@triedotdev/mcp 1.0.97 → 1.0.101

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@triedotdev/mcp",
-  "version": "1.0.97",
+  "version": "1.0.101",
   "description": "Trainable AI Agent for Maintaining AI-Generated Codebases",
   "main": "dist/index.js",
   "type": "module",

package/dist/chunk-FNCCZ3XB.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/cli/checkpoint.ts","../src/config/loader.ts","../src/config/validation.ts","../src/utils/autonomy-config.ts","../src/types/autonomy.ts","../src/agent/git.ts","../src/agent/perceive.ts","../src/agent/diff-analyzer.ts","../src/agent/risk-scorer.ts","../src/agent/pattern-matcher.ts","../src/orchestrator/triager.ts","../src/utils/parallel-executor.ts","../src/utils/cache-manager.ts","../src/orchestrator/executor.ts","../src/agent/reason.ts","../src/bootstrap/files.ts","../src/utils/errors.ts","../src/context/sync.ts","../src/context/incident-index.ts","../src/context/file-trie.ts","../src/agent/confidence.ts","../src/agent/pattern-discovery.ts","../src/agent/learning.ts","../src/guardian/learning-engine.ts","../src/ingest/linear-ingester.ts"],"sourcesContent":["/**\n * Checkpoint CLI\n * \n * Save your work context to .trie/ without running a full scan.\n * Think of it as a quick save - captures what you're working on.\n */\n\nimport { existsSync } from 'fs';\nimport { mkdir, writeFile, readFile } from 'fs/promises';\nimport { join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\n\nexport interface Checkpoint {\n  id: string;\n  timestamp: string;\n  message?: string;\n  files: string[];\n  notes?: string;\n  createdBy: 'cli' | 'mcp';\n}\n\nexport interface CheckpointLog {\n  checkpoints: Checkpoint[];\n  lastCheckpoint?: string;\n}\n\n/**\n * Save a checkpoint\n */\nexport async function saveCheckpoint(options: {\n  message?: string;\n  files?: string[];\n  notes?: string;\n  workDir?: string;\n  createdBy?: 'cli' | 'mcp';\n}): Promise<Checkpoint> {\n  const workDir = options.workDir || getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(workDir);\n  const checkpointPath = join(trieDir, 'checkpoints.json');\n  \n  await mkdir(trieDir, { recursive: true });\n  \n  // Load existing checkpoints\n  let log: CheckpointLog = { checkpoints: [] };\n  try {\n    if (existsSync(checkpointPath)) {\n      log = JSON.parse(await readFile(checkpointPath, 'utf-8'));\n    }\n  } catch {\n    log = { checkpoints: [] };\n  }\n  \n  // Create new checkpoint\n  const checkpoint: Checkpoint = {\n    id: `cp-${Date.now().toString(36)}`,\n    timestamp: new Date().toISOString(),\n    files: options.files || [],\n    createdBy: options.createdBy || 'cli',\n  };\n  if (options.message) checkpoint.message = options.message;\n  if (options.notes) checkpoint.notes = options.notes;\n  \n  // Add to log\n  log.checkpoints.push(checkpoint);\n  log.lastCheckpoint = checkpoint.id;\n  \n  // Keep last 50 checkpoints\n  if (log.checkpoints.length > 50) {\n    log.checkpoints = log.checkpoints.slice(-50);\n  }\n  \n  // Save\n  await writeFile(checkpointPath, JSON.stringify(log, null, 2));\n  \n  // Also update AGENTS.md with checkpoint note\n  await updateAgentsMdWithCheckpoint(checkpoint, workDir);\n  \n  return checkpoint;\n}\n\n/**\n * List checkpoints\n */\nexport async function listCheckpoints(workDir?: string): Promise<Checkpoint[]> {\n  const dir = workDir || getWorkingDirectory(undefined, true);\n  const checkpointPath = join(getTrieDirectory(dir), 'checkpoints.json');\n  \n  try {\n    if (existsSync(checkpointPath)) {\n      const log: CheckpointLog = JSON.parse(await readFile(checkpointPath, 'utf-8'));\n      return log.checkpoints;\n    }\n  } catch {\n    // File doesn't exist or is corrupted\n  }\n  \n  return [];\n}\n\n/**\n * Get the last checkpoint\n */\nexport async function getLastCheckpoint(workDir?: string): Promise<Checkpoint | null> {\n  const checkpoints = await listCheckpoints(workDir);\n  const last = checkpoints[checkpoints.length - 1];\n  return last ?? null;\n}\n\n/**\n * Update AGENTS.md with checkpoint info\n */\nasync function updateAgentsMdWithCheckpoint(checkpoint: Checkpoint, workDir: string): Promise<void> {\n  const agentsPath = join(getTrieDirectory(workDir), 'AGENTS.md');\n  \n  let content = '';\n  try {\n    if (existsSync(agentsPath)) {\n      content = await readFile(agentsPath, 'utf-8');\n    }\n  } catch {\n    content = '';\n  }\n  \n  // Find or create checkpoint section\n  const checkpointSection = `\n## Last Checkpoint\n\n- **ID:** ${checkpoint.id}\n- **Time:** ${checkpoint.timestamp}\n${checkpoint.message ? `- **Message:** ${checkpoint.message}` : ''}\n${checkpoint.files.length > 0 ? `- **Files:** ${checkpoint.files.length} files` : ''}\n${checkpoint.notes ? `- **Notes:** ${checkpoint.notes}` : ''}\n`;\n  \n  // Replace existing checkpoint section or append\n  const checkpointRegex = /## Last Checkpoint[\\s\\S]*?(?=\\n## |\\n---|\\Z)/;\n  if (checkpointRegex.test(content)) {\n    content = content.replace(checkpointRegex, checkpointSection.trim());\n  } else {\n    content = content.trim() + '\\n\\n' + checkpointSection.trim() + '\\n';\n  }\n  \n  await writeFile(agentsPath, content);\n}\n\n/**\n * CLI handler for checkpoint command\n */\nexport async function handleCheckpointCommand(args: string[]): Promise<void> {\n  const subcommand = args[0] || 'save';\n  \n  switch (subcommand) {\n    case 'save': {\n      // Parse options\n      let message: string | undefined;\n      let notes: string | undefined;\n      const files: string[] = [];\n      \n      for (let i = 1; i < args.length; i++) {\n        const arg = args[i];\n        if (arg === '-m' || arg === '--message') {\n          message = args[++i] ?? '';\n        } else if (arg === '-n' || arg === '--notes') {\n          notes = args[++i] ?? '';\n        } else if (arg === '-f' || arg === '--file') {\n          const file = args[++i];\n          if (file) files.push(file);\n        } else if (arg && !arg.startsWith('-')) {\n          // Treat as message if no flag\n          message = arg;\n        }\n      }\n      \n      const opts: { message?: string; files?: string[]; notes?: string } = { files };\n      if (message) opts.message = message;\n      if (notes) opts.notes = notes;\n      const checkpoint = await saveCheckpoint(opts);\n      \n      console.log('\\n  Checkpoint saved\\n');\n      console.log(`  ID: ${checkpoint.id}`);\n      console.log(`  Time: ${checkpoint.timestamp}`);\n      if (checkpoint.message) {\n        console.log(`  Message: ${checkpoint.message}`);\n      }\n      if (checkpoint.files.length > 0) {\n        console.log(`  Files: ${checkpoint.files.join(', ')}`);\n      }\n      console.log('\\n  Context saved to .trie/\\n');\n      break;\n    }\n    \n    case 'list': {\n      const checkpoints = await listCheckpoints();\n      \n      if (checkpoints.length === 0) {\n        console.log('\\n  No checkpoints yet. Run `trie checkpoint` to save one.\\n');\n        return;\n      }\n      \n      console.log('\\n  Checkpoints:\\n');\n      for (const cp of checkpoints.slice(-10).reverse()) {\n        const date = new Date(cp.timestamp).toLocaleString();\n        console.log(`  ${cp.id}  ${date}  ${cp.message || '(no message)'}`);\n      }\n      console.log('');\n      break;\n    }\n    \n    case 'last': {\n      const checkpoint = await getLastCheckpoint();\n      \n      if (!checkpoint) {\n        console.log('\\n  No checkpoints yet. Run `trie checkpoint` to save one.\\n');\n        return;\n      }\n      \n      console.log('\\n  Last Checkpoint:\\n');\n      console.log(`  ID: ${checkpoint.id}`);\n      console.log(`  Time: ${new Date(checkpoint.timestamp).toLocaleString()}`);\n      if (checkpoint.message) {\n        console.log(`  Message: ${checkpoint.message}`);\n      }\n      if (checkpoint.notes) {\n        console.log(`  Notes: ${checkpoint.notes}`);\n      }\n      if (checkpoint.files.length > 0) {\n        console.log(`  Files: ${checkpoint.files.join(', ')}`);\n      }\n      console.log('');\n      break;\n    }\n    \n    default:\n      console.log(`\n  Usage: trie checkpoint [command] [options]\n\n  Commands:\n    save [message]     Save a checkpoint (default)\n    list               List recent checkpoints\n    last               Show the last checkpoint\n\n  Options:\n    -m, --message      Checkpoint message\n    -n, --notes        Additional notes\n    -f, --file         File to include (can be repeated)\n\n  Examples:\n    trie checkpoint \"finished auth flow\"\n    trie checkpoint save -m \"WIP: payment integration\" -n \"needs testing\"\n    trie checkpoint list\n`);\n  }\n}\n","import { readFile, writeFile, mkdir } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join, dirname } from 'path';\nimport { ConfigValidator, DEFAULT_CONFIG, type TrieConfig } from './validation.js';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\nimport { isInteractiveMode } from '../utils/progress.js';\n\nexport async function loadConfig(): Promise<TrieConfig> {\n  const validator = new ConfigValidator();\n  const configPath = join(getTrieDirectory(getWorkingDirectory(undefined, true)), 'config.json');\n\n  try {\n    // Look for config in .trie/config.json\n    if (!existsSync(configPath)) {\n      return DEFAULT_CONFIG;\n    }\n\n    const configFile = await readFile(configPath, 'utf-8');\n    const userConfig = JSON.parse(configFile) as Record<string, unknown>;\n\n    // Deep merge with defaults\n    const merged = mergeConfig(DEFAULT_CONFIG, userConfig);\n\n    // Validate merged config\n    const result = validator.validateConfig(merged);\n    if (!result.success) {\n      // Suppress console output in interactive mode (TUI handles display)\n      if (!isInteractiveMode()) {\n        console.error('Configuration validation failed:');\n        for (const error of result.errors) {\n          console.error(`  - ${error}`);\n        }\n      }\n      return DEFAULT_CONFIG;\n    }\n\n    // Environment validation warnings (skip in interactive mode)\n    if (!isInteractiveMode()) {\n      const envValidation = validator.validateEnvironment();\n      for (const warning of envValidation.warnings) {\n        console.warn(warning);\n      }\n      for (const error of envValidation.errors) {\n        console.error(error);\n      }\n    }\n\n    return result.data;\n  } catch (error) {\n    // If no config found, return defaults (suppress in interactive mode)\n    if (!isInteractiveMode()) {\n      console.error('Failed to load config, using defaults:', error);\n    }\n    return DEFAULT_CONFIG;\n  }\n}\n\nexport async function saveConfig(config: TrieConfig): Promise<void> {\n  const configPath = join(getTrieDirectory(getWorkingDirectory(undefined, true)), 'config.json');\n  const dir = dirname(configPath);\n\n  if (!existsSync(dir)) {\n    await mkdir(dir, { recursive: true });\n  }\n\n  await writeFile(configPath, JSON.stringify(config, null, 2), 'utf-8');\n}\n\nfunction mergeConfig<T extends Record<string, unknown>>(defaults: T, user: Record<string, unknown>): T {\n  if (typeof user !== 'object' || user === null || Array.isArray(user)) {\n    return { ...defaults };\n  }\n\n  const result = { ...defaults } as T;\n\n  for (const [key, value] of Object.entries(user)) {\n    const defaultValue = defaults[key as keyof T];\n    if (typeof value === 'object' && value !== null && !Array.isArray(value) && typeof defaultValue === 'object' && defaultValue !== null) {\n      result[key as keyof T] = mergeConfig(defaultValue as Record<string, unknown>, value as Record<string, unknown>) as T[keyof T];\n    } else {\n      result[key as keyof T] = value as T[keyof T];\n    }\n  }\n\n  return result;\n}","import { z } from 'zod';\nimport { existsSync, readFileSync } from 'fs';\nimport { resolve, join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\n\n// API key validation patterns\nconst API_KEY_PATTERNS = {\n  anthropic: /^sk-ant-api\\d{2}-[\\w-]{95}$/,\n  openai: /^sk-[\\w]{48}$/,\n  github: /^ghp_[\\w]{36}$/,\n  vercel: /^[\\w]{24}$/,\n  linear: /^lin_api_[\\w]{40,60}$/,\n} as const;\n\n// Configuration schemas\nconst ApiKeysSchema = z.object({\n  anthropic: z.string().regex(API_KEY_PATTERNS.anthropic, 'Invalid Anthropic API key format').optional(),\n  openai: z.string().regex(API_KEY_PATTERNS.openai, 'Invalid OpenAI API key format').optional(),\n  github: z.string().regex(API_KEY_PATTERNS.github, 'Invalid GitHub token format').optional(),\n  vercel: z.string().regex(API_KEY_PATTERNS.vercel, 'Invalid Vercel token format').optional(),\n  linear: z.string().optional(), // Linear keys can vary, so we'll be flexible but allow storage\n});\n\nconst AgentConfigSchema = z.object({\n  enabled: z.array(z.string()).optional().default([]),\n  disabled: z.array(z.string()).optional().default([]),\n  parallel: z.boolean().optional().default(true),\n  maxConcurrency: z.number().int().min(1).max(20).optional().default(4),\n  timeout: z.number().int().min(1000).max(300000).optional().default(120000), // 2 minutes\n  cache: z.boolean().optional().default(true),\n});\n\nconst ComplianceSchema = z.object({\n  standards: z.array(z.enum(['SOC2', 'GDPR', 'HIPAA', 'CCPA', 'PCI-DSS'])).optional().default(['SOC2']),\n  enforceCompliance: z.boolean().optional().default(false),\n  reportFormat: z.enum(['json', 'sarif', 'csv', 'html']).optional().default('json'),\n});\n\nconst OutputSchema = z.object({\n  format: z.enum(['console', 'json', 'sarif', 'junit']).optional().default('console'),\n  level: z.enum(['critical', 'serious', 'moderate', 'low', 'all']).optional().default('all'),\n  interactive: z.boolean().optional().default(false),\n  streaming: z.boolean().optional().default(true),\n  colors: z.boolean().optional().default(true),\n});\n\nconst PathsSchema = z.object({\n  include: z.array(z.string()).optional().default([]),\n  exclude: z.array(z.string()).optional().default(['node_modules', 'dist', 'build', '.git']),\n  configDir: z.string().optional().default('.trie'),\n  outputDir: z.string().optional().default('trie-reports'),\n});\n\nconst IntegrationsSchema = z.object({\n  github: z.object({\n    enabled: z.boolean().optional().default(false),\n    token: z.string().optional(),\n    webhook: z.string().url().optional(),\n  }).optional(),\n  slack: z.object({\n    enabled: z.boolean().optional().default(false),\n    webhook: z.string().url().optional(),\n    channel: z.string().optional(),\n  }).optional(),\n  jira: z.object({\n    enabled: z.boolean().optional().default(false),\n    url: z.string().url().optional(),\n    token: z.string().optional(),\n    project: z.string().optional(),\n  }).optional(),\n});\n\n// User identity for attribution tracking\nconst UserSchema = z.object({\n  name: z.string().min(1).optional(),\n  email: z.string().email().optional(),\n  role: z.enum([\n    'developer',\n    'designer', \n    'qa',\n    'devops',\n    'security',\n    'architect',\n    'manager',\n    'contributor'\n  ]).optional().default('developer'),\n  github: z.string().optional(),  // GitHub username\n  url: z.string().url().optional(), // Personal/portfolio URL\n});\n\nexport const TrieConfigSchema = z.object({\n  version: z.string().optional().default('1.0.0'),\n  apiKeys: ApiKeysSchema.optional(),\n  agents: AgentConfigSchema.optional(),\n  compliance: ComplianceSchema.optional(),\n  output: OutputSchema.optional(),\n  paths: PathsSchema.optional(),\n  integrations: IntegrationsSchema.optional(),\n  user: UserSchema.optional(),  // User identity for attribution\n});\n\nexport type TrieConfig = z.infer<typeof TrieConfigSchema>;\nexport type ApiKeys = z.infer<typeof ApiKeysSchema>;\nexport type AgentConfig = z.infer<typeof AgentConfigSchema>;\n\n/**\n * Configuration validator with detailed error reporting\n */\nexport class ConfigValidator {\n  /**\n   * Validate configuration object\n   */\n  validateConfig(config: unknown): { success: true; data: TrieConfig } | { success: false; errors: string[] } {\n    try {\n      const validated = TrieConfigSchema.parse(config);\n\n      // Additional business logic validation\n      const businessErrors = this.validateBusinessLogic(validated);\n      if (businessErrors.length > 0) {\n        return { success: false, errors: businessErrors };\n      }\n\n      return { success: true, data: validated };\n    } catch (error) {\n      if (error instanceof z.ZodError) {\n        const errors = error.errors.map(err =>\n          `${err.path.join('.')