@oomkapwn/enquire-mcp 2.7.0 → 2.8.0

package/CHANGELOG.md

@@ -2,6 +2,57 @@
 
 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).
 
+## [2.8.0] — 2026-05-08
+
+**Sprint 8 — PDF retrieval integration.** v2.7.0 added PDF text-extraction tools (`obsidian_list_pdfs` / `obsidian_read_pdf`); v2.8.0 makes PDFs **first-class citizens of `obsidian_search`**. Index PDFs into the same FTS5 + embedding stores as markdown, blend them in hybrid retrieval (BM25 + TF-IDF + embeddings → RRF fusion), and surface a `kind: "md" | "pdf"` flag on every hit so agents can distinguish content sources at a glance.
+
+### Added — `--include-pdfs` flag on `serve`, `index`, `build-embeddings`
+
+Off by default — opt-in because PDF extraction is ~10-30× slower per file than markdown chunking. When enabled:
+
+- `enquire-mcp serve --vault <path> --persistent-index --include-pdfs` → boots and incrementally syncs PDFs into the FTS5 index alongside markdown.
+- `enquire-mcp index --vault <path> --include-pdfs` → cold-build / refresh the FTS5 index for both markdown and PDFs.
+- `enquire-mcp build-embeddings --vault <path> --include-pdfs` → embed PDF chunks too.
+
+Bad PDFs (encrypted without password / corrupt / image-only / scanned) are caught per-file and surfaced via stderr without taking down the markdown index path. Image-only / scanned PDFs are skipped with a clear log line — OCR is tracked for v2.9+ (Tesseract.js).
+
+### Schema migration — FTS5 v3 → v4, embed-db v1 → v2
+
+Both indexes added a `kind` column (`'md' | 'pdf'`, default `'md'`). Schema bump auto-rebuilds the index on first open after upgrade — same pattern as the `tokenize_mode` / `vault_root` cross-config-change guards. Existing markdown indexes are preserved (they re-sync from the markdown source as kind=md).
+
+### `obsidian_search` returns `kind` on every hit
+
+Both `note` and `block` granularity propagate the kind flag. PDF hits use the filename without the `.pdf` extension as the title (so titles read naturally in agent output). The tool description was updated to flag the v2.8.0 capability so MCP clients introspecting `tools/list` see it immediately.
+
+### Page-citation markers in PDF chunks
+
+When indexing PDFs, page boundaries are preserved as `[page: N]\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 the agent can extract. Same `chunkContent` pipeline as markdown, so chunk identity matches across BM25 / TF-IDF / embeddings (RRF requires stable IDs).
+
+### Independent sync paths via kind-aware diff()
+
+`FtsIndex.diff(live, kind?)` and `EmbedDb.getSourceStates(kind?)` now accept an optional kind filter. Lets the markdown-sync path run independently from the PDF-sync path against the same DB without one's "missing files" being mistakenly deleted by the other. Backward-compat: omitting the kind arg returns all rows (legacy behavior).
+
+### Tests
+
+493 unit tests pass (was 481 in v2.7.0, +12 new):
+- **FTS5 PDF (+6):** indexes PDF chunks with kind='pdf' alongside markdown, page markers travel through chunks for snippets, kind-scoped diff() doesn't see other-kind rows, kind-undefined diff() shows both, reindexPdfFile is atomically idempotent, schema bump v3→v4 auto-rebuilds.
+- **Embed-db PDF (+3):** upserts with kind='pdf' and search returns kind='pdf', getSourceStates(kind=…) doesn't overlap, schema bump v1→v2 idempotent on matching schema.
+- **searchHybrid kind (+3):** blended hits with both kind='md' and kind='pdf', PDF hits use .pdf-stripped titles, kind defaults to 'md' on TF-IDF-only matches.
+
+### Surface delta vs v2.7.0
+
+- **No new tools.** The 38 from v2.7.0 stay. PDF retrieval is a property of `obsidian_search` (and the diagnostic single-ranker tools), not a new tool surface.
+- **+1 CLI flag** (`--include-pdfs`) wired on three subcommands (`serve`, `index`, `build-embeddings`).
+- **Schema bumps** auto-rebuild legacy indexes on first open.
+
+### Migration
+
+**No-op for default users.** PDF indexing is opt-in via `--include-pdfs`. Existing `serve` / `serve-http` / `index` / `build-embeddings` users keep working unchanged. Once you opt in, the FTS5 + embed-db files auto-rebuild on first open (same one-time cost as `tokenize_mode` change in earlier versions).
+
+### Strategic position
+
+v2.7.0 added the foundation (PDF extraction tools); v2.8.0 makes them retrievable. Combined with v2.0-v2.6's hybrid RRF + wikilink graph-boost + breadcrumb chunking + multilingual embeddings + remote MCP transport, **enquire-mcp is the only Obsidian-MCP that searches markdown and PDFs in a unified hybrid retrieval surface**. Smart Connections (paid) doesn't index PDFs. Khoj indexes PDFs but doesn't run on Obsidian's substrate (separate app, separate vault). The intersection is uniquely ours.
+
 ## [2.7.0] — 2026-05-08
 
