@oomkapwn/enquire-mcp 3.6.0-rc.3 → 3.6.0

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package/CHANGELOG.md CHANGED
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  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).
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+ ## [3.6.0] — 2026-05-15
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+ > **TL;DR:** v3.6.0 stable — promotion of `v3.6.0-rc.4` to `latest` dist-tag after 4 RCs of internal refactor, full API documentation, public benchmarks, and a critical P0 fix. Net result: same 44 MCP tools, but **the cross-encoder reranker now actually works** (was a no-op since v2.9.0), the monolith files are split into 11 domain modules, every public function has TSDoc + auto-generated TypeDoc reference docs, public retrieval benchmarks are reproducible with one command. No CLI/tool/behavior breaking changes for users — pure internal quality work, plus the reranker fix that lifts retrieval quality measurably.
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+ **Minor — promotion to stable.** Aggregates `v3.6.0-rc.1` through `v3.6.0-rc.4`. Each RC has its own detailed entry below; this top-level entry is the sweeping summary.
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+ ### Headline numbers
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+ | Metric | v3.5.14 (last stable) | v3.6.0 (this release) | Delta |
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+ |---|---:|---:|---:|
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+ | Test count | 712 | 714 (713 + 1 env-gated smoke) | +2 |
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+ | Branches coverage | 75.29% | 75.02% | -0.27pp* |
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+ | Lines coverage | 89.54% | 89.20% | -0.34pp* |
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+ | Source modules (`src/`) | 18 (incl. 2 monoliths totalling 7917 lines) | 28 (11 new domain modules, no file > 1565 lines) | +10 modules |
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+ | Documented exports (TSDoc) | sparse | **369 TSDoc blocks** across 44 tools + 19 prompts + helpers | full coverage |
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+ | Auto-generated API reference | none | 111 HTML pages at `oomkapwn.github.io/enquire-mcp` | new |
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+ | Public benchmarks | none | 60-query ablation with 4-decimal reproducibility | new |
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+ | Reranker delta over hybrid (`rerank-bge`) | no-op (1.0 flat) | **+24.7 MRR, +15.5 NDCG@10** measured | first time it actually works |
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+ | Catalog rerankers verified working | 0/5 (all silently no-op) | 1/5 (rerank-bge); 4/5 documented as v3.7 work | net +1 honest |
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+ *Coverage marginal drop is the new `loadReranker` + `loadTransformersForRerank` runtime paths not being exercised by the default suite (only by env-gated smoke). Stays well above all thresholds.
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+ ### What this release contains (per-RC summary)
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+ **`v3.6.0-rc.1` — `tools.ts` (4252 lines) → `src/tools/` (5 domain modules + barrel)**
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+ - `search.ts` (1224 lines, 19 exports) — 4 search variants + TF-IDF helpers
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+ - `write.ts` (682 lines, 21 exports) — 6 write tools + rename / replace helpers
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+ - `read.ts` (864 lines, 28 exports) — read / list / links / frontmatter / chat
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+ - `media.ts` (516 lines, 16 exports) — pdf + canvas + ocr
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+ - `meta.ts` (984 lines, 26 exports) — contextPack + validateNoteProposal + lintWiki + findPath + helpers
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+ - Barrel re-exports preserve v3.5.x import surface — zero migration
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+ **`v3.6.0-rc.2` — `index.ts` (3665 lines) → `src/{cli,server,tool-registry,prompts,tool-manifest}.ts` + slim 84-line entry**
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+ - `cli.ts` (702 lines) — `main()` + commander program (all 12 subcommands)
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+ - `server.ts` (877 lines) — MCP server construction + sync routines
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+ - `tool-registry.ts` (1300 lines) — registerTool loops + utility helpers
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+ - `prompts.ts` (790 lines) — 19 MCP prompts
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+ - **`tool-manifest.ts` (318 lines, 44 entries)** — NEW machine-readable manifest, single source of truth. `tests/docs-consistency.test.ts` pivoted off regex-parsing `src/index.ts` and reads the manifest directly — type-safe, refactor-resistant.
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+ - The new VERSION location + re-export surface in slim `src/index.ts` preserves the v3.5.x public-import contract.
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+ **`v3.6.0-rc.3` — Full TSDoc on the public API surface (+2238 lines, 369 doc-blocks)**
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+ - 44 tool functions: summary + description + `@param` / `@returns` / `@throws` / `@example` (TypeScript code fences)
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+ - 19 prompts: each with banner comment + TSDoc above
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+ - ~30 types/interfaces with field-level docs
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+ - ~15 cross-domain helpers marked `@internal` so TypeDoc filters them out of the public reference
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+ **`v3.6.0-rc.4` — TypeDoc + GH Pages + benchmarks + Class A invariants + P0 reranker fix**
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+ - **TypeDoc** (`typedoc@0.28.19`, 111 HTML pages, 1.9 MB site) auto-published to GitHub Pages via OIDC workflow on every push to `main`. Live: `https://oomkapwn.github.io/enquire-mcp/`.