}: ${err.message}`\n        );\n        return { success: false, errors };\n      }\n\n      return {\n        success: false,\n        errors: [`Configuration validation failed: ${error instanceof Error ? error.message : 'Unknown error'}`]\n      };\n    }\n  }\n\n  /**\n   * Validate environment variables for API keys\n   */\n  validateEnvironment(): { valid: boolean; warnings: string[]; errors: string[] } {\n    const warnings: string[] = [];\n    const errors: string[] = [];\n\n    // Check for potentially exposed secrets\n    const exposedPatterns = [\n      'NEXT_PUBLIC_ANTHROPIC',\n      'REACT_APP_ANTHROPIC',\n      'VITE_ANTHROPIC',\n      'PUBLIC_ANTHROPIC'\n    ];\n\n    for (const pattern of exposedPatterns) {\n      const envVars = Object.keys(process.env).filter(key => key.includes(pattern));\n      for (const envVar of envVars) {\n        errors.push(`[!] Security risk: API key in client-side environment variable: ${envVar}`);\n      }\n    }\n\n    // Check API key format if present (check env var first, then config)\n    let anthropicKey = process.env.ANTHROPIC_API_KEY;\n    \n    // Also check config file if available (for validation purposes)\n    // Note: This is a read-only check for validation, actual usage goes through isAIAvailable()\n    if (!anthropicKey) {\n      try {\n        const configPath = join(getTrieDirectory(getWorkingDirectory(undefined, true)), 'config.json');\n        if (existsSync(configPath)) {\n          const config = JSON.parse(readFileSync(configPath, 'utf-8'));\n          anthropicKey = config.apiKeys?.anthropic;\n        }\n      } catch {\n        // Config file check failed, continue with env var only\n      }\n    }\n    \n    if (anthropicKey && !API_KEY_PATTERNS.anthropic.test(anthropicKey)) {\n      errors.push('ANTHROPIC_API_KEY does not match expected format');\n    }\n\n    // Warnings for missing optional keys\n    if (!anthropicKey) {\n      warnings.push('ANTHROPIC_API_KEY not set - AI features will be disabled. Set in environment, .trie/config.json, or .env file');\n    }\n\n    if (!process.env.GITHUB_TOKEN && process.env.CI) {\n      warnings.push('GITHUB_TOKEN not set - GitHub integration disabled');\n    }\n\n    return {\n      valid: errors.length === 0,\n      warnings,\n      errors\n    };\n  }\n\n  /**\n   * Validate file paths in configuration\n   */\n  validatePaths(paths: z.infer<typeof PathsSchema>): { valid: boolean; errors: string[] } {\n    const errors: string[] = [];\n\n    if (paths?.include) {\n      for (const path of paths.include) {\n        const resolvedPath = resolve(path);\n        if (!existsSync(resolvedPath)) {\n          errors.push(`Include path does not exist: ${path}`);\n        }\n      }\n    }\n\n    if (paths?.configDir) {\n      const configPath = resolve(paths.configDir);\n      if (!existsSync(configPath)) {\n        try {\n          // Try to create the directory\n          require('fs').mkdirSync(configPath, { recursive: true });\n        } catch {\n          errors.push(`Cannot create config directory: ${paths.configDir}`);\n        }\n      }\n    }\n\n    return {\n      valid: errors.length === 0,\n      errors\n    };\n  }\n\n  /**\n   * Validate integration configurations\n   */\n  validateIntegrations(integrations: z.infer<typeof IntegrationsSchema>): { valid: boolean; errors: string[] } {\n    const errors: string[] = [];\n\n    // GitHub integration\n    if (integrations?.github?.enabled) {\n      if (!integrations.github.token) {\n        errors.push('GitHub integration enabled but no token provided');\n      }\n    }\n\n    // Slack integration\n    if (integrations?.slack?.enabled) {\n      if (!integrations.slack.webhook) {\n        errors.push('Slack integration enabled but no webhook URL provided');\n      }\n    }\n\n    // JIRA integration\n    if (integrations?.jira?.enabled) {\n      if (!integrations.jira.url || !integrations.jira.token || !integrations.jira.project) {\n        errors.push('JIRA integration enabled but missing required fields (url, token, project)');\n      }\n    }\n\n    return {\n      valid: errors.length === 0,\n      errors\n    };\n  }\n\n  /**\n   * Business logic validation\n   */\n  private validateBusinessLogic(config: TrieConfig): string[] {\n    const errors: string[] = [];\n\n    // Agent configuration validation\n    if (config.agents?.enabled && config.agents?.disabled) {\n      const overlap = config.agents.enabled.filter(agent =>\n        config.agents?.disabled?.includes(agent)\n      );\n      if (overlap.length > 0) {\n        errors.push(`Agents cannot be both enabled and disabled: ${overlap.join(', ')}`);\n      }\n    }\n\n    // Concurrency validation\n    if (config.agents?.maxConcurrency && config.agents.maxConcurrency > 10) {\n      errors.push('maxConcurrency should not exceed 10 for optimal performance');\n    }\n\n    // Compliance standards validation\n    if (config.compliance?.standards) {\n      const invalidStandards = config.compliance.standards.filter(standard =>\n        !['SOC2', 'GDPR', 'HIPAA', 'CCPA', 'PCI-DSS'].includes(standard)\n      );\n      if (invalidStandards.length > 0) {\n        errors.push(`Invalid compliance standards: ${invalidStandards.join(', ')}`);\n      }\n    }\n\n    // Path validation\n    if (config.paths) {\n      const pathValidation = this.validatePaths(config.paths);\n      errors.push(...pathValidation.errors);\n    }\n\n    // Integration validation\n    if (config.integrations) {\n      const integrationValidation = this.validateIntegrations(config.integrations);\n      errors.push(...integrationValidation.errors);\n    }\n\n    return errors;\n  }\n\n  /**\n   * Generate configuration template\n   */\n  generateTemplate(): TrieConfig {\n    return {\n      version: '1.0.0',\n      agents: {\n        enabled: ['security', 'bugs', 'types'],\n        disabled: [],\n        parallel: true,\n        maxConcurrency: 4,\n        timeout: 120000,\n        cache: true\n      },\n      compliance: {\n        standards: ['SOC2'],\n        enforceCompliance: false,\n        reportFormat: 'json'\n      },\n      output: {\n        format: 'console',\n        level: 'all',\n        interactive: false,\n        streaming: true,\n        colors: true\n      },\n      paths: {\n        include: [],\n        exclude: ['node_modules', 'dist', 'build', '.git'],\n        configDir: '.trie',\n        outputDir: 'trie-reports'\n      }\n    };\n  }\n\n  /**\n   * Validate and provide suggestions for improvement\n   */\n  analyze(config: TrieConfig): {\n    score: number;\n    suggestions: string[];\n    securityIssues: string[];\n    optimizations: string[];\n  } {\n    const suggestions: string[] = [];\n    const securityIssues: string[] = [];\n    const optimizations: string[] = [];\n    let score = 100;\n\n    // Check for AI enhancement (check config, env var, and .env files)\n    let hasApiKey = Boolean(config.apiKeys?.anthropic || process.env.ANTHROPIC_API_KEY);\n    if (!hasApiKey) {\n      // Check .env files as well\n      try {\n        const workDir = getWorkingDirectory(undefined, true);\n        const envFiles = ['.env', '.env.local', '.env.production'];\n        for (const envFile of envFiles) {\n          const envPath = join(workDir, envFile);\n          if (existsSync(envPath)) {\n            const envContent = readFileSync(envPath, 'utf-8');\n            if (envContent.includes('ANTHROPIC_API_KEY=')) {\n              hasApiKey = true;\n              break;\n            }\n          }\n        }\n      } catch {\n        // .env check failed, continue\n      }\n    }\n    \n    if (!hasApiKey) {\n      suggestions.push('Add ANTHROPIC_API_KEY to enable AI-powered analysis for better issue detection. Set in environment, .trie/config.json, or .env file');\n      score -= 10;\n    }\n\n    // Check parallel execution\n    if (config.agents?.parallel === false) {\n      optimizations.push('Enable parallel agent execution for 3-5x faster scans');\n      score -= 15;\n    }\n\n    // Check caching\n    if (config.agents?.cache === false) {\n      optimizations.push('Enable result caching to speed up repeated scans');\n      score -= 10;\n    }\n\n    // Check compliance standards\n    if (!config.compliance?.standards || config.compliance.standards.length === 0) {\n      suggestions.push('Configure compliance standards (SOC2, GDPR, etc.) for regulatory requirements');\n      score -= 5;\n    }\n\n    // Check integrations for team collaboration\n    const hasIntegrations = config.integrations && (\n      config.integrations.github?.enabled ||\n      config.integrations.slack?.enabled ||\n      config.integrations.jira?.enabled\n    );\n    if (!hasIntegrations) {\n      suggestions.push('Consider enabling GitHub/Slack/JIRA integrations for better team collaboration');\n      score -= 5;\n    }\n\n    // Security checks\n    if (config.apiKeys) {\n      securityIssues.push('API keys in config file - consider using environment variables instead');\n      score -= 20;\n    }\n\n    return {\n      score: Math.max(0, score),\n      suggestions,\n      securityIssues,\n      optimizations\n    };\n  }\n}\n\n/**\n * Default configuration with security best practices\n */\nexport const DEFAULT_CONFIG: TrieConfig = {\n  version: '1.0.0',\n  agents: {\n    enabled: [],\n    disabled: [],\n    parallel: true,\n    maxConcurrency: 4,\n    timeout: 120000,\n    cache: true,\n  },\n  compliance: {\n    standards: ['SOC2'],\n    enforceCompliance: false,\n    reportFormat: 'json',\n  },\n  output: {\n    format: 'console',\n    level: 'all',\n    interactive: false,\n    streaming: true,\n    colors: true,\n  },\n  paths: {\n    include: [],\n    exclude: ['node_modules', 'dist', 'build', '.git', '.next', '.nuxt', 'coverage'],\n    configDir: '.trie',\n    outputDir: 'trie-reports',\n  },\n};\n\n/**\n * Validate startup configuration\n */\nexport function validateStartupConfig(): {\n  valid: boolean;\n  config: TrieConfig;\n  warnings: string[];\n  errors: string[];\n} {\n  const validator = new ConfigValidator();\n\n  // Validate environment\n  const envValidation = validator.validateEnvironment();\n\n  // Use default config as base\n  const configResult = validator.validateConfig(DEFAULT_CONFIG);\n\n  if (!configResult.success) {\n    return {\n      valid: false,\n      config: DEFAULT_CONFIG,\n      warnings: envValidation.warnings,\n      errors: [...envValidation.errors, ...configResult.errors]\n    };\n  }\n\n  return {\n    valid: envValidation.valid,\n    config: configResult.data,\n    warnings: envValidation.warnings,\n    errors: envValidation.errors\n  };\n}","/**\n * Autonomy Configuration Loader\n * \n * Loads, saves, and manages autonomy settings from .trie/config.json\n */\n\nimport { readFile, writeFile, mkdir } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { getTrieDirectory } from './workspace.js';\nimport type { \n  AutonomyConfig, \n  IssueOccurrence,\n  AutoFixAction,\n  PushBlockResult \n} from '../types/autonomy.js';\nimport { DEFAULT_AUTONOMY_CONFIG } from '../types/autonomy.js';\nimport { createHash } from 'crypto';\n\n// ============================================================================\n// Config Loading/Saving\n// ============================================================================\n\n/**\n * Load autonomy config from .trie/config.json\n */\nexport async function loadAutonomyConfig(projectPath: string): Promise<AutonomyConfig> {\n  const configPath = join(getTrieDirectory(projectPath), 'config.json');\n  \n  try {\n    if (!existsSync(configPath)) {\n      return { ...DEFAULT_AUTONOMY_CONFIG };\n    }\n    \n    const content = await readFile(configPath, 'utf-8');\n    const config = JSON.parse(content);\n    \n    // Merge with defaults to ensure all fields exist\n    return mergeWithDefaults(config.autonomy || {});\n  } catch (error) {\n    console.error('Failed to load autonomy config:', error);\n    return { ...DEFAULT_AUTONOMY_CONFIG };\n  }\n}\n\n/**\n * Save autonomy config to .trie/config.json\n */\nexport async function saveAutonomyConfig(\n  projectPath: string, \n  autonomyConfig: Partial<AutonomyConfig>\n): Promise<void> {\n  const configPath = join(getTrieDirectory(projectPath), 'config.json');\n  const trieDir = getTrieDirectory(projectPath);\n  \n  try {\n    // Ensure .trie directory exists\n    if (!existsSync(trieDir)) {\n      await mkdir(trieDir, { recursive: true });\n    }\n    \n    // Load existing config\n    let fullConfig: Record<string, unknown> = {};\n    if (existsSync(configPath)) {\n      const content = await readFile(configPath, 'utf-8');\n      fullConfig = JSON.parse(content);\n    }\n    \n    // Merge autonomy config\n    fullConfig.autonomy = mergeWithDefaults(autonomyConfig);\n    \n    // Save atomically\n    const tempPath = configPath + '.tmp';\n    await writeFile(tempPath, JSON.stringify(fullConfig, null, 2));\n    await writeFile(configPath, JSON.stringify(fullConfig, null, 2));\n    \n  } catch (error) {\n    console.error('Failed to save autonomy config:', error);\n    throw error;\n  }\n}\n\n/**\n * Merge partial config with defaults\n */\nfunction mergeWithDefaults(partial: Partial<AutonomyConfig>): AutonomyConfig {\n  return {\n    level: partial.level ?? DEFAULT_AUTONOMY_CONFIG.level,\n    autoCheck: {\n      ...DEFAULT_AUTONOMY_CONFIG.autoCheck,\n      ...(partial.autoCheck || {}),\n    },\n    autoFix: {\n      ...DEFAULT_AUTONOMY_CONFIG.autoFix,\n      ...(partial.autoFix || {}),\n    },\n    pushBlocking: {\n      ...DEFAULT_AUTONOMY_CONFIG.pushBlocking,\n      ...(partial.pushBlocking || {}),\n    },\n    progressiveEscalation: {\n      ...DEFAULT_AUTONOMY_CONFIG.progressiveEscalation,\n      ...