promptgraph-mcp 2.5.0 → 2.6.0

package/api.js

@@ -39,7 +39,8 @@ export async function index(sourceDir, sourceName) {
     const path = await import('path');
     const { createHash } = await import('crypto');
     const { parseSkillFile, isSkillFile } = await import('./parser.js');
-    const { embedBatch, BATCH_SIZE } = await import('./embedder.js');
+    const { embedBatch } = await import('./embedder.js');
+    const { BATCH_SIZE } = await import('./config.js');
     const { skillId, vecToBlob } = await import('./db.js');
     const { chunkText } = await import('./chunker.js');
 
@@ -105,7 +106,8 @@ export async function update() {
     const path = await import('path');
     const { createHash } = await import('crypto');
     const { parseSkillFile, isSkillFile } = await import('./parser.js');
-    const { embedBatch, BATCH_SIZE } = await import('./embedder.js');
+    const { embedBatch } = await import('./embedder.js');
+    const { BATCH_SIZE } = await import('./config.js');
     const { skillId, vecToBlob } = await import('./db.js');
     const { chunkText } = await import('./chunker.js');
     const { indexBatch } = await import('./indexer.js');

package/bundle-counts.js

@@ -20,12 +20,13 @@ function httpsGet(url) {
   const headers = { 'User-Agent': 'promptgraph-mcp' };
   if (token && url.startsWith('https://api.github.com/')) headers['Authorization'] = `Bearer ${token}`;
   return new Promise((res, rej) => {
-    const req = https.get(url, { headers }, r => {
+    const req = https.get(url, { headers, timeout: 15000 }, r => {
       if (r.statusCode === 403 || r.statusCode === 429) return rej(new Error(`Rate limited`));
       if (r.statusCode !== 200) { r.resume(); return rej(new Error(`HTTP ${r.statusCode}`)); }
-      let d = ''; r.setEncoding('utf8'); r.on('data', c => d += c); r.on('end', () => res(d));
+      const chunks = []; r.setEncoding('utf8'); r.on('data', c => chunks.push(c)); r.on('end', () => res(chunks.join('')));
     });
     req.on('error', rej);
+    req.on('timeout', () => { req.destroy(new Error('timeout')); });
   });
 }
 

package/db.js

@@ -7,124 +7,138 @@ const DB_PATH = path.join(PROMPTGRAPH_DIR, 'promptgraph.db');
 
 let _db = null;
 
-export function getDb() {
-  if (_db) return _db;
-  fs.mkdirSync(path.dirname(DB_PATH), { recursive: true });
-  const db = new Database(DB_PATH);
-  _db = db;
-  db.pragma('journal_mode = WAL');
-
-  db.exec(`
-    CREATE TABLE IF NOT EXISTS skills (
-      id TEXT PRIMARY KEY,
-      name TEXT NOT NULL,
-      description TEXT,
-      path TEXT NOT NULL,
-      source TEXT NOT NULL,
-      content TEXT NOT NULL,
-      hash TEXT
-    );
-
-    CREATE TABLE IF NOT EXISTS chunks (
-      id INTEGER PRIMARY KEY AUTOINCREMENT,
-      skill_id TEXT NOT NULL,
-      chunk_index INTEGER NOT NULL,
-      text TEXT NOT NULL,
-      embedding BLOB NOT NULL,
-      UNIQUE(skill_id, chunk_index)
-    );
-
-    CREATE TABLE IF NOT EXISTS edges (
-      from_skill TEXT NOT NULL,
-      to_skill TEXT NOT NULL,
-      PRIMARY KEY (from_skill, to_skill)
-    );
-
-    CREATE TABLE IF NOT EXISTS ratings (
-      skill_id TEXT PRIMARY KEY,
-      uses INTEGER DEFAULT 0,
-      success INTEGER DEFAULT 0,
-      fail INTEGER DEFAULT 0
-    );
-
-    CREATE VIRTUAL TABLE IF NOT EXISTS skills_fts USING fts5(
-      id UNINDEXED,
-      name,
-      description,
-      content,
-      content='skills',
-      content_rowid='rowid'
-    );
-  `);
-
-  // migrate: add hash column if missing
-  const cols = db.pragma('table_info(skills)').map(c => c.name);
-  if (!cols.includes('hash')) {
-    db.exec('ALTER TABLE skills ADD COLUMN hash TEXT');
+const MIGRATIONS = [
+  {
+    version: 1, description: 'initial schema',
+    up: db => db.exec(`
+      CREATE TABLE IF NOT EXISTS skills (
+        id TEXT PRIMARY KEY,
+        name TEXT NOT NULL,
+        description TEXT,
+        path TEXT NOT NULL,
+        source TEXT NOT NULL,
+        content TEXT NOT NULL,
+        hash TEXT
+      );
+      CREATE TABLE IF NOT EXISTS chunks (
+        id INTEGER PRIMARY KEY AUTOINCREMENT,
+        skill_id TEXT NOT NULL,
+        chunk_index INTEGER NOT NULL,
+        text TEXT NOT NULL,
+        embedding BLOB NOT NULL,
+        UNIQUE(skill_id, chunk_index)
+      );
+      CREATE TABLE IF NOT EXISTS edges (
+        from_skill TEXT NOT NULL,
+        to_skill TEXT NOT NULL,
+        PRIMARY KEY (from_skill, to_skill)
+      );
+      CREATE TABLE IF NOT EXISTS ratings (
+        skill_id TEXT PRIMARY KEY,
+        uses INTEGER DEFAULT 0,
+        success INTEGER DEFAULT 0,
+        fail INTEGER DEFAULT 0
+      );
+      CREATE VIRTUAL TABLE IF NOT EXISTS skills_fts USING fts5(
+        id UNINDEXED, name, description, content,
+        content='skills', content_rowid='rowid'
+      );
+    `),
+  },
+  {
+    version: 2, description: 'add hash column',
+    up: db => {
+      const cols = db.pragma('table_info(skills)').map(c => c.name);
+      if (!cols.includes('hash')) db.exec('ALTER TABLE skills ADD COLUMN hash TEXT');
+    },
+  },
+  {
+    version: 3, description: 'add registry metadata columns',
+    up: db => {
+      const cols = db.pragma('table_info(skills)').map(c => c.name);
+      for (const [col, def] of [
+        ['version', 'TEXT'],
+        ['author', 'TEXT'],
+        ['license', 'TEXT'],
+        ['updated_at', 'TEXT'],
+        ['downloads', 'INTEGER DEFAULT 0'],
+        ['verified', 'INTEGER DEFAULT 0'],
+        ['trust_level', "TEXT DEFAULT 'unknown'"],
+        ['rating', 'REAL DEFAULT 0'],
+        ['rating_count', 'INTEGER DEFAULT 0'],
+        ['popularity', 'REAL DEFAULT 0'],
+        ['last_update', 'TEXT'],
+      ]) {
+        if (!cols.includes(col)) db.exec(`ALTER TABLE skills ADD COLUMN ${col} ${def}`);
+      }
+    },
+  },
+  {
+    version: 4, description: 'registry_entries table',
+    up: db => db.exec(`
+      CREATE TABLE IF NOT EXISTS registry_entries (
+        id TEXT PRIMARY KEY,
+        trust_level TEXT DEFAULT 'unknown',
+        downloads INTEGER DEFAULT 0,
+        rating REAL DEFAULT 0,
+        rating_count INTEGER DEFAULT 0,
+        popularity REAL DEFAULT 0,
+        last_update TEXT
+      );
+    `),
+  },
+  {
+    version: 5, description: 'convert TEXT embeddings to Float32 BLOB',
+    up: db => {
+      const textEmbeddings = db.prepare("SELECT COUNT(*) as n FROM chunks WHERE typeof(embedding) = 'text'").get();
+      if (textEmbeddings?.n > 0) {
+        const rows = db.prepare("SELECT rowid, embedding FROM chunks WHERE typeof(embedding) = 'text'").all();
+        const upd = db.prepare('UPDATE chunks SET embedding = ? WHERE rowid = ?');
+        db.transaction(() => {
+          for (const row of rows) {
+            const vec = JSON.parse(row.embedding);
+            upd.run(Buffer.from(new Float32Array(vec).buffer), row.rowid);
+          }
+        })();
+        console.error(`[PromptGraph] Migrated ${textEmbeddings.n} embeddings TEXT→BLOB`);
+      }
+    },
+  },
+]
+
+function getSchemaVersion(db) {
+  try {
+    return db.prepare('SELECT MAX(version) as v FROM _schema_version').get().v || 0
+  } catch {
+    return 0
   }
+}
 