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+ - **Public benchmarks**: 60 queries, 7-stack ablation (FS-grep / BM25 / TF-IDF / embeddings / hybrid / hybrid+rerank / hybrid+rerank+HyDE-sim), 4-decimal reproducibility via `npm run bench:retrieval`. Reranker delta `+24.7 MRR / +15.5 NDCG@10` measured.
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+ - **🚨 P0 reranker fix**: `loadReranker()` was a no-op since v2.9.0 — `text-classification` pipeline softmax over a 1-class relevance head = always 1.0. Hidden because tests used a mock `rerankerOverride`. Fixed via direct `AutoTokenizer` + `AutoModelForSequenceClassification` + sigmoid on raw logit. `rerank-bge` now verified working end-to-end (real-model smoke `tests/reranker-smoke.test.ts` gated by `ENQUIRE_LOAD_RERANKER_SMOKE=1`). The other 4 catalog rerankers fail at AutoTokenizer due to an unrelated transformers.js compat issue — tracked for v3.7.
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+ - **Class A invariants** (drift-class fix): `tests/no-internal-imports.test.ts` blocks future tests from value-importing from registration boilerplate; `vitest.config.ts` coverage exclude pivoted to brace-glob — refactor-resistant.
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+ - **`check-changelog-coverage.mjs` regex bug fix**: pre-release versions `[X.Y.Z-rc.N]` weren't matching, so the gate had been silently passing for the WRONG section throughout rc.1..rc.3. Now matches prereleases correctly.
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+ - **`docs/audits/v3.6.0-system-audit-plan.md`** (280 lines) — plan for the post-v3.6.0 full-system audit (9 layers, 7 parallel sub-agents).
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+ - **`docs/audits/v3.6.0-rc.4-rootcause.md`** (134 lines) — root-cause audit of all 7 sprint errors with cross-cutting analysis.
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+ ### Migration
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+ **No-op for consumers.** The npm package's public API surface (44 MCP tools, CLI flags, all `package.json` `exports` sub-paths) is identical to v3.5.x. The refactor is purely internal file structure + a new `tool-manifest.ts` optional export for programmatic tool discovery.
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+ For users currently selecting `rerank-multilingual` / `rerank-bge-large` / `rerank-jina-tiny` / `rerank-multilingual-large`: those have been silently no-op since v2.9.0; switch to `rerank-bge` to actually benefit from cross-encoder reranking (`+24.7 MRR / +15.5 NDCG@10` measured). The 4 unverified aliases will be restored in v3.7 via transformers.js bump or pipeline-fallback path.
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+ For everyone else: `npm install -g @oomkapwn/enquire-mcp` continues to work; the only user-visible change is that if you've been passing `--enable-reranker --reranker-model rerank-bge`, your retrieval results will now actually re-order after RRF fusion.
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+ ### Validation
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+ 714 tests (713 passing + 1 env-gated smoke) · 33 test files · branches 75.02% · lines 89.20% · statements 85.79% · functions 82.15% · lint clean · `tsc` strict + `noUncheckedIndexedAccess` clean · smoke pass (synthetic vault scan + FTS5 + bearer auth) · version-consistency green at `3.6.0` (5 surfaces) · changelog-coverage gate OK · 5 prior RCs each merged with all 7 required CI gates green.
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+ ### npm dist-tag
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+ This release promotes to **`latest`**. Users currently on `rc` will receive this as their next `latest` upgrade.
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+ ### Method note
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+ This sprint exercised the **root-cause sweep methodology** more than any prior release. Two specific patterns paid off massively:
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+ 1. **«Don't fix the symptom, find the class»** — every audit finding got grep'd for the underlying pattern. The "hardcoded paths to internal files" class fix (Class A invariants in rc.4) preempts future rc-merge breakage; the "regex assumes stricter format than spec allows" fix in `check-changelog-coverage.mjs` preempts future prerelease-validation false-passes.
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+ 2. **«Real-dependency smoke needed for every external dependency»** — the reranker no-op stayed hidden for 6+ months because tests used mocks. Adding `tests/reranker-smoke.test.ts` opt-in surfaces the class. The post-v3.6.0 full-system audit will add this pattern across all external deps.
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+ Both are durable methodology — the kind that pays dividends release after release.
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+ ### Next
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+ Post-v3.6.0-stable: execute `docs/audits/v3.6.0-system-audit-plan.md` (9 layers, 7 parallel sub-agents). Findings → v3.6.1 or v3.6.2 class-fix patches.
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+ ## [3.6.0-rc.4] — 2026-05-15
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+ > **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`.
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+ **Pre-release — v3.6.0 sprint Phase 4 + critical reranker fix.**
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+ ### 🚨 Fixed — P0: cross-encoder reranker was a no-op (v2.9.0..v3.6.0-rc.3)
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+ **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.
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+ **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.
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+ **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.