 **Sprint 7 — PDF as a first-class indexable content type.** PDFs are the #1 non-markdown content kind in real research vaults (papers, scanned notes, downloaded references). **No other Obsidian-MCP currently indexes them.** v2.7.0 adds two new read tools that work identically over stdio + `serve-http`, gated behind `pdfjs-dist` as an `optionalDependency` so the markdown-only path stays zero-cost.

package/README.md

@@ -38,13 +38,14 @@ That's it. Your AI now has structured access to wikilinks, backlinks, frontmatte
 | TF-IDF semantic search | ❌ | ❌ | ✅ |
 | **ML embeddings (multilingual)** | ❌ | ✅ paid | ✅ **free** |
 | **Hybrid (BM25+TF-IDF+embeddings, RRF)** | ❌ | ❌ | ✅ **only here** |
+| **PDFs blended into hybrid search** | ❌ | ❌ | ✅ **only here** (v2.8.0) |
 | Per-signal observability on each hit | ❌ | ❌ | ✅ |
 | Privacy filter (`--exclude-glob` / `--read-paths`) | ❌ | n/a | ✅ verified at search + write paths |
 | Standalone (no Obsidian plugin) | varies | ❌ requires Obsidian | ✅ direct vault read |
 | MCP-native (any agent) | varies | ❌ Obsidian-only | ✅ stdio JSON-RPC |
 | **Remote MCP (HTTP transport, bearer auth)** | ❌ | ❌ | ✅ **only here** (v2.6.0) |
 | SLSA-3 provenance | ❌ | n/a | ✅ |
-| Test suite | rare | n/a | ✅ 481 unit tests |
+| Test suite | rare | n/a | ✅ 493 unit tests |
 
 ---
 
@@ -131,7 +132,7 @@ No other Obsidian-MCP currently ships a remote-HTTP transport. Same vault, same
 
 | Tool | What it does |
 |---|---|
-| `obsidian_search` | **Hybrid retrieval** — fuses BM25 + TF-IDF + ML embeddings via RRF. The default search tool. Auto-detects available signals. v2.2.0: `granularity: "block"` arg returns chunks instead of notes. |
+| `obsidian_search` | **Hybrid retrieval** — fuses BM25 + TF-IDF + ML embeddings via RRF. The default search tool. Auto-detects available signals. v2.2.0: `granularity: "block"` arg returns chunks instead of notes. **v2.8.0:** with `--include-pdfs`, PDF chunks blend in alongside markdown — every hit carries `kind: "md" \| "pdf"` and PDF snippets include `[page: N]` markers for citation. |
 | `obsidian_context_pack` | **v2.2.0.** Token-budgeted context bundling: takes a question, runs hybrid search, gathers note bodies + backlinks + optionally recent dailies, returns one ready-to-paste markdown bundle. Saves ~5 tool calls. |
 | `obsidian_chat_thread_read` | **v2.2.0.** Parse a note's `## Chat: <title>` block into structured messages (role/timestamp/content/line-range). Pair with `_append` (write) for note-tethered AI conversations. |
 | `obsidian_frontmatter_get` | **v2.3.0.** Read parsed YAML frontmatter for a note. With `key`, returns just that field. |
@@ -230,7 +231,7 @@ Full posture: [SECURITY.md](./SECURITY.md). Report vulnerabilities to `oomkapwn@
 |---|---|
 | Language | TypeScript strict + `noUncheckedIndexedAccess` |
 | Lint | Biome 2 (zero-warning policy) |
-| Tests | 481 unit tests across 23 files |
+| Tests | 493 unit tests across 23 files |
 | CI | ubuntu × {Node 20, 22, 24} required + macOS advisory job |
 | Coverage | Lines ≥86%, statements ≥82%, functions ≥75%, branches ≥73% (gated) |
 | Audit | `npm audit --audit-level=moderate` for prod; high for dev |

