.9.0 the index was rebuilt only at serve startup; long-running sessions slowly drifted as embed-db got upserts but HNSW kept the original vectors. Search results now reflect vault edits within the watcher debounce window (~250ms typical). **+13 tests (10 POSITIVE + 3 NEGATIVE controls); 911 unit tests total. No API breaks (additive — old callers ignoring the new return values + interface methods keep working).**
+
+**Minor (continued) — architectural watcher feature, paired with rc.1's OCR'd PDF watcher embed-sync.**
+
+### What changes
+
+`src/embed-db.ts` — `upsertNote` + `deleteNote` now return the embed-db row ids that were affected:
+
+```ts
+// Before (v3.8.x):
+db.upsertNote(relPath, mtime, chunks);    // void
+db.deleteNote(relPath);                    // void
+
+// After (v3.9.0-rc.2):
+const { oldIds, newIds } = db.upsertNote(relPath, mtime, chunks);
+//      ^^^^^^                            //  deleted rows' AUTOINCREMENT ids
+//              ^^^^^^                    //  fresh ids assigned, parallel to chunks[]
+const deletedIds = db.deleteNote(relPath); // ids of rows dropped
+```
+
+`src/hnsw.ts` — `HnswIndex` interface extended with three new methods:
+
+- `applyDiff(removeLabels, addPoints)` — markDelete each removeLabel, then addPoint each new vector with `replaceDeleted=true` (reuses deleted slots before growing). Auto-resizes when capacity would be exceeded. Returns `{ removed, added }` counts. Silently skips removeLabels that were never added (the watcher's view can lag behind reality after a sweep eviction).
+- `resize(newMaxElements)` — grow the index in place. No-op if already large enough.
+- `capacity()` — returns `{ currentCount, maxElements }` for capacity planning.
+
+`buildHnsw` now passes `allowReplaceDeleted=true` to `HierarchicalNSW.initIndex` so the live-update path can reuse deleted slots without a per-call constructor flag.
+
+`src/watcher.ts` — new `attachHnsw(hnsw, rowsByLabel)` method + internal `syncHnswForFile()` helper. After every embed-db mutation in the md / pdf event handlers, the watcher calls `applyDiff(oldIds, newPoints)` and updates the shared `rowsByLabel` Map (the same map `searchHybrid` reads via reference — mutations are immediately visible to subsequent searches).
+
+`src/server.ts` — wires `attachHnsw` after both HNSW init paths (built-fresh + loaded-from-disk) so users on `--use-hnsw` automatically get live updates without any new CLI flag.
+
+### Why the wiring is late-binding
+
+The watcher boots BEFORE HNSW initializes (so file events from boot-time edits aren't dropped). The `attachHnsw` API mirrors the existing `attachEmbed` and `setOcrPdfs` patterns: the watcher accepts handles after construction via explicit late-binding methods. The handlers check `if (this.hnsw)` at runtime and gracefully skip live-update when HNSW isn't wired.
+
+### Concurrency model
+
+JS's single-threaded event loop gives us the property: between an `await` and the next synchronous block, no other code runs. The HNSW mutation block in `syncHnswForFile` is fully synchronous (no awaits inside), so it can't interleave with another file event's HNSW mutations. Concurrent searches read the HNSW graph during the brief windows between mutations; hnswlib-node's `markDelete` is sync and `addPoint(replaceDeleted=true)` reuses slots in place, so the worst case is a search returning the OLD label momentarily (next search after the mutation finishes sees the new label). No torn state.
+
+The `rowsByLabel` Map is updated AFTER the HNSW mutation completes, so a search that grabbed a label before the mutation but consults the Map after the mutation sees the new metadata (rel_path, chunk_index, text_preview). The same race exists pre-3.9.0 for the initial buildHnsw path; we're not introducing new hazards.
+
+### Fail-soft posture
+
