@monoes/monograph 1.2.7 → 1.2.9

package/src/search/hybrid-query.ts

@@ -1,27 +1,23 @@
 /**
- * Hybrid BM25 + vector search with Reciprocal Rank Fusion.
+ * BM25 search (FTS5) with the historical "hybrid" entry-point signature.
  *
- * When MONOGRAPH_EMBEDDINGS=true (or an embedder is provided), the query is
- * embedded and cosine similarity is computed in JavaScript against all stored
- * vectors.  Both result lists are merged via RRF(K=60).
- *
- * If embeddings are unavailable (table empty, env not set, no embedder),
- * the function falls back to BM25 only — same behaviour as before.
+ * Monograph search is BM25-only. The former embedding/vector branch
+ * (gated on MONOGRAPH_EMBEDDINGS=true) was removed — it was never run in
+ * practice (the embeddings table stayed empty) and did a JS cosine full
+ * scan. The exported function signatures are unchanged so callers do not
+ * need to change.
  */
 
 import type Database from 'better-sqlite3';
-import type { EmbedderFn } from './embedder.js';
-import { mergeRanks, type RankedResult } from './rrf.js';
-import { getAllEmbeddings, countEmbeddings } from '../storage/embedding-store.js';
-import { embedText } from './embedder.js';
+import type { RankedResult } from './rrf.js';
 import { ftsSearch } from '../storage/fts-store.js';
 import { normalizeSearchTerm } from './diacritic.js';
 
 export interface HybridQueryOptions {
   limit?: number;
   label?: string;
-  /** Explicit embedder — overrides MONOGRAPH_EMBEDDINGS env check */
-  embedder?: EmbedderFn;
+  /** @deprecated Embeddings are disabled — this option is ignored; search is BM25-only. */
+  embedder?: unknown;
 }
 
 export interface HybridResult extends RankedResult {
@@ -38,19 +34,15 @@ export interface HybridResult extends RankedResult {
 }
 
 /**
- * Run a hybrid BM25 + cosine search.
- *
- * Falls back to BM25-only when:
- *  - MONOGRAPH_EMBEDDINGS env var is not 'true' AND no explicit embedder is given
- *  - The embeddings table is empty
- *  - Embedding the query string fails
+ * Run a BM25 (FTS5) search. Despite the name, this is BM25-only — the
+ * vector branch was removed; the `embedder` option is ignored.
  */
 export async function hybridQuery(
   db: Database.Database,
   query: string,
   options: HybridQueryOptions = {},
 ): Promise<HybridResult[]> {
-  const { limit = 20, label, embedder } = options;
+  const { limit = 20, label } = options;
 
   // Normalize the query for text-based lookups (strip diacritics, lowercase, trim)
   const normalizedQuery = normalizeSearchTerm(query);
@@ -69,104 +61,5 @@ export async function hybridQuery(
     endLine: r.endLine,
   }));
 