(partial.progressiveEscalation || {}),\n      thresholds: {\n        ...DEFAULT_AUTONOMY_CONFIG.progressiveEscalation.thresholds,\n        ...(partial.progressiveEscalation?.thresholds || {}),\n      },\n    },\n  };\n}\n\n// ============================================================================\n// Issue Occurrence Tracking (for progressive escalation)\n// ============================================================================\n\nconst occurrenceCache = new Map<string, Map<string, IssueOccurrence>>();\n\n/**\n * Get occurrence tracker for a project\n */\nasync function getOccurrences(projectPath: string): Promise<Map<string, IssueOccurrence>> {\n  if (occurrenceCache.has(projectPath)) {\n    return occurrenceCache.get(projectPath)!;\n  }\n  \n  const occurrencesPath = join(getTrieDirectory(projectPath), 'memory', 'occurrences.json');\n  const occurrences = new Map<string, IssueOccurrence>();\n  \n  try {\n    if (existsSync(occurrencesPath)) {\n      const content = await readFile(occurrencesPath, 'utf-8');\n      const data = JSON.parse(content);\n      for (const [hash, occ] of Object.entries(data)) {\n        occurrences.set(hash, occ as IssueOccurrence);\n      }\n    }\n  } catch {\n    // Start fresh\n  }\n  \n  occurrenceCache.set(projectPath, occurrences);\n  return occurrences;\n}\n\n/**\n * Save occurrences to disk\n */\nasync function saveOccurrences(projectPath: string): Promise<void> {\n  const occurrences = occurrenceCache.get(projectPath);\n  if (!occurrences) return;\n  \n  const occurrencesPath = join(getTrieDirectory(projectPath), 'memory', 'occurrences.json');\n  const memoryDir = join(getTrieDirectory(projectPath), 'memory');\n  \n  try {\n    if (!existsSync(memoryDir)) {\n      await mkdir(memoryDir, { recursive: true });\n    }\n    \n    const data: Record<string, IssueOccurrence> = {};\n    for (const [hash, occ] of occurrences.entries()) {\n      data[hash] = occ;\n    }\n    \n    await writeFile(occurrencesPath, JSON.stringify(data, null, 2));\n  } catch (error) {\n    console.error('Failed to save occurrences:', error);\n  }\n}\n\n/**\n * Create a hash for an issue (for deduplication)\n */\nexport function createIssueHash(file: string, line: number | undefined, issueType: string): string {\n  const input = `${file}:${line || 0}:${issueType}`;\n  return createHash('md5').update(input).digest('hex').slice(0, 12);\n}\n\n/**\n * Track an issue occurrence\n */\nexport async function trackIssueOccurrence(\n  projectPath: string,\n  file: string,\n  line: number | undefined,\n  issueType: string,\n  config: AutonomyConfig\n): Promise<IssueOccurrence> {\n  const occurrences = await getOccurrences(projectPath);\n  const hash = createIssueHash(file, line, issueType);\n  const now = Date.now();\n  \n  let occurrence = occurrences.get(hash);\n  \n  if (occurrence) {\n    // Check if within time window\n    const windowMs = config.progressiveEscalation.windowMs;\n    if (now - occurrence.firstSeen > windowMs) {\n      // Reset if outside window\n      occurrence = {\n        hash,\n        firstSeen: now,\n        lastSeen: now,\n        count: 1,\n        escalationLevel: 'suggest',\n        notified: false,\n        bypassed: false,\n        bypassHistory: occurrence.bypassHistory, // Keep bypass history\n      };\n    } else {\n      // Increment within window\n      occurrence.lastSeen = now;\n      occurrence.count++;\n      \n      // Update escalation level\n      const thresholds = config.progressiveEscalation.thresholds;\n      if (occurrence.count >= thresholds.block) {\n        occurrence.escalationLevel = 'block';\n      } else if (occurrence.count >= thresholds.escalate) {\n        occurrence.escalationLevel = 'escalate';\n      } else if (occurrence.count >= thresholds.autoCheck) {\n        occurrence.escalationLevel = 'autoCheck';\n      }\n    }\n  } else {\n    // New occurrence\n    occurrence = {\n      hash,\n      firstSeen: now,\n      lastSeen: now,\n      count: 1,\n      escalationLevel: 'suggest',\n      notified: false,\n      bypassed: false,\n      bypassHistory: [],\n    };\n  }\n  \n  occurrences.set(hash, occurrence);\n  await saveOccurrences(projectPath);\n  \n  return occurrence;\n}\n\n/**\n * Get escalation level for an issue\n */\nexport async function getEscalationLevel(\n  projectPath: string,\n  file: string,\n  line: number | undefined,\n  issueType: string\n): Promise<IssueOccurrence['escalationLevel']> {\n  const occurrences = await getOccurrences(projectPath);\n  const hash = createIssueHash(file, line, issueType);\n  \n  const occurrence = occurrences.get(hash);\n  return occurrence?.escalationLevel ?? 'suggest';\n}\n\n/**\n * Record a bypass\n */\nexport async function recordBypass(\n  projectPath: string,\n  file: string,\n  line: number | undefined,\n  issueType: string,\n  method: string,\n  reason?: string\n): Promise<void> {\n  const occurrences = await getOccurrences(projectPath);\n  const hash = createIssueHash(file, line, issueType);\n  \n  const occurrence = occurrences.get(hash);\n  if (occurrence) {\n    occurrence.bypassed = true;\n    occurrence.bypassHistory.push({\n      timestamp: Date.now(),\n      method,\n      ...(reason !== undefined ? { reason } : {}),\n    });\n    await saveOccurrences(projectPath);\n  }\n}\n\n// ============================================================================\n// Auto-fix Helpers\n// ============================================================================\n\n/**\n * Check if a fix should be auto-applied based on config\n */\nexport function shouldAutoFix(\n  fix: AutoFixAction,\n  config: AutonomyConfig\n): boolean {\n  if (!config.autoFix.enabled) {\n    return false;\n  }\n  \n  // Check if category is allowed\n  const allowedCategories = config.autoFix.categories as string[];\n  if (!allowedCategories.includes(fix.category) && \n      !allowedCategories.includes('all')) {\n    return false;\n  }\n  \n  // Check if specific fix type is allowed\n  if (config.autoFix.allowedFixTypes.length > 0 &&\n      !config.autoFix.allowedFixTypes.includes(fix.type)) {\n    return false;\n  }\n  \n  // Check confidence threshold (require high confidence for auto-fix)\n  if (fix.confidence < 0.9) {\n    return false;\n  }\n  \n  return true;\n}\n\n/**\n * Group fixes by file for batch application\n */\nexport function groupFixesByFile(fixes: AutoFixAction[]): Map<string, AutoFixAction[]> {\n  const grouped = new Map<string, AutoFixAction[]>();\n  \n  for (const fix of fixes) {\n    const existing = grouped.get(fix.file) || [];\n    existing.push(fix);\n    grouped.set(fix.file, existing);\n  }\n  \n  return grouped;\n}\n\n// ============================================================================\n// Push Blocking Helpers\n// ============================================================================\n\n/**\n * Check if push should be blocked\n */\nexport function shouldBlockPush(\n  issues: Array<{ severity: string; file: string; line?: number; issue: string }>,\n  config: AutonomyConfig\n): PushBlockResult {\n  if (!config.pushBlocking.enabled) {\n    return {\n      blocked: false,\n      blockingIssues: [],\n      bypassed: false,\n    };\n  }\n  \n  // Find blocking issues\n  const blockingIssues = issues.filter(issue => \n    config.pushBlocking.blockOn.includes(issue.severity as 'critical' | 'serious' | 'moderate')\n  );\n  \n  if (blockingIssues.length === 0) {\n    return {\n      blocked: false,\n      blockingIssues: [],\n      bypassed: false,\n    };\n  }\n  \n  // Check for bypass\n  const envBypass = process.env.TRIE_BYPASS === '1' || process.env.TRIE_BYPASS === 'true';\n  \n  if (envBypass && config.pushBlocking.allowBypass) {\n    return {\n      blocked: false,\n      blockingIssues,\n      bypassed: true,\n      bypassMethod: 'env',\n    };\n  }\n  \n  // Build bypass instructions\n  const bypassInstructions = buildBypassInstructions(config);\n  \n  return {\n    blocked: true,\n    reason: `${blockingIssues.length} ${blockingIssues[0]?.severity || 'critical'} issue(s) must be fixed before pushing`,\n    blockingIssues,\n    bypassInstructions,\n    bypassed: false,\n  };\n}\n\n/**\n * Build bypass instructions based on config\n */\nfunction buildBypassInstructions(config: AutonomyConfig): string {\n  const instructions: string[] = [];\n  \n  if (config.pushBlocking.bypassMethods.includes('env')) {\n    instructions.push('• Set TRIE_BYPASS=1 to bypass: TRIE_BYPASS=1 git push');\n  }\n  \n  if (config.pushBlocking.bypassMethods.includes('flag')) {\n    instructions.push('• Use --no-verify flag: git push --no-verify');\n  }\n  \n  if (config.pushBlocking.bypassMethods.includes('confirm')) {\n    instructions.push('• Run: trie bypass --confirm to bypass this push');\n  }\n  \n  return instructions.join('\\n');\n}\n\n// ============================================================================\n// Singleton Config Cache\n// ============================================================================\n\nconst configCache = new Map<string, { config: AutonomyConfig; loadedAt: number }>();\nconst CACHE_TTL = 60000; // 1 minute\n\n/**\n * Get autonomy config with caching\n */\nexport async function getAutonomyConfig(projectPath: string): Promise<AutonomyConfig> {\n  const cached = configCache.get(projectPath);\n  \n  if (cached && Date.now() - cached.loadedAt < CACHE_TTL) {\n    return cached.config;\n  }\n  \n  const config = await loadAutonomyConfig(projectPath);\n  configCache.set(projectPath, { config, loadedAt: Date.now() });\n  \n  return config;\n}\n\n/**\n * Clear config cache (for testing or after config changes)\n */\nexport function clearConfigCache(): void {\n  configCache.clear();\n  occurrenceCache.clear();\n}\n","/**\n * Autonomy Configuration Types\n * \n * Controls how autonomous Trie behaves:\n * - Auto-check: Run full checks when issues detected\n * - Auto-fix: Apply fixes with human confirmation\n * - Push blocking: Block git push on critical issues\n * - Progressive escalation: Escalate based on occurrence count\n */\n\n/**\n * Overall autonomy level\n */\nexport type AutonomyLevel = \n  | 'passive'     // Only report, never act\n  | 'suggest'     // Suggest actions, don't execute\n  | 'proactive'   // Auto-check, ask before fixing\n  | 'aggressive'; // Auto-check, auto-fix trivial, block on critical\n\n/**\n * Auto-check configuration\n */\nexport interface AutoCheckConfig {\n  /** Enable auto-running full checks */\n  enabled: boolean;\n  /** Issue count threshold to trigger auto-check */\n  threshold: number;\n  /** Always trigger on critical issues */\n  onCritical: boolean;\n  /** Cooldown between auto-checks (ms) */\n  cooldownMs: number;\n}\n\n/**\n * Auto-fix configuration\n */\nexport interface AutoFixConfig {\n  /** Enable auto-fix suggestions */\n  enabled: boolean;\n  /** Always ask user before applying fixes (human-in-the-loop) */\n  askFirst: boolean;\n  /** Categories of fixes to auto-apply */\n  categories: ('trivial' | 'safe' | 'moderate' | 'all')[];\n  /** Specific fix types to auto-apply */\n  allowedFixTypes: string[];\n}\n\n/**\n * Push blocking configuration\n */\nexport interface PushBlockingConfig {\n  /** Enable push blocking */\n  enabled: boolean;\n  /** Allow user to bypass with flag */\n  allowBypass: boolean;\n  /** Severities that trigger blocking */\n  blockOn: ('critical' | 'serious' | 'moderate')[];\n  /** Bypass methods */\n  bypassMethods: ('env' | 'flag' | 'confirm')[];\n  /** Log bypasses for audit */\n  logBypasses: boolean;\n}\n\n/**\n * Progressive escalation thresholds\n */\nexport interface ProgressiveEscalationConfig {\n  /** Enable progressive escalation */\n  enabled: boolean;\n  /** Thresholds for different actions */\n  thresholds: {\n    /** First occurrence: suggest fix */\n    suggest: number;\n    /** N occurrences: auto-run full check */\n    autoCheck: number;\n    /** N occurrences: escalate to Slack/email */\n    escalate: number;\n    /** N occurrences: block until fixed */\n    block: number;\n  };\n  /** Time window for counting occurrences (ms) */\n  windowMs: number;\n}\n\n/**\n * Full autonomy configuration\n */\nexport interface AutonomyConfig {\n  /** Overall autonomy level (can be overridden by specific settings) */\n  level: AutonomyLevel;\n  /** Auto-check settings */\n  autoCheck: AutoCheckConfig;\n  /** Auto-fix settings */\n  autoFix: AutoFixConfig;\n  /** Push blocking settings */\n  pushBlocking: PushBlockingConfig;\n  /** Progressive escalation settings */\n  progressiveEscalation: ProgressiveEscalationConfig;\n}\n\n/**\n * Default autonomy configuration - proactive but safe\n */\nexport const DEFAULT_AUTONOMY_CONFIG: AutonomyConfig = {\n  level: 'proactive',\n  autoCheck: {\n    enabled: true,\n    threshold: 5,\n    onCritical: true,\n    cooldownMs: 30000, // 30 seconds\n  },\n  autoFix: {\n    enabled: true,\n    askFirst: true, // Always ask (human-in-the-loop)\n    categories: ['trivial', 'safe'],\n    allowedFixTypes: [\n      'remove-console-log',\n      'remove-unused-import',\n      'add-missing-await',\n      'fix-typo',\n    ],\n  },\n  pushBlocking: {\n    enabled: true,\n    allowBypass: true,\n    blockOn: ['critical'],\n    bypassMethods: ['env', 'flag', 'confirm'],\n    logBypasses: true,\n  },\n  progressiveEscalation: {\n    enabled: true,\n    thresholds: {\n      suggest: 1,\n      autoCheck: 3,\n      escalate: 5,\n      block: 10,\n    },\n    windowMs: 24 * 60 * 60 * 1000, // 24 hours\n  },\n};\n\n/**\n * Issue occurrence tracking for progressive escalation\n */\nexport interface IssueOccurrence {\n  /** Issue hash (file + line + type) */\n  hash: string;\n  /** First seen timestamp */\n  firstSeen: number;\n  /** Last seen timestamp */\n  lastSeen: number;\n  /** Total occurrence count */\n  count: number;\n  /** Current escalation level */\n  escalationLevel: 'suggest' | 'autoCheck' | 'escalate' | 'block';\n  /** Whether user has been notified at current level */\n  notified: boolean;\n  /** Whether issue has been bypassed */\n  bypassed: boolean;\n  /** Bypass history */\n  bypassHistory: Array<{\n    timestamp: number;\n    method: string;\n    reason?: string;\n  }>;\n}\n\n/**\n * Auto-fix action\n */\nexport interface AutoFixAction {\n  /** Unique ID for this fix */\n  id: string;\n  /** File to fix */\n  file: string;\n  /** Line number */\n  line?: number;\n  /** Original code */\n  original: string;\n  /** Fixed code */\n  fixed: string;\n  /** Type of fix */\n  type: string;\n  /** Category of fix */\n  category: 'trivial' | 'safe' | 'moderate' | 'risky';\n  /** Description of what the fix does */\n  description: string;\n  /** Confidence in the fix (0-1) */\n  confidence: number;\n}\n\n/**\n * Push block result\n */\nexport interface PushBlockResult {\n  /** Whether push is blocked */\n  blocked: boolean;\n  /** Reason for blocking */\n  reason?: string;\n  /** Issues causing the block */\n  blockingIssues: Array<{\n    file: string;\n    line?: number;\n    severity: string;\n    issue: string;\n  }>;\n  /** Bypass instructions */\n  bypassInstructions?: string;\n  /** Whether