@oomkapwn/enquire-mcp 2.7.0 → 2.9.0

package/dist/fts5.js

@@ -14,7 +14,7 @@ import { createHash } from "node:crypto";
 import { promises as fs } from "node:fs";
 import * as os from "node:os";
 import * as path from "node:path";
-const SCHEMA_VERSION = 3;
+const SCHEMA_VERSION = 4;
 // Lazy-loaded better-sqlite3 binding so missing native module surfaces only
 // when --persistent-index is actually used.
 //
@@ -133,12 +133,14 @@ export class FtsIndex {
         line_end UNINDEXED,
         tags UNINDEXED,
         raw_content UNINDEXED,
+        kind UNINDEXED,
         tokenize='${tokenizeArg}'
       );
       CREATE TABLE IF NOT EXISTS source_state (
         rel_path TEXT PRIMARY KEY,
         mtime_ms INTEGER NOT NULL,
         n_chunks INTEGER NOT NULL,
+        kind TEXT NOT NULL DEFAULT 'md',
         indexed_at TEXT NOT NULL
       );
     `);
@@ -171,10 +173,19 @@ export class FtsIndex {
      * Diff the on-disk source_state against the live vault snapshot. Returns
      * categorized lists; caller is expected to feed `added` + `updated` paths
      * back into reindexFile() and pass `deleted` to dropFile().
+     *
+     * v2.8.0: optional `kind` filter — when set, the diff only considers
+     * source_state rows of that kind. Lets the markdown-sync and PDF-sync
+     * paths run independently against the same DB without one's "missing
+     * files" being mistakenly deleted by the other. Default `undefined`
+     * means "all kinds" (used by older callers + diff queries that want
+     * a global view).
      */
-    diff(liveEntries) {
+    diff(liveEntries, kind) {
         const db = this.requireDb();
-        const stored = db.prepare("SELECT rel_path, mtime_ms FROM source_state").all();
+        const stored = kind !== undefined
+            ? db.prepare("SELECT rel_path, mtime_ms FROM source_state WHERE kind = ?").all(kind)
+            : db.prepare("SELECT rel_path, mtime_ms FROM source_state").all();
         const storedMap = new Map();
         for (const r of stored)
             storedMap.set(r.rel_path, r.mtime_ms);
@@ -205,12 +216,12 @@ export class FtsIndex {
         db.prepare("DELETE FROM chunks WHERE rel_path = ?").run(relPath);
         db.prepare("DELETE FROM source_state WHERE rel_path = ?").run(relPath);
     }
-    /** Re-chunk a single file, replacing its existing chunks atomically. */
+    /** Re-chunk a single markdown file, replacing its existing chunks atomically. */
     reindexFile(relPath, mtimeMs, content, wikilinkTargets = [], tags = []) {
         const db = this.requireDb();
         const chunks = chunkContent(content);
         db.prepare("DELETE FROM chunks WHERE rel_path = ?").run(relPath);
-        const insert = db.prepare("INSERT INTO chunks (content, rel_path, chunk_index, line_start, line_end, tags, raw_content) VALUES (?, ?, ?, ?, ?, ?, ?)");
+        const insert = db.prepare("INSERT INTO chunks (content, rel_path, chunk_index, line_start, line_end, tags, raw_content, kind) VALUES (?, ?, ?, ?, ?, ?, ?, 'md')");
         // `tags` is a comma-delimited list so the filter LIKE pattern can wrap it
         // with leading/trailing commas for exact-tag matching at query time.
         const tagsSerialized = tags.length ? tags.join(",") : "";
@@ -228,7 +239,36 @@ export class FtsIndex {
             const enriched = `${breadcrumbPrefix}${c.text}${linksSuffix}`;
             insert.run(enriched, relPath, i, c.lineStart, c.lineEnd, tagsSerialized, c.text);
         });
-        db.prepare("INSERT OR REPLACE INTO source_state (rel_path, mtime_ms, n_chunks, indexed_at) VALUES (?, ?, ?, ?)").run(relPath, mtimeMs, chunks.length, new Date().toISOString());
+        db.prepare("INSERT OR REPLACE INTO source_state (rel_path, mtime_ms, n_chunks, kind, indexed_at) VALUES (?, ?, ?, 'md', ?)").run(relPath, mtimeMs, chunks.length, new Date().toISOString());
+        return chunks.length;
+    }
+    /**
+     * v2.8.0 — re-chunk a single PDF, replacing its existing chunks atomically.