-  // migrate: add registry metadata columns
-  if (!cols.includes('version')) {
-    db.exec('ALTER TABLE skills ADD COLUMN version TEXT');
-  }
-  if (!cols.includes('author')) {
-    db.exec('ALTER TABLE skills ADD COLUMN author TEXT');
-  }
-  if (!cols.includes('license')) {
-    db.exec('ALTER TABLE skills ADD COLUMN license TEXT');
-  }
-  if (!cols.includes('updated_at')) {
-    db.exec('ALTER TABLE skills ADD COLUMN updated_at TEXT');
-  }
-  if (!cols.includes('downloads')) {
-    db.exec('ALTER TABLE skills ADD COLUMN downloads INTEGER DEFAULT 0');
-  }
-  if (!cols.includes('verified')) {
-    db.exec('ALTER TABLE skills ADD COLUMN verified INTEGER DEFAULT 0');
-  }
-  if (!cols.includes('trust_level')) {
-    db.exec('ALTER TABLE skills ADD COLUMN trust_level TEXT DEFAULT \'unknown\'');
-  }
-  if (!cols.includes('rating')) {
-    db.exec('ALTER TABLE skills ADD COLUMN rating REAL DEFAULT 0');
-  }
-  if (!cols.includes('rating_count')) {
-    db.exec('ALTER TABLE skills ADD COLUMN rating_count INTEGER DEFAULT 0');
-  }
-  if (!cols.includes('popularity')) {
-    db.exec('ALTER TABLE skills ADD COLUMN popularity REAL DEFAULT 0');
-  }
-  if (!cols.includes('last_update')) {
-    db.exec('ALTER TABLE skills ADD COLUMN last_update TEXT');
-  }
+function runMigrations(db) {
+  const current = getSchemaVersion(db)
+  const pending = MIGRATIONS.filter(m => m.version > current).sort((a, b) => a.version - b.version)
+  if (!pending.length) return
 
-  // migrate: registry entries metadata table
-  db.exec(`
-    CREATE TABLE IF NOT EXISTS registry_entries (
-      id TEXT PRIMARY KEY,
-      trust_level TEXT DEFAULT 'unknown',
-      downloads INTEGER DEFAULT 0,
-      rating REAL DEFAULT 0,
-      rating_count INTEGER DEFAULT 0,
-      popularity REAL DEFAULT 0,
-      last_update TEXT
-    );
-  `);
+  db.exec(`CREATE TABLE IF NOT EXISTS _schema_version (version INTEGER PRIMARY KEY, description TEXT, applied_at TEXT)`)
 
-  // migrate: convert JSON text embeddings to Float32 BLOB (one-time, ~10x smaller)
-  const textEmbeddings = db.prepare("SELECT COUNT(*) as n FROM chunks WHERE typeof(embedding) = 'text'").get();
-  if (textEmbeddings?.n > 0) {
-    const rows = db.prepare("SELECT rowid, embedding FROM chunks WHERE typeof(embedding) = 'text'").all();
-    const upd = db.prepare('UPDATE chunks SET embedding = ? WHERE rowid = ?');
+  for (const migration of pending) {
     db.transaction(() => {
-      for (const row of rows) {
-        const vec = JSON.parse(row.embedding);
-        upd.run(Buffer.from(new Float32Array(vec).buffer), row.rowid);
-      }
-    })();
-    console.error(`[PromptGraph] Migrated ${textEmbeddings.n} embeddings TEXT→BLOB`);
+      migration.up(db)
+      db.prepare('INSERT INTO _schema_version (version, description, applied_at) VALUES (?, ?, ?)').run(
+        migration.version, migration.description, new Date().toISOString()
+      )
+    })()
+    console.error(`[PromptGraph] DB migrated to v${migration.version}: ${migration.description}`)
   }
+}
 