user chose to bypass */\n  bypassed: boolean;\n  /** Bypass method used */\n  bypassMethod?: string;\n}\n","import { existsSync } from 'node:fs';\nimport path from 'node:path';\nimport { runExecFile } from '../utils/command-runner.js';\n\nexport interface Commit {\n  hash: string;\n  author: string;\n  date: string;\n  message: string;\n}\n\nexport interface Change {\n  path: string;\n  status: string;\n  oldPath?: string;\n}\n\nasync function execGit(args: string[], cwd: string): Promise<string | null> {\n  try {\n    const { stdout } = await runExecFile(\n      'git',\n      ['-C', cwd, ...args],\n      { actor: 'internal:git', triggeredBy: 'manual', targetPath: cwd },\n      { maxBuffer: 10 * 1024 * 1024, captureOutput: false }\n    );\n    return stdout.trim();\n  } catch (error: any) {\n    const stderr: string | undefined = error?.stderr?.toString();\n    // Gracefully handle non-git directories and repos with no commits\n    if (stderr?.includes('not a git repository') || stderr?.includes('does not have any commits')) {\n      return null;\n    }\n    throw error;\n  }\n}\n\nasync function ensureRepo(projectPath: string): Promise<boolean> {\n  const result = await execGit(['rev-parse', '--is-inside-work-tree'], projectPath);\n  return result === 'true';\n}\n\nfunction parseNameStatus(output: string): Change[] {\n  return output\n    .split('\\n')\n    .map((line) => line.trim())\n    .filter(Boolean)\n    .map((line) => {\n      const parts = line.split('\\t');\n      const status = parts[0] ?? '';\n      const filePath = parts[1] ?? '';\n      const oldPath = parts[2];\n      const change: Change = { status, path: filePath };\n      if (oldPath) change.oldPath = oldPath;\n      return change;\n    })\n    .filter((entry) => entry.path.length > 0);\n}\n\nexport async function getRecentCommits(projectPath: string, limit: number): Promise<Commit[]> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return [];\n\n  const output = await execGit(\n    ['log', `-n`, String(limit), '--pretty=format:%H%x09%an%x09%ad%x09%s', '--date=iso'],\n    projectPath\n  );\n\n  if (!output) return [];\n\n  return output.split('\\n').map((line) => {\n    const [hash, author, date, message] = line.split('\\t');\n    return { hash, author, date, message } as Commit;\n  });\n}\n\nexport async function getLastCommit(projectPath: string): Promise<Commit | null> {\n  const commits = await getRecentCommits(projectPath, 1);\n  return commits[0] ?? null;\n}\n\nexport async function getStagedChanges(projectPath: string): Promise<Change[]> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return [];\n\n  const output = await execGit(['diff', '--cached', '--name-status'], projectPath);\n  if (!output) return [];\n  return parseNameStatus(output);\n}\n\nexport async function getUncommittedChanges(projectPath: string): Promise<Change[]> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return [];\n\n  const changes: Change[] = [];\n\n  const unstaged = await execGit(['diff', '--name-status'], projectPath);\n  if (unstaged) {\n    changes.push(...parseNameStatus(unstaged));\n  }\n\n  const untracked = await execGit(['ls-files', '--others', '--exclude-standard'], projectPath);\n  if (untracked) {\n    changes.push(\n      ...untracked\n        .split('\\n')\n        .map((p) => p.trim())\n        .filter(Boolean)\n        .map((p) => ({ status: '??', path: p }))\n    );\n  }\n\n  return changes;\n}\n\n/**\n * Get a flat list of changed file paths in the working tree.\n * Convenience helper used by tooling (e.g. cache invalidation).\n *\n * Returns null if not a git repository.\n */\nexport async function getGitChangedFiles(projectPath: string): Promise<string[] | null> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return null;\n\n  const [staged, uncommitted] = await Promise.all([\n    getStagedChanges(projectPath).catch(() => []),\n    getUncommittedChanges(projectPath).catch(() => []),\n  ]);\n\n  const paths = new Set<string>();\n  for (const change of [...staged, ...uncommitted]) {\n    if (change.path) paths.add(change.path);\n    if (change.oldPath) paths.add(change.oldPath);\n  }\n\n  return [...paths];\n}\n\nexport async function getDiff(projectPath: string, commitHash: string): Promise<string> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return '';\n\n  const diff = await execGit(['show', commitHash, '--unified=3', '--no-color'], projectPath);\n  return diff ?? '';\n}\n\nexport async function getWorkingTreeDiff(projectPath: string, stagedOnly = false): Promise<string> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return '';\n\n  const args = stagedOnly ? ['diff', '--cached', '--unified=3', '--no-color'] : ['diff', '--unified=3', '--no-color'];\n  const diff = await execGit(args, projectPath);\n  return diff ?? '';\n}\n\nexport async function getUnpushedCommits(projectPath: string): Promise<Commit[]> {\n  const isRepo = await ensureRepo(projectPath);\n  if (!isRepo) return [];\n\n  // Handles detached HEAD by falling back to HEAD if upstream missing\n  const upstream = await execGit(['rev-parse', '--abbrev-ref', '--symbolic-full-name', '@{u}'], projectPath);\n  if (!upstream) {\n    return getRecentCommits(projectPath, 10);\n  }\n\n  const output = await execGit(['log', `${upstream}..HEAD`, '--pretty=format:%H%x09%an%x09%ad%x09%s', '--date=iso'], projectPath);\n  if (!output) return [];\n\n  return output.split('\\n').filter(Boolean).map((line) => {\n    const [hash, author, date, message] = line.split('\\t');\n    return { hash, author, date, message } as Commit;\n  });\n}\n\nexport function resolveRepoPath(projectPath: string): string {\n  const gitDir = path.join(projectPath, '.git');\n  if (existsSync(gitDir)) return projectPath;\n  return projectPath;\n}\n\n/**\n * Check if the given path is inside a git repository\n */\nexport async function isGitRepo(projectPath: string): Promise<boolean> {\n  const result = await execGit(['rev-parse', '--is-inside-work-tree'], projectPath);\n  return result === 'true';\n}\n\n/**\n * Get files changed since a given timestamp\n * Uses git log to find commits after timestamp, then gets affected files\n * Returns null if not a git repo or on error\n */\nexport async function getChangedFilesSinceTimestamp(\n  projectPath: string,\n  timestamp: number\n): Promise<string[] | null> {\n  const isRepo = await isGitRepo(projectPath);\n  if (!isRepo) return null;\n\n  try {\n    // Convert timestamp to ISO date for git\n    const sinceDate = new Date(timestamp).toISOString();\n    \n    // Set timeout for git operations (5 seconds total)\n    const GIT_TIMEOUT_MS = 5000;\n    const startTime = Date.now();\n    \n    // Get all files that changed in commits since the timestamp\n    // Use Promise.race to timeout if git operations take too long\n    const committedChangesPromise = execGit(\n      ['log', `--since=${sinceDate}`, '--name-only', '--pretty=format:'],\n      projectPath\n    );\n    const committedChangesTimeout = new Promise<string | null>((resolve) => {\n      setTimeout(() => resolve(null), GIT_TIMEOUT_MS);\n    });\n    const committedChanges = await Promise.race([committedChangesPromise, committedChangesTimeout]);\n\n    // Check if we've exceeded timeout\n    if (Date.now() - startTime > GIT_TIMEOUT_MS) {\n      return null;\n    }\n\n    // Get currently modified files (staged + unstaged) - run in parallel with timeout\n    const stagedPromise = execGit(['diff', '--cached', '--name-only'], projectPath);\n    const unstagedPromise = execGit(['diff', '--name-only'], projectPath);\n    const untrackedPromise = execGit(\n      ['ls-files', '--others', '--exclude-standard'],\n      projectPath\n    );\n    \n    const timeoutPromise = new Promise<null>((resolve) => {\n      setTimeout(() => resolve(null), Math.max(0, GIT_TIMEOUT_MS - (Date.now() - startTime)));\n    });\n    \n    const [stagedChanges, unstagedChanges, untrackedFiles] = await Promise.race([\n      Promise.all([stagedPromise, unstagedPromise, untrackedPromise]),\n      timeoutPromise.then(() => [null, null, null] as const)\n    ]);\n\n    // Combine all changed files\n    const changedFiles = new Set<string>();\n    \n    const addFiles = (output: string | null) => {\n      if (output) {\n        output.split('\\n')\n          .map(f => f.trim())\n          .filter(Boolean)\n          .forEach(f => changedFiles.add(path.join(projectPath, f)));\n      }\n    };\n\n    addFiles(committedChanges);\n    addFiles(stagedChanges);\n    addFiles(unstagedChanges);\n    addFiles(untrackedFiles);\n\n    return Array.from(changedFiles);\n  } catch {\n    return null;\n  }\n}\n","import path from 'node:path';\n\nimport { analyzeDiff, type DiffSummary } from './diff-analyzer.js';\nimport {\n  getStagedChanges,\n  getUncommittedChanges,\n  getWorkingTreeDiff,\n  type Change\n} from './git.js';\nimport { ContextGraph } from '../context/graph.js';\nimport type { FileNode, FileNodeData } from '../context/nodes.js';\n\nexport interface PerceptionResult {\n  staged: Change[];\n  unstaged: Change[];\n  diffSummary: DiffSummary;\n  changeNodeId?: string;\n}\n\nexport async function perceiveCurrentChanges(\n  projectPath: string,\n  graph?: ContextGraph\n): Promise<PerceptionResult> {\n  const ctxGraph = graph ?? new ContextGraph(projectPath);\n\n  const [staged, unstaged] = await Promise.all([\n    getStagedChanges(projectPath),\n    getUncommittedChanges(projectPath)\n  ]);\n\n  const stagedDiff = await getWorkingTreeDiff(projectPath, true);\n  const unstagedDiff = await getWorkingTreeDiff(projectPath, false);\n  const combinedDiff = [stagedDiff, unstagedDiff].filter(Boolean).join('\\n');\n  const diffSummary = analyzeDiff(combinedDiff);\n\n  const filesTouched = new Set<string>();\n  staged.forEach((c) => filesTouched.add(c.path));\n  unstaged.forEach((c) => filesTouched.add(c.path));\n  diffSummary.files.forEach((f) => filesTouched.add(f.filePath));\n\n  const changeId = await upsertWorkingChange(ctxGraph, Array.from(filesTouched), projectPath);\n\n  const result: PerceptionResult = {\n    staged,\n    unstaged,\n    diffSummary\n  };\n  if (changeId) result.changeNodeId = changeId;\n  return result;\n}\n\nasync function upsertWorkingChange(\n  graph: ContextGraph,\n  files: string[],\n  projectPath: string\n): Promise<string | undefined> {\n  if (files.length === 0) return undefined;\n\n  const now = new Date().toISOString();\n  const change = await graph.addNode('change', {\n    commitHash: null,\n    files,\n    message: 'workspace changes',\n    diff: null,\n    author: null,\n    timestamp: now,\n    outcome: 'unknown'\n  });\n\n  for (const filePath of files) {\n    const fileNode = await ensureFileNode(graph, filePath, projectPath);\n    await graph.addEdge(change.id, fileNode.id, 'affects');\n  }\n\n  return change.id;\n}\n\nasync function ensureFileNode(\n  graph: ContextGraph,\n  filePath: string,\n  projectPath: string\n): Promise<FileNode> {\n  const normalized = path.resolve(projectPath, filePath);\n  const existing = await graph.getNode('file', normalized);\n\n  const now = new Date().toISOString();\n  if (existing) {\n    const data = existing.data as FileNodeData;\n    await graph.updateNode('file', existing.id, {\n      changeCount: (data.changeCount ?? 0) + 1,\n      lastChanged: now\n    });\n    return (await graph.getNode('file', existing.id)) as FileNode;\n  }\n\n  const data: FileNodeData = {\n    path: filePath,\n    extension: path.extname(filePath),\n    purpose: '',\n    riskLevel: 'medium',\n    whyRisky: null,\n    changeCount: 1,\n    lastChanged: now,\n    incidentCount: 0,\n    createdAt: now\n  };\n\n  return (await graph.addNode('file', data)) as FileNode;\n}\n","export interface DiffFileSummary {\n  filePath: string;\n  added: number;\n  removed: number;\n  functionsModified: string[];\n  riskyPatterns: string[];\n}\n\nexport interface DiffSummary {\n  files: DiffFileSummary[];\n  totalAdded: number;\n  totalRemoved: number;\n  riskyFiles: string[];\n}\n\nconst RISKY_PATTERNS = [/auth/i, /token/i, /password/i, /secret/i, /validate/i, /sanitize/i];\n\nexport function analyzeDiff(diff: string): DiffSummary {\n  const files: DiffFileSummary[] = [];\n  let current: DiffFileSummary | null = null;\n\n  const lines = diff.split('\\n');\n\n  for (const line of lines) {\n    if (line.startsWith('+++ b/')) {\n      const filePath = line.replace('+++ b/', '').trim();\n      current = {\n        filePath,\n        added: 0,\n        removed: 0,\n        functionsModified: [],\n        riskyPatterns: []\n      };\n      files.push(current);\n      continue;\n    }\n\n    if (!current) {\n      continue;\n    }\n\n    if (line.startsWith('@@')) {\n      // Capture function names or signatures in hunk headers\n      const match = line.match(/@@.*?(function\\s+([\\w$]+)|class\\s+([\\w$]+)|([\\w$]+\\s*\\())/i);\n      const fnName = match?.[2] || match?.[3] || match?.[4];\n      if (fnName) {\n        current.functionsModified.push(fnName.replace('(', '').trim());\n      }\n      continue;\n    }\n\n    if (line.startsWith('+') && !line.startsWith('+++')) {\n      current.added += 1;\n      markRisk(line, current);\n    } else if (line.startsWith('-') && !line.startsWith('---')) {\n      current.removed += 1;\n      markRisk(line, current);\n    }\n  }\n\n  const totalAdded = files.reduce((acc, f) => acc + f.added, 0);\n  const totalRemoved = files.reduce((acc, f) => acc + f.removed, 0);\n  const riskyFiles = files.filter((f) => f.riskyPatterns.length > 0).map((f) => f.filePath);\n\n  return {\n    files,\n    totalAdded,\n    totalRemoved,\n    riskyFiles\n  };\n}\n\nfunction markRisk(line: string, file: DiffFileSummary): void {\n  for (const pattern of RISKY_PATTERNS) {\n    if (pattern.test(line)) {\n      const label = pattern.toString();\n      if (!file.riskyPatterns.includes(label)) {\n        file.riskyPatterns.push(label);\n      }\n    }\n  }\n}\n","import path from 'node:path';\n\nimport type { RiskLevel } from '../types/index.js';\nimport type { PatternNode } from '../context/types.js';\nimport type { ContextGraph } from '../context/graph.js';\nimport type { FileNodeData, IncidentNode } from '../context/nodes.js';\n\nexport interface FileRiskResult {\n  file: string;\n  score: number;\n  level: RiskLevel;\n  reasons: string[];\n  incidents: IncidentNode[];\n  matchedPatterns: PatternNode[];\n}\n\nexport interface ChangeRiskResult {\n  files: FileRiskResult[];\n  overall: RiskLevel;\n  score: number;\n  shouldEscalate: boolean;\n}\n\nconst BASE_RISK: Record<RiskLevel, number> = {\n  low: 10,\n  medium: 35,\n  high: 65,\n  critical: 85\n};\n\nconst SENSITIVE_PATHS: { pattern: RegExp; weight: number; reason: string }[] = [\n  { pattern: /auth|login|token|session/i, weight: 20, reason: 'touches authentication' },\n  { pattern: /payment|billing|stripe|paypal|checkout/i, weight: 25, reason: 'touches payments' },\n  { pattern: /secret|credential|env|config\\/security/i, weight: 15, reason: 'touches secrets/security config' },\n];\n\nfunction levelFromScore(score: number): RiskLevel {\n  if (score >= 90) return 'critical';\n  if (score >= 65) return 'high';\n  if (score >= 40) return 'medium';\n  return 'low';\n}\n\nexport async function scoreFile(\n  graph: ContextGraph,\n  filePath: string,\n  matchedPatterns: PatternNode[] = []\n): Promise<FileRiskResult> {\n  const reasons: string[] = [];\n  const normalized = path.resolve(graph.projectRoot, filePath);\n  const node = await graph.getNode('file', normalized);\n  const incidents = await graph.getIncidentsForFile(filePath);\n\n  let score = 10;\n  const data = node?.data as FileNodeData | undefined;\n\n  if (data) {\n    score = BASE_RISK[data.riskLevel] ?? score;\n    reasons.push(`baseline ${data.riskLevel}`);\n\n    if (data.incidentCount > 0) {\n      const incBoost = Math.min(data.incidentCount * 12, 36);\n      score += incBoost;\n      reasons.push(`historical incidents (+${incBoost})`);\n    }\n\n    if (data.changeCount > 5) {\n      const changeBoost = Math.min((data.changeCount - 5) * 2, 12);\n      score += changeBoost;\n      reasons.push(`frequent changes (+${changeBoost})`);\n    }\n\n    if (data.lastChanged) {\n      const lastChanged = new Date(data.lastChanged).getTime();\n      const days = (Date.now() - lastChanged) / (1000 * 60 * 60 * 24);\n      if (days > 60 && data.incidentCount === 0) {\n        score -= 5;\n        reasons.push('stable for 60d (-5)');\n      }\n    }\n  }\n\n  for (const { pattern, weight, reason } of SENSITIVE_PATHS) {\n    if (pattern.test(filePath)) {\n      score += weight;\n      reasons.push(reason);\n    }\n  }\n\n  if (matchedPatterns.length > 0) {\n    const patternBoost = Math.min(\n      matchedPatterns.reduce((acc, p) => acc + (p.data.confidence ?? 