+     * Caller pre-extracts page text via `extractPdfText` (src/pdf.ts) so this
+     * method stays decoupled from pdfjs-dist (which is an optionalDependency).
+     *
+     * Page boundaries are preserved as `[page: N]` markers in the joined text
+     * before chunking — the chunker may split a page across chunks or merge
+     * short pages, but the markers travel with the text so search snippets
+     * carry page citations. Same `chunkContent` pipeline as markdown so chunk
+     * IDs match across the BM25 / TF-IDF / embeddings rankers (RRF requires
+     * stable IDs).
+     */
+    reindexPdfFile(relPath, mtimeMs, pages) {
+        const db = this.requireDb();
+        // Join pages with explicit `[page: N]` markers so the chunker can carry
+        // page provenance through. Empty pages (image-only / scanned) still get
+        // a marker so chunks downstream of them can still cite the right page.
+        const joined = pages.map((p) => `[page: ${p.pageNumber}]\n${p.text}`).join("\n\n");
+        const chunks = chunkContent(joined);
+        db.prepare("DELETE FROM chunks WHERE rel_path = ?").run(relPath);
+        const insert = db.prepare("INSERT INTO chunks (content, rel_path, chunk_index, line_start, line_end, tags, raw_content, kind) VALUES (?, ?, ?, ?, ?, '', ?, 'pdf')");
+        chunks.forEach((c, i) => {
+            // No wikilink/tag enrichment for PDFs (they don't have either). The
+            // page marker is already in c.text so it shows up in snippets.
+            insert.run(c.text, relPath, i, c.lineStart, c.lineEnd, c.text);
+        });
+        db.prepare("INSERT OR REPLACE INTO source_state (rel_path, mtime_ms, n_chunks, kind, indexed_at) VALUES (?, ?, ?, 'pdf', ?)").run(relPath, mtimeMs, chunks.length, new Date().toISOString());
         return chunks.length;
     }
     search(rawQuery, opts = {}) {
@@ -262,6 +302,7 @@ export class FtsIndex {
         const sql = `
       SELECT chunks.rel_path AS rel_path, chunks.chunk_index AS chunk_index,
              chunks.line_start AS line_start, chunks.line_end AS line_end,
+             chunks.kind AS kind,
              snippet(chunks, 0, '«', '»', '…', 25) AS snippet,
              bm25(chunks) AS score
       FROM chunks
@@ -277,6 +318,10 @@ export class FtsIndex {
             chunk_index: r.chunk_index,
             line_start: r.line_start,
             line_end: r.line_end,
+            // v2.8.0: kind defaults to "md" for chunks indexed before the schema
+            // bump (legacy DBs auto-rebuild via SCHEMA_VERSION mismatch, but the
+            // null fallback is defense-in-depth).
