@monoes/monograph 1.2.6 → 1.2.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@monoes/monograph",
-  "version": "1.2.6",
+  "version": "1.2.8",
   "type": "module",
   "description": "Native TypeScript code intelligence engine for monomind",
   "main": "dist/src/index.js",
@@ -15,10 +15,6 @@
     "access": "public",
     "tag": "latest"
   },
-  "scripts": {
-    "build": "tsc",
-    "test": "vitest run"
-  },
   "dependencies": {
     "better-sqlite3": "^12.0.0",
     "chokidar": "^3.6.0",
@@ -55,5 +51,9 @@
     "@types/node": "^20.0.0",
     "typescript": "^5.3.0",
     "vitest": "^4.1.4"
+  },
+  "scripts": {
+    "build": "tsc",
+    "test": "vitest run"
   }
-}
+}

package/src/__tests__/analysis/file-classifier.test.ts

@@ -23,8 +23,8 @@ describe('classifyFile', () => {
   it('classifies arxiv URL as PAPER', () => {
     expect(classifyFile('https://arxiv.org/abs/2401.00001')).toBe('PAPER');
   });
-  it('returns CODE for unknown extension', () => {
-    expect(classifyFile('Makefile')).toBe('CODE');
+  it('returns UNKNOWN for unrecognized extension', () => {
+    expect(classifyFile('Makefile')).toBe('UNKNOWN');
   });
   it('detects paper signals in filename', () => {
     expect(classifyFile('attention_is_all_you_need.pdf')).toBe('PAPER');

package/src/analysis/file-classifier.ts

@@ -1,6 +1,6 @@
 import { extname } from 'path';
 
-export type FileType = 'CODE' | 'DOCUMENT' | 'PAPER' | 'IMAGE' | 'VIDEO';
+export type FileType = 'CODE' | 'DOCUMENT' | 'PAPER' | 'IMAGE' | 'VIDEO' | 'AUDIO' | 'DATA' | 'UNKNOWN';
 
 const CODE_EXTENSIONS = new Set([
   '.ts', '.tsx', '.js', '.jsx', '.mjs', '.cjs',
@@ -28,6 +28,8 @@ const VIDEO_EXTENSIONS = new Set([
   '.wmv', '.m4v',
 ]);
 
+const AUDIO_EXTENSIONS = new Set(['.mp3', '.wav', '.flac', '.aac', '.ogg', '.m4a', '.wma']);
+
 const PAPER_URL_PATTERNS = [
   /arxiv\.org/,
   /semanticscholar\.org/,
@@ -49,6 +51,7 @@ export function classifyFile(pathOrUrl: string): FileType {
 
   if (IMAGE_EXTENSIONS.has(ext)) return 'IMAGE';
   if (VIDEO_EXTENSIONS.has(ext)) return 'VIDEO';
+  if (AUDIO_EXTENSIONS.has(ext)) return 'AUDIO';
 
   if (DOCUMENT_EXTENSIONS.has(ext)) {
     if (ext === '.pdf' && PAPER_FILENAME_SIGNALS.some(p => p.test(pathOrUrl))) return 'PAPER';
@@ -57,7 +60,7 @@ export function classifyFile(pathOrUrl: string): FileType {
 
   if (CODE_EXTENSIONS.has(ext)) return 'CODE';
 
-  return 'CODE';
+  return 'UNKNOWN';
 }
 
 const PAPER_CONTENT_SIGNALS: RegExp[] = [

package/src/pipeline/orchestrator.ts

@@ -42,10 +42,55 @@ export interface BuildOptions extends Partial<PipelineOptions> {
   incremental?: boolean;
 }
 
+// Cross-process build mutex. Callers arrive from several independent entry points
+// (session-start hook, MCP staleness auto-build, CLI, watcher), each with its own
+// ad-hoc lock file that the others don't know about — concurrent builds then fail
+// with "database is locked". Serialize here, the one place all builders pass through.
+async function acquireBuildLock(dbPath: string): Promise<(() => void) | null> {
+  const { writeFileSync, readFileSync, statSync, unlinkSync } = await import('fs');
+  const lockPath = dbPath + '.build-lock';
+  const tryAcquire = (): boolean => {
+    try { writeFileSync(lockPath, String(process.pid), { flag: 'wx' }); return true; }
+    catch { return false; }
+  };
+  if (!tryAcquire()) {
+    // Reclaim if the holder is dead or the lock is older than 30 minutes
+    let stale = false;
+    try {
+      const pid = parseInt(readFileSync(lockPath, 'utf8'), 10);
+      try { process.kill(pid, 0); } catch { stale = true; }
+      if (!stale && Date.now() - statSync(lockPath).mtimeMs > 30 * 60 * 1000) stale = true;
+    } catch { stale = true; }
+    if (!stale) return null;
+    try { unlinkSync(lockPath); } catch { /* raced with another reclaimer */ }
+    if (!tryAcquire()) return null;
+  }
+  return () => { try { unlinkSync(lockPath); } catch { /* already gone */ } };
+}
+
 export async function buildAsync(repoPath: string, options: BuildOptions = {}): Promise<void> {
   const dbPath = resolve(join(repoPath, '.monomind', 'monograph.db'));
   const fullOptions: PipelineOptions = { ...DEFAULT_OPTIONS, ...options };
 