50) / 10, 0),\n      20\n    );\n    score += patternBoost;\n    reasons.push(`pattern match (+${Math.round(patternBoost)})`);\n  }\n\n  if (incidents.length > 0) {\n    const timestamps = incidents\n      .map((i) => new Date(i.data.timestamp).getTime())\n      .sort((a, b) => b - a);\n    const recent = timestamps[0]!;\n    const daysSince = (Date.now() - recent) / (1000 * 60 * 60 * 24);\n    if (daysSince > 90) {\n      score -= 5;\n      reasons.push('no incidents in 90d (-5)');\n    } else {\n      score += 8;\n      reasons.push('recent incident (+8)');\n    }\n  }\n\n  const level = levelFromScore(score);\n  return {\n    file: filePath,\n    score,\n    level,\n    reasons,\n    incidents,\n    matchedPatterns\n  };\n}\n\nexport async function scoreChangeSet(\n  graph: ContextGraph,\n  files: string[],\n  patternMatches: Record<string, PatternNode[]> = {}\n): Promise<ChangeRiskResult> {\n  const fileResults: FileRiskResult[] = [];\n\n  for (const file of files) {\n    const patterns = patternMatches[file] ?? [];\n    fileResults.push(await scoreFile(graph, file, patterns));\n  }\n\n  // Aggregate: use max file score, but boost if many files touched\n  const maxScore = Math.max(...fileResults.map((f) => f.score), 10);\n  const spreadBoost = files.length > 5 ? Math.min((files.length - 5) * 2, 10) : 0;\n  const overallScore = maxScore + spreadBoost;\n  const overall = levelFromScore(overallScore);\n\n  const shouldEscalate = overall === 'critical' || overall === 'high';\n\n  return {\n    files: fileResults,\n    overall,\n    score: overallScore,\n    shouldEscalate\n  };\n}\n","import { ContextGraph } from '../context/graph.js';\nimport type { PatternNode } from '../context/nodes.js';\n\nexport interface PatternMatch {\n  file: string;\n  pattern: PatternNode;\n  confidence: number;\n  isAntiPattern: boolean;\n}\n\nexport async function matchPatternsForFiles(\n  graph: ContextGraph,\n  files: string[]\n): Promise<{ matches: PatternMatch[]; byFile: Record<string, PatternNode[]> }> {\n  const matches: PatternMatch[] = [];\n  const byFile: Record<string, PatternNode[]> = {};\n\n  for (const file of files) {\n    const patterns = await graph.getPatternsForFile(file);\n    if (patterns.length === 0) continue;\n\n    byFile[file] = patterns;\n\n    for (const pattern of patterns) {\n      matches.push({\n        file,\n        pattern,\n        confidence: pattern.data.confidence,\n        isAntiPattern: pattern.data.isAntiPattern\n      });\n    }\n  }\n\n  return { matches, byFile };\n}\n","import type { CodeContext, Agent, TriagingConfig } from '../types/index.js';\n\nexport class Triager {\n  constructor(_config?: Partial<TriagingConfig>) {\n    // Config no longer used - Trie is now purely a decision ledger\n  }\n\n  /**\n   * Triage a change to select appropriate agents\n   * Note: Skills/agents have been removed - Trie is now purely a decision ledger\n   */\n  async triage(\n    _context: CodeContext,\n    _forceAgents?: string[]\n  ): Promise<Agent[]> {\n    // No skills to triage - return empty array\n    // Trie now focuses on decision ledger and learning from incidents\n    return [];\n  }\n\n  /**\n   * Get all available agent names (deprecated - returns empty array)\n   */\n  getAvailableAgents(): string[] {\n    return [];\n  }\n}\n","import { Worker } from 'worker_threads';\nimport { cpus } from 'os';\nimport { existsSync } from 'fs';\nimport { fileURLToPath } from 'url';\nimport type { Agent, AgentResult, ScanContext } from '../types/index.js';\nimport { StreamingManager } from './streaming.js';\nimport { CacheManager } from './cache-manager.js';\nimport { isInteractiveMode } from './progress.js';\n\ninterface ParallelTask {\n  agent: Agent;\n  files: string[];\n  context: ScanContext;\n  priority: number;\n  timeoutMs: number;\n}\n\ninterface ParallelResult {\n  agent: string;\n  result: AgentResult;\n  fromCache: boolean;\n  executionTime: number;\n}\n\n/**\n * Parallel execution engine for Trie agents\n *\n * Features:\n * - True parallel execution using worker threads\n * - Intelligent scheduling based on agent priority\n * - Result caching and cache-aware scheduling\n * - Real-time progress streaming\n * - Dynamic resource management\n */\nexport class ParallelExecutor {\n  private maxWorkers: number;\n  private cache: CacheManager | null;\n  private streaming?: StreamingManager;\n  private activeWorkers: Set<Worker> = new Set();\n  private cacheEnabled: boolean = true;\n  private useWorkerThreads: boolean = false;\n  private workerAvailable: boolean | null = null;\n  private warnedWorkerFallback: boolean = false;\n\n  constructor(\n    cacheManager: CacheManager | null,\n    maxWorkers: number = Math.max(2, Math.min(cpus().length - 1, 8)),\n    options?: { cacheEnabled?: boolean; useWorkerThreads?: boolean }\n  ) {\n    this.maxWorkers = maxWorkers;\n    this.cache = cacheManager;\n    this.cacheEnabled = options?.cacheEnabled ?? true;\n    this.useWorkerThreads = options?.useWorkerThreads ?? false;\n  }\n\n  /**\n   * Set streaming manager for real-time updates\n   */\n  setStreaming(streaming: StreamingManager): void {\n    this.streaming = streaming;\n  }\n\n  /**\n   * Execute agents in parallel with intelligent scheduling\n   */\n  async executeAgents(\n    agents: Agent[],\n    files: string[],\n    context: ScanContext\n  ): Promise<Map<string, AgentResult>> {\n    if (agents.length === 0) {\n      return new Map();\n    }\n\n    // Initialize streaming\n    if (this.streaming && this.streaming.getProgress().totalFiles === 0) {\n      this.streaming.startScan(files.length);\n    }\n\n    // Check cache for existing results\n    const cacheResults = new Map<string, AgentResult>();\n    const uncachedTasks: ParallelTask[] = [];\n\n    for (const agent of agents) {\n      const cached = await this.checkAgentCache(agent, files);\n      if (cached) {\n        cacheResults.set(agent.name, cached);\n        this.streaming?.completeAgent(agent.name, cached.issues);\n      } else {\n        uncachedTasks.push({\n          agent,\n          files,\n          context,\n          priority: agent.priority?.tier || 2,\n          timeoutMs: context?.config?.timeoutMs || 120000\n        });\n      }\n    }\n\n    // Sort tasks by priority (tier 1 = highest priority)\n    uncachedTasks.sort((a, b) => a.priority - b.priority);\n\n    // Execute uncached tasks in parallel\n    const parallelResults = await this.executeTasksParallel(uncachedTasks);\n\n    // Cache new results\n    await this.cacheResults(parallelResults);\n\n    // Combine cached and new results\n    const allResults = new Map<string, AgentResult>();\n\n    // Add cached results\n    for (const [agent, result] of cacheResults) {\n      allResults.set(agent, result);\n    }\n\n    // Add new results\n    for (const result of parallelResults) {\n      allResults.set(result.agent, result.result);\n    }\n\n    // Complete streaming\n    const allIssues = Array.from(allResults.values()).flatMap(r => r.issues);\n    this.streaming?.completeScan(allIssues);\n\n    return allResults;\n  }\n\n  /**\n   * Check if agent has cached results for given files\n   */\n  private async checkAgentCache(agent: Agent, files: string[]): Promise<AgentResult | null> {\n    if (!this.cacheEnabled || !this.cache) {\n      return null;\n    }\n\n    const cachedIssues = await this.cache.getCachedBatch(files, agent.name);\n\n    // Only use cache if we have results for ALL files\n    if (cachedIssues.size === files.length) {\n      const allIssues = Array.from(cachedIssues.values()).flat();\n      return {\n        agent: agent.name,\n        issues: allIssues,\n        executionTime: 0, // Cached\n        success: true,\n        metadata: {\n          filesAnalyzed: files.length,\n          linesAnalyzed: 0\n        }\n      };\n    }\n\n    return null;\n  }\n\n  /**\n   * Execute tasks in parallel batches\n   */\n  private async executeTasksParallel(tasks: ParallelTask[]): Promise<ParallelResult[]> {\n    if (tasks.length === 0) {\n      return [];\n    }\n\n    const results: ParallelResult[] = [];\n    const batches = this.createBatches(tasks, this.maxWorkers);\n\n    for (const batch of batches) {\n      const batchResults = await Promise.all(\n        batch.map(task => this.executeTask(task))\n      );\n      results.push(...batchResults);\n    }\n\n    return results;\n  }\n\n  /**\n   * Create batches for parallel execution\n   */\n  private createBatches(tasks: ParallelTask[], batchSize: number): ParallelTask[][] {\n    const batches: ParallelTask[][] = [];\n\n    for (let i = 0; i < tasks.length; i += batchSize) {\n      batches.push(tasks.slice(i, i + batchSize));\n    }\n\n    return batches;\n  }\n\n  /**\n   * Execute a single task\n   */\n  private async executeTask(task: ParallelTask): Promise<ParallelResult> {\n    const startTime = Date.now();\n\n    this.streaming?.startAgent(task.agent.name);\n\n    try {\n      const result = this.canUseWorkers()\n        ? await this.executeTaskInWorker(task)\n        : await task.agent.scan(task.files, task.context);\n      const executionTime = Date.now() - startTime;\n\n      this.streaming?.completeAgent(task.agent.name, result.issues);\n\n      return {\n        agent: task.agent.name,\n        result,\n        fromCache: false,\n        executionTime\n      };\n    } catch (error) {\n      const executionTime = Date.now() - startTime;\n      const errorMessage = error instanceof Error ? error.message : String(error);\n\n      this.streaming?.reportError(new Error(errorMessage), `Agent: ${task.agent.name}`);\n\n      return {\n        agent: task.agent.name,\n        result: {\n          agent: task.agent.name,\n          issues: [],\n          executionTime,\n          success: false,\n          error: errorMessage\n        },\n        fromCache: false,\n        executionTime\n      };\n    }\n  }\n\n  private canUseWorkers(): boolean {\n    if (!this.useWorkerThreads) {\n      return false;\n    }\n    if (this.workerAvailable !== null) {\n      return this.workerAvailable;\n    }\n    const workerUrl = this.getWorkerUrl();\n    this.workerAvailable = existsSync(fileURLToPath(workerUrl));\n    if (!this.workerAvailable && !this.warnedWorkerFallback && !isInteractiveMode()) {\n      console.error('Worker threads unavailable; falling back to in-process agents.');\n      this.warnedWorkerFallback = true;\n    }\n    return this.workerAvailable;\n  }\n\n  private getWorkerUrl(): URL {\n    const distDir = new URL('.', import.meta.url);\n    return new URL('workers/agent-worker.js', distDir);\n  }\n\n  private async executeTaskInWorker(task: ParallelTask): Promise<AgentResult> {\n    // Use dirname to get the dist folder, then resolve to workers subfolder\n    // This works whether the code is bundled into chunks or in utils/ folder\n    const workerUrl = this.getWorkerUrl();\n\n    return new Promise((resolve, reject) => {\n      const worker = new Worker(workerUrl, {\n        workerData: {\n          agentName: task.agent.name,\n          files: task.files,\n          context: task.context\n        }\n      } as ConstructorParameters<typeof Worker>[1]);\n\n      this.activeWorkers.add(worker);\n\n      const timeout = setTimeout(() => {\n        worker.terminate().catch(() => undefined);\n        reject(new Error(`Agent ${task.agent.name} timed out after ${task.timeoutMs}ms`));\n      }, task.timeoutMs);\n\n      worker.on('message', (message) => {\n        if (message?.type === 'result') {\n          clearTimeout(timeout);\n          resolve(message.result as AgentResult);\n        } else if (message?.type === 'error') {\n          clearTimeout(timeout);\n          reject(new Error(message.error));\n        }\n      });\n\n      worker.on('error', (error) => {\n        clearTimeout(timeout);\n        reject(error);\n      });\n\n      worker.on('exit', (code) => {\n        this.activeWorkers.delete(worker);\n        if (code !== 0) {\n          clearTimeout(timeout);\n          reject(new Error(`Worker stopped with exit code ${code}`));\n        }\n      });\n    });\n  }\n\n  /**\n   * Cache results for future use\n   */\n  private async cacheResults(results: ParallelResult[]): Promise<void> {\n    if (!this.cacheEnabled || !this.cache) {\n      return;\n    }\n\n    const cachePromises = results\n      .filter(r => r.result.success && !r.fromCache)\n      .map(r => {\n        const issuesByFile = this.groupIssuesByFile(r.result.issues);\n        const perFilePromises = Object.entries(issuesByFile).map(([file, issues]) =>\n          this.cache!.setCached(file, r.agent, issues, r.executionTime)\n        );\n        return Promise.all(perFilePromises);\n      });\n\n    await Promise.allSettled(cachePromises);\n  }\n\n  /**\n   * Cleanup resources\n   */\n  async cleanup(): Promise<void> {\n    // Terminate any active workers\n    const terminationPromises = Array.from(this.activeWorkers).map(worker =>\n      worker.terminate()\n    );\n\n    await Promise.allSettled(terminationPromises);\n    this.activeWorkers.clear();\n  }\n\n  private groupIssuesByFile(issues: AgentResult['issues']): Record<string, AgentResult['issues']> {\n    const grouped: Record<string, AgentResult['issues']> = {};\n\n    for (const issue of issues) {\n      if (!grouped[issue.file]) {\n        grouped[issue.file] = [];\n      }\n      grouped[issue.file]!.push(issue);\n    }\n\n    return grouped;\n  }\n}\n\n/**\n * Smart agent prioritization based on dependencies and execution characteristics\n */\nexport function prioritizeAgents(agents: Agent[]): Agent[] {\n  const prioritized = [...agents];\n\n  // Sort by priority tier, then by estimated execution time\n  prioritized.sort((a, b) => {\n    const aTier = a.priority?.tier || 2;\n    const bTier = b.priority?.tier || 2;\n\n    if (aTier !