+            kind: (r.kind === "pdf" ? "pdf" : "md"),
             snippet: r.snippet,
             score: -r.score // BM25 is negative; flip so higher = better for callers
         }));

package/dist/fts5.js.map

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

@@ -19,6 +19,17 @@ export interface ServeOptions {
     disabledTools?: string[];
     enabledTools?: string[];
     diagnosticSearchTools?: boolean;
+    /** v2.8.0 — also index PDFs into FTS5 (and embeddings, if a build-embeddings
+     *  with --include-pdfs ran). Off by default; opt-in because PDF extraction
+     *  is slower than markdown. */
+    includePdfs?: boolean;
+    /** v2.9.0 — enable BGE cross-encoder reranking on top of RRF in
+     *  obsidian_search. Off by default; adds ~30-50ms per query at top-50. */
+    enableReranker?: boolean;
+    /** v2.9.0 — reranker model alias (default "rerank-multilingual"). */
+    rerankerModel?: string;
+    /** v2.9.0 — how many top fused candidates to rerank (default 50). */
+    rerankerTopN?: string;
 }
 declare function main(): Promise<void>;
 /**

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAIA,OAAO,EAAE,SAAS,EAAoB,MAAM,yCAAyC,CAAC;AAMtF,OAAO,EAAkC,QAAQ,EAAE,MAAM,WAAW,CAAC;AAwCrE,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AACnC,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAW5C,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,WAAW,GAAG,SAAS,CAAC;IACnC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,EAAE,CAAC;IACzB,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,qBAAqB,CAAC,EAAE,OAAO,CAAC;IAChC;;mCAE+B;IAC/B,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;8EAC0E;IAC1E,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,qEAAqE;IACrE,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,qEAAqE;IACrE,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAcD,iBAAe,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAsVnC;AAED;;;;;;;;;;GAUG;AACH,MAAM,WAAW,UAAU;IACzB,KAAK,EAAE,KAAK,CAAC;IACb,QAAQ,EAAE,QAAQ,GAAG,IAAI,CAAC;IAC1B,OAAO,EAAE,YAAY,GAAG,IAAI,CAAC;IAC7B,aAAa,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IAC3B,YAAY,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IAC1B,cAAc,EAAE;QAAE,OAAO,EAAE,OAAO,CAAA;KAAE,CAAC;CACtC;AAED;;;;;GAKG;AACH,wBAAsB,iBAAiB,CAAC,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,CAkE/E;AAED;;;;GAIG;AACH,wBAAgB,cAAc,CAAC,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,YAAY,GAAG,SAAS,CA8F9E;AAED,iBAAe,WAAW,CAAC,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,IAAI,CAAC,CAoD5D;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,UAAU,GAAG,MAAM,CAY1D;AAo7DD,iBAAS,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,MAAM,CAM3D;AAsCD,OAAO,EAAE,IAAI,EAAE,gBAAgB,EAAE,WAAW,EAAE,CAAC"}

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, 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 = "2.7.0";
+const VERSION = "2.9.0";
 /** Default location for the persistent embedding index, alongside .fts5.db. */
 function embedDbPath(vaultRoot) {
     // Match the FTS5 location convention by stripping the .fts5.db extension
@@ -43,6 +43,10 @@ async function main() {
         .option("--disabled-tools <name...>", "Skip registration of specific tools by exact name. Useful when you want to expose a smaller surface to a particular agent (e.g. read-only research agent gets only obsidian_search_text + obsidian_read_note). Repeatable. Names are the same as in `tools/list` — `obsidian_*`. Example: `--disabled-tools obsidian_dataview_query obsidian_full_text_search`.")
         .option("--enabled-tools <name...>", "Strict allowlist — when set, ONLY listed tools register. Complement to --disabled-tools (denylist). If both are set: a tool must be in the allowlist AND not in the denylist. Repeatable. Example: `--enabled-tools obsidian_search_text obsidian_read_note obsidian_get_recent_edits`.")
         .option("--diagnostic-search-tools", "Register the four single-ranker search tools (obsidian_search_text, obsidian_full_text_search, obsidian_semantic_search, obsidian_embeddings_search) IN ADDITION to the default obsidian_search hybrid tool. Off by default in v2.0+ — the umbrella obsidian_search auto-detects available signals and produces consistent recall. Enable when you need single-ranker output for diagnostics or A/B benchmarking.")
+        .option("--include-pdfs", 'v2.8.0 — also index PDF files into FTS5 (and embeddings, if `enquire-mcp build-embeddings --include-pdfs` ran). With `--persistent-index`, PDF chunks become first-class hits in `obsidian_search` results, surfaced with `kind: "pdf"` flag. Off by default — opt-in because PDF text extraction is slower than markdown (~50-200ms per page on M1 cold). Requires the `pdfjs-dist` optionalDependency (default-installed unless you used `--omit=optional`).')
