@oomkapwn/enquire-mcp 3.6.0-rc.2 → 3.6.0-rc.4

package/CHANGELOG.md

@@ -2,6 +2,149 @@
 
 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).
 
+## [3.6.0-rc.4] — 2026-05-15
+
+> **TL;DR:** v3.6.0 Phase 4 of 4 — TypeDoc + GitHub Pages auto-publish of API reference, public retrieval benchmarks (60 queries, ablation across 7 stack configs, **+24.7 MRR / +15.5 NDCG@10 reranker delta measured**), Class A invariants for hardcoded-paths, full-system audit plan committed, AND a **P0 fix to the BGE cross-encoder reranker which had been a no-op for all 5 catalog models since v2.9.0**. Published under npm dist-tag `rc`.
+
+**Pre-release — v3.6.0 sprint Phase 4 + critical reranker fix.**
+
+### 🚨 Fixed — P0: cross-encoder reranker was a no-op (v2.9.0..v3.6.0-rc.3)
+
+**The bug.** `src/embeddings.ts:loadReranker()` used the high-level `text-classification` pipeline from `@huggingface/transformers`. The pipeline softmax'es over the model's classification head. BGE-style cross-encoders have a **single output class** (the relevance logit); softmax over 1 class is always 1.0 by definition. The reranker returned `score: 1.0` for every input regardless of query/passage relevance — i.e., it didn't re-order anything. The hybrid-search pipeline downstream sorted by tied 1.0s, so the reranker's contribution was effectively null.
+
+**How it stayed hidden for 6+ months.** `tests/reranker.test.ts` (introduced in v2.9.0) tested the reranker integration by injecting a mock `rerankerOverride` with hand-authored score functions. The mock path verified that `ctx.reranker` was called, that errors surfaced via `signal_errors.reranker`, that scores re-ordered hits. But the REAL model path (`loadReranker()` → pipeline → score) was never tested end-to-end. The bench-driven rediscovery this release (rc.4 benchmarks) finally exercised the real path and surfaced the no-op.
+
+**The fix.** `loadReranker()` now uses `AutoTokenizer.from_pretrained` + `AutoModelForSequenceClassification.from_pretrained` directly, reads the raw relevance logit from `logits.data[i]`, and applies sigmoid `1/(1+exp(-x))` to map to a `[0, 1]` relevance score that's comparable across queries. Empirically: on `Xenova/bge-reranker-base`, a RAG-relevant passage gets score ~0.93 vs an off-topic Tokyo passage at ~0.0001 — a 4-order-of-magnitude discrimination that the old code returned as exactly tied 1.0.
+
+**Catalog impact.**
+| Alias | HuggingFace ID | Pre-fix behavior | Post-fix behavior |
+|---|---|---|---|
+| `rerank-bge` | `Xenova/bge-reranker-base` | no-op (1.0 flat) | ✅ **verified working end-to-end** |
+| `rerank-multilingual` | `Xenova/mxbai-rerank-xsmall-v1` | no-op (1.0 flat) | ⚠️ fails on `AutoTokenizer.from_pretrained` — transformers.js compatibility issue, NOT this fix's regression. Tracked for v3.7. |
+| `rerank-bge-large` | `Xenova/bge-reranker-large` | no-op (1.0 flat) | ⏳ unverified — model download timed out in CI smoke (560 MB). Tracked for v3.7. |
+| `rerank-jina-tiny` | `Xenova/jina-reranker-v1-tiny-en` | no-op (1.0 flat) | ⚠️ same `tokenizer_class` error. Tracked for v3.7. |
+| `rerank-multilingual-large` | `Xenova/mxbai-rerank-large-v2` | no-op (1.0 flat) | ⚠️ same `tokenizer_class` error. Tracked for v3.7. |
+
+**For v3.6.0**: the fix lands for `rerank-bge` (the project's primary documented reranker — also the one the benchmark numbers in `docs/benchmarks.md` are measured against). The 4 other catalog aliases were no-ops before this release and remain non-functional at the model-load layer due to an unrelated transformers.js compatibility issue uncovered by the fix. Users who selected those aliases got the same (broken) behavior they had before; users on `rerank-bge` now get the +24.7 MRR / +15.5 NDCG@10 boost the project always advertised.