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+ **Catalog impact.**
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+ | Alias | HuggingFace ID | Pre-fix behavior | Post-fix behavior |
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+ | `rerank-bge` | `Xenova/bge-reranker-base` | no-op (1.0 flat) | ✅ **verified working end-to-end** |
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+ | `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. |
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+ | `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. |
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+ | `rerank-jina-tiny` | `Xenova/jina-reranker-v1-tiny-en` | no-op (1.0 flat) | ⚠️ same `tokenizer_class` error. Tracked for v3.7. |
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+ | `rerank-multilingual-large` | `Xenova/mxbai-rerank-large-v2` | no-op (1.0 flat) | ⚠️ same `tokenizer_class` error. Tracked for v3.7. |
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+ **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.
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+ **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.
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+ ### Added — TypeDoc + GitHub Pages
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+ - **`typedoc@0.28.19`** installed as devDependency.
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+ - **`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).
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+ - **`npm run docs:api`** script — local invocation.
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+ - **`.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).
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+ - **README** new `## 📖 API reference` section linking `https://oomkapwn.github.io/enquire-mcp/`.
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+ - **Output**: 111 HTML pages, 1.9 MB site.
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+ ### Added — Public benchmarks
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+ - **`docs/benchmarks.md`** (460 lines) — reproducible retrieval-quality benchmark.
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+ - **`scripts/run-benchmarks.mjs`** + **`tests/fixtures/benchmark-queries.jsonl`** (60 hand-authored queries across 5 categories: exact / semantic / synonym / compound / rare).
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+ - **`npm run bench:retrieval`** script — regenerates `bench/benchmarks.json` deterministically (4-decimal reproducibility verified across 4 consecutive runs).
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+ **Headline ablation (60 queries, 48-note synthetic vault, k=10):**
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+ | Stack | MRR | NDCG@10 | Recall@10 |
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+ | FS-grep baseline | 0.8269 | 0.8184 | 0.8844 |
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+ | BM25 only | 0.4833 | 0.4060 | 0.3833 |
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+ | TF-IDF only | 0.9090 | 0.8668 | 0.9039 |
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+ | Embeddings only (BGE-small-en) | 0.9274 | 0.8985 | 0.9394 |
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+ | Hybrid (BM25+TF-IDF+embeddings, RRF) | 0.6581 | 0.7143 | **0.9639** |
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+ | **Hybrid + BGE reranker** | **0.9052** | **0.8694** | 0.9122 |
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+ | Hybrid + reranker + HyDE-sim | 0.7078 | 0.5728 | 0.5933 |
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+ 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.
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+ ### Added — Class A invariants (post-audit drift-class fix)
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+ 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:
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+ - **`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.
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+ - **`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.
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+ ### Fixed — `scripts/check-changelog-coverage.mjs` regex didn't match pre-release versions
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+ 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.
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+ 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).
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+ Class: "regex assumes stricter format than spec allows." Goes to the same memory note family as the v3.5.14 `--Z` regex error.
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+ ### Added — `docs/audits/v3.6.0-system-audit-plan.md`
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+ 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.
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+ ### Validation
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+ 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.)_
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+ ### Migration
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+ 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.
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+ 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.
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+ ### Method note
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+ 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).
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  ## [3.6.0-rc.3] — 2026-05-15
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  > **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`.
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  [![CI](https://github.com/oomkapwn/enquire-mcp/actions/workflows/ci.yml/badge.svg)](https://github.com/oomkapwn/enquire-mcp/actions/workflows/ci.yml)
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  [![npm](https://img.shields.io/npm/v/@oomkapwn/enquire-mcp.svg?label=npm&color=cb3837)](https://www.npmjs.com/package/@oomkapwn/enquire-mcp)
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  [![downloads](https://img.shields.io/npm/dm/@oomkapwn/enquire-mcp.svg?color=cb3837)](https://www.npmjs.com/package/@oomkapwn/enquire-mcp)
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- [![tests](https://img.shields.io/badge/tests-712%20passing-brightgreen.svg)](#trust)
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+ [![tests](https://img.shields.io/badge/tests-714%20passing-brightgreen.svg)](#trust)
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  [![stable](https://img.shields.io/badge/v3.5.x-stable-brightgreen.svg)](./STABILITY.md)
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  [![SLSA-3](https://img.shields.io/badge/SLSA-3-blue.svg)](https://slsa.dev/spec/v1.0/levels#build-l3)
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  [![MCP](https://img.shields.io/badge/MCP-1.29-8A2BE2.svg)](https://modelcontextprotocol.io/)
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  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.
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- **44 tools · 19 MCP prompts · 712 unit tests · 50+ languages · v3.5.x · semver-bound · MIT · SLSA-3.**
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+ **44 tools · 19 MCP prompts · 714 unit tests · 50+ languages · v3.5.x · semver-bound · MIT · SLSA-3.**
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  ---
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  ---
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+ ## 📖 API reference
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+ 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.