+        .option("--enable-reranker", "v2.9.0 — enable BGE cross-encoder reranking on top of RRF in `obsidian_search`. After fusion, top-N candidates (default 50) are re-scored by a cross-encoder model and re-sorted. Adds ~30-50ms per query on M1 CPU; +5-10 NDCG@10 typical for retrieval quality. Off by default — opt-in because the cross-encoder model is downloaded from HuggingFace on first call (~25-110 MB depending on alias). Requires the `@huggingface/transformers` optionalDependency.")
+        .option("--reranker-model <alias>", "v2.9.0 — reranker alias from RERANKER_MODELS. `rerank-multilingual` (default; Xenova/mxbai-rerank-xsmall-v1, ~25 MB, multilingual) or `rerank-bge` (Xenova/bge-reranker-base, ~110 MB, English-only). Only effective with `--enable-reranker`.")
+        .option("--reranker-top-n <n>", "v2.9.0 — how many top RRF-fused candidates to rerank (default 50). Larger N improves recall ceiling but costs more reranker compute (~30-50ms per 50 pairs on M1). Only effective with `--enable-reranker`.")
         .action(async (opts) => {
         await startServer(opts);
     });
@@ -159,6 +163,7 @@ async function main() {
         .requiredOption("--vault <path>", "Path to the Obsidian vault root")
         .option("--index-file <path>", "Override the FTS5 index file location")
         .option("--tokenize <mode>", "FTS5 tokenize mode: 'unicode61' (default) or 'trigram'")
+        .option("--include-pdfs", "v2.8.0 — also index PDFs into the FTS5 index. Off by default; PDF extraction is slower than markdown.")
         .action(async (opts) => {
         const tokenize = opts.tokenize === "trigram" ? "trigram" : "unicode61";
         const vault = new Vault(opts.vault);
@@ -168,7 +173,11 @@ async function main() {
         await idx.open();
         try {
             const report = await syncFtsIndex(vault, idx);
-            process.stdout.write(`enquire: index ${indexFile} — added=${report.added} updated=${report.updated} deleted=${report.deleted} unchanged=${report.unchanged} total_chunks=${report.total_chunks}\n`);
+            process.stdout.write(`enquire: index ${indexFile} (md) — added=${report.added} updated=${report.updated} deleted=${report.deleted} unchanged=${report.unchanged} total_chunks=${report.total_chunks}\n`);
+            if (opts.includePdfs) {
+                const pdfReport = await syncPdfFtsIndex(vault, idx);
+                process.stdout.write(`enquire: index ${indexFile} (pdf) — added=${pdfReport.added} updated=${pdfReport.updated} deleted=${pdfReport.deleted} unchanged=${pdfReport.unchanged} total_chunks=${pdfReport.total_chunks}\n`);
+            }
         }
         finally {
             idx.close();
@@ -203,6 +212,7 @@ async function main() {
         .option("--embed-file <path>", "Override the .embed.db file location")
         .option("--exclude-glob <pattern...>", "Exclude paths matching glob (repeatable)")
         .option("--read-paths <pattern...>", "Strict allowlist of glob patterns (repeatable)")
+        .option("--include-pdfs", "v2.8.0 — also embed PDF chunks. Off by default; PDF extraction + embedding is ~10-30x slower than markdown per file.")