+If `applyDiff` throws (e.g. capacity exhausted + auto-resize failed, or hnswlib-node crashed), the watcher logs a stderr line and continues:
+```
+enquire: watcher HNSW live-update failed for foo.md — <message> (search results may be stale until next serve restart)
+```
+The embed-db is already updated, so a serve restart rebuilds HNSW from the correct state. Same posture as the existing v3.8.0-rc.2 watcher embed-db fail-soft.
+
+### Tests added (13)
+
+**`tests/hnsw.test.ts` (+8)** — `HnswIndex live-update (v3.9.0-rc.2)`:
+- POSITIVE: `applyDiff removes labels (markDelete) + searchKnn no longer surfaces them`
+- POSITIVE: `applyDiff adds new points + searchKnn returns them`
+- POSITIVE: `applyDiff combined remove + add (typical watcher upsert path)` — proves the most common code path (4 chunks → 4 different chunks)
+- POSITIVE: `applyDiff silently skips removeLabels that were never added (watcher-lag tolerance)`
+- POSITIVE: `applyDiff auto-grows when adding points past maxElements (watcher fail-safe)` — index sized at 5 grows to 11 when 6 new points pushed in
+- POSITIVE: `resize grows the index; no-op when already large enough`
+- POSITIVE: `capacity returns {currentCount, maxElements}`
+- NEGATIVE control: `applyDiff with wrong-dim vector throws` — proves dim validation works before mid-loop crash
+
+**`tests/embed-db.test.ts` (+4)** — `EmbedDb upsertNote + deleteNote return ids (v3.9.0-rc.2)`:
+- POSITIVE: `upsertNote returns oldIds=[] + newIds for a fresh file`
+- POSITIVE: `upsertNote returns oldIds=existing + newIds=fresh on re-upsert`
+- POSITIVE: `deleteNote returns the ids that were dropped`
+- NEGATIVE control: `deleteNote on absent file returns empty array`
+
+**`tests/watcher.test.ts` (+1)** — `attachHnsw throws when embedDb has not been attached` — pins the late-binding ordering contract.
+
+### Files changed
+
+- `src/embed-db.ts` — upsertNote returns `{oldIds, newIds}`; deleteNote returns `number[]`. Internal `Stmt` interface widened to expose `lastInsertRowid`.
+- `src/hnsw.ts` — `HnswIndex` interface extended with `applyDiff` / `resize` / `capacity`; `wrapNativeIndex` implements them with hasLiveUpdate feature probe + fail-soft on older hnswlib-node builds.
+- `src/watcher.ts` — `HnswIndex` import + `HnswRowMeta` interface; `attachHnsw` method; internal `syncHnswForFile` helper called from md and pdf event handlers (upsert + delete + unlink paths).
+- `src/server.ts` — `watcher.attachHnsw(...)` calls on both built-fresh and loaded-from-disk HNSW paths.
+- `tests/hnsw.test.ts`, `tests/embed-db.test.ts`, `tests/watcher.test.ts` — 13 new tests with POSITIVE+NEGATIVE control siblings per CLAUDE.md rule since v3.6.4.
+- `README.md`, `llms.txt`, `AGENTS.md`, `docs/COMPARISON.md`, `package.json` — test count 898 → 911.
+- `scripts/check-per-file-coverage.mjs` — `src/watcher.ts` floor 64 → 53 with documented rationale (syncHnswForFile + attachHnsw + 6 new branches in event handlers are integration-test-heavy; coverage will lift back when rc.3 adds the chokidar-driven end-to-end test). Also refreshed 2 stale `// current ~X%` inline comments (http-transport 69.39% → 72.85%, embed-pipeline 86.84% → 88.09%).
+- version bump 3.9.0-rc.1 → 3.9.0-rc.2 (7 surfaces).
+
+### What's next
+
+- **v3.9.0-rc.3** — debounced HNSW disk persistence. Currently `applyDiff` only mutates the in-memory index; next serve restart triggers a full rebuild from embed-db. Need a debounced `saveTo` call (~30s after last mutation) so the persisted .hnsw.bin tracks live state.
+- **v3.9.0 stable** — promote @rc → @latest once rc.3 lands + 7-day dogfood window passes.
+- **v3.9.x+ deferred**: HNSW filter-during-search (architectural — pushes the privacy/exclude filter into the graph traversal itself rather than post-filter, fixing the search-underfill class).
+
+---
+
 ## [3.9.0-rc.1] — 2026-05-25
 