+export function getDb() {
+  if (_db) return _db;
+  fs.mkdirSync(path.dirname(DB_PATH), { recursive: true });
+  const db = new Database(DB_PATH);
+  _db = db;
+  db.pragma('journal_mode = WAL');
+  runMigrations(db);
   return db;
 }
 

package/github-import.js

@@ -25,21 +25,22 @@ function getRepoStats(ownerRepo) {
   return repoStats.get(ownerRepo)
 }
 
-function streamDownload(url, maxSize = MAX_DOWNLOAD_SIZE) {
+function streamDownload(url, maxSize = MAX_DOWNLOAD_SIZE, redirects = 0) {
+  if (redirects > 5) return Promise.reject(new Error('Too many redirects'))
   return new Promise((res, rej) => {
     const token = process.env.GITHUB_TOKEN;
     const headers = { 'User-Agent': 'promptgraph-mcp' };
     if (token && url.startsWith('https://raw.')) headers['Authorization'] = `Bearer ${token}`;
     const req = https.get(url, { headers }, r => {
       if (r.statusCode >= 300 && r.statusCode < 400 && r.headers.location)
-        return streamDownload(r.headers.location, maxSize).then(res, rej);
+        return streamDownload(r.headers.location, maxSize, redirects + 1).then(res, rej);
       if (r.statusCode !== 200) { r.resume(); return rej(new Error(`HTTP ${r.statusCode}`)); }
       const cl = parseInt(r.headers['content-length'], 10);
       if (!isNaN(cl) && cl > maxSize) {
         r.resume();
         return rej(new Error(`Content-Length ${cl} exceeds max ${maxSize}`));
       }
-      let d = ''
+      const chunks = []
       let total = 0
       r.setEncoding('utf8')
       r.on('data', c => {
@@ -48,15 +49,16 @@ function streamDownload(url, maxSize = MAX_DOWNLOAD_SIZE) {
           r.destroy()
           return rej(new Error(`Download exceeded ${maxSize} bytes`))
         }
-        d += c
+        chunks.push(c)
       })
-      r.on('end', () => res(d))
+      r.on('end', () => res(chunks.join('')))
     })
     req.on('error', rej)
   })
 }
 
-async function httpsGet(url) {
+async function httpsGet(url, redirects = 0) {
+  if (redirects > 5) return Promise.reject(new Error('Too many redirects'))
   await githubRateLimiter.acquire()
   const token = process.env.GITHUB_TOKEN;
   const headers = { 'User-Agent': 'promptgraph-mcp' };
@@ -64,9 +66,9 @@ async function httpsGet(url) {
   return new Promise((res, rej) => {
     const req = https.get(url, { headers }, r => {
       if (r.statusCode >= 300 && r.statusCode < 400 && r.headers.location)
-        return httpsGet(r.headers.location).then(res, rej);
+        return httpsGet(r.headers.location, redirects + 1).then(res, rej);
       if (r.statusCode !== 200) { r.resume(); return rej(new Error(`HTTP ${r.statusCode}`)); }
-      let d = ''; r.setEncoding('utf8'); r.on('data', c => d += c); r.on('end', () => res(d));
+      const chunks = []; r.setEncoding('utf8'); r.on('data', c => chunks.push(c)); r.on('end', () => res(chunks.join('')));
     });
     req.on('error', rej);
   });

package/index.js

@@ -70,605 +70,25 @@ if (args[0] && !KNOWN_COMMANDS.has(args[0])) {
   process.exit(1);
 }
 
