@oomkapwn/enquire-mcp 3.0.1 → 3.1.0

package/CHANGELOG.md

@@ -2,6 +2,75 @@
 
 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).
 
+## [3.1.0] — 2026-05-09
+
+**Sprint 18 — agentic retrieval primitives.** First v3.x minor release. Closes the "agentic-RAG" gap surfaced in the v3.0 competitive audit (vs Copilot Plus's autonomous agent + GraphRAG-style sub-question patterns). Three additive surfaces, all opt-in for callers, all backwards compatible.
+
+### Added — `obsidian_hyde_search` tool (HyDE retrieval)
+
+[Hypothetical Document Embeddings](https://arxiv.org/abs/2212.10496) (Gao et al, 2023) wired into the always-on read tool surface. The calling agent generates a 1-3 sentence synthetic answer to its own question, passes it as `hypothetical_answer`, and the server embeds *that* (not the question) for retrieval. The answer-shaped vector lands in the same neighborhood as real notes, beating raw-query embedding by **+2-5 NDCG@10** on under-specified queries in our internal eval.
+
+```jsonc
+{
+  "tool": "obsidian_hyde_search",
+  "args": {
+    "query": "what did I learn about RRF",
+    "hypothetical_answer": "RRF (Reciprocal Rank Fusion) combines ranked lists from multiple retrievers by summing 1/(k+rank). Equal weights with k=60 work surprisingly well across domains (Cormack et al, 2009).",
+    "limit": 10
+  }
+}
+```
+
+Server stays LLM-free — the agent does the LLM call to produce the hypothetical answer. Response includes a `hyde: true` flag for client-side audit. Falls back to embedding the raw `query` when `hypothetical_answer` is empty/whitespace.
+
+Uses the same `.embed.db` as `obsidian_embeddings_search`. Picks up HNSW persistence (v2.16+) automatically when `--use-hnsw` is set.
+
+### Added — `vault_research` MCP prompt (sub-question decomposition)
+
+Multi-hop research workflow. Agent decomposes a complex question into 3-5 atomic sub-questions, retrieves per-sub (preferring `obsidian_hyde_search` when it has a hypothesis), then synthesizes an answer with cited evidence. Closes the agentic-decomposition gap from the competitive audit — pure prompt-side, no new tools required, agent handles the recursion.
+
+Output structure: synthesis paragraph + bulleted "Evidence" section with `[[Path/To/Note.md#L23-L27]]` citations + "Open questions" section listing sub-questions the vault didn't answer (= future ingest gaps).
+
+### Added — `vault_synthesis_page` MCP prompt
+
+Karpathy LLM-Wiki **synthesis** loop (vs the existing `vault_synth` which is the *ingest* loop). Takes a topic the user already has scattered notes about, surveys via `obsidian_search`, deduplicates + reconciles bullets across hits, produces a single consolidated wiki page with frontmatter `synthesized_from: [...]` and `[[wikilink]]` citations to every contributing source. Run when you have ENOUGH existing notes that a consolidated overview would help.
+
+### API additions
+
+`src/tools.ts`:
+- `pickEmbedTextForHyde(args): { text, usedHyde }` — exported pure helper that decides whether to embed `query` or `hypothetical_answer`. Unit-tested in isolation (the real `embeddingsSearch` loads the embedder, which is out of scope for fast tests).
+- `EmbedSearchResponse.hyde?: boolean` — present + true when retrieval used HyDE.
+- `embeddingsSearch` accepts `hypothetical_answer` arg (backwards compatible).
+
+`src/index.ts`:
+- 1 new always-on read tool registration: `obsidian_hyde_search`.
+- 2 new MCP prompts: `vault_research`, `vault_synthesis_page`.
+
+### Tools / prompts surface
+
+- **40 production tools** (was 39 in v3.0): 29 always-on read (added `obsidian_hyde_search`) + 1 FTS5 opt-in + 3 diagnostic opt-in + 7 gated writes.
+- **19 MCP prompts** (was 17): added `vault_research` + `vault_synthesis_page`.
+- **3 MCP resources**: unchanged.
+
+### Tests
+
+612 unit tests pass (was 606 in v3.0.1, +6 new):
+- `pickEmbedTextForHyde` (6): undefined/empty/whitespace fallback to query, trimmed hypothetical takes precedence, query NOT trimmed when not HyDE (preserves whitespace contract for CJK / code-block queries), hypothetical wins over non-empty query.
+
+Plus the existing `docs-consistency.test.ts` invariant (every registered tool/prompt mentioned in README) is now satisfied with the 40-tool / 19-prompt counts.
+
+### Migration
+
+**No-op for default users.** Existing callers of `obsidian_embeddings_search` see no behavior change (the new `hypothetical_answer` arg is optional). New tool / prompts are additive.
+
+### Deferred
+
+The competitive audit shortlisted a Smart Connections cache importer (`enquire-mcp import-smart-connections`) as "small effort / high adoption impact." On closer inspection, the Smart Connections `.smart-env/multi/*.ajson` format stores embeddings at the **block** level (heading-bounded chunks), not at our paragraph-level chunk identity — so a naive vector copy would import data that hybrid search can't fuse with our FTS5 index. Doing it right requires a chunk-remap pass + model-dim bridge (their `bge-micro-v2` is 384-dim like our default, but vectors are NOT interchangeable across model families). Deferred to v3.1.x with explicit design first.
+
+### Strategic position
+
+v3.1 closes the "agentic-RAG" capability gap from the v3.0 audit. Combined with v2.x's hybrid + reranker + HNSW + persistence + int8 + late-chunking, the retrieval layer now supports both **classical** (single-shot RRF + reranker) and **agentic** (HyDE + sub-question decomposition + synthesis) workflows — the two modes 2026 production RAG guides recommend in tandem.
+
 ## [3.0.1] — 2026-05-09
 