+
+**Regression catch.** New `tests/reranker-smoke.test.ts` (opt-in via `ENQUIRE_LOAD_RERANKER_SMOKE=1`) exercises the real model path: every catalog alias must score a RAG-relevant passage HIGHER than an off-topic passage. If the no-op class returns in any form, this test fails.
+
+### Added — TypeDoc + GitHub Pages
+
+- **`typedoc@0.28.19`** installed as devDependency.
+- **`typedoc.json`** at repo root: entry points `src/index.ts`, `src/tools/index.ts`, `src/tool-manifest.ts`. `excludeInternal: true` honors the `@internal` markers from rc.3. Output: `docs/api-reference/` (gitignored — generated content; CI regenerates each release).
+- **`npm run docs:api`** script — local invocation.
+- **`.github/workflows/publish-docs.yml`** (57 lines) — pushes to `main` trigger build + deploy to GitHub Pages via `actions/configure-pages@v6` + `actions/upload-pages-artifact@v5` + `actions/deploy-pages@v5` (OIDC-based).
+- **README** new `## 📖 API reference` section linking `https://oomkapwn.github.io/enquire-mcp/`.
+- **Output**: 111 HTML pages, 1.9 MB site.
+
+### Added — Public benchmarks
+
+- **`docs/benchmarks.md`** (460 lines) — reproducible retrieval-quality benchmark.
+- **`scripts/run-benchmarks.mjs`** + **`tests/fixtures/benchmark-queries.jsonl`** (60 hand-authored queries across 5 categories: exact / semantic / synonym / compound / rare).
+- **`npm run bench:retrieval`** script — regenerates `bench/benchmarks.json` deterministically (4-decimal reproducibility verified across 4 consecutive runs).
+
+**Headline ablation (60 queries, 48-note synthetic vault, k=10):**
+
+| Stack | MRR | NDCG@10 | Recall@10 |
+|---|---|---|---|
+| FS-grep baseline | 0.8269 | 0.8184 | 0.8844 |
+| BM25 only | 0.4833 | 0.4060 | 0.3833 |
+| TF-IDF only | 0.9090 | 0.8668 | 0.9039 |
+| Embeddings only (BGE-small-en) | 0.9274 | 0.8985 | 0.9394 |
+| Hybrid (BM25+TF-IDF+embeddings, RRF) | 0.6581 | 0.7143 | **0.9639** |
+| **Hybrid + BGE reranker** | **0.9052** | **0.8694** | 0.9122 |
+| Hybrid + reranker + HyDE-sim | 0.7078 | 0.5728 | 0.5933 |
+
+The reranker delta (**+24.7 MRR, +15.5 NDCG@10** over plain hybrid) is the measured payoff of the cross-encoder layer on the new (fixed) code path. The HyDE row is simulated with hand-authored hypothetical answers (no LLM call) so it represents a floor rather than realistic LLM-driven HyDE.
+
+### Added — Class A invariants (post-audit drift-class fix)
+
+The audit pass after rc.1+rc.2 identified that 4 of 7 sprint errors had a single root cause: **hardcoded paths to internal modules in code outside `package.json#exports`**. This release closes that class:
+
+- **`tests/no-internal-imports.test.ts`** (NEW) — invariant: test files cannot value-import from `src/{cli,server,tool-registry,prompts}.ts` (registration boilerplate). Future refactor of those files can't break tests by moving content.
+- **`vitest.config.ts`** coverage exclude pivoted from 6 exact paths to a single brace-glob: `src/{index,cli,server,tool-registry,prompts,tool-manifest}.ts` — refactor-resistant.
+
+### Fixed — `scripts/check-changelog-coverage.mjs` regex didn't match pre-release versions
+
+Discovered during rc.4 self-audit: the script's section-detection regex `\[\d+\.\d+\.\d+\]` required the closing bracket immediately after the third version digit. Pre-release headings like `## [3.6.0-rc.4]` have `-rc.4` between the third digit and the closing bracket, so the regex didn't match. The script silently fell through to the first STABLE-semver section (`[3.5.14]`) and validated CHANGELOG against ITS coverage claims — which never drift because they were fixed at write time. **The gate was passing for the wrong reason** during the entire rc.1..rc.3 sequence.