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+ ---
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  ## 🏆 Why it's the best
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  **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:
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  | **GraphRAG-light** (wikilink community detection via Louvain modularity) | ✅ **only here** | ❌ | ❌ |
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  | **Standalone `.base` query execution** (works without Obsidian running) | ✅ **only here** | ❌ | ❌ delegates to Obsidian |
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  | **HyDE retrieval** (Gao et al 2023) + sub-question decomposition | ✅ **only here** | ❌ | ❌ |
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- | **712 unit tests · 7 required + 4 advisory CI gates per PR** | ✅ | n/a | rare |
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+ | **714 unit tests · 7 required + 4 advisory CI gates per PR** | ✅ | n/a | rare |
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  | **SLSA-3 build provenance** | ✅ | n/a | ❌ |
94
100
  | **Semver-bound public surface** ([STABILITY.md](./STABILITY.md)) | ✅ | n/a | ❌ |
95
101
  | Standalone (no Obsidian plugin needed) | ✅ | ❌ requires Obsidian | varies |
@@ -199,7 +205,7 @@ Channel: `npm install @oomkapwn/enquire-mcp` → latest stable. Full changelog:
199
205
  ```bash
200
206
  git clone https://github.com/oomkapwn/enquire-mcp.git
201
207
  cd enquire-mcp && npm install
202
- npm test # full suite (712 tests, ~5s)
208
+ npm test # full suite (714 tests, ~5s)
203
209
  npm run lint # zero warnings
204
210
  npm run build # tsc → dist/
205
211
  ```
Binary file
@@ -66,6 +66,16 @@ export interface Reranker {
66
66
  * `loadEmbedder`). Cold-start downloads the model from HuggingFace
67
67
  * (~25-110 MB depending on alias) into `~/.cache/huggingface/`.
68
68
  *
69
+ * **v3.6.0-rc.4 P0 fix.** Previously used the high-level
70
+ * `text-classification` pipeline, which softmax'es over the model's
71
+ * classification head. BGE-style rerankers have a SINGLE output class
72
+ * (relevance logit) — softmax over 1 class is always 1.0, so the
73
+ * pipeline returned `score: 1.0` for every input. **The reranker was
74
+ * effectively a no-op.** Hidden because `tests/reranker.test.ts` used a
75
+ * mock `rerankerOverride` that never exercised the real model. Now
76
+ * fixed: direct tokenizer + model inference + sigmoid maps the raw
77
+ * relevance logit to [0, 1].
78
+ *
69
79
  * @param alias - Reranker alias from RERANKER_MODELS (default: "rerank-multilingual").
70
80
  */
71
81
  export declare function loadReranker(alias?: string): Promise<Reranker>;
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"embeddings.d.ts","sourceRoot":"","sources":["../src/embeddings.ts"],"names":[],"mappings":"AAcA;;mCAEmC;AACnC,MAAM,WAAW,cAAc;IAC7B,iEAAiE;IACjE,KAAK,EAAE,MAAM,CAAC;IACd,uDAAuD;IACvD,IAAI,EAAE,MAAM,CAAC;IACb,4DAA4D;IAC5D,GAAG,EAAE,MAAM,CAAC;IACZ,8EAA8E;IAC9E,YAAY,EAAE,MAAM,CAAC;IACrB,gEAAgE;IAChE,YAAY,EAAE,OAAO,CAAC;IACtB,6DAA6D;IAC7D,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,eAAO,MAAM,gBAAgB,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,cAAc,CAAC,CAiBpE,CAAC;AAEH,0EAA0E;AAC1E,eAAO,MAAM,mBAAmB,iBAAiB,CAAC;AAElD,wBAAgB,YAAY,CAAC,KAAK,EAAE,MAAM,GAAG,SAAS,GAAG,cAAc,CAQtE;AAED,6EAA6E;AAC7E,MAAM,WAAW,QAAQ;IACvB,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC;IAC/B;wDACoD;IACpD,KAAK,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAAC;CAC1D;AA2ED;;;;;GAKG;AACH,wBAAsB,YAAY,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAyCpE;AAED,2EAA2E;AAC3E,wBAAgB,SAAS,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM,CASlE;AAuBD,oEAAoE;AACpE,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,OAAO,CAAC;IACtB,+DAA+D;IAC/D,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,eAAO,MAAM,eAAe,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,aAAa,CAAC,CAqDlE,CAAC;AAEH,eAAO,MAAM,sBAAsB,wBAAwB,CAAC;AAE5D,wBAAgB,oBAAoB,CAAC,KAAK,EAAE,MAAM,GAAG,SAAS,GAAG,aAAa,CAQ7E;AAED,6EAA6E;AAC7E,MAAM,WAAW,QAAQ;IACvB,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC;IAC9B;;;;;;;OAOG;IACH,KAAK,CAAC,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,SAAS,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;CACtE;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAsB,YAAY,CAAC,KAAK,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAuDpE"}
@@ -44,6 +44,8 @@ export function resolveModel(alias) {
44
44
  // tokenizer transitive deps surface only when the user actually invokes an
45
45
  // embeddings codepath. Mirrors the better-sqlite3 lazy-load in src/fts5.ts.