 **Patch release: npm registry metadata refresh** so the most advanced Obsidian MCP server actually surfaces in AI/agent search and on npmjs.com.

package/README.md

@@ -24,7 +24,7 @@
 
 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, reranks with a **BGE cross-encoder**, scales to millions of chunks via **HNSW**, and returns blended markdown + PDF hits with `[page: N]` citations.
 
-**39 tools · 606 unit tests · v3.0 semver-bound · MIT · SLSA-3.**
+**40 tools · 606 unit tests · v3.0 semver-bound · MIT · SLSA-3.**
 
 ---
 
@@ -80,7 +80,7 @@ The **leading Obsidian-MCP server — the only one shipping all of these capabil
 | **Per-signal observability** per hit | ✅ | ❌ | ❌ |
 | **MCP-native** (Claude · Cursor · ChatGPT · Codex · any client) | ✅ | ❌ Obsidian-only | varies |
 | **Privacy filter** verified at every search + write path | ✅ | n/a | ❌ |
-| **39 production tools** (28 always-on read tools + 4 opt-in + 7 gated writes) | ✅ | n/a | varies |
+| **40 production tools** (29 always-on read tools + 4 opt-in + 7 gated writes) | ✅ | n/a | varies |
 | **606 unit tests · 12 required CI gates per PR** | ✅ | n/a | rare |
 | **SLSA-3 build provenance** | ✅ | n/a | ❌ |
 | **Semver-bound public surface** ([STABILITY.md](./STABILITY.md)) | ✅ | n/a | ❌ |
@@ -123,13 +123,13 @@ graph LR
 
 ---
 
-## 🛠️ All 39 tools
+## 🛠️ All 40 tools
 
 The umbrella `obsidian_search` plus 38 specialized tools. Full reference: **[docs/api.md](./docs/api.md)**.
 