+  const releaseLock = await acquireBuildLock(dbPath);
+  if (!releaseLock) {
+    options.onProgress?.({ phase: 'skip', message: 'Another build is in progress — skipping' });
+    return;
+  }
+  try {
+    await buildAsyncLocked(repoPath, dbPath, fullOptions, options);
+  } finally {
+    releaseLock();
+  }
+}
+
+async function buildAsyncLocked(
+  repoPath: string,
+  dbPath: string,
+  fullOptions: PipelineOptions,
+  options: BuildOptions,
+): Promise<void> {
+
   // Incremental guard: if the caller requested skip-when-fresh and force is
   // not set, check staleness before opening the DB for a full write cycle.
   if (options.incremental && !options.force) {
@@ -97,7 +142,7 @@ export async function buildAsync(repoPath: string, options: BuildOptions = {}):
         db.prepare('SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL').all() as { file_path: string }[]
       )
         .map((r) => r.file_path)
-        .filter((f) => !liveFiles.has(resolve(f)));
+        .filter((f) => !liveFiles.has(resolve(ctx.repoPath, f)));
       if (staleFiles.length > 0) {
         const deleteStale = db.transaction((files: string[]) => {
           // Edges FK-reference nodes with no ON DELETE CASCADE, and a stale node

package/src/pipeline/phases/god-nodes.ts

@@ -5,6 +5,13 @@ import type { CrossFileOutput } from './cross-file.js';
 
 const EXCLUDED_LABELS = new Set(['File', 'Folder', 'Community', 'Concept']);
 
+// Test files stay in the graph (useful for impact/navigation) but are excluded
+// from centrality rankings — a heavily-importing test suite is not a god node.
+const TEST_PATH_RE = /(\.test\.|\.spec\.|__tests__|__mocks__)/;
+function isTestNode(n: { filePath?: string | null }): boolean {
+  return !!(n.filePath && TEST_PATH_RE.test(n.filePath));
+}
+
 export type GodNodeCategory =
   | 'HIGH_CENTRALITY'
   | 'BRIDGE_NODE'
@@ -58,7 +65,7 @@ export const godNodesPhase: PipelinePhase<GodNodesOutput> = {
     const allFanIn: number[] = [];
     const allFanOut: number[] = [];
     for (const n of symbolNodes) {
-      if (EXCLUDED_LABELS.has(n.label)) continue;
+      if (EXCLUDED_LABELS.has(n.label) || isTestNode(n)) continue;
       allFanIn.push(inDeg.get(n.id) ?? 0);
       allFanOut.push(outDeg.get(n.id) ?? 0);
     }
@@ -78,7 +85,8 @@ export const godNodesPhase: PipelinePhase<GodNodesOutput> = {
     const p75FanOut = thresholds.p75FanOut;
 
     const godNodes = symbolNodes
-      .filter(n => !EXCLUDED_LABELS.has(n.label) && (inDeg.get(n.id) ?? 0) + (outDeg.get(n.id) ?? 0) > p95FanIn)
+      .filter(n => !EXCLUDED_LABELS.has(n.label) && !isTestNode(n)
+        && (inDeg.get(n.id) ?? 0) + (outDeg.get(n.id) ?? 0) > p95FanIn)
       .map(n => {
         const fanIn = inDeg.get(n.id) ?? 0;
         const fanOut = outDeg.get(n.id) ?? 0;

package/src/pipeline/phases/scan.ts

@@ -55,6 +55,8 @@ export const scanPhase: PipelinePhase<ScanOutput> = {
 
       for (const entry of entries) {
         if (ignoreDirs.has(entry)) continue;
+        // Skip macOS AppleDouble resource fork files (._*) — common on ExFAT/network volumes
+        if (entry.startsWith('._')) continue;
         const fullPath = join(dir, entry);
         let stat: ReturnType<typeof statSync>;
         try { stat = statSync(fullPath); } catch { continue; }