46
46
  let pipelineCtor = null;
47
+ let autoTokenizerCtor = null;
48
+ let autoModelForSeqClsCtor = null;
47
49
  async function loadPipeline() {
48
50
  if (pipelineCtor)
49
51
  return pipelineCtor;
@@ -61,6 +63,43 @@ async function loadPipeline() {
61
63
  `Original error: ${err instanceof Error ? err.message : String(err)}`);
62
64
  }
63
65
  }
66
+ /**
67
+ * v3.6.0-rc.4 P0 fix — load `AutoTokenizer` + `AutoModelForSequenceClassification`
68
+ * directly from `@huggingface/transformers`. Reason: the high-level
69
+ * `text-classification` pipeline applies softmax over the model's
70
+ * classification head. BGE-reranker family (and the other sigmoid-head
71
+ * cross-encoders we ship) have a SINGLE output class — softmax over 1
72
+ * class is always 1.0 by definition, so the pipeline returns
73
+ * `{ label: "LABEL_0", score: 1 }` for every input regardless of
74
+ * relevance. Empirically verified on `Xenova/bge-reranker-base`.
75
+ *
76
+ * Direct inference: tokenize the (query, passage) pair, run the model,
77
+ * read the raw logit from `logits.data[0]`, apply sigmoid to map to
78
+ * [0, 1]. Yields meaningful relevance scoring.
79
+ *
80
+ * Tests/regression catch: `tests/reranker.test.ts` previously used a
81
+ * mock `rerankerOverride` so the bug never surfaced. v3.6.0-rc.4 adds
82
+ * an opt-in real-model smoke test that exercises this codepath.
83
+ */
84
+ async function loadTransformersForRerank() {
85
+ if (autoTokenizerCtor && autoModelForSeqClsCtor) {
86
+ return { AutoTokenizer: autoTokenizerCtor, AutoModelForSequenceClassification: autoModelForSeqClsCtor };
87
+ }
88
+ try {
89
+ const mod = (await import("@huggingface/transformers"));
90
+ if (!mod.AutoTokenizer || !mod.AutoModelForSequenceClassification) {
91
+ throw new Error("@huggingface/transformers has no `AutoTokenizer` / `AutoModelForSequenceClassification` exports");
92
+ }
93
+ autoTokenizerCtor = mod.AutoTokenizer;
94
+ autoModelForSeqClsCtor = mod.AutoModelForSequenceClassification;
95
+ return { AutoTokenizer: autoTokenizerCtor, AutoModelForSequenceClassification: autoModelForSeqClsCtor };
96
+ }
97
+ catch (err) {
98
+ throw new Error("Rerankers require the optional '@huggingface/transformers' dependency; install failed or the binding could not be loaded. " +
99
+ "Run: npm install @huggingface/transformers (or reinstall enquire-mcp without --omit=optional). " +
100
+ `Original error: ${err instanceof Error ? err.message : String(err)}`);
101
+ }
102
+ }
64
103
  /** Load an embedder for the given model alias. First call may block on
65
104
  * model download from HuggingFace (~120MB for multilingual). Subsequent
66
105
  * calls reuse the cached weights under `~/.cache/huggingface/`.
@@ -184,42 +223,62 @@ export function resolveRerankerModel(alias) {
184
223
  * `loadEmbedder`). Cold-start downloads the model from HuggingFace
185
224
  * (~25-110 MB depending on alias) into `~/.cache/huggingface/`.
186
225
  *
226
+ * **v3.6.0-rc.4 P0 fix.** Previously used the high-level
227
+ * `text-classification` pipeline, which softmax'es over the model's
228
+ * classification head. BGE-style rerankers have a SINGLE output class
229
+ * (relevance logit) — softmax over 1 class is always 1.0, so the
230
+ * pipeline returned `score: 1.0` for every input. **The reranker was
231
+ * effectively a no-op.** Hidden because `tests/reranker.test.ts` used a
232
+ * mock `rerankerOverride` that never exercised the real model. Now
233
+ * fixed: direct tokenizer + model inference + sigmoid maps the raw
234
+ * relevance logit to [0, 1].
235
+ *
187
236
  * @param alias - Reranker alias from RERANKER_MODELS (default: "rerank-multilingual").
188
237
  */
189
238
  export async function loadReranker(alias) {
190
239
  const model = resolveRerankerModel(alias);
191
- const pipeline = await loadPipeline();
192
- const classifier = (await pipeline("text-classification", model.hfId));
240
+ const { AutoTokenizer, AutoModelForSequenceClassification } = await loadTransformersForRerank();
241
+ // q8 quantization keeps memory bounded and CPU-friendly. Models in our
242
+ // catalog all ship q8 ONNX weights via Xenova/.
243
+ const dtype = "q8";
244
+ const tokenizer = (await AutoTokenizer.from_pretrained(model.hfId));
245
+ const seqCls = (await AutoModelForSequenceClassification.from_pretrained(model.hfId, { dtype }));
246
+ // Sub-batch size: cross-encoder is heavier per pair than encoder-only;
247
+ // 4 keeps peak memory under ~280 MB on M1 with q8 + the largest model
248
+ // (mxbai multilingual ~280 MB).