+
+Fixed: regex extended to `\[\d+\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?\]`. Now actually validates the rc.4 section's claims (lines 89.20% / statements 85.79% / functions 82.15% / branches 75.02% — those are what `npm run test:coverage` actually produces on this commit).
+
+Class: "regex assumes stricter format than spec allows." Goes to the same memory note family as the v3.5.14 `--Z` regex error.
+
+### Added — `docs/audits/v3.6.0-system-audit-plan.md`
+
+A 280-line plan for the post-v3.6.0-stable **full-system audit** (9 layers: code / arch / tests / CI/CD / security / docs / ops / reproducibility / process). Includes severity grading, class-identification methodology, failure handling, sign-off criteria. Will be executed when `npm view <pkg> version` reports `3.6.0` and the GH release "v3.6.0" is marked Latest.
+
+### Validation
+
+714 tests (713 passing + 1 skipped, the env-gated reranker smoke) · 33 test files · branches 75.02% · lines 89.20% · statements 85.79% · functions 82.15% · lint clean · `tsc` strict clean · smoke pass · version-consistency green at `3.6.0-rc.4` (5 surfaces). _(Coverage dropped marginally vs rc.3 because the new `loadReranker` + `loadTransformersForRerank` runtime paths aren't exercised by the default test suite — only by the opt-in smoke. Stays well above all thresholds.)_
+
+### Migration
+
+For users actively using a non-`rerank-bge` catalog alias: your reranker has been a no-op since v2.9.0; this release doesn't change that observed behavior (still no-op due to a separate compatibility issue) but at least surfaces it explicitly. Switch to `rerank-bge` to actually benefit from cross-encoder reranking. The 4 broken aliases will be addressed in v3.7 via either a transformers.js bump or a `pipeline`-fallback-with-correct-score-extraction path.
+
+For users on `rerank-bge` (default in many configs): the reranker now actually does what it claims. Expect retrieval results to re-order meaningfully after RRF fusion. The benchmark numbers above quantify the impact.
+
+### Method note
+
+The reranker bug exposes a class we haven't named before: **"tests pass against a mock but the real production code path is untested."** The fix here is the new smoke test gated by env var. As a general pattern: any production code path that goes through an external dependency (HuggingFace model, SQLite, native binding) should have at least ONE end-to-end test that exercises the real dependency, not just a mock. Mocks are useful for fast unit tests; they're not a substitute for integration verification. Added to memory note `method_real_vs_mock_coverage.md` (post-v3.6.0).
+
+## [3.6.0-rc.3] — 2026-05-15
+
+> **TL;DR:** v3.6.0 Phase 3 of 4 — **+2238 lines of Full TSDoc** added across 44 MCP tool functions, 19 prompt definitions, and ~50 exported helpers/types. Every exported function now ships with one-sentence summary + detailed description + `@param` / `@returns` / `@throws` / `@example`. Internal cross-domain helpers marked `@internal` so v3.6.0-rc.4's TypeDoc auto-generation keeps them out of the public surface. Pure documentation addition: 712 tests pass, zero behavior change. Published under npm dist-tag `rc`.
+
+**Pre-release — v3.6.0 sprint Phase 3.**
+
+### Added — Full TSDoc on the public API surface
+
+Every exported function in `src/tools/*` and every prompt in `src/prompts.ts` now has comprehensive TSDoc. Per-file expansion:
+
+| File | Before | After | TSDoc blocks |
+|---|---:|---:|---:|
+| `src/tools/search.ts` | 1224 | 1565 (+341) | 62 |
+| `src/tools/read.ts` | 864 | 1384 (+520) | 111 |
+| `src/tools/write.ts` | 682 | 1094 (+412) | 47 |
+| `src/tools/media.ts` | 516 | 725 (+209) | 53 |
+| `src/tools/meta.ts` | 984 | 1425 (+441) | 76 |
+| `src/prompts.ts` | 790 | 1105 (+315) | 20 |
+| **Total** | **5060** | **7298** | **369 TSDoc blocks** |
+
+The 369 TSDoc blocks include:
+- **44 MCP tool functions** (the public API surface) — each with summary, description distinguishing it from alternatives, `@param` per parameter with type-aware description, `@returns`, `@throws` where applicable, and ` ```ts ``` ` `@example` showing realistic usage.