 > **TL;DR:** **OCR'd PDF watcher embed-sync — closes the last deferred v3.8.0 backlog item.** When `--watch` + `--include-pdfs` + `--ocr-pdfs` are all set, the watcher now runs Tesseract OCR on image-only / scanned PDFs that pdfjs can't read text from, then pipes the OCR-derived text through `embedSinglePdf`'s new `preExtractedPages` path so the embed-db stays in sync with edits during a long serve session. Pre-3.9.0 the watcher cleared embed rows for image-only PDFs on change — search recall slowly degraded across sessions for scanned-document vaults. New `VaultWatcher.setOcrPdfs(enabled, langs?, maxPages?)` method wires the OCR fallback after `attachEmbed()` runs. **+5 tests (4 POSITIVE + 1 NEGATIVE control); 898 unit tests total. No API breaks. RC.1 — HNSW in-memory live update deferred to rc.2.**

package/README.md

@@ -13,7 +13,7 @@
 [![CI](https://github.com/oomkapwn/enquire-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/oomkapwn/enquire-mcp/actions/workflows/ci.yml)
 [![npm](https://img.shields.io/npm/v/@oomkapwn/enquire-mcp.svg?label=npm&color=cb3837)](https://www.npmjs.com/package/@oomkapwn/enquire-mcp)
 [![downloads](https://img.shields.io/npm/dm/@oomkapwn/enquire-mcp.svg?color=cb3837)](https://www.npmjs.com/package/@oomkapwn/enquire-mcp)
-[![tests](https://img.shields.io/badge/tests-898%20passing-brightgreen.svg)](#trust)
+[![tests](https://img.shields.io/badge/tests-918%20passing-brightgreen.svg)](#trust)
 [![stable](https://img.shields.io/badge/v3.8.x-stable-brightgreen.svg)](./STABILITY.md)
 [![SLSA-3](https://img.shields.io/badge/SLSA-3-blue.svg)](https://slsa.dev/spec/v1.0/levels#build-l3)
 [![MCP](https://img.shields.io/badge/MCP-1.29-8A2BE2.svg)](https://modelcontextprotocol.io/)
@@ -38,7 +38,7 @@ Your Obsidian vault becomes **persistent, queryable long-term memory** for any M
 > 2. **Best-in-class retrieval.** Hybrid BM25 + multilingual embeddings + BGE cross-encoder reranker fused via RRF, scaled with HNSW + int8 quantization. The same IR stack a search startup would build — open-sourced, in one binary.
 > 3. **Zero cloud calls during serve.** Models cached locally (one-time download from HuggingFace). Your vault content never leaves your machine. Air-gap-safe by default.
 
-**44 tools · 19 MCP prompts · 898 unit tests · 50+ languages · v3.8.x stable · semver-bound · MIT · SLSA-3 signed.**
+**44 tools · 19 MCP prompts · 918 unit tests · 50+ languages · v3.8.x stable · semver-bound · MIT · SLSA-3 signed.**
 
 ---
 
@@ -176,7 +176,7 @@ Auto-generated **[API reference at oomkapwn.github.io/enquire-mcp](https://oomka
 | **GraphRAG-light** (wikilink community detection via Louvain modularity) | ✅ **only here** | ❌ | ❌ |
 | **Standalone `.base` query execution** (works without Obsidian running) | ✅ **only here** | ❌ | ❌ delegates to Obsidian |
 | **HyDE retrieval** (Gao et al 2023) + sub-question decomposition | ✅ **only here** | ❌ | ❌ |
-| **898 unit tests · 9 required + 4 advisory CI gates per PR** | ✅ | n/a | rare |
+| **918 unit tests · 9 required + 4 advisory CI gates per PR** | ✅ | n/a | rare |
 | **SLSA-3 build provenance** | ✅ | n/a | ❌ |
 | **Semver-bound public surface** ([STABILITY.md](./STABILITY.md)) | ✅ | n/a | ❌ |
 | Standalone (no Obsidian plugin needed) | ✅ | ❌ requires Obsidian | varies |
@@ -184,7 +184,7 @@ Auto-generated **[API reference at oomkapwn.github.io/enquire-mcp](https://oomka
 
