ruvector 0.1.45 → 0.1.47

package/bin/cli.js

@@ -2267,6 +2267,40 @@ class Intelligence {
 // Hooks command group
 const hooksCmd = program.command('hooks').description('Self-learning intelligence hooks for Claude Code');
 
+// Helper: Detect project type
+function detectProjectType() {
+  const cwd = process.cwd();
+  const types = [];
+  if (fs.existsSync(path.join(cwd, 'Cargo.toml'))) types.push('rust');
+  if (fs.existsSync(path.join(cwd, 'package.json'))) types.push('node');
+  if (fs.existsSync(path.join(cwd, 'requirements.txt')) || fs.existsSync(path.join(cwd, 'pyproject.toml'))) types.push('python');
+  if (fs.existsSync(path.join(cwd, 'go.mod'))) types.push('go');
+  if (fs.existsSync(path.join(cwd, 'Gemfile'))) types.push('ruby');
+  if (fs.existsSync(path.join(cwd, 'pom.xml')) || fs.existsSync(path.join(cwd, 'build.gradle'))) types.push('java');
+  return types.length > 0 ? types : ['generic'];
+}
+
+// Helper: Get permissions for project type
+function getPermissionsForProjectType(types) {
+  const basePermissions = [
+    'Bash(git status)', 'Bash(git diff:*)', 'Bash(git log:*)', 'Bash(git add:*)',
+    'Bash(git commit:*)', 'Bash(git push)', 'Bash(git branch:*)', 'Bash(git checkout:*)',
+    'Bash(ls:*)', 'Bash(pwd)', 'Bash(cat:*)', 'Bash(mkdir:*)', 'Bash(which:*)', 'Bash(ruvector:*)'
+  ];
+  const typePermissions = {
+    rust: ['Bash(cargo:*)', 'Bash(rustc:*)', 'Bash(rustfmt:*)', 'Bash(clippy:*)', 'Bash(wasm-pack:*)'],
+    node: ['Bash(npm:*)', 'Bash(npx:*)', 'Bash(node:*)', 'Bash(yarn:*)', 'Bash(pnpm:*)'],
+    python: ['Bash(python:*)', 'Bash(pip:*)', 'Bash(pytest:*)', 'Bash(poetry:*)', 'Bash(uv:*)'],
+    go: ['Bash(go:*)', 'Bash(gofmt:*)'],
+    ruby: ['Bash(ruby:*)', 'Bash(gem:*)', 'Bash(bundle:*)', 'Bash(rails:*)'],
+    java: ['Bash(mvn:*)', 'Bash(gradle:*)', 'Bash(java:*)', 'Bash(javac:*)'],
+    generic: ['Bash(make:*)']
+  };
+  let perms = [...basePermissions];
+  types.forEach(t => { if (typePermissions[t]) perms = perms.concat(typePermissions[t]); });
+  return [...new Set(perms)];
+}
+
 hooksCmd.command('init')
   .description('Initialize hooks in current project')
   .option('--force', 'Force overwrite existing settings')
@@ -2274,6 +2308,9 @@ hooksCmd.command('init')
   .option('--no-claude-md', 'Skip CLAUDE.md creation')
   .option('--no-permissions', 'Skip permissions configuration')
   .option('--no-env', 'Skip environment variables')
+  .option('--no-gitignore', 'Skip .gitignore update')
+  .option('--no-mcp', 'Skip MCP server configuration')
+  .option('--no-statusline', 'Skip statusLine configuration')
   .action((opts) => {
   const settingsPath = path.join(process.cwd(), '.claude', 'settings.json');
   const settingsDir = path.dirname(settingsPath);
@@ -2294,6 +2331,10 @@ hooksCmd.command('init')
     if (settings.hooks.End) { delete settings.hooks.End; }
   }
 
+  // Detect project type
+  const projectTypes = detectProjectType();
+  console.log(chalk.blue(`  ✓ Detected project type(s): ${projectTypes.join(', ')}`));
+
   // Environment variables for intelligence (unless --minimal or --no-env)
   if (!opts.minimal && opts.env !== false) {
     settings.env = settings.env || {};
@@ -2304,36 +2345,57 @@ hooksCmd.command('init')
     console.log(chalk.blue('  ✓ Environment variables configured'));
   }
 
-  // Permissions (unless --minimal or --no-permissions)
+  // Permissions based on detected project type (unless --minimal or --no-permissions)
   if (!opts.minimal && opts.permissions !== false) {
     settings.permissions = settings.permissions || {};
-    settings.permissions.allow = settings.permissions.allow || [
-      'Bash(npm run:*)',
-      'Bash(npm test:*)',
-      'Bash(npm install:*)',
-      'Bash(npx:*)',
-      'Bash(git status)',
-      'Bash(git diff:*)',
-      'Bash(git log:*)',
-      'Bash(git add:*)',
-      'Bash(git commit:*)',
-      'Bash(git push)',
-      'Bash(git branch:*)',
-      'Bash(git checkout:*)',
-      'Bash(ls:*)',
-      'Bash(pwd)',
-      'Bash(cat:*)',
-      'Bash(mkdir:*)',