+- **19 prompt registrations** in `src/prompts.ts` — each with a `// === prompt_name ============` banner header above the registration call + a TSDoc block above the banner describing purpose, expected args (read from `argsSchema`), and intended use case.
+- **~30 exported types/interfaces** (e.g., `SearchHit`, `SearchHybridResponse`, `RenameNoteResult`, `ContextPackResult`) — each with description and field-level docs where the field-doc convention was already in place.
+- **~15 cross-domain helpers** (e.g., `tokenizeForTfidf`, `findBestMatch`, `resolveTarget`, `rewriteRawTarget`, `jaccard`) — marked `@internal` so the v3.6.0-rc.4 TypeDoc pass keeps them out of the public API reference.
+
+Distinct-from cross-references are present where two functions could be confused:
+- `searchText` / `semanticSearch` / `embeddingsSearch` / `searchHybrid` — each TSDoc explicitly contrasts the variant and points readers at `{@link searchHybrid}` as the recommended umbrella entry.
+- `vault_synth` / `vault_synthesis_page` / `vault_research` / `search_with_query_expansion` — prompt-to-prompt cross-references explaining when each is the right pick.
+
+### Validation
+
+712 unit tests pass · branches 75.29% · lines 89.54% · statements 86.07% · functions 82.15% · lint clean · `tsc` strict + `noUncheckedIndexedAccess` clean · smoke pass · version-consistency green at `3.6.0-rc.3` (5 surfaces).
+
+### Migration
+
+**No-op for consumers.** No function signatures changed, no behavior changed, no exports added or removed. Pure documentation addition.
+
+For contributors:
+- IDE hovers now display full descriptions + examples for every tool function.
+- VS Code, Cursor, IntelliJ, Vim+lsp all surface the TSDoc instantly.
+
+### npm dist-tag
+
+Published under **`rc`** dist-tag. Users on `latest` stay on v3.5.14. Try: `npm install @oomkapwn/enquire-mcp@rc`.
+
+### Next RC
+
+`v3.6.0-rc.4`: TypeDoc auto-generation of API reference docs + publish to GitHub Pages. Plus public benchmarks (MRR / NDCG@10 / Recall@K on a BEIR/TREC subset, with comparison vs main competitors).
+
+### Method note
+
+This is the second phase that ships **without any logic change** — pure structural/documentation work that compounds value: the TSDoc written here becomes the source for rc.4's auto-generated API docs site. The maintenance burden going forward is low because the TSDoc lives next to the code (drift requires actively writing wrong docs vs. doing nothing).
+
 ## [3.6.0-rc.2] — 2026-05-15
 
 > **TL;DR:** v3.6.0 Phase 2 of 4 — `src/index.ts` (3665 lines) split into 5 domain modules (`cli.ts` 702 + `server.ts` 877 + `tool-registry.ts` 1300 + `prompts.ts` 790) plus a slim 84-line entry point. NEW `src/tool-manifest.ts` (318 lines, 44 machine-readable tool entries) becomes the single source of truth — `tests/docs-consistency.test.ts` pivoted off regex-parsing source code and reads the manifest directly. Pure refactor: same CLI surface, same registered tools, same 712 tests pass. Published under npm dist-tag `rc`.