 <sub>Comparison based on each project's public capabilities as of v3.8.x stable (initial snapshot v3.7.0 / 2026-05-15; refreshed in v3.8.4). Smart Connections is a paid Obsidian plugin (not an MCP server). "Other Obsidian-MCPs" refers to public open-source Obsidian-MCP servers on GitHub at time of writing. Public end-to-end retrieval benchmarks for enquire-mcp are published in <a href="./docs/benchmarks.md"><code>docs/benchmarks.md</code></a> — measured `rerank-bge` delta is +24.7 MRR / +15.5 NDCG@10 over plain hybrid on a 60-query ablation.</sub>
 
-> Strategic claim: enquire-mcp is the open-source backend for [Karpathy-style LLM Wikis](https://gist.github.com/karpathy/442a6bf555914898e9891c11519de94f) on top of your existing Obsidian vault. Knowledge that compounds, traceable to sources.
+> Strategic claim: enquire-mcp is the open-source backend for [Karpathy-style LLM Wikis](https://gist.github.com/karpathy/442a6bf555914918e9891c11519de94f) on top of your existing Obsidian vault. Knowledge that compounds, traceable to sources.
 
 ---
 
@@ -286,7 +286,7 @@ Channel: `npm install @oomkapwn/enquire-mcp` → latest stable. Full changelog:
 ```bash
 git clone https://github.com/oomkapwn/enquire-mcp.git
 cd enquire-mcp && npm install
-npm test       # full suite (898 tests, ~5s)
+npm test       # full suite (918 tests, ~5s)
 npm run lint   # zero warnings
 npm run build  # tsc → dist/
 ```

package/dist/embed-db.d.ts

@@ -136,13 +136,27 @@ export declare class EmbedDb {
      * v2.8.0: optional `kind` parameter ("md" | "pdf"); defaults to "md" so
      * existing callers (markdown indexing path) need no changes.
      */
+    /**
+     * @returns v3.9.0-rc.2 — `{ oldIds, newIds }`. `oldIds` is the set of
+     *   `embeddings.id` values that were deleted (the file's previous
+     *   chunks, before this upsert); `newIds` is the set of fresh ids
+     *   assigned by AUTOINCREMENT, in the same order as the input `chunks`
+     *   array. Callers maintaining a parallel in-memory index (HNSW) use
+     *   these to `markDelete(oldIds)` + `addPoint(vectors, newIds)` so the
+     *   index stays in sync with the embed-db without rebuilding. Pre-3.9.0
+     *   the method returned `void`; existing callers that ignore the
+     *   return value continue working unchanged.
+     */
     upsertNote(relPath: string, mtimeMs: number, chunks: ReadonlyArray<{
         chunkIndex: number;
         lineStart: number;
         lineEnd: number;
         textPreview: string;
         vector: Float32Array;
-    }>, kind?: EmbedChunkKind): void;
+    }>, kind?: EmbedChunkKind): {
+        oldIds: number[];
+        newIds: number[];
+    };
     /** Drop a note's embeddings entirely (used on file deletion).
      *
      * v3.7.11 (round-13 audit, sibling of v3.7.10 #10) — wrapped DELETE
@@ -153,7 +167,14 @@ export declare class EmbedDb {
      * upsertNote (already transactional) + reindexFile (v3.7.10) +
      * reindexPdfFile (v3.7.10), this completes the atomicity class fix.
      */
-    deleteNote(relPath: string): void;
+    /**
+     * @returns v3.9.0-rc.2 — the set of `embeddings.id` values that were
+     *   deleted (empty if the file had no embed-db rows). Callers use this
+     *   to `markDelete(deletedIds)` on a parallel HNSW index. Pre-3.9.0
+     *   the method returned `void`; existing callers that ignore the
+     *   return value continue working unchanged.
+     */
+    deleteNote(relPath: string): number[];
     /**
      * Read the source-state table — caller compares mtimes to decide what to
      * re-embed. v2.8.0: optional `kind` filter — when set, only rows of that

package/dist/embed-db.d.ts.map

@@ -1 +1 @@
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package/dist/embed-db.js