-if (args[0] === 'doctor') {
-  const { runDoctor } = await import('./doctor.js');
-  const spin = (await import('./cli.js')).spinner('Checking database...');
-  spin.start();
-  const r = runDoctor();
-  spin.stop();
-  success('Database checked');
-  info(`Removed: ${r.orphanChunks} chunks, ${r.orphanRatings} ratings, ${r.orphanFromEdges + r.danglingEdges} edges`);
-  if (r.duplicatePaths > 0) info(chalk.yellow(`Warning: ${r.duplicatePaths} duplicate paths`));
-  info(chalk.gray(`Now: ${r.totalSkills} skills, ${r.totalChunks} chunks, ${r.totalEdges} edges`));
-  process.exit(0);
-}
-
-if (args[0] === 'status') {
-  const { loadConfig: _lc } = await import('./config.js');
-  const { getDb } = await import('./db.js');
-  const { fetchText } = await import('./marketplace.js');
-  const purple = chalk.hex('#7C3AED');
-  const cfg = _lc();
-  const db = getDb();
-
-  // Skills per source from DB
-  const sourceCounts = new Map();
-  for (const row of db.prepare('SELECT source, COUNT(*) as n FROM skills GROUP BY source').all()) {
-    sourceCounts.set(row.source, row.n);
-  }
-  const totalSkills = db.prepare('SELECT COUNT(*) as n FROM skills').get().n;
-  const totalBundles = cfg.sources.filter(s => s.source.startsWith('github:')).length;
-
-  // Fetch marketplace totals for comparison
-  let marketSkills = 0, marketBundles = 0;
-  try {
-    const REGISTRY_URL = 'https://raw.githubusercontent.com/NeiP4n/promptgraph-registry/main/registry.json';
-    const reg = JSON.parse(await fetchText(REGISTRY_URL));
-    marketSkills = reg.skills?.length || 0;
-    marketBundles = reg.bundles?.length || 0;
-  } catch {}
-
-  console.log();
-  console.log('  ' + purple.bold('◆ PromptGraph Status'));
-  console.log('  ' + chalk.gray('─'.repeat(56)));
-  console.log();
-
-  // Summary row
-  const skillsLine = chalk.bold.white(`${totalSkills} skills`) +
-    (marketSkills ? chalk.gray(` / ${marketSkills} in registry`) : '');
-  const bundlesLine = chalk.bold.white(`${totalBundles} repos`) +
-    (marketBundles ? chalk.gray(` / ${marketBundles} in marketplace`) : '');
-  console.log('  ' + skillsLine + chalk.gray('   ·   ') + bundlesLine);
-  console.log();
-
-  // Sources grouped by type
-  const githubSources = cfg.sources.filter(s => s.source.startsWith('github:'));
-  const localSources  = cfg.sources.filter(s => !s.source.startsWith('github:'));
-
-  if (localSources.length) {
-    console.log('  ' + purple('📁  Local'));
-    for (const s of localSources) {
-      const n = sourceCounts.get(s.source) || 0;
-      const exists = fs.existsSync(s.dir);
-      const label = exists ? chalk.white(s.source) : chalk.gray(s.source + ' (missing)');
-      console.log('    ' + label + chalk.gray(`  ${n} skills  ·  ${s.dir}`));
-    }
-    console.log();
-  }
-
-  if (githubSources.length) {
-    console.log('  ' + purple('🌐  GitHub repos'));
-    for (const s of githubSources) {
-      const n = sourceCounts.get(s.source) || 0;
-      const repoName = s.source.replace('github:', '');
-      const exists = fs.existsSync(s.dir);
-      const label = exists ? chalk.white(repoName) : chalk.gray(repoName + ' (not cloned)');
-      console.log('    ' + label + chalk.gray(`  ${n} skills`));
-      console.log('      ' + chalk.dim(s.dir));
-    }
-    console.log();
-  }
-
-  // Marketplace skill-list bundles (installed individually, not whole repos)
-  const marketplaceDir = path.join(os.homedir(), '.claude', 'skills-store', 'marketplace');
-  const installedBundles = fs.existsSync(marketplaceDir)
-    ? fs.readdirSync(marketplaceDir, { withFileTypes: true }).filter(d => d.isDirectory()).map(d => d.name)
-    : [];
-
-  if (installedBundles.length) {
-    let registryBundles = [];
-    try {
-      const REGISTRY_URL = 'https://raw.githubusercontent.com/NeiP4n/promptgraph-registry/main/registry.json';
-      const text = await fetchText(REGISTRY_URL);
-      registryBundles = JSON.parse(text).bundles || [];
-    } catch {}
-
-    console.log('  ' + purple('📦  Installed marketplace bundles'));
-    for (const b of installedBundles) {
-      const bundle = registryBundles.find(rb => rb.id === b);
-      const name = bundle ? chalk.white.bold(bundle.name || b) : chalk.white(b);
-      const cat  = bundle?.category ? chalk.dim(` [${bundle.category}]`) : '';
-      const n    = sourceCounts.get('marketplace') || 0;
-      console.log(`    ${name}${cat}  ${chalk.gray(n + ' skills')}`);
-    }
-    console.log();
-  }
-
-  // Not-yet-indexed repos hint
-  const emptyRepos = githubSources.filter(s => (sourceCounts.get(s.source) || 0) === 0 && fs.existsSync(s.dir));
-  if (emptyRepos.length) {
-    console.log('  ' + chalk.yellow(`⚠  ${emptyRepos.length} repo(s) not indexed`) + chalk.gray('  →  run: ') + chalk.cyan(`${bin} reindex`));
-    console.log();
-  }
-
-  console.log(
-    boxen(
-      chalk.dim('full reindex   ') + chalk.cyan(`${bin} reindex`) + '\n' +
-      chalk.dim('install bundle ') + chalk.cyan(`${bin} bundle install <id>`) + '\n' +
-      chalk.dim('browse market  ') + chalk.cyan(`${bin} marketplace bundles`),
-      { padding: { top: 0, bottom: 0, left: 1, right: 1 }, borderStyle: 'round', borderColor: '#4B5563', dimBorder: true }
-    )
-  );
-  console.log();
-  process.exit(0);
-}
-
-if (args[0] === 'marketplace') {
-  if (!process.stdout.isTTY) {
-    error('marketplace TUI requires an interactive terminal');
-    process.exit(1);
-  }
-  const { browseMarketplace, browseBundles, installSkill, installBundle } = await import('./marketplace.js');
-  const { loadConfig: _lcMkt } = await import('./config.js');
-  const { getDb: _getDbMkt } = await import('./db.js');
-  const { spinner: spin2 } = await import('./cli.js');
-  const sp = spin2('Fetching marketplace...');
-  sp.start();
-  const [skills, bundles] = await Promise.all([browseMarketplace(1000), browseBundles(1000)]);
-  sp.stop();
-
-  if (skills?.error) { error(skills.error); process.exit(1); }
-
-  // Apply cached skillCounts and refresh stale ones in background
-  const { getCachedCount, refreshCountsInBackground } = await import('./bundle-counts.js');
-  const bundlesWithCounts = (Array.isArray(bundles) ? bundles : []).map(b => {
-    if (!b.repo_url) return b;
-    const cached = getCachedCount(b.repo_url);
-    return cached !== null ? { ...b, skillCount: cached } : b;
-  });
-  refreshCountsInBackground(bundlesWithCounts);
-
-  // Build installed set — source of truth is the FILESYSTEM, not DB/config
-  const installedSet = new Set();
-  try {
-    const cfg = _lcMkt();
-    const db = _getDbMkt();
-    const { SKILLS_STORE_DIR } = await import('./config.js');
-    const githubDir = path.join(SKILLS_STORE_DIR, 'github');
-
-    for (const b of (Array.isArray(bundles) ? bundles : [])) {
-      if (b.repo_url) {
-        // Check actual cloned directory exists and has files
-        const owner = b.repo_url.split('/')[0];