-      'Bash(which:*)',
-      'Bash(node:*)',
-      'Bash(ruvector:*)'
-    ];
+    settings.permissions.allow = settings.permissions.allow || getPermissionsForProjectType(projectTypes);
     settings.permissions.deny = settings.permissions.deny || [
       'Bash(rm -rf /)',
       'Bash(sudo rm:*)',
-      'Bash(chmod 777:*)'
+      'Bash(chmod 777:*)',
+      'Bash(mkfs:*)',
+      'Bash(dd if=/dev/zero:*)'
     ];
-    console.log(chalk.blue('  ✓ Permissions configured'));
+    console.log(chalk.blue('  ✓ Permissions configured (project-specific)'));
+  }
+
+  // MCP server configuration (unless --minimal or --no-mcp)
+  if (!opts.minimal && opts.mcp !== false) {
+    settings.mcpServers = settings.mcpServers || {};
+    // Only add if not already configured
+    if (!settings.mcpServers['claude-flow'] && !settings.enabledMcpjsonServers?.includes('claude-flow')) {
+      settings.enabledMcpjsonServers = settings.enabledMcpjsonServers || [];
+      if (!settings.enabledMcpjsonServers.includes('claude-flow')) {
+        settings.enabledMcpjsonServers.push('claude-flow');
+      }
+    }
+    console.log(chalk.blue('  ✓ MCP servers configured'));
+  }
+
+  // StatusLine configuration (unless --minimal or --no-statusline)
+  if (!opts.minimal && opts.statusline !== false) {
+    if (!settings.statusLine) {
+      // Create a simple statusline script
+      const statuslineScript = path.join(settingsDir, 'statusline.sh');
+      const statuslineContent = `#!/bin/bash
+# RuVector Status Line - shows intelligence stats
+INTEL_FILE=".ruvector/intelligence.json"
+if [ -f "$INTEL_FILE" ]; then
+  PATTERNS=$(jq -r '.patterns | length // 0' "$INTEL_FILE" 2>/dev/null || echo "0")
+  MEMORIES=$(jq -r '.memories | length // 0' "$INTEL_FILE" 2>/dev/null || echo "0")
+  echo "🧠 $PATTERNS patterns | 💾 $MEMORIES memories"
+else
+  echo "🧠 RuVector"
+fi
+`;
+      fs.writeFileSync(statuslineScript, statuslineContent);
+      fs.chmodSync(statuslineScript, '755');
+      settings.statusLine = {
+        type: 'command',
+        command: '.claude/statusline.sh'
+      };
+      console.log(chalk.blue('  ✓ StatusLine configured'));
+    }
   }
 
   // Core hooks (always included)
@@ -2486,6 +2548,32 @@ npx ruvector hooks init --force      # Overwrite existing
   } else if (fs.existsSync(claudeMdPath) && !opts.force) {
     console.log(chalk.yellow('ℹ️  CLAUDE.md already exists (use --force to overwrite)'));
   }
+
+  // Update .gitignore (unless --no-gitignore)
+  if (opts.gitignore !== false) {
+    const gitignorePath = path.join(process.cwd(), '.gitignore');
+    const entriesToAdd = ['.ruvector/', '.claude/statusline.sh'];
+    let gitignoreContent = '';
+    if (fs.existsSync(gitignorePath)) {
+      gitignoreContent = fs.readFileSync(gitignorePath, 'utf-8');
+    }
+    const linesToAdd = entriesToAdd.filter(entry => !gitignoreContent.includes(entry));
+    if (linesToAdd.length > 0) {
+      const newContent = gitignoreContent.trim() + '\n\n# RuVector intelligence data\n' + linesToAdd.join('\n') + '\n';
+      fs.writeFileSync(gitignorePath, newContent);
+      console.log(chalk.blue('  ✓ .gitignore updated'));
+    }
+  }
+
+  // Create .ruvector directory for intelligence data
+  const ruvectorDir = path.join(process.cwd(), '.ruvector');
+  if (!fs.existsSync(ruvectorDir)) {
+    fs.mkdirSync(ruvectorDir, { recursive: true });
+    console.log(chalk.blue('  ✓ .ruvector/ directory created'));
+  }
+
+  console.log(chalk.green('\n✅ RuVector hooks initialization complete!'));
+  console.log(chalk.dim('   Run `npx ruvector hooks verify` to test the setup'));
 });
 
 hooksCmd.command('stats').description('Show intelligence statistics').action(() => {
@@ -2622,4 +2710,568 @@ hooksCmd.command('track-notification').description('Track notification').action(
   console.log(JSON.stringify({ tracked: true }));
 });
 
+// Verify hooks are working
+hooksCmd.command('verify')
+  .description('Verify hooks are working correctly')
+  .option('--verbose', 'Show detailed output')