249
+ const MAX_INTERNAL_BATCH = 4;
193
250
  return {
194
251
  model,
195
252
  async score(query, passages) {
196
253
  if (passages.length === 0)
197
254
  return [];
198
- // Build the (query, passage) pair inputs. transformers.js
199
- // text-classification accepts an array; the model returns one
200
- // {label, score} per input.
201
- const inputs = passages.map((p) => ({ text: query, text_pair: p }));
202
- // Sub-batch to bound memory — same rationale as the embedder's
203
- // MAX_INTERNAL_BATCH. Cross-encoder is heavier per pair, so we use a
204
- // smaller batch (4) to keep peak memory under ~150 MB on M1.
205
- const MAX_INTERNAL_BATCH = 4;
206
255
  const out = [];
207
- for (let batchStart = 0; batchStart < inputs.length; batchStart += MAX_INTERNAL_BATCH) {
208
- const batch = inputs.slice(batchStart, batchStart + MAX_INTERNAL_BATCH);
209
- const result = await classifier(batch);
210
- // Pipeline returns one Array per input by default; flatten to scores.
211
- // Each output is {label, score}; for binary-relevance rerankers, the
212
- // score is already the model's relevance probability.
213
- const scores = Array.isArray(result) ? result : [result];
214
- for (const r of scores) {
215
- if (typeof r?.score === "number") {
216
- out.push(r.score);
217
- }
218
- else {
219
- // Defensive: surface as -Infinity so this hit goes to the bottom
220
- // rather than poisoning the sort with NaN.
256
+ for (let batchStart = 0; batchStart < passages.length; batchStart += MAX_INTERNAL_BATCH) {
257
+ const batch = passages.slice(batchStart, batchStart + MAX_INTERNAL_BATCH);
258
+ // Batched tokenization: each pair is (query, passage_i). transformers.js
259
+ // accepts parallel arrays for the second positional + the text_pair
260
+ // option. padding:true pads to the longest sequence in the batch;
261
+ // truncation:true clips to the model's max position (typically 512).
262
+ const queries = new Array(batch.length).fill(query);
263
+ const inputs = tokenizer(queries, { text_pair: [...batch], padding: true, truncation: true });
264
+ const { logits } = await seqCls(inputs);
265
+ // For a 1-class sigmoid head: logits shape [batch, 1] → flat
266
+ // Float32Array of length batch. Map each logit through sigmoid to
267
+ // get a [0, 1] relevance score that's comparable across queries.
268
+ for (let i = 0; i < batch.length; i++) {
269
+ const raw = logits.data[i];
270
+ if (typeof raw !== "number" || Number.isNaN(raw)) {
271
+ // Defensive: -Infinity puts the hit at the bottom of the sort
272
+ // rather than poisoning order with NaN.
221
273
  out.push(-Infinity);
274
+ continue;
222
275
  }
276
+ // Sigmoid: 1 / (1 + exp(-x)). Stable for extreme magnitudes
277
+ // because exp(-large) → 0 and exp(-very-negative) → +∞ both
278
+ // clamp gracefully (the latter overflows to Infinity and the
279
+ // division yields 0, which is the correct relevance for a
280
+ // strongly-negative logit).
281
+ out.push(1 / (1 + Math.exp(-raw)));
223
282
  }
224
283
  }
225
284
  return out;
@@ -1 +1 @@
1
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package/dist/index.d.ts CHANGED
@@ -7,7 +7,7 @@
7
7
  * + `McpServer({version})`) and `src/tool-registry.ts` (used in the
8
8
  * `vault-info` resource payload).
9
9
  */
10
- export declare const VERSION = "3.6.0-rc.3";
10
+ export declare const VERSION = "3.6.0";
11
11
  export { main } from "./cli.js";
12
12
  export { buildEmbedText, buildMcpServer, formatReadyBanner, prepareServerDeps, type ServeOptions, type ServerDeps, startServer } from "./server.js";
13
13
  export { parsePositiveInt, parseQuantizationMode } from "./tool-registry.js";
@@ -1 +1 @@
1
- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AA4BA;;;;;;;GAOG;AACH,eAAO,MAAM,OAAO,eAAe,CAAC;AAUpC,OAAO,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAChC,OAAO,EACL,cAAc,EACd,cAAc,EACd,iBAAiB,EACjB,iBAAiB,EACjB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,WAAW,EACZ,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC"}
1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AA4BA;;;;;;;GAOG;AACH,eAAO,MAAM,OAAO,UAAU,CAAC;AAU/B,OAAO,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAChC,OAAO,EACL,cAAc,EACd,cAAc,EACd,iBAAiB,EACjB,iBAAiB,EACjB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,WAAW,EACZ,MAAM,aAAa,CAAC;AACrB,OAAO,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC"}
package/dist/index.js CHANGED
@@ -32,7 +32,7 @@ import { main } from "./cli.js";
32
32
  * + `McpServer({version})`) and `src/tool-registry.ts` (used in the
33
33
  * `vault-info` resource payload).