== bTier) {\n      return aTier - bTier; // Lower tier = higher priority\n    }\n\n    // Within same tier, prioritize faster agents\n    const aTime = a.priority?.estimatedTimeMs || 1000;\n    const bTime = b.priority?.estimatedTimeMs || 1000;\n\n    return aTime - bTime;\n  });\n\n  return prioritized;\n}\n\n/**\n * Calculate optimal concurrency based on system resources and agent characteristics\n */\nexport function calculateOptimalConcurrency(): number {\n  const numCPUs = cpus().length;\n  const availableMemoryGB = process.memoryUsage().rss / 1024 / 1024 / 1024;\n\n  // Conservative concurrency for stability\n  let optimal = Math.max(2, Math.min(numCPUs - 1, 8));\n\n  // Reduce concurrency if low memory\n  if (availableMemoryGB < 2) {\n    optimal = Math.max(2, Math.floor(optimal / 2));\n  }\n\n  // Increase slightly for systems with lots of CPU cores\n  if (numCPUs > 8) {\n    optimal = Math.min(optimal + 2, 12);\n  }\n\n  return optimal;\n}","import { readFile, writeFile, mkdir, stat } from 'fs/promises';\nimport { join } from 'path';\nimport { createHash } from 'crypto';\nimport type { Issue } from '../types/index.js';\nimport { isInteractiveMode } from './progress.js';\nimport { getTrieDirectory } from './workspace.js';\n\ninterface CacheEntry {\n  version: string;\n  timestamp: number;\n  fileHash: string;\n  fileSize: number;\n  agent: string;\n  issues: Issue[];\n  executionTime: number;\n}\n\ninterface CacheIndex {\n  version: string;\n  created: number;\n  entries: Record<string, CacheEntry>;\n}\n\nexport class CacheManager {\n  private cacheDir: string;\n  private indexPath: string;\n  private readonly VERSION = '1.0.0';\n  private readonly MAX_AGE_MS = 24 * 60 * 60 * 1000; // 24 hours\n  private readonly MAX_ENTRIES = 1000;\n\n  constructor(baseDir: string) {\n    this.cacheDir = join(getTrieDirectory(baseDir), 'cache');\n    this.indexPath = join(this.cacheDir, 'index.json');\n  }\n\n  /**\n   * Generate cache key for a file and agent combination\n   */\n  private generateCacheKey(filePath: string, agent: string, fileHash: string): string {\n    const key = `${filePath}:${agent}:${fileHash}`;\n    return createHash('sha256').update(key).digest('hex').slice(0, 16);\n  }\n\n  /**\n   * Get file hash for cache validation\n   */\n  private async getFileHash(filePath: string): Promise<{ hash: string; size: number; mtime: number }> {\n    try {\n      const content = await readFile(filePath, 'utf-8');\n      const stats = await stat(filePath);\n      const hash = createHash('sha256').update(content).digest('hex').slice(0, 16);\n      return {\n        hash,\n        size: stats.size,\n        mtime: stats.mtime.getTime()\n      };\n    } catch {\n      return { hash: '', size: 0, mtime: 0 };\n    }\n  }\n\n  /**\n   * Load cache index\n   */\n  private async loadIndex(): Promise<CacheIndex> {\n    try {\n      const content = await readFile(this.indexPath, 'utf-8');\n      return JSON.parse(content);\n    } catch {\n      return {\n        version: this.VERSION,\n        created: Date.now(),\n        entries: {}\n      };\n    }\n  }\n\n  /**\n   * Save cache index\n   */\n  private async saveIndex(index: CacheIndex): Promise<void> {\n    try {\n      await mkdir(this.cacheDir, { recursive: true });\n      await writeFile(this.indexPath, JSON.stringify(index, null, 2));\n    } catch (error) {\n      if (!isInteractiveMode()) {\n        console.warn('Failed to save cache index:', error);\n      }\n    }\n  }\n\n  /**\n   * Clean up expired entries\n   */\n  private cleanupExpired(index: CacheIndex): CacheIndex {\n    const now = Date.now();\n    const validEntries: Record<string, CacheEntry> = {};\n\n    for (const [key, entry] of Object.entries(index.entries)) {\n      if (now - entry.timestamp < this.MAX_AGE_MS) {\n        validEntries[key] = entry;\n      }\n    }\n\n    // If still too many, keep the most recent ones\n    const entries = Object.entries(validEntries);\n    if (entries.length > this.MAX_ENTRIES) {\n      entries.sort((a, b) => b[1].timestamp - a[1].timestamp);\n      const limited = entries.slice(0, this.MAX_ENTRIES);\n      return {\n        ...index,\n        entries: Object.fromEntries(limited)\n      };\n    }\n\n    return {\n      ...index,\n      entries: validEntries\n    };\n  }\n\n  /**\n   * Get cached result for a file and agent\n   * \n   * Cache automatically invalidates when files change:\n   * - Cache key includes file hash: hash(filePath:agent:fileHash)\n   * - When file changes, hash changes, so cache key changes\n   * - Old cache entry won't be found (different key)\n   * - File is automatically rescanned\n   * \n   * This means cache auto-updates when Claude fixes code - no manual invalidation needed!\n   */\n  async getCached(filePath: string, agent: string): Promise<Issue[] | null> {\n    try {\n      const { hash, size: _size, mtime: _mtime } = await this.getFileHash(filePath);\n      if (!hash) return null;\n\n      const index = await this.loadIndex();\n      const cacheKey = this.generateCacheKey(filePath, agent, hash);\n      const entry = index.entries[cacheKey];\n\n      if (!entry) return null;\n\n      // Validate entry is still fresh\n      // Double-check hash matches (defense in depth)\n      const isValid = entry.fileHash === hash &&\n                     entry.version === this.VERSION &&\n                     (Date.now() - entry.timestamp) < this.MAX_AGE_MS;\n\n      if (!isValid) {\n        delete index.entries[cacheKey];\n        await this.saveIndex(index);\n        return null;\n      }\n\n      return entry.issues;\n    } catch {\n      return null;\n    }\n  }\n\n  /**\n   * Cache result for a file and agent\n   */\n  async setCached(\n    filePath: string,\n    agent: string,\n    issues: Issue[],\n    executionTime: number\n  ): Promise<void> {\n    try {\n      const { hash, size } = await this.getFileHash(filePath);\n      if (!hash) return;\n\n      const index = await this.loadIndex();\n      const cacheKey = this.generateCacheKey(filePath, agent, hash);\n\n      index.entries[cacheKey] = {\n        version: this.VERSION,\n        timestamp: Date.now(),\n        fileHash: hash,\n        fileSize: size,\n        agent,\n        issues,\n        executionTime\n      };\n\n      // Clean up old entries\n      const cleanedIndex = this.cleanupExpired(index);\n      await this.saveIndex(cleanedIndex);\n    } catch (error) {\n      if (!isInteractiveMode()) {\n        console.warn('Failed to cache result:', error);\n      }\n    }\n  }\n\n  /**\n   * Check if multiple files have cached results\n   */\n  async getCachedBatch(files: string[], agent: string): Promise<Map<string, Issue[]>> {\n    const results = new Map<string, Issue[]>();\n\n    await Promise.all(\n      files.map(async (file) => {\n        const cached = await this.getCached(file, agent);\n        if (cached) {\n          results.set(file, cached);\n        }\n      })\n    );\n\n    return results;\n  }\n\n  /**\n   * Get cache statistics\n   */\n  async getStats(): Promise<{\n    totalEntries: number;\n    totalSizeKB: number;\n    oldestEntry: number | null;\n    newestEntry: number | null;\n    agents: string[];\n    hitRate?: number;\n  }> {\n    try {\n      const index = await this.loadIndex();\n      const entries = Object.values(index.entries);\n\n      const totalSizeKB = entries.reduce((acc, entry) => acc + entry.fileSize, 0) / 1024;\n      const timestamps = entries.map(e => e.timestamp);\n      const agents = [...new Set(entries.map(e => e.agent))];\n\n      return {\n        totalEntries: entries.length,\n        totalSizeKB: Math.round(totalSizeKB),\n        oldestEntry: timestamps.length > 0 ? Math.min(...timestamps) : null,\n        newestEntry: timestamps.length > 0 ? Math.max(...timestamps) : null,\n        agents\n      };\n    } catch {\n      return {\n        totalEntries: 0,\n        totalSizeKB: 0,\n        oldestEntry: null,\n        newestEntry: null,\n        agents: []\n      };\n    }\n  }\n\n  /**\n   * Clean up stale cache entries by verifying file hashes\n   * This removes entries where files have changed or no longer exist\n   * Called periodically to keep cache clean\n   * \n   * Note: Since cache keys are hashed, we can't easily reverse-engineer file paths.\n   * However, when getCached() is called, it naturally invalidates stale entries\n   * by checking if the current file hash matches the cached hash. This method\n   * proactively cleans up entries for known changed files.\n   */\n  async cleanupStaleEntries(filePaths?: string[]): Promise<number> {\n    try {\n      const index = await this.loadIndex();\n      let removedCount = 0;\n      const keysToRemove: string[] = [];\n\n      // If specific files provided, check those files against all cache entries\n      // We can't perfectly match entries to files without storing paths, but we can\n      // try to identify likely matches by checking if regenerating keys matches\n      if (filePaths && filePaths.length > 0) {\n        // Get all unique agents from cache entries\n        const agents = new Set<string>();\n        for (const entry of Object.values(index.entries)) {\n          agents.add(entry.agent);\n        }\n\n        // For each file+agent combination, check if cache entry is stale\n        for (const filePath of filePaths) {\n          try {\n            const { hash: currentHash } = await this.getFileHash(filePath);\n            if (!currentHash) {\n              // File doesn't exist - can't clean up without knowing which entries are for it\n              continue;\n            }\n\n            // Check each agent's potential cache entries for this file\n            for (const agent of agents) {\n              // Check all entries to find ones that might be for this file\n              for (const [key, entry] of Object.entries(index.entries)) {\n                if (entry.agent !== agent) continue;\n                \n                // If entry hash doesn't match current hash, it might be stale\n                if (entry.fileHash !== currentHash) {\n                  // Check if this key was generated with the old hash for this file\n                  const oldKey = this.generateCacheKey(filePath, agent, entry.fileHash);\n                  if (oldKey === key) {\n                    // This entry is for this file but hash doesn't match - stale!\n                    keysToRemove.push(key);\n                    removedCount++;\n                  }\n                }\n              }\n            }\n          } catch {\n            // File doesn't exist or can't be read - skip\n            continue;\n          }\n        }\n      }\n\n      // Remove stale entries (avoid duplicates)\n      const uniqueKeys = [...new Set(keysToRemove)];\n      for (const key of uniqueKeys) {\n        delete index.entries[key];\n      }\n\n      if (removedCount > 0) {\n        await this.saveIndex(index);\n      }\n\n      return removedCount;\n    } catch (error) {\n      if (!isInteractiveMode()) {\n        console.warn('Failed to cleanup stale cache entries:', error);\n      }\n      return 0;\n    }\n  }\n\n  /**\n   * Clear all cache\n   */\n  async clear(): Promise<void> {\n    try {\n      const emptyIndex: CacheIndex = {\n        version: this.VERSION,\n        created: Date.now(),\n        entries: {}\n      };\n      await this.saveIndex(emptyIndex);\n    } catch (error) {\n      if (!isInteractiveMode()) {\n        console.warn('Failed to clear cache:', error);\n      }\n    }\n  }\n}","import type { Agent, AgentResult, ScanContext } from '../types/index.js';\nimport { ParallelExecutor, calculateOptimalConcurrency } from '../utils/parallel-executor.js';\nimport { CacheManager } from '../utils/cache-manager.js';\nimport type { StreamingManager } from '../utils/streaming.js';\nimport { isInteractiveMode } from '../utils/progress.js';\n\nexport class Executor {\n  async executeAgents(\n    agents: Agent[],\n    files: string[],\n    context: ScanContext,\n    options?: {\n      streaming?: StreamingManager;\n      parallel?: boolean;\n      cacheEnabled?: boolean;\n      maxConcurrency?: number;\n      useWorkerThreads?: boolean;\n      timeoutMs?: number;\n    }\n  ): Promise<AgentResult[]> {\n    const parallel = options?.parallel ?? true;\n    const cacheEnabled = options?.cacheEnabled ?? true;\n    const maxConcurrency = options?.maxConcurrency ?? calculateOptimalConcurrency();\n    const useWorkerThreads = options?.useWorkerThreads ?? false;\n\n    if (!isInteractiveMode()) {\n      console.error(`Executing ${agents.length} scouts ${parallel ? 'in parallel' : 'sequentially'}...`);\n    }\n\n    if (parallel) {\n      const cacheManager = cacheEnabled ? new CacheManager(context.workingDir) : null;\n      const executor = new ParallelExecutor(cacheManager, maxConcurrency, {\n        cacheEnabled,\n        useWorkerThreads\n      });\n\n      if (options?.streaming) {\n        executor.setStreaming(options.streaming);\n      }\n\n      const results = await executor.executeAgents(agents, files, {\n        ...context,\n        config: { timeoutMs: options?.timeoutMs ?? 120000 }\n      });\n\n      return agents.map(agent => results.get(agent.name)!).filter(Boolean);\n    }\n\n    // Execute scouts in parallel with timeout\n    const promises = agents.map(agent =>\n      this.executeAgentWithTimeout(agent, files, context, options?.timeoutMs ?? 