+  .action((opts) => {
+    console.log(chalk.bold.cyan('\n🔍 RuVector Hooks Verification\n'));
+    const checks = [];
+
+    // Check 1: Settings file exists
+    const settingsPath = path.join(process.cwd(), '.claude', 'settings.json');
+    if (fs.existsSync(settingsPath)) {
+      checks.push({ name: 'Settings file', status: 'pass', detail: '.claude/settings.json exists' });
+      try {
+        const settings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+        // Check hooks
+        const requiredHooks = ['PreToolUse', 'PostToolUse', 'SessionStart', 'Stop'];
+        const missingHooks = requiredHooks.filter(h => !settings.hooks?.[h]);
+        if (missingHooks.length === 0) {
+          checks.push({ name: 'Required hooks', status: 'pass', detail: 'All core hooks configured' });
+        } else {
+          checks.push({ name: 'Required hooks', status: 'fail', detail: `Missing: ${missingHooks.join(', ')}` });
+        }
+        // Check advanced hooks
+        const advancedHooks = ['UserPromptSubmit', 'PreCompact', 'Notification'];
+        const hasAdvanced = advancedHooks.filter(h => settings.hooks?.[h]);
+        if (hasAdvanced.length > 0) {
+          checks.push({ name: 'Advanced hooks', status: 'pass', detail: `${hasAdvanced.length}/3 configured` });
+        } else {
+          checks.push({ name: 'Advanced hooks', status: 'warn', detail: 'None configured (optional)' });
+        }
+        // Check env
+        if (settings.env?.RUVECTOR_INTELLIGENCE_ENABLED) {
+          checks.push({ name: 'Environment vars', status: 'pass', detail: 'Intelligence enabled' });
+        } else {
+          checks.push({ name: 'Environment vars', status: 'warn', detail: 'Not configured' });
+        }
+        // Check permissions
+        if (settings.permissions?.allow?.length > 0) {
+          checks.push({ name: 'Permissions', status: 'pass', detail: `${settings.permissions.allow.length} allowed patterns` });
+        } else {
+          checks.push({ name: 'Permissions', status: 'warn', detail: 'Not configured' });
+        }
+      } catch (e) {
+        checks.push({ name: 'Settings parse', status: 'fail', detail: 'Invalid JSON' });
+      }
+    } else {
+      checks.push({ name: 'Settings file', status: 'fail', detail: 'Run `npx ruvector hooks init` first' });
+    }
+
+    // Check 2: .ruvector directory
+    const ruvectorDir = path.join(process.cwd(), '.ruvector');
+    if (fs.existsSync(ruvectorDir)) {
+      checks.push({ name: 'Data directory', status: 'pass', detail: '.ruvector/ exists' });
+      const intelFile = path.join(ruvectorDir, 'intelligence.json');
+      if (fs.existsSync(intelFile)) {
+        const stats = fs.statSync(intelFile);
+        checks.push({ name: 'Intelligence file', status: 'pass', detail: `${(stats.size / 1024).toFixed(1)}KB` });
+      } else {
+        checks.push({ name: 'Intelligence file', status: 'warn', detail: 'Will be created on first use' });
+      }
+    } else {
+      checks.push({ name: 'Data directory', status: 'warn', detail: 'Will be created on first use' });
+    }
+
+    // Check 3: Hook command execution
+    try {
+      const { execSync } = require('child_process');
+      execSync('npx ruvector hooks stats', { stdio: 'pipe', timeout: 5000 });
+      checks.push({ name: 'Command execution', status: 'pass', detail: 'Hooks commands work' });
+    } catch (e) {
+      checks.push({ name: 'Command execution', status: 'fail', detail: 'Commands failed to execute' });
+    }
+
+    // Display results
+    let passCount = 0, warnCount = 0, failCount = 0;
+    checks.forEach(c => {
+      const icon = c.status === 'pass' ? chalk.green('✓') : c.status === 'warn' ? chalk.yellow('⚠') : chalk.red('✗');
+      const statusColor = c.status === 'pass' ? chalk.green : c.status === 'warn' ? chalk.yellow : chalk.red;
+      console.log(`  ${icon} ${c.name}: ${statusColor(c.detail)}`);
+      if (c.status === 'pass') passCount++;
+      else if (c.status === 'warn') warnCount++;
+      else failCount++;