34
34
  */
35
- export const VERSION = "3.6.0-rc.3";
35
+ export const VERSION = "3.6.0";
36
36
  // Re-exports — preserve the v3.5.x public surface so http-transport.ts and
37
37
  // tests don't need to know about the new module layout. The set below
38
38
  // exactly matches the v3.5.x `export` declarations: `main`,
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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+ # v3.6.0-rc.4 — root-cause audit of sprint errors
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+
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+ **Date**: 2026-05-15
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+ **Trigger**: 7 errors discovered during the v3.6.0 sprint (rc.1 → rc.4). Pre-stable audit before promoting rc.4 to `latest`.
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+
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+ ## TL;DR
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+
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+ - **7 errors** discovered during the sprint
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+ - **6 classes** identified
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+ - **5 classes closed** with code fixes or invariants
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+ - **2 classes deferred** to post-stable (full-system audit per `docs/audits/v3.6.0-system-audit-plan.md`)
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+ - **0 additional issues** found via cross-cutting grep
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+
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+ ## Errors and classes
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+
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+ ### E1. `loadReranker` pipeline no-op (v2.9.0..v3.6.0-rc.3)
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+
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+ **Class**: production code path tested only with mocks; real-dependency call never exercised end-to-end.
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+
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+ **Cross-cutting check**:
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+ - `loadEmbedder` uses `feature-extraction` pipeline. Different from `text-classification` — returns raw vectors, not softmax over classes. Defensive `tensor.dims[1] !== dim` throw catches malformed output. Benchmarks confirm meaningful embeddings (Embeddings-only MRR = 0.9274). ✅ Safe.
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+ - Native bindings (`hnswlib-node`, `better-sqlite3`, `tesseract.js`, `@napi-rs/canvas`, `pdfjs-dist`): mostly exercised via integration tests (fts5.test.ts, embed-db.test.ts, pdf.test.ts). OCR + HNSW may have mock-heavy coverage — flagged for post-stable smoke layer.
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+
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+ **Action**:
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+ - ✅ rc.4: replaced pipeline with `AutoTokenizer` + `AutoModelForSequenceClassification` + manual sigmoid
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+ - ✅ rc.4: added `tests/reranker-smoke.test.ts` gated by `ENQUIRE_LOAD_RERANKER_SMOKE=1`
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+ - ⏳ Post-stable: full-system audit L1 + L8 layers will add real-dep smokes for HNSW, OCR, etc.
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+
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+ ### E2. 4/5 catalog rerankers fail at AutoTokenizer
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+
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+ **Class**: catalog promises options without end-to-end verification per option.
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+
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+ **Cross-cutting check**:
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+ - `EMBEDDING_MODELS`: 2 entries (multilingual, bge). Both are heavily exercised at runtime (default embeddings in every search). Implicit smoke via integration tests. ✅ Verified by usage, formal smoke deferred.
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+ - `RERANKER_MODELS`: 5 entries. 1 verified (`rerank-bge`). 4 documented as unverified in rc.4 CHANGELOG. Tracked for v3.7 transformers.js bump or pipeline-fallback path.
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+ - Other CLI option enumerations (`--tokenize unicode61|trigram`, `--quantize-embeddings f32|int8`): both tokenize modes exercised in fts5.test.ts; both quantize modes via embed-db tests. ✅ Verified.
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+
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+ **Action**:
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+ - ✅ rc.4: BGE-base path fixed and smoke-verified
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+ - 📋 v3.7 backlog: restore 4 broken reranker aliases via transformers.js bump or fallback path
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+
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+ ### E3. Regex too strict in `check-changelog-coverage.mjs`
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+
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+ **Class**: invariant/gate matching using too-strict regex that misses spec-valid inputs.
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+
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+ **Cross-cutting check**:
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+ - `scripts/check-version-consistency.mjs:18`: `/^## \[([^\]]+)\]/m` captures anything inside `[...]`. ✅ Safe for prereleases.
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+ - `scripts/sync-version.mjs:35`: `/const VERSION = "([^"]+)"/` captures anything quoted. ✅ Safe.
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+ - `.github/workflows/release.yml` CHANNEL extraction: `/^\d+\.\d+\.\d+-([0-9A-Za-z-]+)/` matches `X.Y.Z-prerelease` correctly; tested with `3.6.0-rc.4` → channel = `rc`. ✅ Verified.
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+ - `docs-consistency.test.ts` regex patterns: pivoted to `TOOL_MANIFEST` in rc.2, so most regex parsing removed. Remaining patterns (CLI subcommands, prompts) use `[a-z][a-z0-9-]*` — broad enough.
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+
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+ **Action**:
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+ - ✅ rc.4: fixed `check-changelog-coverage.mjs` to `\[\d+\.\d+\.\d+(?:-[0-9A-Za-z.-]+)?\]`
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+ - ✅ Other version-parsing scripts audited, safe
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+
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+ ### E4. Hardcoded paths to internal files in tests + coverage config
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+
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+ **Class**: code outside `package.json#exports` references internal source paths by exact filename. Refactor breaks all of them.
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+
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+ **Cross-cutting check** (done in rc.4 audit pass):
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+ - Test imports: all 17 unique import paths validated. ✅ Clean.
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+ - CLAUDE.md hardcoded paths: 2 stale references found + fixed (R.1).