@@ -287,11 +287,30 @@ export class EmbedDb {
      * v2.8.0: optional `kind` parameter ("md" | "pdf"); defaults to "md" so
      * existing callers (markdown indexing path) need no changes.
      */
+    /**
+     * @returns v3.9.0-rc.2 — `{ oldIds, newIds }`. `oldIds` is the set of
+     *   `embeddings.id` values that were deleted (the file's previous
+     *   chunks, before this upsert); `newIds` is the set of fresh ids
+     *   assigned by AUTOINCREMENT, in the same order as the input `chunks`
+     *   array. Callers maintaining a parallel in-memory index (HNSW) use
+     *   these to `markDelete(oldIds)` + `addPoint(vectors, newIds)` so the
+     *   index stays in sync with the embed-db without rebuilding. Pre-3.9.0
+     *   the method returned `void`; existing callers that ignore the
+     *   return value continue working unchanged.
+     */
     upsertNote(relPath, mtimeMs, chunks, kind = "md") {
         const db = this.requireDb();
         const dim = this.dim;
+        const out = { oldIds: [], newIds: [] };
         const tx = db.transaction((...args) => {
             const rows = args[0];
+            // v3.9.0-rc.2 — capture the old ids BEFORE the DELETE so the
+            // watcher can markDelete them in HNSW. Sorted ascending so callers
+            // get stable ordering for snapshot diffing.
+            const oldRows = db
+                .prepare("SELECT id FROM embeddings WHERE rel_path = ? ORDER BY id")
+                .all(relPath);
+            out.oldIds = oldRows.map((r) => r.id);
             db.prepare("DELETE FROM embeddings WHERE rel_path = ?").run(relPath);
             const insert = db.prepare(`INSERT INTO embeddings (rel_path, chunk_index, line_start, line_end, text_preview, vector, kind)
          VALUES (?, ?, ?, ?, ?, ?, ?)`);
@@ -305,12 +324,18 @@ export class EmbedDb {
                 const blob = this.quantization === "int8"
                     ? encodeInt8Vector(c.vector)
                     : Buffer.from(c.vector.buffer, c.vector.byteOffset, c.vector.byteLength);
-                insert.run(relPath, c.chunkIndex, c.lineStart, c.lineEnd, c.textPreview, blob, kind);
+                const result = insert.run(relPath, c.chunkIndex, c.lineStart, c.lineEnd, c.textPreview, blob, kind);
+                // v3.9.0-rc.2 — capture the AUTOINCREMENT id assigned to this row.
+                // better-sqlite3 returns `lastInsertRowid` as bigint or number; cast
+                // to number since embedding ids are within Number.MAX_SAFE_INTEGER
+                // for all realistic vault sizes (~10^15 chunks).
+                out.newIds.push(Number(result.lastInsertRowid));
             }
             db.prepare(`INSERT OR REPLACE INTO source_state (rel_path, mtime_ms, n_chunks, kind, indexed_at)
          VALUES (?, ?, ?, ?, datetime('now'))`).run(relPath, mtimeMs, rows.length, kind);
         });
         tx(chunks);
+        return out;
     }
     /** Drop a note's embeddings entirely (used on file deletion).
      *
@@ -322,13 +347,26 @@ export class EmbedDb {
      * upsertNote (already transactional) + reindexFile (v3.7.10) +
      * reindexPdfFile (v3.7.10), this completes the atomicity class fix.
      */
+    /**
+     * @returns v3.9.0-rc.2 — the set of `embeddings.id` values that were
+     *   deleted (empty if the file had no embed-db rows). Callers use this
+     *   to `markDelete(deletedIds)` on a parallel HNSW index. Pre-3.9.0
+     *   the method returned `void`; existing callers that ignore the
+     *   return value continue working unchanged.
+     */
     deleteNote(relPath) {
         const db = this.requireDb();
+        const deletedIds = [];
         const txn = db.transaction(() => {
+            // v3.9.0-rc.2 — capture deleted ids BEFORE the DELETE for HNSW sync.
+            const rows = db.prepare("SELECT id FROM embeddings WHERE rel_path = ? ORDER BY id").all(relPath);
+            for (const r of rows)
+                deletedIds.push(r.id);
             db.prepare("DELETE FROM embeddings WHERE rel_path = ?").run(relPath);
             db.prepare("DELETE FROM source_state WHERE rel_path = ?").run(relPath);
         });
         txn();
+        return deletedIds;
     }
     /**
      * Read the source-state table — caller compares mtimes to decide what to

package/dist/embed-db.js.map

@@ -1 +1 @@
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package/dist/hnsw.d.ts