-  // ── Decide whether to add vector results ──────────────────────────────────
-  const embeddingsEnabled =
-    embedder !== undefined || process.env['MONOGRAPH_EMBEDDINGS'] === 'true';
-
-  if (!embeddingsEnabled) return sliceHybrid(bm25Results, limit);
-
-  const embeddingCount = countEmbeddings(db);
-  if (embeddingCount === 0) return sliceHybrid(bm25Results, limit);
-
-  // ── Embed the query ────────────────────────────────────────────────────────
-  let queryVec: Float32Array;
-  try {
-    const fn: import('./embedder.js').EmbedderFn = embedder ?? (await import('./embedder.js').then((m) => m.getEmbedder()));
-    queryVec = await embedText(normalizedQuery, fn);
-  } catch {
-    // Embedding failed — degrade gracefully to BM25
-    return sliceHybrid(bm25Results, limit);
-  }
-
-  // ── Cosine similarity against stored vectors ──────────────────────────────
-  const allVecs = getAllEmbeddings(db);
-  const vectorScored: { id: string; cosine: number }[] = [];
-
-  for (const [nodeId, vec] of allVecs) {
-    const sim = dotProduct(queryVec, vec); // valid because vectors are L2-normalised
-    vectorScored.push({ id: nodeId, cosine: sim });
-  }
-
-  // Sort descending by cosine similarity
-  vectorScored.sort((a, b) => b.cosine - a.cosine);
-
-  // Build vector RankedResult list with node metadata joined from BM25 cache
-  const bm25ById = new Map(bm25Results.map((r) => [r.id, r]));
-  const vectorResults: RankedResult[] = vectorScored.map((vs) => {
-    const meta = bm25ById.get(vs.id);
-    return {
-      id: vs.id,
-      name: (meta?.name as string | undefined) ?? '',
-      normLabel: (meta?.normLabel as string | undefined) ?? '',
-      filePath: (meta?.filePath as string | null | undefined) ?? null,
-      label: (meta?.label as string | undefined) ?? '',
-      score: vs.cosine,
-    };
-  });
-
-  // ── Merge via RRF ──────────────────────────────────────────────────────────
-  const merged = mergeRanks(bm25Results, vectorResults);
-
-  // Enrich nodes not in bm25 cache with a DB lookup
-  const enrichable = merged as Partial<HybridResult>[];
-  const unknownIds = enrichable
-    .filter((r) => !r.name)
-    .map((r) => r.id as string);
-
-  if (unknownIds.length > 0) {
-    const placeholders = unknownIds.map(() => '?').join(',');
-    const rows = db
-      .prepare(
-        `SELECT id, name, norm_label, file_path, label, start_line, end_line FROM nodes WHERE id IN (${placeholders})`,
-      )
-      .all(...unknownIds) as {
-      id: string;
-      name: string;
-      norm_label: string;
-      file_path: string | null;
-      label: string;
-      start_line: number | null;
-      end_line: number | null;
-    }[];
-
-    const rowMap = new Map(rows.map((r) => [r.id, r]));
-    for (const item of enrichable) {
-      if (!item.name) {
-        const row = rowMap.get(item.id as string);
-        if (row) {
-          item.name = row.name;
-          item.normLabel = row.norm_label;
-          item.filePath = row.file_path;
-          item.label = row.label;
-          (item as HybridResult).startLine = row.start_line;
-          (item as HybridResult).endLine = row.end_line;
-        }
-      }
-    }
-  }
-
-  return sliceHybrid(merged, limit);
-}
-
-// ── Helpers ───────────────────────────────────────────────────────────────────
-
-function sliceHybrid(results: RankedResult[], limit: number): HybridResult[] {
-  return results.slice(0, limit) as HybridResult[];
-}
-
-function dotProduct(a: Float32Array, b: Float32Array): number {
-  let sum = 0;
-  const len = Math.min(a.length, b.length);
-  for (let i = 0; i < len; i++) sum += a[i] * b[i];
-  return sum;
+  return bm25Results.slice(0, limit) as HybridResult[];
 }

package/src/storage/db.ts

@@ -16,6 +16,14 @@ export function openDb(dbPath: string): MonographDb {
     const db = new Database(dbPath);
     db.pragma('journal_mode = WAL');
     db.pragma('foreign_keys = ON');
+    // Concurrent pipeline phases + long-lived MCP connections share this DB —
+    // without a busy timeout, writers fail immediately with "database is locked".
+    db.pragma('busy_timeout = 10000');
+    db.pragma('synchronous = NORMAL');
+    // node-store uses INSERT OR REPLACE; without recursive_triggers the implicit
+    // DELETE never fires the nodes_fts delete trigger, leaving ghost FTS rows that
+    // corrupt queries ("missing row N from content table") and bloat the index.
+    db.pragma('recursive_triggers = ON');
     applyMigrations(db);
     return db;
   } catch (err) {

package/src/watch/watcher.ts

@@ -3,7 +3,6 @@ import { EventEmitter } from 'events';
 import { isSupportedExtension } from '../parsers/loader.js';
 import type { PipelineProgress } from '../types.js';
 import { extname } from 'path';
-import { platform } from 'os';
 
 export interface WatcherOptions {
   debounceMs?: number;  // default 3000ms
@@ -24,10 +23,23 @@ export async function watchAsync(
   const { buildAsync } = await import('../pipeline/orchestrator.js');
   const watcher = new MonographWatcher(repoPath, { debounceMs: opts.debounceMs ?? 3000 });
 
+  // monolean: full rebuild per change-batch, serialized — true incremental rebuild
+  // (re-parse only changed files) requires restructuring the phase pipeline.
+  let building = false;
+  let rerun = false;
   watcher.on('monograph:updated', async (files: string[]) => {
-    opts.onProgress?.({ phase: 'watch', message: `Changed: ${files.slice(0, 3).join(', ')}` });
-    await buildAsync(repoPath, { onProgress: opts.onProgress, force: opts.force, codeOnly: opts.codeOnly, llmMaxSections: opts.llmMaxSections ?? 0 });
-    opts.onProgress?.({ phase: 'watch', message: 'Graph rebuilt.' });
+    if (building) { rerun = true; return; } // coalesce saves that land mid-build
+    building = true;
+    try {
+      do {
+        rerun = false;
+        opts.onProgress?.({ phase: 'watch', message: `Changed: ${files.slice(0, 3).join(', ')}` });
+        await buildAsync(repoPath, { onProgress: opts.onProgress, force: opts.force, codeOnly: opts.codeOnly, llmMaxSections: opts.llmMaxSections ?? 0 });
+        opts.onProgress?.({ phase: 'watch', message: 'Graph rebuilt.' });
+      } while (rerun);
+    } finally {
+      building = false;
+    }
   });
 