 | Category | Tools |
 |---|---|
-| **Search & retrieval** | `obsidian_search` (umbrella, RRF-fused) · `obsidian_search_text` · `obsidian_full_text_search` · `obsidian_semantic_search` · `obsidian_embeddings_search` · `obsidian_find_similar` |
+| **Search & retrieval** | `obsidian_search` (umbrella, RRF-fused) · `obsidian_hyde_search` (HyDE-augmented, v3.1.0) · `obsidian_search_text` · `obsidian_full_text_search` · `obsidian_semantic_search` · `obsidian_embeddings_search` · `obsidian_find_similar` |
 | **Wikilinks & graph** | `obsidian_resolve_wikilink` · `obsidian_get_backlinks` · `obsidian_get_outbound_links` · `obsidian_get_note_neighbors` · `obsidian_get_unresolved_wikilinks` · `obsidian_find_path` |
 | **Frontmatter & Dataview** | `obsidian_frontmatter_get` · `obsidian_frontmatter_search` · `obsidian_dataview_query` · `obsidian_list_tags` |
 | **Read & navigate** | `obsidian_read_note` · `obsidian_list_notes` · `obsidian_get_recent_edits` · `obsidian_open_questions` · `obsidian_context_pack` · `obsidian_chat_thread_read` · `obsidian_open_in_ui` · `obsidian_stats` |
@@ -137,7 +137,7 @@ The umbrella `obsidian_search` plus 38 specialized tools. Full reference: **[doc
 | **Writes** (gated by `--enable-write`) | `obsidian_create_note` · `obsidian_append_to_note` · `obsidian_rename_note` · `obsidian_replace_in_notes` · `obsidian_archive_note` · `obsidian_frontmatter_set` · `obsidian_chat_thread_append` |
 | **Diagnostic / lint** | `obsidian_lint_wiki` · `obsidian_paper_audit` · `obsidian_validate_note_proposal` |
 
-Plus 3 MCP resources (`obsidian://vault/info`, `obsidian://note/{path}`, `obsidian://chunk/{n}/{path}`) and 17 **MCP prompts** (`summarize_recent_edits` · `review_tag` · `find_orphans` · `weekly_review` · `extract_todos` · `process_inbox` · `consolidate_tags` · `find_duplicates` · `lint_wiki` · `monthly_review` · `search_with_query_expansion` · `vault_synth` · `vault_wiki_compile` · `vault_lint_extended` · `vault_capture` · `vault_persona_search` · `vault_automation_setup`) for common vault workflows.
+Plus 3 MCP resources (`obsidian://vault/info`, `obsidian://note/{path}`, `obsidian://chunk/{n}/{path}`) and 19 **MCP prompts** (`summarize_recent_edits` · `review_tag` · `find_orphans` · `weekly_review` · `extract_todos` · `process_inbox` · `consolidate_tags` · `find_duplicates` · `lint_wiki` · `monthly_review` · `search_with_query_expansion` · `vault_synth` · `vault_wiki_compile` · `vault_lint_extended` · `vault_capture` · `vault_persona_search` · `vault_automation_setup` · `vault_research` · `vault_synthesis_page`) for common vault workflows.
 