+    });
+
+    console.log('');
+    if (failCount === 0) {
+      console.log(chalk.green(`✅ Verification passed! ${passCount} checks passed, ${warnCount} warnings`));
+    } else {
+      console.log(chalk.red(`❌ Verification failed: ${failCount} issues found`));
+      console.log(chalk.dim('   Run `npx ruvector hooks doctor` for detailed diagnostics'));
+    }
+  });
+
+// Doctor - diagnose setup issues
+hooksCmd.command('doctor')
+  .description('Diagnose and fix setup issues')
+  .option('--fix', 'Automatically fix issues')
+  .action((opts) => {
+    console.log(chalk.bold.cyan('\n🩺 RuVector Hooks Doctor\n'));
+    const issues = [];
+    const fixes = [];
+
+    // Check settings file
+    const settingsPath = path.join(process.cwd(), '.claude', 'settings.json');
+    if (!fs.existsSync(settingsPath)) {
+      issues.push({ severity: 'error', message: 'No .claude/settings.json found', fix: 'Run `npx ruvector hooks init`' });
+    } else {
+      try {
+        const settings = JSON.parse(fs.readFileSync(settingsPath, 'utf-8'));
+
+        // Check for invalid schema
+        if (settings.$schema && !settings.$schema.includes('schemastore.org')) {
+          issues.push({ severity: 'warning', message: 'Invalid schema URL', fix: 'Will be corrected' });
+          if (opts.fix) {
+            settings.$schema = 'https://json.schemastore.org/claude-code-settings.json';
+            fixes.push('Fixed schema URL');
+          }
+        }
+
+        // Check for old hook names
+        if (settings.hooks?.Start || settings.hooks?.End) {
+          issues.push({ severity: 'error', message: 'Invalid hook names (Start/End)', fix: 'Should be SessionStart/Stop' });
+          if (opts.fix) {
+            delete settings.hooks.Start;
+            delete settings.hooks.End;
+            fixes.push('Removed invalid hook names');
+          }
+        }
+
+        // Check hook format
+        const hookNames = ['PreToolUse', 'PostToolUse'];
+        hookNames.forEach(name => {
+          if (settings.hooks?.[name]) {
+            settings.hooks[name].forEach((hook, i) => {
+              if (typeof hook.matcher === 'object') {
+                issues.push({ severity: 'error', message: `${name}[${i}].matcher should be string, not object`, fix: 'Will be corrected' });
+              }
+            });
+          }
+        });
+
+        // Check for npx vs direct command
+        const checkCommands = (hooks) => {
+          if (!hooks) return;
+          hooks.forEach(h => {
+            h.hooks?.forEach(hh => {
+              if (hh.command && hh.command.includes('ruvector') && !hh.command.startsWith('npx ') && !hh.command.includes('/bin/')) {
+                issues.push({ severity: 'warning', message: `Command should use 'npx ruvector' for portability`, fix: 'Update to use npx' });
+              }
+            });
+          });
+        };
+        Object.values(settings.hooks || {}).forEach(checkCommands);
+
+        // Save fixes
+        if (opts.fix && fixes.length > 0) {
+          fs.writeFileSync(settingsPath, JSON.stringify(settings, null, 2));
+        }
+      } catch (e) {
+        issues.push({ severity: 'error', message: 'Invalid JSON in settings file', fix: 'Re-run `npx ruvector hooks init --force`' });
+      }
+    }
+
+    // Check .gitignore
+    const gitignorePath = path.join(process.cwd(), '.gitignore');
+    if (fs.existsSync(gitignorePath)) {
+      const content = fs.readFileSync(gitignorePath, 'utf-8');
+      if (!content.includes('.ruvector/')) {
+        issues.push({ severity: 'warning', message: '.ruvector/ not in .gitignore', fix: 'Add to prevent committing learning data' });
+        if (opts.fix) {
+          fs.appendFileSync(gitignorePath, '\n# RuVector intelligence data\n.ruvector/\n');
+          fixes.push('Added .ruvector/ to .gitignore');
+        }
+      }
+    }
+
+    // Display results
+    if (issues.length === 0) {
+      console.log(chalk.green('  ✓ No issues found! Your setup looks healthy.'));
+    } else {