package/README.md

@@ -11,7 +11,7 @@
 [![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-712%20passing-brightgreen.svg)](#trust)
+[![tests](https://img.shields.io/badge/tests-714%20passing-brightgreen.svg)](#trust)
 [![stable](https://img.shields.io/badge/v3.5.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/)
@@ -29,7 +29,7 @@
 
 A **production-ready MCP server** that gives any AI agent — Claude Code, Claude Desktop, Cursor, ChatGPT custom GPT, Codex, mobile MCP clients — structured access to your Obsidian vault. The umbrella `obsidian_search` tool fuses **BM25 + TF-IDF + multilingual ML embeddings** via Reciprocal Rank Fusion (Cormack et al, 2009), reranks with a **BGE cross-encoder** (5 model options), scales to millions of chunks via **HNSW with int8 quantization**, and returns blended markdown + PDF hits with `[page: N]` citations.
 
-**44 tools · 19 MCP prompts · 712 unit tests · 50+ languages · v3.5.x · semver-bound · MIT · SLSA-3.**
+**44 tools · 19 MCP prompts · 714 unit tests · 50+ languages · v3.5.x · semver-bound · MIT · SLSA-3.**
 
 ---
 
@@ -65,6 +65,12 @@ enquire-mcp doctor --vault <path>    # color-coded ✓/⚠/✗ health check
 
 ---
 
+## 📖 API reference
+
+Auto-generated **[API reference at oomkapwn.github.io/enquire-mcp](https://oomkapwn.github.io/enquire-mcp/)** — every tool, prompt, and exported helper with full TSDoc (`@param` / `@returns` / `@example`). Rebuilt from source on every push to `main` via [`publish-docs.yml`](./.github/workflows/publish-docs.yml) (TypeDoc → GitHub Pages). Drift-free by construction: the same TSDoc that AI agents and IDEs see is what's published.
+
+---
+
 ## 🏆 Why it's the best
 
 **Six features no other Obsidian-MCP has at all** (GraphRAG-light, standalone `.base` execution, HyDE, int8 quantization, late-chunking, built-in eval harness). **Plus the entire modern IR stack** (BM25 + ML embeddings + cross-encoder reranking + HNSW) that competitors ship at most one or two of. Side-by-side:
@@ -89,7 +95,7 @@ enquire-mcp doctor --vault <path>    # color-coded ✓/⚠/✗ health check
 | **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** | ❌ | ❌ |
-| **712 unit tests · 7 required + 4 advisory CI gates per PR** | ✅ | n/a | rare |
+| **714 unit tests · 7 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 |
@@ -199,7 +205,7 @@ 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 (712 tests, ~5s)
+npm test       # full suite (714 tests, ~5s)
 npm run lint   # zero warnings
 npm run build  # tsc → dist/
 ```

package/STABILITY.md

@@ -50,8 +50,9 @@ The package exports a few symbols for advanced embedding / programmatic use. The
 - `EmbedDb` / `EmbedDbOptions` / `EmbedQuantization` / `encodeInt8Vector` / `decodeInt8Vector` (`src/embed-db.ts`)
 - `FtsIndex` / `chunkContent` / `defaultIndexFile` (`src/fts5.ts`)
 - `Vault` (`src/vault.ts`)
-- `ServeOptions` / `parsePositiveInt` / `parseQuantizationMode` / `startServer` / `main` / `buildMcpServer` / `prepareServerDeps` / `formatReadyBanner` / `buildEmbedText` (`src/index.ts`)
+- `ServeOptions` / `parsePositiveInt` / `parseQuantizationMode` / `startServer` / `main` / `buildMcpServer` / `prepareServerDeps` / `formatReadyBanner` / `buildEmbedText` — re-exported from `src/index.ts` (since v3.6.0-rc.2 they live in `src/server.ts` / `src/cli.ts` / `src/tool-registry.ts`, with `src/index.ts` keeping the re-export surface for v3.5.x BC).
 - `HnswIndex` / `loadHnswFromDisk` / `HnswPersistedMeta` (`src/hnsw.ts`)
+- `TOOL_MANIFEST` / `ToolManifestEntry` (`src/tool-manifest.ts`) — machine-readable manifest of all MCP tools (added in v3.6.0-rc.2). New stable surface — guaranteed to retain `name`, `kind`, `gating`, `summary` fields per entry across all v3.x.
 
 Anything not listed here (private fields, internal helpers, test fixtures) is **not** semver-bound.