-        const repo  = b.repo_url.split('/')[1];
-        const clonedName = `${owner}-${repo}`;
-        const clonedDir  = path.join(githubDir, clonedName);
-        const dirExists  = fs.existsSync(clonedDir) &&
-          fs.readdirSync(clonedDir).length > 0; // not empty
-        if (dirExists) installedSet.add(b.id);
-      } else if (Array.isArray(b.skills)) {
-        // skill-list bundle: check files exist on disk via DB path column
-        const allOnDisk = b.skills.every(sid => {
-          const row = db.prepare('SELECT path FROM skills WHERE id = ?').get(sid);
-          return row && fs.existsSync(row.path);
-        });
-        if (b.skills.length > 0 && allOnDisk) installedSet.add(b.id);
-      }
-    }
-
-    // Individual marketplace skills — check file exists on disk
-    for (const row of db.prepare('SELECT id, path FROM skills WHERE source = ?').all('marketplace')) {
-      if (fs.existsSync(row.path)) installedSet.add(row.id);
-    }
-  } catch {}
-
-  const { runTUI } = await import('./tui.js');
-  const { loadConfig: _lcR, saveConfig: _scR, SKILLS_STORE_DIR: _ssR } = await import('./config.js');
-  const { getDb: _getDbR } = await import('./db.js');
-
-  await runTUI(
-    Array.isArray(skills) ? skills : [],
-    bundlesWithCounts,
-    async (item) => {
-      if (item.type === 'bundle') {
-        const r = await installBundle(item.id);
-        if (r?.error) throw new Error(r.error);
-        installedSet.add(item.id);
-      } else {
-        const r = await installSkill(item.code || item.id);
-        if (r?.error) throw new Error(r.error);
-        installedSet.add(item.id);
-        if (item.code) installedSet.add(item.code);
-      }
-    },
-    installedSet,
-    async (item) => {
-      const cfg = _lcR();
-      const db  = _getDbR();
-      if (item.type === 'bundle' && item.repo_url) {
-        // Remove cloned directory
-        const owner = item.repo_url.split('/')[0];
-        const repo  = item.repo_url.split('/')[1];
-        const clonedName = `${owner}-${repo}`;
-        const clonedDir  = path.join(_ssR, 'github', clonedName);
-        if (fs.existsSync(clonedDir)) fs.rmSync(clonedDir, { recursive: true, force: true });
-        // Remove from config + DB
-        const src = `github:${clonedName}`;
-        cfg.sources = cfg.sources.filter(s => s.source !== src && !s.dir.startsWith(clonedDir));
-        _scR(cfg);
-        db.prepare('DELETE FROM skills WHERE source = ?').run(src);
-        db.prepare('DELETE FROM chunks WHERE skill_id NOT IN (SELECT id FROM skills)').run();
-      } else if (item.type === 'bundle') {
-        // skill-list bundle — remove each skill file
-        const mktDir = path.join(_ssR, 'marketplace');
-        for (const sid of (item.skills || [])) {
-          const row = db.prepare('SELECT path FROM skills WHERE id = ?').get(sid);
-          if (row?.path && fs.existsSync(row.path)) fs.unlinkSync(row.path);
-          db.prepare('DELETE FROM skills WHERE id = ?').run(sid);
-          db.prepare('DELETE FROM chunks WHERE skill_id = ?').run(sid);
-        }
-      } else {
-        // individual skill
-        const row = db.prepare('SELECT path FROM skills WHERE id = ?').get(item.id);
-        if (row?.path && fs.existsSync(row.path)) fs.unlinkSync(row.path);
-        db.prepare('DELETE FROM skills WHERE id = ?').run(item.id);
-        db.prepare('DELETE FROM chunks WHERE skill_id = ?').run(item.id);
-      }
-      installedSet.delete(item.id);
-      if (item.code) installedSet.delete(item.code);
-    }
-  );
-  process.exit(0);
-}
-
-if (args[0] === 'validate') {
-  const { validateSkill } = await import('./validator.js');
-  const { isSkillFile } = await import('./parser.js');
-  const file = args[1];
-  if (!file) { error('Usage: ' + bin + ' validate <skill.md>'); process.exit(1); }
-
-  const raw = fs.existsSync(file) ? fs.readFileSync(file, 'utf8') : null;
-
-  if (raw) {
-    const { filterWithClassifier, isSkillFile: _isSkill } = await import('./parser.js');
-    const { hardFilter } = await import('./src/filter/hard-filter.js');
-    const { loadModel } = await import('./src/filter/train.js');
-    const { embed } = await import('./embedder.js');
-    const { classify } = await import('./src/filter/classifier.js');
-
-    const hfResult = hardFilter(file, raw);
-    const willIndex = _isSkill(file, raw);
-    const scoreLabel = willIndex ? chalk.green('✓ will be indexed') : chalk.red('✗ will be skipped by indexer');
-    console.log(chalk.bold('\n  Indexing check: ') + scoreLabel);
-
-    const signals = [];
-    if (!hfResult.pass) {
-      signals.push(chalk.red(`✗ hard filter: ${hfResult.reason}`));
-    } else {
-      signals.push(chalk.green('✓ hard filter passed'));
-    }
-
-    const centroids = loadModel();
-    if (centroids) {
-      try {
-        const vec = await embed(raw);
-        const decision = classify(vec, centroids, raw, file);
-        const pct = (decision.score * 100).toFixed(0);
-        if (decision.label === 'skill') signals.push(chalk.green(`✓ classifier: skill (${pct}%)`));
-        else if (decision.label === 'unsure') signals.push(chalk.yellow(`? classifier: unsure (${pct}%)`));
-        else signals.push(chalk.red(`✗ classifier: reject (${pct}%)`));
-      } catch {
-        signals.push(chalk.gray('  classifier: embed failed (skip)'));
-      }
-    } else {
-      signals.push(chalk.gray('  classifier: no model (run `pg train`)'));
-    }
-
-    if (signals.length) {
-      signals.forEach(s => console.log('    ' + s));
-    }
-    console.log();
-  }
-
-  const result = validateSkill(file);
-  result.warnings.forEach(w => console.log(chalk.yellow('⚠') + '  ' + chalk.gray(w)));
-  if (result.ok) {
-    success('Skill is valid — ready to publish');
-    process.exit(0);
-  } else {
-    error('Validation failed:');
-    result.errors.forEach(e => console.log('   ' + chalk.red('•') + ' ' + e));
-    process.exit(1);
-  }
-}
-
-if (args[0] === 'train') {
-  const { train: trainModel } = await import('./src/filter/train.js');
-  const spin = (await import('./cli.js')).spinner('Training classifier...');
-  spin.start();
-  try {
-    const model = await trainModel();
-    spin.stop();
-    success(`Classifier trained (${model.counts.good} good, ${model.counts.bad} bad examples)`);
-  } catch (e) {
-    spin.stop();
-    error(`Training failed: ${e.message}`);
-    process.exit(1);
-  }
-  process.exit(0);
+const COMMAND_MAP = {
+  doctor:    './commands/doctor.js',
+  status:    './commands/status.js',
+  marketplace: './commands/marketplace.js',
+  validate:  './commands/validate.js',
+  train:     './commands/train.js',
+  search:    './commands/search.js',
+  bundle:    './commands/bundle.js',
+  import:    './commands/import.js',
+  setup:     './commands/setup.js',
+  init:      './commands/init.js',
+  update:    './commands/update.js',
+  reindex:   './commands/reindex.js',
 }
 