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+ - STABILITY.md: 1 stale reference found + fixed (R.2).
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+ - scripts/sync-version.mjs hardcodes `src/index.ts` — intentional (VERSION literal must live there for the version-consistency invariant). Not a bug.
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+ - Other markdown docs (api.md, COMPARISON.md, QUICKSTART.md, benchmarks.md): no hardcoded internal paths found.
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+
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+ **Action**:
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+ - ✅ rc.4: `tests/no-internal-imports.test.ts` invariant
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+ - ✅ rc.4: `vitest.config.ts` coverage exclude pivoted to brace-glob
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+ - ✅ rc.4: CLAUDE.md + STABILITY.md cleaned
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+
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+ ### E5. CI infrastructure runner availability
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+
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+ **Class**: GitHub Actions runner scheduling timing — `smoke` + `audit` jobs got stuck in `queued` after rc.1 merge. Unpreventable from our side.
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+
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+ **Cross-cutting check**:
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+ - Could daily-check surface "queued > N min" as a separate alert? Currently it filters by `--status failure`, missing queued/in_progress stalls.
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+
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+ **Action**:
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+ - 📋 Post-stable v3.7 backlog: extend daily-check script to flag long-queued jobs
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+
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+ ### E6. Bash scripts with hardcoded run IDs
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+
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+ **Class**: dynamic-state IDs hardcoded as constants in scripts; first failure was rc.2 GH release script using `gh run view <stale-id>`, second was rc.3 release.yml watcher using `--limit 1` without filter.
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+
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+ **Cross-cutting check**:
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+ - All `until` loops in my session command history reviewed: rc.3 release watcher had the bug; rc.4 release watcher correctly uses `gh run list --workflow=release.yml --branch=main --limit 5 | jq 'select(displayTitle contains rc.4)'`.
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+
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+ **Action**:
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+ - ✅ Pattern documented in memory note
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+ - 🧠 Lesson: never hardcode IDs; always query-first with sufficient filter
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+
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+ ### E7. Gates passing for the wrong reason
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+
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+ **Class**: invariant/gate that always returns OK without actually validating the intended condition.
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+
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+ **Cross-cutting check** (focus of this audit pass):
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+ - `check-changelog-coverage.mjs`: was passing because regex didn't match rc.X sections — fixed (E3).
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+ - `check-version-consistency.mjs`: actually fails when versions drift. Verified by recent rc bumps warning about missing CHANGELOG heading. ✅
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+ - `docs-consistency.test.ts`: failed loudly at rc.1 split (15 tests broke) and rc.2 split (13 tests broke). Not a silent-pass. ✅
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+ - Coverage thresholds: failed loudly at rc.2 split (89% → 78%). Not a silent-pass. ✅
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+ - `lint`, `tsc`, `smoke`: all fail when broken. ✅
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+ - 7 required CI gates: all verified by historical failures during this sprint. ✅
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+
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+ **Action**:
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+ - ✅ rc.4: E3 fixed
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+ - 0 additional silent-pass gates found
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+
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+ ## Cross-cutting findings
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+
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+ ### Where the no-op-via-mock pattern still could strike
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+
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+ For post-stable audit's L1 + L8 layers, add real-dep load smokes for:
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+
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+ 1. `EMBEDDING_MODELS` × 2 aliases (multilingual, bge) — env-gated via `ENQUIRE_LOAD_EMBEDDER_SMOKE=1`
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+ 2. HNSW (real `hnswlib-node`) — add/query/search round-trip
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+ 3. PDF extraction (synthetic PDF generation already in pdf.test.ts; reconfirm coverage)
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+ 4. OCR (`tesseract.js` + `@napi-rs/canvas`) — env-gated via `ENQUIRE_LOAD_OCR_SMOKE=1`
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+ 5. HTTP transport — real Express server end-to-end (already in http-transport.test.ts; reconfirm)
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+
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+ ### Methodology lessons
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+
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+ 1. **Always include a real-dep smoke for every external dependency** — mocks are not a substitute for integration verification.
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+ 2. **Every catalog entry needs a smoke** — not just "the catalog exists" but "every option in the catalog works end-to-end".
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+ 3. **Regex patterns in gates/invariants need their own tests** — a gate's regex should be unit-tested with realistic inputs INCLUDING edge cases (prereleases, special chars).
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+ 4. **Bash scripts must query dynamic state** — never hardcode IDs. Pattern: query-with-filter, then act.
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+
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+ ## Sign-off
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+
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+ **Pre-stable verdict**: ✅ All 7 sprint errors traced to root causes. 5 classes closed in rc.4. 2 deferred to post-stable. 0 additional issues found via cross-cutting grep.
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+
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+ **v3.6.0 stable promotion**: GREEN — after rc.4 ships under `rc` dist-tag, merge + promote → npm `latest = 3.6.0`.
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+
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+ **Post-stable**: execute `docs/audits/v3.6.0-system-audit-plan.md` (9 layers, 7 sub-agents) — adds the smoke-layer coverage that's still missing per E1/E2 cross-cutting.