 

package/dist/embeddings.d.ts

@@ -66,6 +66,16 @@ export interface Reranker {
  * `loadEmbedder`). Cold-start downloads the model from HuggingFace
  * (~25-110 MB depending on alias) into `~/.cache/huggingface/`.
  *
+ * **v3.6.0-rc.4 P0 fix.** Previously used the high-level
+ * `text-classification` pipeline, which softmax'es over the model's
+ * classification head. BGE-style rerankers have a SINGLE output class
+ * (relevance logit) — softmax over 1 class is always 1.0, so the
+ * pipeline returned `score: 1.0` for every input. **The reranker was
+ * effectively a no-op.** Hidden because `tests/reranker.test.ts` used a
+ * mock `rerankerOverride` that never exercised the real model. Now
+ * fixed: direct tokenizer + model inference + sigmoid maps the raw
+ * relevance logit to [0, 1].
+ *
  * @param alias - Reranker alias from RERANKER_MODELS (default: "rerank-multilingual").
  */
 export declare function loadReranker(alias?: string): Promise<Reranker>;

package/dist/embeddings.d.ts.map

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package/dist/embeddings.js

@@ -44,6 +44,8 @@ export function resolveModel(alias) {
 // tokenizer transitive deps surface only when the user actually invokes an
 // embeddings codepath. Mirrors the better-sqlite3 lazy-load in src/fts5.ts.
 let pipelineCtor = null;
+let autoTokenizerCtor = null;
+let autoModelForSeqClsCtor = null;
 async function loadPipeline() {
     if (pipelineCtor)
         return pipelineCtor;
@@ -61,6 +63,43 @@ async function loadPipeline() {
             `Original error: ${err instanceof Error ? err.message : String(err)}`);
     }
 }
+/**
+ * v3.6.0-rc.4 P0 fix — load `AutoTokenizer` + `AutoModelForSequenceClassification`
+ * directly from `@huggingface/transformers`. Reason: the high-level
+ * `text-classification` pipeline applies softmax over the model's
+ * classification head. BGE-reranker family (and the other sigmoid-head
+ * cross-encoders we ship) have a SINGLE output class — softmax over 1
+ * class is always 1.0 by definition, so the pipeline returns
+ * `{ label: "LABEL_0", score: 1 }` for every input regardless of
+ * relevance. Empirically verified on `Xenova/bge-reranker-base`.
+ *
+ * Direct inference: tokenize the (query, passage) pair, run the model,
+ * read the raw logit from `logits.data[0]`, apply sigmoid to map to
+ * [0, 1]. Yields meaningful relevance scoring.
+ *
+ * Tests/regression catch: `tests/reranker.test.ts` previously used a
+ * mock `rerankerOverride` so the bug never surfaced. v3.6.0-rc.4 adds
+ * an opt-in real-model smoke test that exercises this codepath.
+ */
+async function loadTransformersForRerank() {
+    if (autoTokenizerCtor && autoModelForSeqClsCtor) {
+        return { AutoTokenizer: autoTokenizerCtor, AutoModelForSequenceClassification: autoModelForSeqClsCtor };
+    }
+    try {
+        const mod = (await import("@huggingface/transformers"));
+        if (!mod.AutoTokenizer || !mod.AutoModelForSequenceClassification) {
+            throw new Error("@huggingface/transformers has no `AutoTokenizer` / `AutoModelForSequenceClassification` exports");
+        }
+        autoTokenizerCtor = mod.AutoTokenizer;
+        autoModelForSeqClsCtor = mod.AutoModelForSequenceClassification;
+        return { AutoTokenizer: autoTokenizerCtor, AutoModelForSequenceClassification: autoModelForSeqClsCtor };
+    }
+    catch (err) {
+        throw new Error("Rerankers require the optional '@huggingface/transformers' dependency; install failed or the binding could not be loaded. " +
+            "Run: npm install @huggingface/transformers (or reinstall enquire-mcp without --omit=optional). " +
+            `Original error: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
 /** Load an embedder for the given model alias. First call may block on
  *  model download from HuggingFace (~120MB for multilingual). Subsequent
  *  calls reuse the cached weights under `~/.cache/huggingface/`.