         .action(async (opts) => {
         const model = resolveModel(opts.embeddingModel);
         const vault = new Vault(opts.vault, { excludeGlobs: opts.excludeGlob, readPaths: opts.readPaths });
@@ -214,7 +224,11 @@ async function main() {
             process.stderr.write(`enquire: loading embedder ${model.alias} (${model.hfId})...\n`);
             const embedder = await loadEmbedder(opts.embeddingModel);
             const report = await syncEmbedDb(vault, db, embedder);
-            process.stdout.write(`enquire: embed db ${embedFile} — added=${report.added} updated=${report.updated} deleted=${report.deleted} unchanged=${report.unchanged} total_chunks=${report.total_chunks}\n`);
+            process.stdout.write(`enquire: embed db ${embedFile} (md) — added=${report.added} updated=${report.updated} deleted=${report.deleted} unchanged=${report.unchanged} total_chunks=${report.total_chunks}\n`);
+            if (opts.includePdfs) {
+                const pdfReport = await syncPdfEmbedDb(vault, db, embedder);
+                process.stdout.write(`enquire: embed db ${embedFile} (pdf) — added=${pdfReport.added} updated=${pdfReport.updated} deleted=${pdfReport.deleted} unchanged=${pdfReport.unchanged} total_chunks=${pdfReport.total_chunks}\n`);
+            }
         }
         finally {
             db.close();
@@ -270,6 +284,23 @@ export async function prepareServerDeps(opts) {
         try {
             await ftsIndex.open();
             await syncFtsIndex(vault, ftsIndex);
+            // v2.8.0: opt-in PDF indexing. Runs after the markdown sync so
+            // partial-progress logs interleave naturally. PDF extraction is
+            // ~10-30x slower than markdown chunk-and-index, so we surface a
+            // separate progress line for each .pdf processed.
+            if (opts.includePdfs) {
+                try {
+                    const pdfReport = await syncPdfFtsIndex(vault, ftsIndex);
+                    if (pdfReport.added + pdfReport.updated + pdfReport.deleted > 0) {
+                        process.stderr.write(`enquire: pdf-fts5 sync — added=${pdfReport.added} updated=${pdfReport.updated} deleted=${pdfReport.deleted} unchanged=${pdfReport.unchanged}\n`);
+                    }
+                }
+                catch (err) {
+                    // Bad PDF / missing pdfjs-dist — don't take down the markdown
+                    // index path. Markdown search keeps working without PDFs.
+                    process.stderr.write(`enquire: pdf-fts5 sync skipped — ${err instanceof Error ? err.message : String(err)}\n`);
+                }
+            }
         }
         catch (err) {
             // Don't leak the SQLite handle if open() succeeded but sync threw.
@@ -348,7 +379,16 @@ export function buildMcpServer(deps, opts) {
             return origRegisterTool(name, ...rest);
         };
     }
-    registerReadTools(server, deps.vault, deps.ftsIndex, opts.diagnosticSearchTools ?? false);
+    // v2.9.0: build reranker config from CLI opts. Off when `--enable-reranker`
+    // wasn't passed; otherwise we pass through alias + top-n. The reranker
+    // model itself is lazy-loaded on first search call (no boot cost).
+    const rerankerConfig = opts.enableReranker
+        ? {
+            ...(opts.rerankerModel ? { alias: opts.rerankerModel } : {}),
+            ...(opts.rerankerTopN ? { topN: parsePositiveInt(opts.rerankerTopN, "--reranker-top-n") } : {})
+        }
+        : null;
+    registerReadTools(server, deps.vault, deps.ftsIndex, opts.diagnosticSearchTools ?? false, rerankerConfig);
     if (deps.vault.writeEnabled)
         registerWriteTools(server, deps.vault);
     if (deps.ftsIndex && opts.diagnosticSearchTools)
@@ -460,7 +500,9 @@ export function formatReadyBanner(deps) {
 async function syncEmbedDb(vault, db, embedder) {
     const entries = await vault.listMarkdown();
     const known = new Map();
-    for (const s of db.getSourceStates())
+    // v2.8.0: scope to kind="md" so the markdown-sync path doesn't see (and
+    // potentially delete) PDF rows added by syncPdfEmbedDb.