package/dist/embed-db.d.ts

@@ -1,3 +1,5 @@
+/** Content-source kind. Mirrors ChunkKind in src/fts5.ts. */
+export type EmbedChunkKind = "md" | "pdf";
 export interface EmbedSearchHit {
     rel_path: string;
     chunk_index: number;
@@ -7,6 +9,8 @@ export interface EmbedSearchHit {
     text_preview: string;
     /** Cosine similarity (since vectors are L2-normalized at insert time). */
     score: number;
+    /** v2.8.0 — content-source kind. Defaults to "md" for backward compat. */
+    kind: EmbedChunkKind;
 }
 export interface EmbedSyncReport {
     added: number;
@@ -44,19 +48,27 @@ export declare class EmbedDb {
     private readMeta;
     private writeMeta;
     private requireDb;
-    /** Replace all embeddings for a single note. Caller computes vectors. */
+    /**
+     * Replace all embeddings for a single note. Caller computes vectors.
+     * v2.8.0: optional `kind` parameter ("md" | "pdf"); defaults to "md" so
+     * existing callers (markdown indexing path) need no changes.
+     */
     upsertNote(relPath: string, mtimeMs: number, chunks: ReadonlyArray<{
         chunkIndex: number;
         lineStart: number;
         lineEnd: number;
         textPreview: string;
         vector: Float32Array;
-    }>): void;
+    }>, kind?: EmbedChunkKind): void;
     /** Drop a note's embeddings entirely (used on file deletion). */
     deleteNote(relPath: string): void;
-    /** Read the source-state table — caller compares mtimes to decide what to
-     *  re-embed. */
-    getSourceStates(): SourceStateRow[];
+    /**
+     * Read the source-state table — caller compares mtimes to decide what to
+     * re-embed. v2.8.0: optional `kind` filter — when set, only rows of that
+     * kind are returned. Lets the markdown-sync and PDF-sync paths run
+     * independently without one's "missing files" being deleted by the other.
+     */
+    getSourceStates(kind?: EmbedChunkKind): SourceStateRow[];
     /** Brute-force cosine top-K. Vectors are L2-normalized at insert time so
      *  cosine == dot product. Acceptable up to ~50K chunks; v2.1 will swap to
      *  HNSW if real vaults hit that ceiling. */

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

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

@@ -13,7 +13,7 @@
 // on 50K × 384 floats). HNSW comes in v2.1 if real users hit that ceiling.
 import { promises as fs } from "node:fs";
 import * as path from "node:path";
-const SCHEMA_VERSION = 1;
+const SCHEMA_VERSION = 2;
 // v2.0.0-beta.1 P2 fix: probe the native binding via :memory: open so the
 // "JS package present but *.node binary missing" failure mode produces a
 // clean error pointing at `npm rebuild`, not a raw bindings stack trace.
@@ -120,6 +120,7 @@ export class EmbedDb {
         line_end INTEGER NOT NULL,
         text_preview TEXT NOT NULL,
         vector BLOB NOT NULL,
+        kind TEXT NOT NULL DEFAULT 'md',
         UNIQUE(rel_path, chunk_index)
       );
       CREATE INDEX IF NOT EXISTS embeddings_rel_path ON embeddings(rel_path);
@@ -127,6 +128,7 @@ export class EmbedDb {
         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
       );
     `);
@@ -156,23 +158,27 @@ export class EmbedDb {
             throw new Error("EmbedDb is not open — call .open() first");
         return this.db;
     }
-    /** Replace all embeddings for a single note. Caller computes vectors. */
-    upsertNote(relPath, mtimeMs, chunks) {
+    /**
+     * Replace all embeddings for a single note. Caller computes vectors.
+     * v2.8.0: optional `kind` parameter ("md" | "pdf"); defaults to "md" so
+     * existing callers (markdown indexing path) need no changes.
+     */
+    upsertNote(relPath, mtimeMs, chunks, kind = "md") {
         const db = this.requireDb();
         const dim = this.dim;
         const tx = db.transaction((...args) => {
             const rows = args[0];
             db.prepare("DELETE FROM embeddings WHERE rel_path = ?").run(relPath);
-            const insert = db.prepare(`INSERT INTO embeddings (rel_path, chunk_index, line_start, line_end, text_preview, vector)
-         VALUES (?, ?, ?, ?, ?, ?)`);
+            const insert = db.prepare(`INSERT INTO embeddings (rel_path, chunk_index, line_start, line_end, text_preview, vector, kind)
+         VALUES (?, ?, ?, ?, ?, ?, ?)`);
             for (const c of rows) {
                 if (c.vector.length !== dim) {
                     throw new Error(`vector dim mismatch for ${relPath} chunk ${c.chunkIndex}: got ${c.vector.length}, expected ${dim}`);
                 }
-                insert.run(relPath, c.chunkIndex, c.lineStart, c.lineEnd, c.textPreview, Buffer.from(c.vector.buffer, c.vector.byteOffset, c.vector.byteLength));
+                insert.run(relPath, c.chunkIndex, c.lineStart, c.lineEnd, c.textPreview, Buffer.from(c.vector.buffer, c.vector.byteOffset, c.vector.byteLength), kind);
             }
-            db.prepare(`INSERT OR REPLACE INTO source_state (rel_path, mtime_ms, n_chunks, indexed_at)
-         VALUES (?, ?, ?, datetime('now'))`).run(relPath, mtimeMs, rows.length);
+            db.prepare(`INSERT OR REPLACE INTO source_state (rel_path, mtime_ms, n_chunks, kind, indexed_at)
+         VALUES (?, ?, ?, ?, datetime('now'))`).run(relPath, mtimeMs, rows.length, kind);
         });
         tx(chunks);
     }
@@ -182,10 +188,17 @@ export class EmbedDb {
         db.prepare("DELETE FROM embeddings WHERE rel_path = ?").run(relPath);
         db.prepare("DELETE FROM source_state WHERE rel_path = ?").run(relPath);
     }
-    /** Read the source-state table — caller compares mtimes to decide what to
-     *  re-embed. */
-    getSourceStates() {
+    /**
+     * Read the source-state table — caller compares mtimes to decide what to
+     * re-embed. v2.8.0: optional `kind` filter — when set, only rows of that
+     * kind are returned. Lets the markdown-sync and PDF-sync paths run
+     * independently without one's "missing files" being deleted by the other.
+     */
+    getSourceStates(kind) {
         const db = this.requireDb();
+        if (kind !== undefined) {
+            return db.prepare("SELECT rel_path, mtime_ms FROM source_state WHERE kind = ?").all(kind);
+        }
         return db.prepare("SELECT rel_path, mtime_ms FROM source_state").all();
     }
     /** Brute-force cosine top-K. Vectors are L2-normalized at insert time so
@@ -204,9 +217,9 @@ export class EmbedDb {
         // FtsIndex.search() in fts5.ts.
         const rows = db
             .prepare(folderPrefix
-            ? `SELECT rel_path, chunk_index, line_start, line_end, text_preview, vector
+            ? `SELECT rel_path, chunk_index, line_start, line_end, text_preview, vector, kind
              FROM embeddings WHERE substr(rel_path, 1, ?) = ?`
-            : `SELECT rel_path, chunk_index, line_start, line_end, text_preview, vector FROM embeddings`)
+            : `SELECT rel_path, chunk_index, line_start, line_end, text_preview, vector, kind FROM embeddings`)
             .all(...(folderPrefix ? [folderPrefix.length, folderPrefix] : []));
         const expectedBytes = this.dim * 4; // Float32 = 4 bytes
         const heap = [];
@@ -232,7 +245,8 @@ export class EmbedDb {
                 line_start: r.line_start,
                 line_end: r.line_end,
                 text_preview: r.text_preview,
-                score
+                score,
+                kind: (r.kind === "pdf" ? "pdf" : "md")
             });
         }
         heap.sort((a, b) => b.score - a.score);