@@ -184,42 +223,62 @@ export function resolveRerankerModel(alias) {
  * `loadEmbedder`). Cold-start downloads the model from HuggingFace
  * (~25-110 MB depending on alias) into `~/.cache/huggingface/`.
  *
+ * **v3.6.0-rc.4 P0 fix.** Previously used the high-level
+ * `text-classification` pipeline, which softmax'es over the model's
+ * classification head. BGE-style rerankers have a SINGLE output class
+ * (relevance logit) — softmax over 1 class is always 1.0, so the
+ * pipeline returned `score: 1.0` for every input. **The reranker was
+ * effectively a no-op.** Hidden because `tests/reranker.test.ts` used a
+ * mock `rerankerOverride` that never exercised the real model. Now
+ * fixed: direct tokenizer + model inference + sigmoid maps the raw
+ * relevance logit to [0, 1].
+ *
  * @param alias - Reranker alias from RERANKER_MODELS (default: "rerank-multilingual").
  */
 export async function loadReranker(alias) {
     const model = resolveRerankerModel(alias);
-    const pipeline = await loadPipeline();
-    const classifier = (await pipeline("text-classification", model.hfId));
+    const { AutoTokenizer, AutoModelForSequenceClassification } = await loadTransformersForRerank();
+    // q8 quantization keeps memory bounded and CPU-friendly. Models in our
+    // catalog all ship q8 ONNX weights via Xenova/.
+    const dtype = "q8";
+    const tokenizer = (await AutoTokenizer.from_pretrained(model.hfId));
+    const seqCls = (await AutoModelForSequenceClassification.from_pretrained(model.hfId, { dtype }));
+    // Sub-batch size: cross-encoder is heavier per pair than encoder-only;
+    // 4 keeps peak memory under ~280 MB on M1 with q8 + the largest model
+    // (mxbai multilingual ~280 MB).
+    const MAX_INTERNAL_BATCH = 4;
     return {
         model,
         async score(query, passages) {
             if (passages.length === 0)
                 return [];
-            // Build the (query, passage) pair inputs. transformers.js
-            // text-classification accepts an array; the model returns one
-            // {label, score} per input.
-            const inputs = passages.map((p) => ({ text: query, text_pair: p }));
-            // Sub-batch to bound memory — same rationale as the embedder's
-            // MAX_INTERNAL_BATCH. Cross-encoder is heavier per pair, so we use a
-            // smaller batch (4) to keep peak memory under ~150 MB on M1.
-            const MAX_INTERNAL_BATCH = 4;
             const out = [];
-            for (let batchStart = 0; batchStart < inputs.length; batchStart += MAX_INTERNAL_BATCH) {
-                const batch = inputs.slice(batchStart, batchStart + MAX_INTERNAL_BATCH);
-                const result = await classifier(batch);
-                // Pipeline returns one Array per input by default; flatten to scores.
-                // Each output is {label, score}; for binary-relevance rerankers, the
-                // score is already the model's relevance probability.
-                const scores = Array.isArray(result) ? result : [result];
-                for (const r of scores) {
-                    if (typeof r?.score === "number") {
-                        out.push(r.score);
-                    }
-                    else {
-                        // Defensive: surface as -Infinity so this hit goes to the bottom
-                        // rather than poisoning the sort with NaN.
+            for (let batchStart = 0; batchStart < passages.length; batchStart += MAX_INTERNAL_BATCH) {
+                const batch = passages.slice(batchStart, batchStart + MAX_INTERNAL_BATCH);
+                // Batched tokenization: each pair is (query, passage_i). transformers.js
+                // accepts parallel arrays for the second positional + the text_pair
+                // option. padding:true pads to the longest sequence in the batch;
+                // truncation:true clips to the model's max position (typically 512).
+                const queries = new Array(batch.length).fill(query);
+                const inputs = tokenizer(queries, { text_pair: [...batch], padding: true, truncation: true });
+                const { logits } = await seqCls(inputs);
+                // For a 1-class sigmoid head: logits shape [batch, 1] → flat
+                // Float32Array of length batch. Map each logit through sigmoid to
+                // get a [0, 1] relevance score that's comparable across queries.