-if (args[0] === 'search') {
-  const query = args.slice(1).join(' ');
-  if (!query) { error('Usage: ' + bin + ' search <query>'); process.exit(1); }
-  const { search: searchSkills } = await import('./search.js');
-  const spin = (await import('./cli.js')).spinner('Searching...');
-  spin.start();
-  const results = await searchSkills(query, 10);
-  spin.stop();
-  if (!results.length) { info('No results for: ' + query); process.exit(0); }
-  const purple = chalk.hex('#7C3AED');
-  console.log();
-  results.forEach((s, i) => {
-    const score = chalk.dim((s.score * 100).toFixed(0) + '%');
-    console.log('  ' + chalk.dim(String(i + 1) + '.') + ' ' + chalk.bold.white(s.name) + '  ' + score);
-    console.log('     ' + chalk.dim(s.description || ''));
-    console.log('     ' + purple(s.source) + '  ' + chalk.dim(s.path));
-    console.log();
-  });
-  process.exit(0);
-}
-
-if (args[0] === 'bundle') {
-  if (args[1] === 'update') {
-    const { loadConfig: _lcUpd, SKILLS_STORE_DIR: _ssDir } = await import('./config.js');
-    const { indexSource } = await import('./indexer.js');
-    const cfg = _lcUpd();
-    const githubSources = cfg.sources.filter(s => s.source.startsWith('github:'));
-
-    if (!githubSources.length) { info('No GitHub bundles installed.'); process.exit(0); }
-
-    const targetId = args[2]; // optional: pg bundle update <id>
-    const toUpdate = targetId
-      ? githubSources.filter(s => s.source.toLowerCase().includes(targetId.toLowerCase()))
-      : githubSources;
-
-    if (!toUpdate.length) { error(`No installed bundle matching "${targetId}"`); process.exit(1); }
-
-    let updated = 0, unchanged = 0, failed = 0;
-
-    for (const src of toUpdate) {
-      const repoName = src.source.replace('github:', '');
-      const dest = src.dir.replace(/[/\\]skills$|[/\\]commands$|[/\\]prompts$/, ''); // get repo root
-      const repoRoot = fs.existsSync(path.join(dest, '.git')) ? dest : src.dir;
-
-      if (!fs.existsSync(path.join(repoRoot, '.git'))) {
-        console.log(chalk.gray(`  skip ${repoName} (not a git repo)`));
-        continue;
-      }
-
-      process.stdout.write(`  Checking ${chalk.white(repoName)}... `);
-
-      // Get current HEAD hash
-      const before = spawnSync('git', ['-C', repoRoot, 'rev-parse', 'HEAD'], { encoding: 'utf8' }).stdout.trim();
-
-      // Fetch + reset (same as install)
-      const fetch = spawnSync('git', ['-C', repoRoot, 'fetch', '--depth=1', 'origin'], { stdio: 'pipe' });
-      if (fetch.status !== 0) {
-        console.log(chalk.red('fetch failed'));
-        failed++;
-        continue;
-      }
-      const reset = spawnSync('git', ['-C', repoRoot, 'reset', '--hard', 'origin/HEAD'], { stdio: 'pipe' });
-      if (reset.status !== 0) {
-        spawnSync('git', ['-C', repoRoot, 'reset', '--hard', 'origin/main'], { stdio: 'pipe' });
-      }
-
-      const after = spawnSync('git', ['-C', repoRoot, 'rev-parse', 'HEAD'], { encoding: 'utf8' }).stdout.trim();
-
-      if (before === after) {
-        console.log(chalk.gray('already up to date'));
-        unchanged++;
-        continue;
-      }
-
-      // Count changed .md files
-      const diff = spawnSync('git', ['-C', repoRoot, 'diff', '--name-only', before, after], { encoding: 'utf8' });
-      const changedMd = (diff.stdout || '').split('\n').filter(f => f.endsWith('.md')).length;
-      console.log(chalk.green(`${changedMd} files changed`) + chalk.gray(` (${before.slice(0,7)} → ${after.slice(0,7)})`));
-
-      // Reindex only this source — incremental hash check skips unchanged files
-      await indexSource(src.dir, src.source);
-      updated++;
-    }
-
-    console.log();
-    if (updated)   success(`Updated ${updated} bundle(s)`);
-    if (unchanged) info(chalk.gray(`${unchanged} already up to date`));
-    if (failed)    error(`${failed} failed`);
-    process.exit(failed > 0 ? 1 : 0);
-  }
-
-  if (args[1] === 'install') {
-    const { installBundle } = await import('./marketplace.js');
-    const result = await installBundle(args[2]);
-    if (result?.error) { error(result.error); process.exit(1); }
-    success(result.type === 'repo_import' ? `Imported from ${result.repo_url}` : `Installed ${result.installed?.length || 0} skills`);
-    process.exit(0);
-  }
-  if (args[1] === 'add-repo') {
-    const doPush = args[args.length - 1] === '--push';
-    const repoArg = doPush ? args[2] : args[2];
-    if (!repoArg || !repoArg.includes('/')) { error('Usage: pg bundle add-repo <owner/repo> [--push]'); process.exit(1); }
-    const repo = repoArg.replace('https://github.com/', '').replace('.git', '');
-
-    // Validate repo has a skill subdirectory before publishing
-    const { detectSkillsDirFromAPI: _detectDir } = await import('./github-import.js');
-    process.stdout.write(chalk.gray(`  Checking ${repo} for skill subdirectory... `));
-    const detected = await _detectDir(repo);
-    if (!detected) {
-      console.log(chalk.red('none found'));
-      error(
-        `Cannot publish: no skill subdirectory found in ${repo}\n` +
-        `  Expected: skills/, prompts/, commands/, agents/, or any folder with .md files\n` +
-        `  Visit: https://github.com/${repo}`
-      );
-      process.exit(1);
-    }
-    console.log(chalk.green(`found: ${detected.label}/`));
-    const name = repo.split('/')[1].replace(/-/g, ' ').replace(/\b\w/g, c => c.toUpperCase());
-    const id = repo.replace('/', '-').toLowerCase();
-    const bundle = {
-      id, name, repo_url: repo, author: repo.split('/')[0],
-      description: `Skills from ${repo}`,
-      tags: ['community'],
-      stars: 0
-    };
-    const json = JSON.stringify(bundle, null, 2);
-
-    if (doPush) {
-      const registryDir = path.join(os.tmpdir(), 'pg-push-registry');
-      const gitEnv = { ...process.env, GIT_TERMINAL_PROMPT: '0' };
-      const git = (args, opts = {}) => { const r = spawnSync('git', args, { ...opts, env: gitEnv, stdio: 'pipe' }); if (r.status !== 0) { error(r.stderr?.toString() || r.stdout?.toString() || 'git error'); process.exit(1); } return r; };
-      if (fs.existsSync(registryDir)) {
-        git(['-C', registryDir, 'pull']);
-      } else {
-        git(['clone', 'https://github.com/NeiP4n/promptgraph-registry.git', registryDir]);
-      }
-      const regFile = path.join(registryDir, 'registry.json');