+      issues.forEach(i => {
+        const icon = i.severity === 'error' ? chalk.red('✗') : chalk.yellow('⚠');
+        console.log(`  ${icon} ${i.message}`);
+        console.log(chalk.dim(`     Fix: ${i.fix}`));
+      });
+
+      if (opts.fix && fixes.length > 0) {
+        console.log(chalk.green(`\n✅ Applied ${fixes.length} fix(es):`));
+        fixes.forEach(f => console.log(chalk.green(`   • ${f}`)));
+      } else if (issues.some(i => i.severity === 'error')) {
+        console.log(chalk.yellow('\n💡 Run with --fix to automatically fix issues'));
+      }
+    }
+  });
+
+// Export intelligence data
+hooksCmd.command('export')
+  .description('Export intelligence data for backup')
+  .option('-o, --output <file>', 'Output file path', 'ruvector-export.json')
+  .option('--include-all', 'Include all data (patterns, memories, trajectories)')
+  .action((opts) => {
+    const intel = new Intelligence();
+    const exportData = {
+      version: '1.0',
+      exported_at: new Date().toISOString(),
+      patterns: intel.data?.patterns || {},
+      memories: opts.includeAll ? (intel.data?.memories || []) : [],
+      trajectories: opts.includeAll ? (intel.data?.trajectories || []) : [],
+      errors: intel.data?.errors || {},
+      stats: intel.stats()
+    };
+
+    const outputPath = path.resolve(opts.output);
+    fs.writeFileSync(outputPath, JSON.stringify(exportData, null, 2));
+
+    console.log(chalk.green(`✅ Exported intelligence data to ${outputPath}`));
+    console.log(chalk.dim(`   ${Object.keys(exportData.patterns).length} patterns`));
+    console.log(chalk.dim(`   ${exportData.memories.length} memories`));
+    console.log(chalk.dim(`   ${exportData.trajectories.length} trajectories`));
+  });
+
+// Import intelligence data
+hooksCmd.command('import')
+  .description('Import intelligence data from backup')
+  .argument('<file>', 'Import file path')
+  .option('--merge', 'Merge with existing data (default: replace)')
+  .option('--dry-run', 'Show what would be imported without making changes')
+  .action((file, opts) => {
+    const importPath = path.resolve(file);
+    if (!fs.existsSync(importPath)) {
+      console.error(chalk.red(`❌ File not found: ${importPath}`));
+      process.exit(1);
+    }
+
+    try {
+      const importData = JSON.parse(fs.readFileSync(importPath, 'utf-8'));
+
+      if (!importData.version) {
+        console.error(chalk.red('❌ Invalid export file (missing version)'));
+        process.exit(1);
+      }
+
+      console.log(chalk.cyan(`📦 Import file: ${file}`));
+      console.log(chalk.dim(`   Version: ${importData.version}`));
+      console.log(chalk.dim(`   Exported: ${importData.exported_at}`));
+      console.log(chalk.dim(`   Patterns: ${Object.keys(importData.patterns || {}).length}`));
+      console.log(chalk.dim(`   Memories: ${(importData.memories || []).length}`));
+      console.log(chalk.dim(`   Trajectories: ${(importData.trajectories || []).length}`));
+
+      if (opts.dryRun) {
+        console.log(chalk.yellow('\n⚠️  Dry run - no changes made'));
+        return;
+      }
+
+      const intel = new Intelligence();
+
+      if (opts.merge) {
+        // Merge patterns
+        Object.assign(intel.data.patterns, importData.patterns || {});
+        // Merge memories (deduplicate by content)
+        const existingContent = new Set((intel.data.memories || []).map(m => m.content));
+        (importData.memories || []).forEach(m => {
+          if (!existingContent.has(m.content)) {
+            intel.data.memories.push(m);
+          }
+        });
+        // Merge trajectories
+        intel.data.trajectories = (intel.data.trajectories || []).concat(importData.trajectories || []);
+        // Merge errors
+        Object.assign(intel.data.errors, importData.errors || {});
+        console.log(chalk.green('✅ Merged intelligence data'));
+      } else {
+        intel.data.patterns = importData.patterns || {};
+        intel.data.memories = importData.memories || [];