+                for (let i = 0; i < batch.length; i++) {
+                    const raw = logits.data[i];
+                    if (typeof raw !== "number" || Number.isNaN(raw)) {
+                        // Defensive: -Infinity puts the hit at the bottom of the sort
+                        // rather than poisoning order with NaN.
                         out.push(-Infinity);
+                        continue;
                     }
+                    // Sigmoid: 1 / (1 + exp(-x)). Stable for extreme magnitudes
+                    // because exp(-large) → 0 and exp(-very-negative) → +∞ both
+                    // clamp gracefully (the latter overflows to Infinity and the
+                    // division yields 0, which is the correct relevance for a
+                    // strongly-negative logit).
+                    out.push(1 / (1 + Math.exp(-raw)));
                 }
             }
             return out;

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package/dist/index.d.ts

@@ -7,7 +7,7 @@
  * + `McpServer({version})`) and `src/tool-registry.ts` (used in the
  * `vault-info` resource payload).
  */
-export declare const VERSION = "3.6.0-rc.2";
+export declare const VERSION = "3.6.0-rc.4";
 export { main } from "./cli.js";
 export { buildEmbedText, buildMcpServer, formatReadyBanner, prepareServerDeps, type ServeOptions, type ServerDeps, startServer } from "./server.js";
 export { parsePositiveInt, parseQuantizationMode } from "./tool-registry.js";

package/dist/index.js

@@ -32,7 +32,7 @@ import { main } from "./cli.js";
  * + `McpServer({version})`) and `src/tool-registry.ts` (used in the
  * `vault-info` resource payload).
  */
-export const VERSION = "3.6.0-rc.2";
+export const VERSION = "3.6.0-rc.4";
 // Re-exports — preserve the v3.5.x public surface so http-transport.ts and
 // tests don't need to know about the new module layout. The set below
 // exactly matches the v3.5.x `export` declarations: `main`,

package/dist/prompts.d.ts

@@ -1,3 +1,35 @@
 import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+/**
+ * Register all enquire-mcp prompt templates on the given MCP server.
+ *
+ * Prompts are agent-side orchestration recipes — each one expands into a
+ * structured `user`-role message that tells the LLM how to chain
+ * `obsidian_*` tools to accomplish a higher-level workflow (weekly review,
+ * Karpathy-style wiki maintenance, captcha-style ingest, sub-question
+ * decomposition, etc.). No server-side LLM calls happen here; the prompts
+ * are pure prompt engineering that the calling client surfaces to its own
+ * model.
+ *
+ * Total: 19 prompts grouped roughly into:
+ * - Day-to-day vault hygiene (`summarize_recent_edits`, `weekly_review`,
+ *   `monthly_review`, `extract_todos`, `process_inbox`, `consolidate_tags`,
+ *   `find_orphans`, `find_duplicates`)
+ * - Wiki maintenance (`lint_wiki`, `vault_synth`, `vault_wiki_compile`,
+ *   `vault_lint_extended`, `vault_synthesis_page`)
+ * - Retrieval orchestration (`search_with_query_expansion`, `vault_research`,
+ *   `vault_persona_search`)
+ * - Knowledge capture / automation (`vault_capture`, `vault_automation_setup`)
+ * - Reading-list helpers (`review_tag`)
+ *
+ * Called once at server startup by `tool-registry.ts`.
+ *
+ * @param server - The MCP server to register prompts on. Mutated in place.
+ * @example
+ * ```ts
+ * const server = new McpServer({ name: "enquire-mcp", version: "3.6.0" });
+ * registerPrompts(server);
+ * registerTools(server, vault, ctx);
+ * ```
+ */
 export declare function registerPrompts(server: McpServer): void;
 //# sourceMappingURL=prompts.d.ts.map

package/dist/prompts.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"prompts.d.ts","sourceRoot":"","sources":["../src/prompts.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAGzE;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CA6iCvD"}