package/src/pipeline/phases/surprises.ts

@@ -62,7 +62,7 @@ export const surprisesPhase: PipelinePhase<SurprisesOutput> = {
         if (srcFilePath && tgtFilePath) {
           const srcFileType = classifyFile(srcFilePath);
           const tgtFileType = classifyFile(tgtFilePath);
-          if (srcFileType !== tgtFileType) {
+          if (srcFileType !== tgtFileType && srcFileType !== 'UNKNOWN' && tgtFileType !== 'UNKNOWN') {
             score += WEIGHTS.crossRepo;  // reuse unused crossRepo weight (0.15)
             reasons.push(`cross-filetype (${srcFileType}→${tgtFileType})`);
           }

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/.monomind/data/ranked-context.json

@@ -1,5 +0,0 @@
-{
-  "version": 1,
-  "computedAt": 1778102154767,
-  "entries": []
-}

package/.monomind/loops/mastermind-review-1782162423447.json

@@ -1,16 +0,0 @@
-{
-  "id": "mastermind-review-1782162423447",
-  "sessionId": "mastermind-review-1782162423447",
-  "type": "tillend",
-  "command": "/mastermind:review",
-  "prompt": "check the updates on monograph and monoplaybook",
-  "maxReps": 50,
-  "interval": 1,
-  "wait": 60,
-  "currentRep": 1,
-  "startedAt": 1782162423447,
-  "lastRunAt": 1782162423447,
-  "nextRunAt": 1782162423447,
-  "status": "running",
-  "source": "_repeat.md"
-}

package/.monomind/sessions/session-1777578175215.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1777578175215",
-  "startedAt": "2026-04-30T19:42:55.215Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 42,
-    "commands": 0,
-    "tasks": 10,
-    "errors": 0
-  },
-  "endedAt": "2026-05-03T15:52:50.959Z",
-  "duration": 245395745
-}

package/.monomind/sessions/session-1777823684507.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1777823684507",
-  "startedAt": "2026-05-03T15:54:44.507Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 34,
-    "commands": 0,
-    "tasks": 0,
-    "errors": 0
-  },
-  "endedAt": "2026-05-04T21:07:59.511Z",
-  "duration": 105195004
-}

package/.monomind/sessions/session-1777928944749.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1777928944749",
-  "startedAt": "2026-05-04T21:09:04.749Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 18,
-    "commands": 0,
-    "tasks": 3,
-    "errors": 0
-  },
-  "endedAt": "2026-05-06T07:32:36.650Z",
-  "duration": 123811901
-}

package/.monomind/sessions/session-1778052902210.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1778052902210",
-  "startedAt": "2026-05-06T07:35:02.210Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 29,
-    "commands": 0,
-    "tasks": 2,
-    "errors": 0
-  },
-  "endedAt": "2026-05-06T08:37:15.370Z",
-  "duration": 3733161
-}

package/.monomind/sessions/session-1778056744636.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1778056744636",
-  "startedAt": "2026-05-06T08:39:04.636Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 30,
-    "commands": 0,
-    "tasks": 2,
-    "errors": 0
-  },
-  "endedAt": "2026-05-06T09:49:21.825Z",
-  "duration": 4217190
-}

package/.monomind/sessions/session-1778061077599.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1778061077599",
-  "startedAt": "2026-05-06T09:51:17.599Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 11,
-    "commands": 0,
-    "tasks": 0,
-    "errors": 0
-  },
-  "endedAt": "2026-05-06T21:13:36.832Z",
-  "duration": 40939234
-}

package/.monomind/sessions/session-1778102154764.json

@@ -1,15 +0,0 @@
-{
-  "id": "session-1778102154764",
-  "startedAt": "2026-05-06T21:15:54.764Z",
-  "platform": "darwin",
-  "cwd": "/Users/morteza/Desktop/tools/monomind/packages/@monomind/monograph",
-  "context": {},
-  "metrics": {
-    "edits": 12,
-    "commands": 0,
-    "tasks": 0,
-    "errors": 0
-  },
-  "endedAt": "2026-05-09T05:42:40.302Z",
-  "duration": 203205539
-}

package/dist/src/claude-cli.d.ts

@@ -1,3 +0,0 @@
-export declare function isClaudeCliAvailable(): boolean;
-export declare function claudeCliCall(prompt: string, timeoutMs?: number): Promise<string>;
-//# sourceMappingURL=claude-cli.d.ts.map