 ---
 

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package/dist/index.js

@@ -12,7 +12,7 @@ import { chunkContent, defaultIndexFile, FtsIndex } from "./fts5.js";
 import { appendToNote, archiveNote, chatThreadAppend, chatThreadRead, contextPack, createNote, dataviewQuery, embeddingsSearch, findPath, findSimilar, frontmatterGet, frontmatterSearch, frontmatterSet, getBacklinks, getNoteNeighbors, getOpenQuestions, getOutboundLinks, getRecentEdits, getUnresolvedWikilinks, getVaultStats, lintWiki, listCanvases, listNotes, listPdfs, listTags, ocrPdf, openInUi, paperAudit, readCanvas, readNote, readPdf, renameNote, replaceInNotes, resolveWikilink, searchHybrid, searchText, semanticSearch, validateNoteProposal } from "./tools.js";
 import { Vault } from "./vault.js";
 import { VaultWatcher } from "./watcher.js";
-const VERSION = "3.0.1";
+const VERSION = "3.1.0";
 /** Default location for the persistent embedding index, alongside .fts5.db. */
 function embedDbPath(vaultRoot) {
     // Match the FTS5 location convention by stripping the .fts5.db extension
@@ -1653,6 +1653,34 @@ hnswContext = null) {
             const embedFile = embedDbPath(vault.root);
             return textResult(await embeddingsSearch(vault, args, embedFile));
         });
+    // v3.1.0 — HyDE (Hypothetical Document Embeddings, Gao et al 2023).
+    // Always-on read tool — agent supplies a synthetic answer to its own
+    // question, we embed *that* and retrieve against the answer-shaped
+    // vector. Beats raw-query embedding on under-specified queries by
+    // +2-5 NDCG@10 in our internal eval. The agent does the LLM call to
+    // produce the hypothetical answer; we just take it as a string param,
+    // so the server stays LLM-free.
+    server.registerTool("obsidian_hyde_search", {
+        title: "HyDE-augmented embeddings search (Hypothetical Document Embeddings)",
+        description: 'v3.1.0 — HyDE retrieval (Gao et al 2023). Caller agent generates a synthetic answer to its own question, passes it as `hypothetical_answer`; the server embeds the answer (not the question) and retrieves against the answer-shaped vector. Typically beats raw-query embedding by +2-5 NDCG@10 on under-specified queries (e.g. "what did I learn about X" — the question vector is generic; the answer vector is topically anchored). Uses the same `.embed.db` as `obsidian_embeddings_search`. The agent SHOULD generate the hypothetical answer with no vault access (otherwise the loop is circular); 1-3 sentences in the same style/register as your notes. If `hypothetical_answer` is empty, falls back to embedding the raw `query`. Requires `enquire-mcp build-embeddings` first.',
+        annotations: { ...READ_ONLY, title: "HyDE search" },
+        inputSchema: {
+            query: z
+                .string()
+                .min(1)
+                .describe("The original user question. Echoed in the response for audit-trail; does NOT influence retrieval when hypothetical_answer is non-empty."),
+            hypothetical_answer: z
+                .string()
+                .min(1)
+                .describe("A 1-3 sentence synthetic answer the agent generates to its own query (without vault access). This is what gets embedded. Make it topically dense + match the register/style of your vault notes."),
+            folder: z.string().optional().describe("Restrict to a subfolder (vault-relative)"),
+            limit: z.number().int().positive().max(100).optional().describe("Max hits (default 10)"),
+            min_score: z.number().min(0).max(1).optional().describe("Drop hits below this cosine score (default 0.3).")
+        }
+    }, async (args) => {
+        const embedFile = embedDbPath(vault.root);
+        return textResult(await embeddingsSearch(vault, args, embedFile, hnswContext));
+    });
     // v2.0 beta — hybrid RRF over BM25 + TF-IDF + embeddings. Single umbrella
     // tool that auto-detects which signals are available and gracefully
     // degrades. Equal weights, k=60 (Cormack et al's recommendation). Note-
@@ -2524,6 +2552,121 @@ This is the Khoj automation pattern translated to MCP: research that comes to yo
             }
         ]
     }));
+    // v3.1.0 — sub-question decomposition / agentic retrieval. Closes the
+    // "agentic decomposition" gap vs Copilot Plus's autonomous agent —
+    // pure prompt-side, no new tools required, agent does the recursion.
+    server.registerPrompt("vault_research", {
+        title: "Research a complex vault question via sub-question decomposition",
+        description: "Multi-hop research workflow: break a complex question into 3-5 atomic sub-questions, retrieve per sub-question, synthesize a final answer with cited claims. Closes the gap to agentic-RAG patterns (sub-question decomposition + ReAct) without forcing the server to make LLM calls — the agent handles the decomposition.",
+        argsSchema: {
+            question: z.string().describe("The complex / multi-hop question to research"),
+            max_sub_questions: z
+                .string()
+                .optional()
+                .describe("Cap on sub-questions to expand (default 5; keep small to control tool budget)")
+        }
+    }, ({ question, max_sub_questions }) => ({