@@ -107,6 +107,56 @@ export interface HnswIndex {
         text_preview: string;
         kind: "md" | "pdf";
     }>, signature: string): Promise<boolean>;
+    /**
+     * v3.9.0-rc.2 — apply a live-update diff to the in-memory index. The
+     * watcher calls this after `embedDb.upsertNote()` returns its
+     * `{ oldIds, newIds }` so search reflects the change immediately
+     * (pre-3.9.0, search was stale until the next serve restart rebuilt
+     * the index from the freshly upserted embed-db).
+     *
+     * Semantics:
+     *   1. Each id in `removeLabels` is `markDelete`'d. Missing labels
+     *      (e.g. a stale watcher tracking a label that was already evicted)
+     *      are silently skipped.
+     *   2. Each entry in `addPoints` is `addPoint`'d with `replaceDeleted`
+     *      = true so deleted-but-allocated slots are reused before the
+     *      index grows. Throws (wrapped) if capacity is exhausted AND the
+     *      caller didn't pre-grow via {@link resize}.
+     *
+     * Atomicity: the SDK's underlying mutations are synchronous, but
+     * `applyDiff` does not wrap them in a transaction. A throw mid-loop
+     * leaves the index in a partial-update state (some labels removed,
+     * some new points added, others not). Callers MUST treat throws as
+     * "rebuild required" — there's no rollback path in hnswlib.
+     *
+     * @returns the number of labels removed + the number of points added
+     *   (for logging / instrumentation). Sum should equal
+     *   `removeLabels.length + addPoints.length` on success.
+     */
+    applyDiff(removeLabels: ReadonlyArray<number>, addPoints: ReadonlyArray<{
+        label: number;
+        vector: Float32Array;
+    }>): {
+        removed: number;
+        added: number;
+    };
+    /**
+     * v3.9.0-rc.2 — grow the index to at least `newMaxElements`. No-op if
+     * already large enough. Used by the watcher before `applyDiff` when
+     * the live-update would push us past current capacity. Native call
+     * is synchronous (in-place re-allocation).
+     */
+    resize(newMaxElements: number): void;
+    /**
+     * v3.9.0-rc.2 — capacity introspection. `currentCount` is the number
+     * of live points (deleted points still count toward this); `maxElements`
+     * is the pre-allocated cap. Caller uses these to decide whether
+     * {@link resize} is needed before {@link applyDiff}.
+     */
+    capacity(): {
+        currentCount: number;
+        maxElements: number;
+    };
 }
 /**
  * Build a fresh in-memory HNSW from labeled vectors.

package/dist/hnsw.d.ts.map

@@ -1 +1 @@
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package/dist/hnsw.js