-      const reg = JSON.parse(fs.readFileSync(regFile, 'utf8'));
-      if (reg.bundles.find(b => b.id === id)) { error(`Bundle "${id}" already exists`); process.exit(1); }
-      reg.bundles.push(bundle);
-      reg.updated = new Date().toISOString().slice(0, 10);
-      fs.writeFileSync(regFile, JSON.stringify(reg, null, 2) + '\n');
-      fs.writeFileSync(path.join(registryDir, 'bundles', `${id}.json`), json + '\n');
-      git(['-C', registryDir, 'config', 'user.email', 'pg-bot@promptgraph.ai']);
-      git(['-C', registryDir, 'config', 'user.name', 'PromptGraph Bot']);
-      git(['-C', registryDir, 'add', '-A']);
-      git(['-C', registryDir, 'commit', '-m', `bundle: ${name} (${repo})`]);
-      git(['-C', registryDir, 'push']);
-      success(`Bundle "${id}" pushed to registry`);
-    } else {
-      const tmp = path.join(os.tmpdir(), `pg-bundle-${id}.json`);
-      fs.writeFileSync(tmp, json);
-      const { publishBundle } = await import('./marketplace.js');
-      const result = await publishBundle(tmp);
-      fs.unlinkSync(tmp);
-      if (result?.error) { error(result.error); process.exit(1); }
-      if (result.gh_not_installed) {
-        console.log('\n' + result.instructions);
-        console.log(chalk.gray('\nBundle JSON:\n') + chalk.white(json));
-      } else {
-        success(`Bundle proposed! Submit: ${result.submit_url}`);
-      }
-    }
-    process.exit(0);
-  }
-  error('Usage: pg bundle install <id>  |  pg bundle add-repo <owner/repo> [--push]');
-  process.exit(1);
-}
-
-if (args[0] === 'import') {
-  const { importFromGitHub } = await import('./github-import.js');
-  await importFromGitHub(args[1]);
-  process.exit(0);
-}
-
-if (args[0] === 'setup') {
-  const { detectPlatforms, PLATFORMS } = await import('./platform.js');
-  const platformId = args[1];
-  if (!platformId) {
-    section('Detected platforms');
-    detectPlatforms().forEach(p => info(`${chalk.white(p.id.padEnd(16))} ${chalk.gray(p.name)}`));
-    console.log(chalk.gray('\n  Usage: promptgraph-mcp setup <platform-id>\n'));
-  } else {
-    const platform = PLATFORMS[platformId];
-    if (!platform) { error(`Unknown platform: ${platformId}`); process.exit(1); }
-    platform.addMcp(platform);
-    success(`Registered in ${chalk.white(platform.name)}`);
-    info(chalk.gray(platform.configPath));
-  }
-  process.exit(0);
-}
-
-if (args[0] === 'init') {
-  const { promptConfig } = await import('./config.js');
-  const { indexAll } = await import('./indexer.js');
-  const os = await import('os');
-  const fs = await import('fs');
-  const path = await import('path');
-  const commandsDir = path.default.join(os.default.homedir(), '.claude', 'commands');
-  if (!fs.default.existsSync(commandsDir)) {
-    console.log(chalk.yellow('⚠') + '  ' + chalk.gray('~/.claude/commands/ not found — is Claude Code installed?'));
-    console.log(chalk.gray('   Install from: https://claude.ai/download\n'));
-  }
-  if (!args.includes('--yes') && !args.includes('-y')) {
-    const readline = await import('readline');
-    const rl = readline.default.createInterface({ input: process.stdin, output: process.stdout });
-    const answer = await new Promise(r => rl.question(
-      chalk.yellow('  ⚠') + chalk.gray('  First run downloads ~23 MB embedding model (BGE-Small-EN).\n  Proceed? [Y/n] '), r
-    ));
-    rl.close();
-    if (answer.trim().toLowerCase() === 'n') { info('Aborted.'); process.exit(0); }
-  }
-  console.log(chalk.gray('\n  Downloading embedding model (~23 MB, one-time)...\n'));
-  const config = await promptConfig();
-  await indexAll();
-  console.log();
-  console.log(
-    boxen(
-      chalk.white.bold('Add to Claude Code settings.json:') + '\n\n' +
-      chalk.gray(JSON.stringify({ mcpServers: { promptgraph: { command: 'npx', args: ['promptgraph-mcp'] } } }, null, 2)),
-      { padding: 1, borderStyle: 'round', borderColor: '#7C3AED', dimBorder: true }
-    )
-  );
-  process.exit(0);
-}
-
-if (args[0] === 'update') {
-  const { spawnSync } = await import('child_process');
-  const { createRequire } = await import('module');
-  const https = (await import('https')).default;
-  const req = createRequire(import.meta.url);
-  const currentVersion = req('./package.json').version;
-
-  // Check latest version via registry API (works behind proxies/VPN, no npm spawn needed)
-  const spin = (await import('./cli.js')).spinner('Checking latest version...');
-  spin.start();
-  let latest = null;
-  try {
-    latest = await new Promise((res, rej) => {
-      const r = https.get('https://registry.npmjs.org/promptgraph-mcp/latest',
-        { headers: { Accept: 'application/json' }, timeout: 8000 },
-        (resp) => {
-          let d = ''; resp.setEncoding('utf8');
-          resp.on('data', c => d += c);
-          resp.on('end', () => { try { res(JSON.parse(d).version); } catch { rej(new Error('bad response')); } });
-        }
-      );
-      r.on('error', rej);
-      r.on('timeout', () => { r.destroy(new Error('timeout')); });
-    });
-  } catch {}
-  spin.stop();
-
-  if (!latest) { error('Could not reach npm registry. Check your network.'); process.exit(1); }
-  if (latest === currentVersion) {
-    success(`Already on latest version ${chalk.white.bold('v' + currentVersion)}`);
-    process.exit(0);
-  }
-
-  info(`Current: ${chalk.gray('v' + currentVersion)}  →  Latest: ${chalk.white.bold('v' + latest)}`);
-  const updateSpin = (await import('./cli.js')).spinner(`Installing promptgraph-mcp@latest (v${latest})...`);
-  updateSpin.start();
-  const result = spawnSync('npm', ['install', '-g', 'promptgraph-mcp@latest'], { encoding: 'utf8', stdio: 'pipe', shell: true });
-  updateSpin.stop();
-
-  if (result.status !== 0) {
-    error('Update failed:');
-    console.log(chalk.gray(result.stderr || result.stdout));
-    process.exit(1);
-  }
-  success(`Updated to ${chalk.white.bold('v' + latest)}`);
-  process.exit(0);
-}
-
-if (args[0] === 'reindex') {
-  const { indexAll } = await import('./indexer.js');
-  const fast = args.includes('--fast');
-  if (fast) info(chalk.yellow('Fast mode — skipping embeddings (keyword search only)'));
-  await indexAll({ fast });
-  process.exit(0);
+if (COMMAND_MAP[args[0]]) {
+  const mod = await import(COMMAND_MAP[args[0]])
+  await mod.handler(args, bin)
+  // handler calls process.exit() internally
 }
 