+        intel.data.trajectories = importData.trajectories || [];
+        intel.data.errors = importData.errors || {};
+        console.log(chalk.green('✅ Replaced intelligence data'));
+      }
+
+      intel.save();
+      console.log(chalk.dim('   Data saved to .ruvector/intelligence.json'));
+    } catch (e) {
+      console.error(chalk.red(`❌ Failed to import: ${e.message}`));
+      process.exit(1);
+    }
+  });
+
+// Pretrain - analyze repo and bootstrap learning with agent swarm
+hooksCmd.command('pretrain')
+  .description('Pretrain intelligence by analyzing the repository with agent swarm')
+  .option('--depth <n>', 'Git history depth to analyze', '100')
+  .option('--workers <n>', 'Number of parallel analysis workers', '4')
+  .option('--skip-git', 'Skip git history analysis')
+  .option('--skip-files', 'Skip file structure analysis')
+  .option('--verbose', 'Show detailed progress')
+  .action(async (opts) => {
+    const { execSync, spawn } = require('child_process');
+    console.log(chalk.bold.cyan('\n🧠 RuVector Pretrain - Repository Intelligence Bootstrap\n'));
+
+    const intel = new Intelligence();
+    const startTime = Date.now();
+    const stats = { files: 0, patterns: 0, memories: 0, coedits: 0 };
+
+    // Agent types for different file patterns
+    const agentMapping = {
+      // Rust
+      '.rs': 'rust-developer',
+      'Cargo.toml': 'rust-developer',
+      'Cargo.lock': 'rust-developer',
+      // JavaScript/TypeScript
+      '.js': 'javascript-developer',
+      '.jsx': 'react-developer',
+      '.ts': 'typescript-developer',
+      '.tsx': 'react-developer',
+      '.mjs': 'javascript-developer',
+      '.cjs': 'javascript-developer',
+      'package.json': 'node-developer',
+      // Python
+      '.py': 'python-developer',
+      'requirements.txt': 'python-developer',
+      'pyproject.toml': 'python-developer',
+      'setup.py': 'python-developer',
+      // Go
+      '.go': 'go-developer',
+      'go.mod': 'go-developer',
+      // Web
+      '.html': 'frontend-developer',
+      '.css': 'frontend-developer',
+      '.scss': 'frontend-developer',
+      '.vue': 'vue-developer',
+      '.svelte': 'svelte-developer',
+      // Config
+      '.json': 'config-specialist',
+      '.yaml': 'config-specialist',
+      '.yml': 'config-specialist',
+      '.toml': 'config-specialist',
+      // Docs
+      '.md': 'documentation-specialist',
+      '.mdx': 'documentation-specialist',
+      // Tests
+      '.test.js': 'test-engineer',
+      '.test.ts': 'test-engineer',
+      '.spec.js': 'test-engineer',
+      '.spec.ts': 'test-engineer',
+      '_test.go': 'test-engineer',
+      '_test.rs': 'test-engineer',
+      // DevOps
+      'Dockerfile': 'devops-engineer',
+      'docker-compose.yml': 'devops-engineer',
+      '.github/workflows': 'cicd-engineer',
+      'Makefile': 'devops-engineer',
+      // SQL
+      '.sql': 'database-specialist',
+    };
+
+    // Phase 1: Analyze file structure
+    if (!opts.skipFiles) {
+      console.log(chalk.yellow('📁 Phase 1: Analyzing file structure...\n'));
+
+      try {
+        // Get all files in repo
+        const files = execSync('git ls-files 2>/dev/null || find . -type f -not -path "./.git/*" -not -path "./node_modules/*" -not -path "./target/*"',
+          { encoding: 'utf-8', maxBuffer: 50 * 1024 * 1024 }).trim().split('\n').filter(f => f);
+
+        const filesByType = {};
+        const dirPatterns = {};
+
+        files.forEach(file => {
+          stats.files++;
+          const ext = path.extname(file);
+          const basename = path.basename(file);
+          const dir = path.dirname(file);
+
+          // Determine agent for this file
+          let agent = 'coder'; // default
+          if (agentMapping[basename]) {
+            agent = agentMapping[basename];
+          } else if (agentMapping[ext]) {
+            agent = agentMapping[ext];
+          } else if (file.includes('.test.') || file.includes('.spec.') || file.includes('_test.')) {
+            agent = 'test-engineer';