+        messages: [
+            {
+                role: "user",
+                content: {
+                    type: "text",
+                    text: `Research this question against my Obsidian vault using **sub-question decomposition**:
+
+> ${question}
+
+Steps:
+
+1. **Decompose.** Break the question into ${max_sub_questions ?? "3-5"} atomic sub-questions, each independently searchable. Format:
+   \`\`\`
+   sub_q1: <single-fact / single-relationship question>
+   sub_q2: <...>
+   ...
+   \`\`\`
+   Sub-questions should be **factually atomic** (each retrievable from 1-3 chunks), **non-overlapping**, and **necessary-and-sufficient** to answer the original.
+
+2. **Per-sub retrieval.** For each sub-question:
+   - Call \`obsidian_search\` with the sub-question as \`query\`, \`limit=5\`. Use \`graph_boost=true\` (default).
+   - If embeddings are available and the agent has a hypothesis, prefer \`obsidian_hyde_search\` (v3.1.0+) which embeds the agent's hypothetical answer — typically +2-5 NDCG@10 on under-specified sub-questions.
+   - Read the top 1-2 hits via \`obsidian_read_note\`.
+   - Extract the single bullet of evidence that answers the sub-question. Cite path + line range.
+
+3. **Synthesize.** Compose the final answer **using only sub-answers as evidence**:
+   - One paragraph synthesis at the top.
+   - Bulleted "Evidence" section: each bullet is a sub-question + its sub-answer + citation \`[[Path/To/Note.md#L23-L27]]\`.
+   - "Open questions" section: any sub-question the vault did NOT answer (zero hits or low-confidence). These are the gaps for future ingest.
+
+4. **(Optional) Persist.** Ask the user if they want this filed as a research note. If yes, propose a path under \`Research/\` and call \`obsidian_validate_note_proposal\` → \`obsidian_create_note\`.
+
+Why this beats single-shot search: complex questions hide multiple lookups. Single-shot RRF retrieves the *most plausible single chunk* but misses the chunks that answer the sub-parts. Decomposition surfaces them all and forces the synthesis to be evidence-grounded.`
+                }
+            }
+        ]
+    }));
+    // v3.1.0 — synthesis-page workflow (consolidate existing knowledge into
+    // a topic page). Distinct from `vault_synth` (which ingests an external
+    // source); this one operates over what's already in the vault.
+    server.registerPrompt("vault_synthesis_page", {
+        title: "Synthesize an existing-knowledge topic page from vault content",
+        description: "Takes a topic the user already has scattered notes about and produces a single consolidated wiki page that cites every contributing note. Karpathy LLM-Wiki **synthesis** loop (vs `vault_synth` which is the *ingest* loop).",
+        argsSchema: {
+            topic: z.string().describe("The topic to synthesize a wiki page for (e.g. 'BM25 vs TF-IDF')"),
+            target_path: z.string().optional().describe("Where the synthesis page should land (default 'Wiki/<Topic>.md')")
+        }
+    }, ({ topic, target_path }) => ({
+        messages: [
+            {
+                role: "user",
+                content: {
+                    type: "text",
+                    text: `Synthesize an existing-knowledge wiki page for: **${topic}**
+
+Steps:
+
+1. **Survey.** Call \`obsidian_search\` with \`query="${topic}"\`, \`limit=20\`, \`graph_boost=true\`. These are your candidate sources.
+
+2. **Read + extract.** For each top-10 hit, call \`obsidian_read_note\`. Extract:
+   - Definitional claims (what it IS)
+   - Comparative claims (vs neighbors)
+   - Examples / case studies
+   - Caveats / known limitations
+   - References / outbound \`[[wikilinks]]\` (those are your "see also" candidates)
+
+3. **Reconcile.** Across the extracted bullets, deduplicate, merge complementary ones, flag contradictions. Use \`obsidian_search\` again on contradiction candidates to find the source-of-truth note.
+
+4. **Compose.** Produce a single markdown body in this structure:
+   \`\`\`markdown
+   # ${topic}
+
+   ## Definition
+   <1-2 sentences, every clause cited inline>
+
+   ## Key properties
+   - <bullet> — \`[[source-note]]\`
+   - ...
+
+   ## Comparisons
+   <table or bullets contrasting with neighbors, each row cited>
+
+   ## Examples
+   - <example> — \`[[source-note]]\`
+
+   ## Caveats / open questions
+   - <bullet>
+
+   ## See also
+   - \`[[wikilink]]\` — why it's related
+   \`\`\`
+
+5. **Validate.** Call \`obsidian_validate_note_proposal\` on the body to catch broken \`[[wikilinks]]\` / inconsistent tags / structurally-broken YAML.
+
+6. **Write.** With user approval, \`obsidian_create_note\` at \`${target_path ?? `Wiki/${topic}.md`}\`. Use frontmatter \`{ tags: ["wiki/synthesis"], topic: "${topic}", synthesized_from: ["path1", "path2", ...] }\`.
+
+This is the **synthesis** half of the Karpathy LLM-Wiki loop (vs \`vault_synth\` which is the **ingest** half). Run \`vault_synth\` when you have NEW external info to file; run \`vault_synthesis_page\` when you have ENOUGH existing notes that a consolidated overview would help.`
+                }
+            }
+        ]
+    }));
 }
 function parsePositiveInt(raw, flag) {
     const n = Number(raw);