   await watcher.start();
@@ -46,7 +58,10 @@ export class MonographWatcher extends EventEmitter {
   }
 
   async start(): Promise<void> {
-    const usePolling = platform() === 'darwin';
+    // FSEvents works natively on macOS — polling the whole tree every second is
+    // far more expensive (especially on external/exFAT volumes). Poll only when
+    // explicitly requested via env (e.g. network mounts where events don't fire).
+    const usePolling = process.env.MONOGRAPH_WATCH_POLL === '1';
 
     this.watcher = chokidar.watch(this.repoPath, {
       ignored: [

package/vitest.config.ts

@@ -4,6 +4,7 @@ export default defineConfig({
   test: {
     environment: 'node',
     include: ['__tests__/**/*.test.ts', 'src/__tests__/**/*.test.ts'],
+    exclude: ['node_modules', 'dist', '**/._*'],
     globals: true,
     coverage: {
       enabled: false,

package/dist/src/__tests__/mcp-tools/embed.test.d.ts

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=embed.test.d.ts.map

package/dist/src/__tests__/mcp-tools/embed.test.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"embed.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/mcp-tools/embed.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/mcp-tools/embed.test.js

@@ -1,12 +0,0 @@
-import { describe, it, expect } from 'vitest';
-describe('embed tool exports', () => {
-    it('runEmbed is exported from mcp-tools index', async () => {
-        const mod = await import('../../mcp-tools/index.js');
-        expect(typeof mod.runEmbed).toBe('function');
-    });
-    it('runEmbed is directly importable from embed.js', async () => {
-        const { runEmbed } = await import('../../mcp-tools/embed.js');
-        expect(typeof runEmbed).toBe('function');
-    });
-});
-//# sourceMappingURL=embed.test.js.map

package/dist/src/__tests__/mcp-tools/embed.test.js.map

@@ -1 +0,0 @@
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package/dist/src/__tests__/search/embed-stale.test.d.ts

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=embed-stale.test.d.ts.map

package/dist/src/__tests__/search/embed-stale.test.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"embed-stale.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/search/embed-stale.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/search/embed-stale.test.js

@@ -1,38 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import Database from 'better-sqlite3';
-import { upsertEmbedding, getEmbeddingContentHash, isEmbeddingStale } from '../../storage/embedding-store.js';
-function makeDb() {
-    const db = new Database(':memory:');
-    db.exec(`
-    CREATE TABLE IF NOT EXISTS embeddings (
-      node_id TEXT PRIMARY KEY,
-      vector BLOB NOT NULL,
-      content_hash TEXT,
-      created_at INTEGER DEFAULT (unixepoch())
-    );
-  `);
-    return db;
-}
-describe('embedding stale detection', () => {
-    it('stores content hash with embedding', () => {
-        const db = makeDb();
-        upsertEmbedding(db, 'n1', new Float32Array([0.1, 0.2]), 'hash_abc');
-        const stored = getEmbeddingContentHash(db, 'n1');
-        expect(stored).toBe('hash_abc');
-    });
-    it('isEmbeddingStale returns true when hash differs', () => {
-        const db = makeDb();
-        upsertEmbedding(db, 'n1', new Float32Array([0.1, 0.2]), 'old_hash');
-        expect(isEmbeddingStale(db, 'n1', 'new_hash')).toBe(true);
-    });
-    it('isEmbeddingStale returns false when hash matches', () => {
-        const db = makeDb();
-        upsertEmbedding(db, 'n1', new Float32Array([0.1, 0.2]), 'same_hash');
-        expect(isEmbeddingStale(db, 'n1', 'same_hash')).toBe(false);
-    });
-    it('isEmbeddingStale returns true when no embedding exists', () => {
-        const db = makeDb();
-        expect(isEmbeddingStale(db, 'n1', 'any_hash')).toBe(true);
-    });
-});
-//# sourceMappingURL=embed-stale.test.js.map

package/dist/src/__tests__/search/embed-stale.test.js.map

@@ -1 +0,0 @@
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package/dist/src/__tests__/search/exact-search.test.d.ts