+    for (const s of db.getSourceStates("md"))
         known.set(s.rel_path, s.mtime_ms);
     const live = new Set();
     let added = 0;
@@ -551,7 +593,9 @@ async function syncEmbedDb(vault, db, embedder) {
 async function syncFtsIndex(vault, idx) {
     const entries = await vault.listMarkdown();
     const live = entries.map((e) => ({ relPath: e.relPath, mtimeMs: e.mtimeMs }));
-    const diff = idx.diff(live);
+    // v2.8.0: scope to kind="md" so markdown-sync doesn't try to delete PDF
+    // rows added by syncPdfFtsIndex.
+    const diff = idx.diff(live, "md");
     for (const relPath of diff.deleted)
         idx.dropFile(relPath);
     for (const relPath of [...diff.added, ...diff.updated]) {
@@ -575,6 +619,164 @@ async function syncFtsIndex(vault, idx) {
         total_chunks: idx.totalChunks()
     };
 }
+/**
+ * v2.8.0 — sync PDF chunks into the FTS5 index. Same incremental-mtime
+ * pattern as syncFtsIndex but for PDFs: list .pdf files, diff against
+ * source_state rows where kind="pdf", reindex the changed ones via
+ * `extractPdfText` + `reindexPdfFile`.
+ *
+ * pdfjs-dist is an optionalDependency — extraction failures (missing dep
+ * / corrupt PDF / encrypted without password) are caught per-file and
+ * surfaced via stderr so one bad PDF doesn't poison the whole index.
+ */
+async function syncPdfFtsIndex(vault, idx) {
+    const pdfEntries = await vault.listFilesByExtension(".pdf");
+    const live = pdfEntries.map((e) => ({ relPath: e.relPath, mtimeMs: e.mtimeMs }));
+    const diff = idx.diff(live, "pdf");
+    for (const relPath of diff.deleted)
+        idx.dropFile(relPath);
+    if (diff.added.length + diff.updated.length === 0) {
+        return {
+            added: diff.added.length,
+            updated: diff.updated.length,
+            deleted: diff.deleted.length,
+            unchanged: diff.unchanged.length,
+            total_chunks: idx.totalChunks()
+        };
+    }
+    // Lazy import — keeps the markdown-only path zero-cost when pdfjs-dist
+    // isn't installed (--omit=optional users).
+    const { extractPdfText } = await import("./pdf.js");
+    for (const relPath of [...diff.added, ...diff.updated]) {
+        const entry = pdfEntries.find((e) => e.relPath === relPath);
+        if (!entry)
+            continue;
+        try {
+            const buf = await vault.readBinaryFile(entry.absPath);
+            const result = await extractPdfText(buf);
+            // Skip image-only PDFs (no extractable text). They'd produce a chunk
+            // with only `[page: N]` markers and waste index space.
+            if (!result.hasText) {
+                process.stderr.write(`enquire: skipping ${relPath} during pdf-fts5 sync — image-only / scanned (no extractable text; use OCR via v2.9+)\n`);
+                continue;
+            }
+            idx.reindexPdfFile(relPath, entry.mtimeMs, result.pages);
+        }
+        catch (err) {
+            process.stderr.write(`enquire: skipping ${relPath} during pdf-fts5 sync — ${err instanceof Error ? err.message : String(err)}\n`);
+        }
+    }
+    return {
+        added: diff.added.length,
+        updated: diff.updated.length,
+        deleted: diff.deleted.length,
+        unchanged: diff.unchanged.length,
+        total_chunks: idx.totalChunks()
+    };
+}
+/**
+ * v2.8.0 — sync PDF chunks into the embedding index. Mirrors syncEmbedDb
+ * but for PDFs. Page boundaries are preserved as `[page: N]` markers
+ * before chunking so embeddings carry page-citation context.
+ */
+async function syncPdfEmbedDb(vault, db, embedder) {
+    const pdfEntries = await vault.listFilesByExtension(".pdf");
+    const known = new Map();
+    for (const s of db.getSourceStates("pdf"))
+        known.set(s.rel_path, s.mtime_ms);
+    const live = new Set();
+    let added = 0;
+    let updated = 0;
+    let unchanged = 0;
+    let skipped = 0;
+    const totalToProcess = pdfEntries.length;
+    if (totalToProcess === 0) {
+        // Still need to handle deletions — PDFs that vanished from disk.