30000)\n    );\n\n    try {\n      const results = await Promise.allSettled(promises);\n      return results.map((result, index) => {\n        if (result.status === 'fulfilled') {\n          if (!isInteractiveMode()) {\n            console.error(`${agents[index]!.name} completed in ${result.value.executionTime}ms`);\n          }\n          return result.value;\n        } else {\n          if (!isInteractiveMode()) {\n            console.error(`${agents[index]!.name} failed:`, result.reason);\n          }\n          return {\n            agent: agents[index]!.name,\n            issues: [],\n            executionTime: 0,\n            success: false,\n            error: result.reason instanceof Error ? result.reason.message : String(result.reason)\n          };\n        }\n      });\n    } catch (error) {\n      if (!isInteractiveMode()) {\n        console.error('Executor error:', error);\n      }\n      return agents.map(agent => ({\n        agent: agent.name,\n        issues: [],\n        executionTime: 0,\n        success: false,\n        error: 'Execution failed'\n      }));\n    }\n  }\n\n  private async executeAgentWithTimeout(\n    agent: Agent,\n    files: string[],\n    context: ScanContext,\n    timeoutMs: number = 30000 // 30 second timeout\n  ): Promise<AgentResult> {\n    return new Promise(async (resolve, reject) => {\n      const timeout = setTimeout(() => {\n        reject(new Error(`Agent ${agent.name} timed out after ${timeoutMs}ms`));\n      }, timeoutMs);\n\n      try {\n        const result = await agent.scan(files, context);\n        clearTimeout(timeout);\n        resolve(result);\n      } catch (error) {\n        clearTimeout(timeout);\n        reject(error);\n      }\n    });\n  }\n}","import { ContextGraph } from '../context/graph.js';\nimport type { IncidentNode, PatternNode } from '../context/nodes.js';\nimport type { RiskLevel, AgentResult, CodeContext, ScanContext } from '../types/index.js';\nimport { scoreChangeSet, type ChangeRiskResult, type FileRiskResult } from './risk-scorer.js';\nimport { matchPatternsForFiles } from './pattern-matcher.js';\nimport { Triager } from '../orchestrator/triager.js';\nimport { Executor } from '../orchestrator/executor.js';\n\nexport interface Reasoning {\n  riskLevel: RiskLevel;\n  shouldBlock: boolean;\n  explanation: string;\n  relevantIncidents: IncidentNode[];\n  matchedPatterns: PatternNode[];\n  recommendation: string;\n  files: FileRiskResult[];\n  agentResults?: AgentResult[];\n}\n\nexport interface ReasonOptions {\n  runAgents?: boolean;\n  codeContext?: CodeContext;\n  scanContext?: Partial<ScanContext>;\n}\n\nfunction buildDefaultCodeContext(): CodeContext {\n  return {\n    changeType: 'general',\n    isNewFeature: false,\n    touchesUserData: false,\n    touchesAuth: false,\n    touchesPayments: false,\n    touchesDatabase: false,\n    touchesAPI: false,\n    touchesUI: false,\n    touchesHealthData: false,\n    touchesSecurityConfig: false,\n    linesChanged: 50,\n    filePatterns: [],\n    framework: 'unknown',\n    language: 'typescript',\n    touchesCrypto: false,\n    touchesFileSystem: false,\n    touchesThirdPartyAPI: false,\n    touchesLogging: false,\n    touchesErrorHandling: false,\n    hasTests: false,\n    complexity: 'medium',\n    patterns: {\n      hasAsyncCode: false,\n      hasFormHandling: false,\n      hasFileUploads: false,\n      hasEmailHandling: false,\n      hasRateLimiting: false,\n      hasWebSockets: false,\n      hasCaching: false,\n      hasQueue: false\n    }\n  };\n}\n\nfunction buildExplanation(result: ChangeRiskResult): string {\n  const top = [...result.files].sort((a, b) => b.score - a.score)[0];\n  if (!top) return `Risk level ${result.overall} (no files provided)`;\n  return `Risk level ${result.overall} because ${top.file} ${top.reasons.join(', ')}`;\n}\n\nfunction buildRecommendation(risk: RiskLevel, hasAntiPattern: boolean): string {\n  if (hasAntiPattern || risk === 'critical') {\n    return 'Block until reviewed: address anti-patterns and rerun targeted tests.';\n  }\n  if (risk === 'high') {\n    return 'Require senior review and run full test suite before merge.';\n  }\n  if (risk === 'medium') {\n    return 'Proceed with caution; run impacted tests and sanity checks.';\n  }\n  return 'Low risk; proceed but keep an eye on recent changes.';\n}\n\nexport async function reasonAboutChanges(\n  projectPath: string,\n  files: string[],\n  options: ReasonOptions = {}\n): Promise<Reasoning> {\n  const graph = new ContextGraph(projectPath);\n  const { matches, byFile } = await matchPatternsForFiles(graph, files);\n  const changeRisk = await scoreChangeSet(graph, files, byFile);\n\n  const incidents: IncidentNode[] = [];\n  for (const file of files) {\n    const fileIncidents = await graph.getIncidentsForFile(file);\n    incidents.push(...fileIncidents);\n  }\n\n  const hasAntiPattern = matches.some((m) => m.isAntiPattern);\n  const riskLevel: RiskLevel = hasAntiPattern ? 'critical' : changeRisk.overall;\n  const shouldBlock = hasAntiPattern || riskLevel === 'critical' || riskLevel === 'high';\n\n  const reasoning: Reasoning = {\n    riskLevel,\n    shouldBlock,\n    explanation: buildExplanation(changeRisk),\n    relevantIncidents: incidents,\n    matchedPatterns: matches.map((m) => m.pattern),\n    recommendation: buildRecommendation(riskLevel, hasAntiPattern),\n    files: changeRisk.files\n  };\n\n  if (options.runAgents) {\n    const codeContext = options.codeContext ?? buildDefaultCodeContext();\n    const triager = new Triager();\n    // Skills removed - decision ledger now handles risk analysis\n    const agents = await triager.triage(codeContext);\n\n    if (agents.length > 0) {\n      const executor = new Executor();\n      const scanContext: ScanContext = {\n        workingDir: projectPath,\n        ...options.scanContext\n      };\n      if (codeContext.framework) scanContext.framework = codeContext.framework;\n      if (codeContext.language) scanContext.language = codeContext.language;\n\n      reasoning.agentResults = await executor.executeAgents(agents, files, scanContext, {\n        parallel: true,\n        timeoutMs: options.scanContext?.config?.timeoutMs ?? 60000\n      });\n    } else {\n      reasoning.agentResults = [];\n    }\n  }\n\n  return reasoning;\n}\n\n// Convenience wrapper to keep future CLI/MCP integration simple\nexport async function reasonAboutChangesHumanReadable(\n  projectPath: string,\n  files: string[],\n  options: ReasonOptions = {}\n) {\n  const reasoning = await reasonAboutChanges(projectPath, files, options);\n  const { humanizeReasoning } = await import('../comprehension/index.js');\n  return humanizeReasoning(reasoning);\n}\n","/**\n * Bootstrap File System\n * \n * Manages workspace files that inject context at scan start.\n * Files: BOOTSTRAP.md, RULES.md, TEAM.md\n */\n\nimport { readFile, writeFile, unlink, mkdir } from 'fs/promises';\nimport { existsSync } from 'fs';\nimport { join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from '../utils/workspace.js';\nimport { detectStack, type DetectedStack } from './stack-detector.js';\n\nexport interface BootstrapFile {\n  name: string;\n  path: string;\n  type: 'user' | 'auto' | 'one-time';\n  exists: boolean;\n  content?: string;\n}\n\nexport interface BootstrapContext {\n  files: BootstrapFile[];\n  injectedContent: string;\n  needsBootstrap: boolean;\n}\n\ninterface BootstrapFileSpec {\n  name: string;\n  type: 'user' | 'auto' | 'one-time';\n  description: string;\n}\n\nconst BOOTSTRAP_FILES: BootstrapFileSpec[] = [\n  { name: 'PROJECT.md', type: 'user', description: 'Project overview and conventions' },\n  { name: 'RULES.md', type: 'user', description: 'Coding standards agents enforce' },\n  { name: 'TEAM.md', type: 'user', description: 'Team ownership and escalation' },\n  { name: 'BOOTSTRAP.md', type: 'one-time', description: 'First-run setup (deleted after)' },\n  { name: 'AGENTS.md', type: 'auto', description: 'Auto-generated scan context' },\n];\n\n/**\n * Load bootstrap files and inject into agent context\n */\nexport async function loadBootstrapContext(workDir?: string): Promise<BootstrapContext> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(projectDir);\n  const files: BootstrapFile[] = [];\n  const contentParts: string[] = [];\n  let needsBootstrap = false;\n\n  for (const file of BOOTSTRAP_FILES) {\n    const filePath = join(trieDir, file.name);\n    const exists = existsSync(filePath);\n    \n    if (file.name === 'BOOTSTRAP.md' && exists) {\n      needsBootstrap = true;\n    }\n    \n    let content: string | undefined;\n    if (exists) {\n      try {\n        content = await readFile(filePath, 'utf-8');\n        if (content.trim() && file.type !== 'one-time') {\n          contentParts.push(`<!-- ${file.name} -->\\n${content}`);\n        }\n      } catch {\n        // Skip files that can't be read\n      }\n    }\n\n    const fileEntry: BootstrapFile = {\n      name: file.name,\n      path: filePath,\n      type: file.type,\n      exists,\n    };\n    if (content) fileEntry.content = content;\n    files.push(fileEntry);\n  }\n\n  return {\n    files,\n    injectedContent: contentParts.join('\\n\\n---\\n\\n'),\n    needsBootstrap,\n  };\n}\n\n/**\n * Initialize bootstrap files for a new project\n */\nexport async function initializeBootstrapFiles(options: {\n  workDir?: string;\n  force?: boolean;\n  skipBootstrap?: boolean;\n} = {}): Promise<{ created: string[]; skipped: string[]; stack: DetectedStack }> {\n  const projectDir = options.workDir || getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(projectDir);\n  await mkdir(trieDir, { recursive: true });\n\n  const created: string[] = [];\n  const skipped: string[] = [];\n\n  const stack = await detectStack(projectDir);\n\n  for (const file of BOOTSTRAP_FILES) {\n    const filePath = join(trieDir, file.name);\n    const exists = existsSync(filePath);\n\n    if (exists && !options.force) {\n      skipped.push(file.name);\n      continue;\n    }\n\n    if (file.name === 'BOOTSTRAP.md' && options.skipBootstrap) {\n      skipped.push(file.name);\n      continue;\n    }\n\n    if (file.name === 'AGENTS.md') {\n      skipped.push(file.name);\n      continue;\n    }\n\n    const template = getFileTemplate(file.name, stack);\n    if (template) {\n      await writeFile(filePath, template);\n      created.push(file.name);\n    }\n  }\n\n  return { created, skipped, stack };\n}\n\n/**\n * Mark bootstrap as complete (delete BOOTSTRAP.md)\n */\nexport async function completeBootstrap(workDir?: string): Promise<boolean> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const bootstrapPath = join(getTrieDirectory(projectDir), 'BOOTSTRAP.md');\n\n  try {\n    await unlink(bootstrapPath);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Check if bootstrap is needed (BOOTSTRAP.md exists)\n */\nexport function needsBootstrap(workDir?: string): boolean {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const bootstrapPath = join(getTrieDirectory(projectDir), 'BOOTSTRAP.md');\n  return existsSync(bootstrapPath);\n}\n\n/**\n * Get rules from RULES.md\n */\nexport async function loadRules(workDir?: string): Promise<string | null> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const rulesPath = join(getTrieDirectory(projectDir), 'RULES.md');\n  \n  try {\n    if (existsSync(rulesPath)) {\n      return await readFile(rulesPath, 'utf-8');\n    }\n  } catch {\n    // Rules file doesn't exist or can't be read\n  }\n  \n  return null;\n}\n\n/**\n * Get team info from TEAM.md\n */\nexport async function loadTeamInfo(workDir?: string): Promise<string | null> {\n  const projectDir = workDir || getWorkingDirectory(undefined, true);\n  const teamPath = join(getTrieDirectory(projectDir), 'TEAM.md');\n  \n  try {\n    if (existsSync(teamPath)) {\n      return await readFile(teamPath, 'utf-8');\n    }\n  } catch {\n    // Team file doesn't exist or can't be read\n  }\n  \n  return null;\n}\n\nfunction getFileTemplate(fileName: string, stack: DetectedStack): string | null {\n  switch (fileName) {\n    case 'PROJECT.md':\n      return getProjectTemplate(stack);\n    case 'RULES.md':\n      return getRulesTemplate(stack);\n    case 'TEAM.md':\n      return getTeamTemplate();\n    case 'BOOTSTRAP.md':\n      return getBootstrapTemplate(stack);\n    default:\n      return null;\n  }\n}\n\nfunction getProjectTemplate(stack: DetectedStack): string {\n  const lines: string[] = ['# Project Overview', '', '> Define your project context here. AI assistants read this first.', ''];\n  \n  lines.push('## Description', '', '[Describe what this project does and who it\\'s for]', '');\n  \n  lines.push('## Technology Stack', '');\n  if (stack.framework) lines.push(`- **Framework:** ${stack.framework}`);\n  if (stack.language) lines.push(`- **Language:** ${stack.language}`);\n  if (stack.database) lines.push(`- **Database:** ${stack.database}`);\n  if (stack.auth) lines.push(`- **Auth:** ${stack.auth}`);\n  if (!stack.framework && !stack.language && !stack.database) {\n    lines.push('[Add your technology stack]');\n  }\n  lines.push('');\n  \n  lines.push('## Architecture', '', '[Key patterns and design decisions]', '');\n  lines.push('## Coding Conventions', '', '[Style rules agents should follow]', '');\n  lines.push('## AI Instructions', '', 'When working on this project:', '1. [Instruction 1]', '2. [Instruction 2]', '3. [Instruction 3]', '');\n  lines.push('---', '', '*Edit this file to provide project context to AI assistants.*');\n  \n  return lines.join('\\n');\n}\n\nfunction getRulesTemplate(stack: DetectedStack): string {\n  const packageManager = stack.packageManager || 'npm';\n  \n  return `# Project Rules\n\n> These rules are enforced by Trie agents during scans.\n> Violations appear as issues with [RULES] prefix.\n\n## Code Style\n\n1. Use named exports, not default exports\n2. Prefer \\`${packageManager}\\` for package management\n3. Maximum file length: 300 lines\n4. Use TypeScript strict mode\n\n## Testing Requirements\n\n1. Critical paths require unit tests\n2. API endpoints require integration tests\n3. Minimum coverage: 70%\n\n## Security Rules\n\n1. Never log sensitive data (passwords, tokens, PII)\n2. All API routes require authentication\n3. Rate limiting required on public endpoints\n4. SQL queries must use parameterized statements\n\n## Review Requirements\n\n1. All PRs require at least 1 reviewer\n2. Security-sensitive changes require security review\n3. Database migrations require review\n\n---\n\n*Edit this file to define your project's coding standards.*\n`;\n}\n\nfunction getTeamTemplate(): string {\n  return `# Team Structure\n\n## Code Ownership\n\n| Area | Owner | Backup | Review Required |\n|------|-------|--------|-----------------|\n| \\`/src/api/\\` | @backend-team | - | 1 approver |\n| \\`/src/ui/\\` | @frontend-team | - | 1 approver |\n| \\`/src/auth/\\` | @security-team | - | Security review |\n\n## Escalation\n\n| Severity | First Contact | Escalate To | SLA |\n|----------|--------------|-------------|-----|\n| Critical | Team lead | CTO | 1 hour |\n| Serious | PR reviewer | Team lead | 4 hours |\n| Moderate | Self-serve | - | 1 day |\n\n## Contacts\n\n- **Security:** [email/slack]\n- **Privacy:** [email/slack]\n- **Emergencies:** [phone/pager]\n\n---\n\n*Edit this file to define your team structure.*\n`;\n}\n\nfunction getBootstrapTemplate(stack: DetectedStack): string {\n  const skillCommands = stack.suggestedSkills\n    .map(s => `trie skills add ${s}`)\n    .join('\\n');\n\n  const agentList = stack.suggestedAgents.join(', ');\n\n  const lines: string[] = [\n    '# Trie Bootstrap Checklist',\n    '',\n    'This file guides your first scan setup. **Delete when complete.**',\n    '',\n    '## Auto-Detected Stack',\n    '',\n    'Based on your project, Trie detected:',\n  ];\n  \n  if (stack.framework) lines.push(`- **Framework:** ${stack.framework}`);\n  if (stack.language) lines.push(`- **Language:** ${stack.language}`);\n  if (stack.database) lines.push(`- **Database:** ${stack.database}`);\n  if (stack.auth) lines.push(`- **Auth:** ${stack.auth}`);\n  \n  lines.push('', '## Recommended Actions', '', '### 1. Skills to Install', 'Based on your stack, consider installing:', '```bash');\n  lines.push(skillCommands || '# No specific skills detected - browse https://skills.sh');\n  lines.push('```', '', '### 2. Agents to Enable', `Your stack suggests these agents: ${agentList || 'security, bugs'}`, '');\n  lines.push('### 3. Configure Rules', 'Add your coding standards to `.trie/RULES.md`.', '');\n  lines.push('### 4. Run First Scan', '```bash', 'trie scan', '```', '');\n  lines.push('---', '', '**Delete this file after completing setup.