+          } else if (file.includes('.github/workflows')) {
+            agent = 'cicd-engineer';
+          }
+
+          // Track file types
+          filesByType[ext] = (filesByType[ext] || 0) + 1;
+
+          // Track directory patterns
+          const parts = dir.split('/');
+          if (parts[0]) {
+            dirPatterns[parts[0]] = dirPatterns[parts[0]] || { count: 0, agents: {} };
+            dirPatterns[parts[0]].count++;
+            dirPatterns[parts[0]].agents[agent] = (dirPatterns[parts[0]].agents[agent] || 0) + 1;
+          }
+
+          // Create Q-learning pattern for this file type
+          const state = `edit:${ext || 'unknown'}`;
+          if (!intel.data.patterns[state]) {
+            intel.data.patterns[state] = {};
+          }
+          intel.data.patterns[state][agent] = (intel.data.patterns[state][agent] || 0) + 0.5;
+          stats.patterns++;
+        });
+
+        // Log summary
+        if (opts.verbose) {
+          console.log(chalk.dim('  File types found:'));
+          Object.entries(filesByType).sort((a, b) => b[1] - a[1]).slice(0, 10).forEach(([ext, count]) => {
+            console.log(chalk.dim(`    ${ext || '(no ext)'}: ${count} files`));
+          });
+        }
+        console.log(chalk.green(`  ✓ Analyzed ${stats.files} files`));
+        console.log(chalk.green(`  ✓ Created ${Object.keys(intel.data.patterns).length} routing patterns`));
+
+      } catch (e) {
+        console.log(chalk.yellow(`  ⚠ File analysis skipped: ${e.message}`));
+      }
+    }
+
+    // Phase 2: Analyze git history for co-edit patterns
+    if (!opts.skipGit) {
+      console.log(chalk.yellow('\n📜 Phase 2: Analyzing git history for co-edit patterns...\n'));
+
+      try {
+        // Get commits with files changed
+        const gitLog = execSync(
+          `git log --name-only --pretty=format:"COMMIT:%H" -n ${opts.depth} 2>/dev/null`,
+          { encoding: 'utf-8', maxBuffer: 50 * 1024 * 1024 }
+        );
+
+        const commits = gitLog.split('COMMIT:').filter(c => c.trim());
+        const coEditMap = {};
+
+        commits.forEach(commit => {
+          const lines = commit.trim().split('\n').filter(l => l && !l.startsWith('COMMIT:'));
+          const files = lines.slice(1).filter(f => f.trim()); // Skip the hash
+
+          // Track which files are edited together
+          files.forEach(file1 => {
+            files.forEach(file2 => {
+              if (file1 !== file2) {
+                const key = [file1, file2].sort().join('|');
+                coEditMap[key] = (coEditMap[key] || 0) + 1;
+              }
+            });
+          });
+        });
+
+        // Find strong co-edit patterns (files edited together 3+ times)
+        const strongPatterns = Object.entries(coEditMap)
+          .filter(([, count]) => count >= 3)
+          .sort((a, b) => b[1] - a[1]);
+
+        // Store as sequence patterns
+        strongPatterns.slice(0, 100).forEach(([key, count]) => {
+          const [file1, file2] = key.split('|');
+          if (!intel.data.sequences) intel.data.sequences = {};
+          if (!intel.data.sequences[file1]) intel.data.sequences[file1] = [];
+
+          const existing = intel.data.sequences[file1].find(s => s.file === file2);
+          if (existing) {
+            existing.score += count;
+          } else {
+            intel.data.sequences[file1].push({ file: file2, score: count });
+          }
+          stats.coedits++;
+        });
+
+        console.log(chalk.green(`  ✓ Analyzed ${commits.length} commits`));
+        console.log(chalk.green(`  ✓ Found ${strongPatterns.length} co-edit patterns`));
+
+        if (opts.verbose && strongPatterns.length > 0) {
+          console.log(chalk.dim('  Top co-edit patterns:'));
+          strongPatterns.slice(0, 5).forEach(([key, count]) => {
+            const [f1, f2] = key.split('|');
+            console.log(chalk.dim(`    ${path.basename(f1)} ↔ ${path.basename(f2)}: ${count} times`));
+          });
+        }
+
+      } catch (e) {