+        let deleted = 0;
+        for (const relPath of known.keys()) {
+            db.deleteNote(relPath);
+            deleted += 1;
+        }
+        return { added: 0, updated: 0, deleted, unchanged: 0, total_chunks: db.totalChunks() };
+    }
+    const { extractPdfText } = await import("./pdf.js");
+    const logEvery = Math.max(1, Math.floor(totalToProcess / 20));
+    let processed = 0;
+    const startMs = Date.now();
+    for (const e of pdfEntries) {
+        live.add(e.relPath);
+        const prevMtime = known.get(e.relPath);
+        if (prevMtime !== undefined && prevMtime === e.mtimeMs) {
+            unchanged += 1;
+            processed += 1;
+            continue;
+        }
+        try {
+            const buf = await vault.readBinaryFile(e.absPath);
+            const extracted = await extractPdfText(buf);
+            if (!extracted.hasText) {
+                process.stderr.write(`enquire: skipping ${e.relPath} during pdf-embed sync — image-only / scanned\n`);
+                skipped += 1;
+                processed += 1;
+                continue;
+            }
+            // Reuse the same chunker as markdown so chunk identity matches across
+            // BM25 / TF-IDF / embeddings rankers. Page markers travel inline.
+            const joined = extracted.pages.map((p) => `[page: ${p.pageNumber}]\n${p.text}`).join("\n\n");
+            const chunks = chunkContent(joined);
+            if (chunks.length === 0) {
+                db.deleteNote(e.relPath);
+                processed += 1;
+                continue;
+            }
+            // Same breadcrumb-prepending logic as syncEmbedDb (no-op for PDFs
+            // since chunkContent returns no breadcrumb on non-markdown).
+            const vectors = await embedder.embed(chunks.map((c) => (c.breadcrumb ? `${c.breadcrumb}\n\n${c.text}` : c.text)));
+            const rows = chunks.map((c, i) => {
+                const vector = vectors[i];
+                if (!vector)
+                    throw new Error(`embedder returned no vector for chunk ${i} of ${e.relPath}`);
+                return {
+                    chunkIndex: i,
+                    lineStart: c.lineStart,
+                    lineEnd: c.lineEnd,
+                    textPreview: c.text.slice(0, 480),
+                    vector
+                };
+            });
+            db.upsertNote(e.relPath, e.mtimeMs, rows, "pdf");
+            if (prevMtime === undefined)
+                added += 1;
+            else
+                updated += 1;
+        }
+        catch (err) {
+            process.stderr.write(`enquire: skipping ${e.relPath} during pdf-embed sync — ${err instanceof Error ? err.message : String(err)}\n`);
+            skipped += 1;
+        }
+        processed += 1;
+        if (processed % logEvery === 0 || processed === totalToProcess) {
+            const elapsed = (Date.now() - startMs) / 1000;
+            const rate = processed / elapsed;
+            const eta = totalToProcess - processed > 0 ? (totalToProcess - processed) / rate : 0;
+            process.stderr.write(`enquire: pdf-embed sync ${processed}/${totalToProcess} (${rate.toFixed(2)} pdfs/s; ETA ${eta.toFixed(0)}s${skipped > 0 ? `; ${skipped} skipped` : ""})\n`);
+        }
+    }
+    let deleted = 0;
+    for (const relPath of known.keys()) {
+        if (!live.has(relPath)) {
+            db.deleteNote(relPath);
+            deleted += 1;
+        }
+    }
+    return {
+        added,
+        updated,
+        deleted,
+        unchanged,
+        total_chunks: db.totalChunks()
+    };
+}
 function registerFtsTools(server, idx, vault) {
     const READ_ONLY = { readOnlyHint: true, idempotentHint: true, openWorldHint: false };
     server.registerTool("obsidian_full_text_search", {
@@ -633,7 +835,13 @@ function registerFtsTools(server, idx, vault) {
         });
     });
 }
-function registerReadTools(server, vault, ftsIndex, diagnosticSearchTools) {
+function registerReadTools(server, vault, ftsIndex, diagnosticSearchTools, 
+/**
+ * v2.9.0 — optional cross-encoder reranker config. When set, obsidian_search
+ * post-RRF reranks the top-N candidates with a BGE-style cross-encoder.