package/dist/embed-db.js.map

@@ -1 +1 @@
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package/dist/fts5.d.ts

@@ -1,4 +1,6 @@
 export type TokenizeMode = "unicode61" | "trigram";
+/** Content-source kind. v2.7.0 added `pdf`; v2.8.0 indexes them. */
+export type ChunkKind = "md" | "pdf";
 export interface FtsSearchHit {
     rel_path: string;
     chunk_index: number;
@@ -6,6 +8,8 @@ export interface FtsSearchHit {
     line_end: number;
     snippet: string;
     score: number;
+    /** v2.8.0 — content-source kind. Defaults to "md" for backward compat. */
+    kind: ChunkKind;
 }
 export interface FtsSyncReport {
     added: number;
@@ -36,11 +40,18 @@ export declare 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: Array<{
         relPath: string;
         mtimeMs: number;
-    }>): {
+    }>, kind?: ChunkKind): {
         added: string[];
         updated: string[];
         deleted: string[];
@@ -48,8 +59,24 @@ export declare class FtsIndex {
     };
     /** Drop a file's chunks + state row. Idempotent. */
     dropFile(relPath: string): void;
-    /** Re-chunk a single file, replacing its existing chunks atomically. */
+    /** Re-chunk a single markdown file, replacing its existing chunks atomically. */
     reindexFile(relPath: string, mtimeMs: number, content: string, wikilinkTargets?: string[], tags?: string[]): number;
+    /**
+     * 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: string, mtimeMs: number, pages: ReadonlyArray<{
+        pageNumber: number;
+        text: string;
+    }>): number;
     search(rawQuery: string, opts?: {
         limit?: number;
         folder?: string;

package/dist/fts5.d.ts.map

@@ -1 +1 @@
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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 +19,10 @@ 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;
 }
 declare function main(): Promise<void>;
 /**

package/dist/index.d.ts.map

@@ -1 +1 @@
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