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=exact-search.test.d.ts.map

package/dist/src/__tests__/search/exact-search.test.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"exact-search.test.d.ts","sourceRoot":"","sources":["../../../../src/__tests__/search/exact-search.test.ts"],"names":[],"mappings":""}

package/dist/src/__tests__/search/exact-search.test.js

@@ -1,49 +0,0 @@
-import { describe, it, expect } from 'vitest';
-import Database from 'better-sqlite3';
-import { exactVectorSearch } from '../../search/exact-search.js';
-function makeDb() {
-    const db = new Database(':memory:');
-    db.exec(`
-    CREATE TABLE nodes (id TEXT PRIMARY KEY, label TEXT NOT NULL, name TEXT NOT NULL,
-      norm_label TEXT, file_path TEXT, start_line INTEGER, end_line INTEGER,
-      community_id INTEGER, is_exported INTEGER DEFAULT 0, language TEXT, properties TEXT);
-    CREATE TABLE embeddings (node_id TEXT PRIMARY KEY, vector BLOB NOT NULL, content_hash TEXT, created_at INTEGER);
-  `);
-    db.prepare(`INSERT INTO nodes VALUES ('n1','Function','doAuth',null,'/auth.ts',1,5,null,1,null,null)`).run();
-    db.prepare(`INSERT INTO nodes VALUES ('n2','Function','renderUI',null,'/ui.ts',1,3,null,1,null,null)`).run();
-    // Store simple 3-dim embeddings: n1 ~ [1, 0, 0], n2 ~ [0, 1, 0]
-    const v1 = new Float32Array([1, 0, 0]);
-    const v2 = new Float32Array([0, 1, 0]);
-    db.prepare(`INSERT INTO embeddings VALUES ('n1', ?, null, 0)`).run(Buffer.from(v1.buffer));
-    db.prepare(`INSERT INTO embeddings VALUES ('n2', ?, null, 0)`).run(Buffer.from(v2.buffer));
-    return db;
-}
-describe('exactVectorSearch', () => {
-    it('returns closest node to query vector', () => {
-        const db = makeDb();
-        const query = new Float32Array([0.9, 0.1, 0]);
-        const results = exactVectorSearch(db, query, { limit: 2 });
-        expect(results[0]?.id).toBe('n1');
-    });
-    it('respects limit', () => {
-        const db = makeDb();
-        const query = new Float32Array([1, 0, 0]);
-        const results = exactVectorSearch(db, query, { limit: 1 });
-        expect(results).toHaveLength(1);
-    });
-    it('returns score between 0 and 1', () => {
-        const db = makeDb();
-        const query = new Float32Array([1, 0, 0]);
-        const results = exactVectorSearch(db, query, { limit: 2 });
-        expect(results[0].score).toBeGreaterThan(0);
-        expect(results[0].score).toBeLessThanOrEqual(1);
-    });
-    it('returns empty array when no embeddings', () => {
-        const db = new Database(':memory:');
-        db.exec(`CREATE TABLE embeddings (node_id TEXT PRIMARY KEY, vector BLOB NOT NULL, content_hash TEXT, created_at INTEGER);
-             CREATE TABLE nodes (id TEXT PRIMARY KEY, label TEXT NOT NULL, name TEXT NOT NULL, norm_label TEXT, file_path TEXT, start_line INTEGER, end_line INTEGER, community_id INTEGER, is_exported INTEGER DEFAULT 0, language TEXT, properties TEXT);`);
-        const results = exactVectorSearch(db, new Float32Array([1, 0, 0]), { limit: 5 });
-        expect(results).toHaveLength(0);
-    });
-});
-//# sourceMappingURL=exact-search.test.js.map

package/dist/src/__tests__/search/exact-search.test.js.map

@@ -1 +0,0 @@
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package/dist/src/mcp-tools/embed.d.ts

@@ -1,25 +0,0 @@
-/**
- * monograph_embed MCP tool
- *
- * Embeds all symbol nodes in the Monograph knowledge graph using
- * Snowflake/snowflake-arctic-embed-xs (384 dimensions).
- *
- * Requires @huggingface/transformers to be installed.
- * Returns { embedded, skipped, model } on success or an error message.
- */
-import type Database from 'better-sqlite3';
-export interface EmbedToolInput {
-    codeOnly?: boolean;
-    force?: boolean;
-}
-export interface EmbedToolResult {
-    embedded: number;
-    skipped: number;
-    model: string;
-}
-/**
- * Run the embedding pipeline on the open database.
- * Exported so the CLI handler can call it after opening the DB.
- */
-export declare function runEmbed(db: Database.Database, options?: EmbedToolInput): Promise<EmbedToolResult>;
-//# sourceMappingURL=embed.d.ts.map

package/dist/src/mcp-tools/embed.d.ts.map

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