+ * `null` means reranker disabled (default).
+ */
+rerankerConfig = null) {
     const READ_ONLY = { readOnlyHint: true, idempotentHint: true, openWorldHint: false };
     server.registerTool("obsidian_list_notes", {
         title: "List notes",
@@ -999,7 +1207,7 @@ function registerReadTools(server, vault, ftsIndex, diagnosticSearchTools) {
     // level fusion: chunk hits collapse to best-rank-per-note before fusion.
     server.registerTool("obsidian_search", {
         title: "Hybrid search (BM25 + TF-IDF + embeddings, RRF-fused)",
-        description: "**The default search tool for v2.0.** Auto-detects every available retrieval signal — BM25 via FTS5 (if `--persistent-index`), TF-IDF cosine (always), and ML embeddings (if `enquire-mcp build-embeddings` ran) — and fuses them with Reciprocal Rank Fusion (Cormack et al, 2009) for higher recall and better paraphrase / synonym matching than any single ranker. Equal weights, k=60. Gracefully degrades: with only TF-IDF available it produces TF-IDF-style ranking; with BM25+TF-IDF it does keyword-augmented retrieval; with all 3 it matches Smart Connections-quality retrieval — free / offline / open-source. Returns per-signal observability (`per_signal: { bm25, tfidf, embeddings }`) so you can see WHY each hit ranked. Use this instead of the individual `_search_text` / `_full_text_search` / `_semantic_search` / `_embeddings_search` tools unless you specifically need single-ranker output for diagnostics.",
+        description: '**The default search tool for v2.0.** Auto-detects every available retrieval signal — BM25 via FTS5 (if `--persistent-index`), TF-IDF cosine (always), and ML embeddings (if `enquire-mcp build-embeddings` ran) — and fuses them with Reciprocal Rank Fusion (Cormack et al, 2009) for higher recall and better paraphrase / synonym matching than any single ranker. Equal weights, k=60. Gracefully degrades: with only TF-IDF available it produces TF-IDF-style ranking; with BM25+TF-IDF it does keyword-augmented retrieval; with all 3 it matches Smart Connections-quality retrieval — free / offline / open-source. Returns per-signal observability (`per_signal: { bm25, tfidf, embeddings }`) so you can see WHY each hit ranked. **v2.8.0:** when `--include-pdfs` was passed to `serve` (or `enquire-mcp index --include-pdfs` ran), PDF chunks are blended into results — each hit carries a `kind: "md" | "pdf"` flag and PDF chunks include `[page: N]` markers in snippets so agents can cite the right page. Use this instead of the individual `_search_text` / `_full_text_search` / `_semantic_search` / `_embeddings_search` tools unless you specifically need single-ranker output for diagnostics.',
         annotations: { ...READ_ONLY, title: "Hybrid search" },
         inputSchema: {
             query: z.string().min(1).describe("Free-form query — multi-word natural language is the sweet spot"),
@@ -1027,7 +1235,11 @@ function registerReadTools(server, vault, ftsIndex, diagnosticSearchTools) {
         }
     }, async (args) => {
         const embedFile = embedDbPath(vault.root);
-        return textResult(await searchHybrid(vault, args, { ftsIndex, embedFile }));
+        return textResult(await searchHybrid(vault, args, {
+            ftsIndex,
+            embedFile,
+            ...(rerankerConfig ? { reranker: rerankerConfig } : {})
+        }));
     });
     server.registerTool("obsidian_chat_thread_read", {
         title: "Read parsed chat thread from a note",