 // ── MCP server mode (no CLI command) ──
@@ -680,8 +100,10 @@ const { loadConfig: _loadConfig, saveConfig: _saveConfig } = await import('./con
 const { startWatcher } = await import('./watcher.js');
 const { browseMarketplace, installSkill, installSkillFromUrl, publishSkill, publishBundle, getTopRated, recordUse, recordSuccess, recordFail, browseBundles, installBundle } = await import('./marketplace.js');
 
+const { createRequire } = await import('module');
+const pkg = createRequire(import.meta.url)('./package.json');
 const server = new Server(
-  { name: 'promptgraph', version: '1.0.0' },
+  { name: 'promptgraph', version: pkg.version },
   { capabilities: { tools: {} } }
 );
 

package/indexer.js

@@ -19,7 +19,7 @@ function sanitizePath(filePath) {
   return path.resolve(filePath);
 }
 
-async function indexBatch(db, skills, { fast = false } = {}) {
+export async function indexBatch(db, skills, { fast = false } = {}) {
   const upsertSkill = db.prepare(`
     INSERT INTO skills (id, name, description, path, source, content, hash, version, author, license, updated_at, downloads, verified)
     VALUES (@id, @name, @description, @path, @source, @content, @hash, @version, @author, @license, @updated_at, @downloads, @verified)
@@ -107,21 +107,15 @@ export async function indexAll({ fast = false } = {}) {
     normDir: path.resolve(s.dir),
   })).sort((a, b) => b.normDir.length - a.normDir.length); // longest first
 
-  console.error('DEBUG normalizedSources count:', normalizedSources.length);
-  console.error('DEBUG first dir:', normalizedSources[0]?.dir);
-
   const seenFiles = new Set();
   const allFiles = [];
   for (const { dir, source } of normalizedSources) {
     const files = globSync(`${dir}/**/*.md`);
-    console.error('DEBUG source:', source, 'dir:', dir, 'count:', files.length);
     for (const f of files) {
       const norm = sanitizePath(f);
       if (!seenFiles.has(norm)) {
         seenFiles.add(norm);
         allFiles.push({ file: norm, source });
-      } else {
-        console.error('DEBUG duplicate:', norm);
       }
     }
     if (allFiles.length > MAX_FILE_COUNT) {
@@ -130,7 +124,6 @@ export async function indexAll({ fast = false } = {}) {
     }
   }
   const total = allFiles.length;
-  console.error('DEBUG total files found:', total);
   info(`Found ${chalk.white.bold(total)} files`);
 
   // reconcile: remove skills whose files no longer exist OR whose name changed

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "promptgraph-mcp",
-  "version": "2.5.0",
+  "version": "2.6.0",
   "files": [
     "*.js",
     "src/**/*.js",

package/src/reranker/reranker.js

@@ -4,12 +4,13 @@ export class Reranker {
     this.device = device
   }
 
-  // Cross-encoder style reranker
-  // Plug-in point for BGE Reranker / MiniLM Reranker via ONNX
+  // Term-overlap boost on top of hybrid search scores
+  // This is a lightweight reranker that ranks by term overlap ratio.
+  // Replace with BGE Reranker / MiniLM cross-encoder via ONNX for deeper semantic reranking.
   async rerank(query, results) {
     if (!results || results.length === 0) return []
 
-    const queryTerms = (query.toLowerCase().match(/\w+/g) || [])
+    const queryTerms = (query.toLowerCase().match(/\w+/g) || []).slice(0, 50)
     const queryTermCount = queryTerms.length || 1
 
     const scored = results.map(r => {