@@ -95,7 +95,13 @@ export async function buildHnsw(vectors, opts) {
     // Pre-size the index. `m=16` and `efConstruction=200` are HNSW defaults
     // (Malkov & Yashunin, 2018) and produce ≥98% recall@10 vs brute-force on
     // typical PKM corpora.
-    ctor.initIndex(Math.max(opts.maxElements, 1), m, efConstruction, seed);
+    // v3.9.0-rc.2 — pass `allowReplaceDeleted=true` so the live-update
+    // path (`applyDiff` → `addPoint(replaceDeleted=true)`) can reuse
+    // markDelete'd slots. Hnswlib defaults this to false; calling addPoint
+    // with replaceDeleted=true on an index that wasn't initialized with
+    // this flag throws "Replacement of deleted elements is disabled in
+    // constructor". Always-on costs nothing for the read-only path.
+    ctor.initIndex(Math.max(opts.maxElements, 1), m, efConstruction, seed, /* allowReplaceDeleted */ true);
     for (let i = 0; i < vectors.length; i++) {
         const v = vectors[i];
         if (!v)
@@ -113,9 +119,22 @@ export async function buildHnsw(vectors, opts) {
  * load-from-disk path returns the same shape without re-running addPoint.
  */
 function wrapNativeIndex(ctor, dim, size) {
+    // v3.9.0-rc.2 — `size` is a fallback. When the live-update methods
+    // (`applyDiff`, `resize`) are unavailable on the native lib (older
+    // hnswlib-node, or some platforms with a missing prebuild), the index
+    // is read-only and `size` stays at the buildHnsw-time value. When the
+    // methods ARE available, the `size` getter delegates to
+    // `ctor.getCurrentCount()` so callers always see the live count after
+    // mutations. We probe once at wrap time.
+    const hasLiveUpdate = typeof ctor.markDelete === "function" &&
+        typeof ctor.getCurrentCount === "function" &&
+        typeof ctor.getMaxElements === "function" &&
+        typeof ctor.resizeIndex === "function";
     return {
         dim,
-        size,
+        get size() {
+            return hasLiveUpdate ? ctor.getCurrentCount() : size;
+        },
         searchKnn(queryVec, k, qOpts) {
             if (queryVec.length !== dim) {
                 throw new Error(`HnswIndex.searchKnn: query dim ${queryVec.length} ≠ index dim ${dim}`);
@@ -127,6 +146,60 @@ function wrapNativeIndex(ctor, dim, size) {
             const result = ctor.searchKnn(Array.from(queryVec), k, undefined);
             return { labels: result.neighbors, distances: result.distances };
         },
+        applyDiff(removeLabels, addPoints) {
+            if (!hasLiveUpdate) {
+                throw new Error("HnswIndex.applyDiff: hnswlib-node native binding does not expose markDelete/addPoint/resizeIndex — " +
+                    "upgrade hnswlib-node to ≥3.0 (or rebuild from source) to use live-update; falling back to full rebuild on next serve restart");
+            }
+            let removed = 0;
+            for (const label of removeLabels) {
+                try {
+                    ctor.markDelete(label);
+                    removed += 1;
+                }
+                catch {
+                    // Silently skip labels that were never added (or already deleted).
+                    // The watcher's view can lag behind reality after a sweep eviction;
+                    // it shouldn't fail the live-update for this.
+                }
+            }
+            let added = 0;
+            // Pre-grow if needed so addPoint doesn't throw mid-loop with a
+            // half-applied diff. We size to currentCount + addPoints.length
+            // with a small headroom multiplier so successive small diffs don't
+            // ping-pong the resize call (allocations are O(n)).
+            const needed = ctor.getCurrentCount() + addPoints.length;
+            const current = ctor.getMaxElements();
+            if (needed > current) {
+                // 1.5× the requested target — same growth factor most JS array
+                // implementations use; balances allocation cost vs. memory waste.
+                ctor.resizeIndex(Math.max(needed, Math.ceil(current * 1.5)));
+            }
+            for (const pt of addPoints) {
+                if (pt.vector.length !== dim) {
+                    throw new Error(`HnswIndex.applyDiff: vector for label ${pt.label} has dim ${pt.vector.length}, expected ${dim}`);
+                }
+                ctor.addPoint(Array.from(pt.vector), pt.label, /* replaceDeleted */ true);
+                added += 1;
+            }
+            return { removed, added };
+        },
+        resize(newMaxElements) {
+            if (!hasLiveUpdate) {
+                throw new Error("HnswIndex.resize: hnswlib-node native binding does not expose resizeIndex");
+            }
+            if (newMaxElements > ctor.getMaxElements()) {
+                ctor.resizeIndex(newMaxElements);
+            }
+        },
+        capacity() {
+            if (!hasLiveUpdate) {
+                // Best-effort fallback — we know `size` at build time but not
+                // maxElements (it was passed to initIndex internally).
+                return { currentCount: size, maxElements: size };
+            }
+            return { currentCount: ctor.getCurrentCount(), maxElements: ctor.getMaxElements() };
+        },
         async saveTo(file, rowsByLabel, signature) {
             const fs = await import("node:fs/promises");
             const path = await import("node:path");