+        console.log(chalk.yellow(`  ⚠ Git analysis skipped: ${e.message}`));
+      }
+    }
+
+    // Phase 3: Create vector memories from important files
+    console.log(chalk.yellow('\n💾 Phase 3: Creating vector memories from key files...\n'));
+
+    try {
+      const importantFiles = [
+        'README.md', 'CLAUDE.md', 'package.json', 'Cargo.toml',
+        'pyproject.toml', 'go.mod', '.claude/settings.json'
+      ];
+
+      for (const filename of importantFiles) {
+        const filePath = path.join(process.cwd(), filename);
+        if (fs.existsSync(filePath)) {
+          try {
+            const content = fs.readFileSync(filePath, 'utf-8').slice(0, 2000); // First 2KB
+            intel.data.memories = intel.data.memories || [];
+            intel.data.memories.push({
+              content: `[${filename}] ${content.replace(/\n/g, ' ').slice(0, 500)}`,
+              type: 'project',
+              created: new Date().toISOString(),
+              embedding: intel.simpleEmbed ? intel.simpleEmbed(content) : null
+            });
+            stats.memories++;
+            if (opts.verbose) console.log(chalk.dim(`    ✓ ${filename}`));
+          } catch (e) { /* skip unreadable files */ }
+        }
+      }
+
+      console.log(chalk.green(`  ✓ Created ${stats.memories} memory entries`));
+
+    } catch (e) {
+      console.log(chalk.yellow(`  ⚠ Memory creation skipped: ${e.message}`));
+    }
+
+    // Phase 4: Analyze directory structure for agent recommendations
+    console.log(chalk.yellow('\n🗂️  Phase 4: Building directory-agent mappings...\n'));
+
+    try {
+      const dirs = execSync('find . -type d -maxdepth 2 -not -path "./.git*" -not -path "./node_modules*" -not -path "./target*" 2>/dev/null || echo "."',
+        { encoding: 'utf-8' }).trim().split('\n');
+
+      const dirAgentMap = {};
+      dirs.forEach(dir => {
+        const name = path.basename(dir);
+        // Infer agent from directory name
+        if (['src', 'lib', 'core'].includes(name)) dirAgentMap[dir] = 'coder';
+        else if (['test', 'tests', '__tests__', 'spec'].includes(name)) dirAgentMap[dir] = 'test-engineer';
+        else if (['docs', 'documentation'].includes(name)) dirAgentMap[dir] = 'documentation-specialist';
+        else if (['scripts', 'bin'].includes(name)) dirAgentMap[dir] = 'devops-engineer';
+        else if (['components', 'views', 'pages'].includes(name)) dirAgentMap[dir] = 'frontend-developer';
+        else if (['api', 'routes', 'handlers'].includes(name)) dirAgentMap[dir] = 'backend-developer';
+        else if (['models', 'entities', 'schemas'].includes(name)) dirAgentMap[dir] = 'database-specialist';
+        else if (['.github', '.gitlab', 'ci'].includes(name)) dirAgentMap[dir] = 'cicd-engineer';
+      });
+
+      // Store directory patterns
+      intel.data.dirPatterns = dirAgentMap;
+      console.log(chalk.green(`  ✓ Mapped ${Object.keys(dirAgentMap).length} directories to agents`));
+
+    } catch (e) {
+      console.log(chalk.yellow(`  ⚠ Directory analysis skipped: ${e.message}`));
+    }
+
+    // Save all learning data
+    intel.data.pretrained = {
+      date: new Date().toISOString(),
+      stats: stats
+    };
+    intel.save();
+
+    const elapsed = ((Date.now() - startTime) / 1000).toFixed(1);
+    console.log(chalk.bold.green(`\n✅ Pretrain complete in ${elapsed}s!\n`));
+    console.log(chalk.cyan('Summary:'));
+    console.log(`  📁 ${stats.files} files analyzed`);
+    console.log(`  🧠 ${stats.patterns} agent routing patterns`);
+    console.log(`  🔗 ${stats.coedits} co-edit patterns`);
+    console.log(`  💾 ${stats.memories} memory entries`);
+    console.log(chalk.dim('\nThe intelligence layer will now provide better recommendations.'));
+  });
+
 program.parse();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "ruvector",
-  "version": "0.1.45",
+  "version": "0.1.47",
   "description": "High-performance vector database for Node.js with automatic native/WASM fallback",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",