** Run:', '```bash', 'rm .trie/BOOTSTRAP.md', '```');\n  \n  return lines.join('\\n');\n}\n","export class TrieError extends Error {\n  code: string;\n  recoverable: boolean;\n  userMessage: string;\n\n  constructor(message: string, code: string, userMessage: string, recoverable = true) {\n    super(message);\n    this.code = code;\n    this.recoverable = recoverable;\n    this.userMessage = userMessage;\n  }\n}\n\nexport class GraphError extends TrieError {\n  constructor(message: string) {\n    super(\n      message,\n      'GRAPH_ERROR',\n      'Trie had trouble accessing its memory. Try again or re-run trie reconcile.',\n      true\n    );\n  }\n}\n\nexport class GitError extends TrieError {\n  constructor(message: string) {\n    super(\n      message,\n      'GIT_ERROR',\n      'Git info is unavailable. Is this a git repo? Commit once, or pass --files to trie check.',\n      true\n    );\n  }\n}\n\nexport class NetworkError extends TrieError {\n  constructor(message: string) {\n    super(\n      message,\n      'NETWORK_ERROR',\n      'Network unavailable. Running in offline mode; AI calls skipped.',\n      true\n    );\n  }\n}\n\nexport class MissingAPIKeyError extends TrieError {\n  constructor(message = 'Missing ANTHROPIC_API_KEY') {\n    super(\n      message,\n      'MISSING_API_KEY',\n      'No API key detected. Set ANTHROPIC_API_KEY for AI-powered analysis (deeper issue detection, smarter fixes). Running in pattern-only mode.',\n      true\n    );\n  }\n}\n\nexport function formatFriendlyError(error: unknown): { userMessage: string; code: string } {\n  if (error instanceof TrieError) {\n    return { userMessage: error.userMessage, code: error.code };\n  }\n  return {\n    userMessage: 'Something went wrong. Try again or run with --offline.',\n    code: 'UNKNOWN'\n  };\n}\n","import fs from 'node:fs/promises';\nimport path from 'node:path';\nimport { getTrieDirectory } from '../utils/workspace.js';\n\nimport { ContextGraph } from './graph.js';\nimport type { ContextSnapshot } from './types.js';\n\nconst DEFAULT_JSON_NAME = 'context.json';\n\nexport async function exportToJson(graph: ContextGraph, targetPath?: string): Promise<string> {\n  const snapshot = await graph.getSnapshot();\n  const json = JSON.stringify(snapshot, null, 2);\n\n  const outputPath = targetPath ?? path.join(getTrieDirectory(graph.projectRoot), DEFAULT_JSON_NAME);\n  await fs.mkdir(path.dirname(outputPath), { recursive: true });\n  await fs.writeFile(outputPath, json, 'utf8');\n\n  return json;\n}\n\nexport async function importFromJson(\n  graph: ContextGraph,\n  json: string,\n  sourcePath?: string\n): Promise<void> {\n  const payload =\n    json.trim().length > 0\n      ? json\n      : await fs.readFile(sourcePath ?? path.join(getTrieDirectory(graph.projectRoot), DEFAULT_JSON_NAME), 'utf8');\n\n  const snapshot = JSON.parse(payload) as ContextSnapshot;\n  await graph.applySnapshot(snapshot);\n}\n","import path from 'node:path';\n\nimport type { IncidentNode } from './nodes.js';\nimport type { ContextGraph } from './graph.js';\nimport { FilePathTrie, type IncidentMetadata } from './file-trie.js';\nimport { getTrieDirectory } from '../utils/workspace.js';\n\nexport interface IncidentIndexOptions {\n  persistPath?: string;\n}\n\nexport class IncidentIndex {\n  private readonly graph: ContextGraph;\n  private readonly trie: FilePathTrie;\n  private readonly projectRoot: string;\n\n  constructor(graph: ContextGraph, projectRoot: string, options?: IncidentIndexOptions) {\n    this.graph = graph;\n    this.projectRoot = projectRoot;\n    this.trie = new FilePathTrie(\n      options?.persistPath ?? path.join(getTrieDirectory(projectRoot), 'incident-trie.json')\n    );\n  }\n\n  static async build(graph: ContextGraph, projectRoot: string, options?: IncidentIndexOptions): Promise<IncidentIndex> {\n    const index = new IncidentIndex(graph, projectRoot, options);\n    await index.rebuild();\n    return index;\n  }\n\n  async rebuild(): Promise<void> {\n    const nodes = await this.graph.listNodes();\n    const incidents = nodes.filter((n) => n.type === 'incident') as IncidentNode[];\n\n    for (const incident of incidents) {\n      const files = await this.getFilesForIncident(incident.id);\n      this.addIncidentToTrie(incident, files);\n    }\n  }\n\n  addIncidentToTrie(incident: IncidentNode, files: string[]): void {\n    const meta: IncidentMetadata = {\n      id: incident.id,\n      file: '',\n      description: incident.data.description,\n      severity: incident.data.severity,\n      timestamp: incident.data.timestamp,\n    };\n\n    for (const file of files) {\n      const normalized = this.normalizePath(file);\n      this.trie.addIncident(normalized, { ...meta, file: normalized });\n    }\n  }\n\n  getFileTrie(): FilePathTrie {\n    return this.trie;\n  }\n\n  private async getFilesForIncident(incidentId: string): Promise<string[]> {\n    const files = new Set<string>();\n    const edges = await this.graph.getEdges(incidentId, 'both');\n\n    // Traverse connected changes to pull file lists\n    for (const edge of edges) {\n      if (edge.type === 'causedBy' || edge.type === 'leadTo') {\n        // Identify the change node id regardless of direction\n        const changeId = edge.type === 'causedBy' ? edge.to_id : edge.from_id;\n        const change = await this.graph.getNode('change', changeId);\n        if (change?.data && 'files' in change.data && Array.isArray(change.data.files)) {\n          (change.data.files as string[]).forEach((f: string) => files.add(f));\n        }\n      }\n\n      // If there are direct file links, capture them as well\n      if (edge.type === 'affects') {\n        const fileNode =\n          (await this.graph.getNode('file', edge.to_id)) ||\n          (await this.graph.getNode('file', edge.from_id));\n        if (fileNode && typeof (fileNode as any).data?.path === 'string') {\n          files.add((fileNode as any).data.path);\n        }\n      }\n    }\n\n    return Array.from(files);\n  }\n\n  private normalizePath(filePath: string): string {\n    const absolute = path.isAbsolute(filePath) ? filePath : path.join(this.projectRoot, filePath);\n    const relative = path.relative(this.projectRoot, absolute);\n    return relative.replace(/\\\\/g, '/');\n  }\n}\n","import fs from 'node:fs';\nimport path from 'node:path';\nimport { performance } from 'node:perf_hooks';\n\nimport { Trie } from '../trie/trie.js';\n\nexport interface IncidentMetadata {\n  id: string;\n  file: string;\n  description: string;\n  severity: 'minor' | 'major' | 'critical' | string;\n  timestamp: string;\n}\n\nexport interface HotZone {\n  path: string;\n  incidentCount: number;\n  confidence: number;\n}\n\nfunction normalizePath(filePath: string): string {\n  const normalized = filePath.replace(/\\\\/g, '/');\n  return normalized.startsWith('./') ? normalized.slice(2) : normalized;\n}\n\nexport class FilePathTrie {\n  private trie: Trie<IncidentMetadata[]> = new Trie();\n  private persistPath?: string;\n\n  constructor(persistPath?: string) {\n    if (persistPath) this.persistPath = persistPath;\n    if (persistPath && fs.existsSync(persistPath)) {\n      try {\n        const raw = fs.readFileSync(persistPath, 'utf-8');\n        if (raw.trim().length > 0) {\n          const json = JSON.parse(raw);\n          this.trie = Trie.fromJSON<IncidentMetadata[]>(json);\n        }\n      } catch {\n        this.trie = new Trie();\n      }\n    }\n  }\n\n  addIncident(filePath: string, incident: IncidentMetadata): void {\n    const key = normalizePath(filePath);\n    const existing = this.trie.search(key);\n    const incidents = existing.found && Array.isArray(existing.value) ? existing.value : [];\n    incidents.push(incident);\n    this.trie.insert(key, incidents);\n    this.persist();\n  }\n\n  getIncidents(filePath: string): IncidentMetadata[] {\n    const key = normalizePath(filePath);\n    const result = this.trie.search(key);\n    return result.found && Array.isArray(result.value) ? result.value : [];\n  }\n\n  getDirectoryIncidents(prefix: string): IncidentMetadata[] {\n    const normalizedPrefix = normalizePath(prefix);\n    const matches = this.trie.getWithPrefix(normalizedPrefix);\n    return matches.flatMap((m) => (Array.isArray(m.value) ? m.value : [])).filter(Boolean);\n  }\n\n  getHotZones(threshold: number): HotZone[] {\n    const matches = this.trie.getWithPrefix('');\n    const zones: HotZone[] = [];\n\n    for (const match of matches) {\n      const incidents = Array.isArray(match.value) ? match.value : [];\n      if (incidents.length >= threshold) {\n        zones.push({\n          path: match.pattern,\n          incidentCount: incidents.length,\n          confidence: this.calculateConfidence(incidents.length),\n        });\n      }\n    }\n\n    return zones.sort((a, b) => b.incidentCount - a.incidentCount);\n  }\n\n  suggestPaths(partial: string, limit = 5): Array<{ path: string; incidentCount: number }> {\n    const normalized = normalizePath(partial);\n    const results = this.trie.getWithPrefix(normalized);\n    return results\n      .map((r) => ({\n        path: r.pattern,\n        incidentCount: Array.isArray(r.value) ? r.value.length : 0,\n      }))\n      .sort((a, b) => b.incidentCount - a.incidentCount)\n      .slice(0, limit);\n  }\n\n  timeLookup(path: string): number {\n    const start = performance.now();\n    this.getIncidents(path);\n    return performance.now() - start;\n  }\n\n  toJSON(): object {\n    return this.trie.toJSON();\n  }\n\n  private calculateConfidence(count: number): number {\n    const capped = Math.min(count, 10);\n    return Math.round((capped / 10) * 100) / 100; // 0-1 scale\n  }\n\n  private persist(): void {\n    if (!this.persistPath) return;\n    try {\n      const dir = path.dirname(this.persistPath);\n      if (!fs.existsSync(dir)) {\n        fs.mkdirSync(dir, { recursive: true });\n      }\n      fs.writeFileSync(this.persistPath, JSON.stringify(this.trie.toJSON()), 'utf-8');\n    } catch {\n      // Persistence is best-effort; ignore failures\n    }\n  }\n}\n","/**\n * Lightweight Bayesian-style confidence updater.\n * Treats confidence as probability in [0,1].\n */\n\nexport function bayesianUpdate(prior: number, evidence: number, weight = 1): number {\n  const p = clamp(prior);\n  const e = clamp(evidence);\n  const w = Math.max(0, weight);\n  // Blend prior with evidence weighted by w\n  const posterior = (p * (1 - w)) + (e * w);\n  return clamp(posterior);\n}\n\nexport function adjustConfidence(current: number, outcome: 'positive' | 'negative', step = 0.1): number {\n  const delta = outcome === 'positive' ? step : -step;\n  return clamp(current + delta);\n}\n\nfunction clamp(value: number): number {\n  if (Number.isNaN(value)) return 0.5;\n  return Math.min(1, Math.max(0, value));\n}\n","import { IncidentIndex } from '../context/incident-index.js';\nimport type { ContextGraph } from '../context/graph.js';\nimport type { ChangeNode, IncidentNode } from '../context/nodes.js';\n\nexport interface HotPattern {\n  type: 'file' | 'directory';\n  path: string;\n  incidentCount: number;\n  confidence: number;\n  relatedFiles?: string[];\n}\n\nexport interface CoOccurrencePattern {\n  files: [string, string];\n  coOccurrences: number;\n  confidence: number;\n}\n\nexport class TriePatternDiscovery {\n  constructor(\n    private graph: ContextGraph,\n    private incidentIndex: IncidentIndex\n  ) {}\n\n  discoverHotPatterns(threshold = 3): HotPattern[] {\n    const trie = this.incidentIndex.getFileTrie();\n    const hotZones = trie.getHotZones(threshold);\n\n    return hotZones.map((zone) => ({\n      type: zone.path.endsWith('/') ? 'directory' : 'file',\n      path: zone.path,\n      incidentCount: zone.incidentCount,\n      confidence: zone.confidence,\n      relatedFiles: trie.getDirectoryIncidents(zone.path).map((i) => i.file)\n    }));\n  }\n\n  async discoverCoOccurrences(minCount = 3): Promise<CoOccurrencePattern[]> {\n    const incidents = await this.getAllIncidents();\n    const coOccurrences: Map<string, Map<string, number>> = new Map();\n\n    for (const inc of incidents) {\n      const files = await this.getFilesForIncident(inc);\n      for (let i = 0; i < files.length; i++) {\n        for (let j = i + 1; j < files.length; j++) {\n          const a = files[i]!;\n          const b = files[j]!;\n          if (!coOccurrences.has(a)) coOccurrences.set(a, new Map());\n          const counts = coOccurrences.get(a)!;\n          counts.set(b, (counts.get(b) || 0) + 1);\n        }\n      }\n    }\n\n    const patterns: CoOccurrencePattern[] = [];\n    for (const [a, map] of coOccurrences.entries()) {\n      for (const [b, count] of map.entries()) {\n        if (count >= minCount) {\n          const denom = Math.min(\n            this.incidentIndex.getFileTrie().getIncidents(a).length || 1,\n            this.incidentIndex.getFileTrie().getIncidents(b).length || 1\n          );\n          patterns.push({\n            files: [a, b],\n            coOccurrences: count,\n            confidence: Math.min(1, count / denom)\n          });\n        }\n      }\n    }\n\n    return patterns.sort((x, y) => y.confidence - x.confidence);\n  }\n\n  private async getAllIncidents(): Promise<IncidentNode[]> {\n    const nodes = await this.graph.listNodes();\n    return nodes.filter((n) => n.type === 'incident') as IncidentNode[];\n  }\n\n  private async getFilesForIncident(incident: IncidentNode): Promise<string[]> {\n    const files = new Set<string>();\n    const edges = await this.graph.getEdges(incident.id, 'both');\n\n    for (const edge of edges) {\n      if (edge.type === 'causedBy' || edge.type === 'leadTo') {\n        const changeId = edge.type === 'causedBy' ? edge.to_id : edge.from_id;\n        const change = await this.graph.getNode('change', changeId) as ChangeNode | null;\n        if (change?.data?.files && Array.isArray(change.data.files)) {\n          change.data.files.forEach((f: string) => files.add(f));\n        }\n      }\n    }\n\n    return Array.from(files).map((f) => f.replace(/\\\\/g, '/'));\n  }\n}\n","import { ContextGraph } from '../context/graph.js';\nimport type { IncidentNode, PatternNode } from '../context/nodes.js';\nimport { IncidentIndex } from '../context/incident-index.js';\nimport { adjustConfidence } from './confidence.js';\nimport { TriePatternDiscovery } from './pattern-discovery.js';\n\nexport class LearningSystem {\n  private incidentIndex: IncidentIndex;\n  private discovery: TriePatternDiscovery;\n\n  constructor(private graph: ContextGraph, projectPath: string) {\n    this.incidentIndex = new IncidentIndex(graph, projectPath);\n    this.discovery = new TriePatternDiscovery(graph, this.incidentIndex);\n  }\n\n  async onWarningHeeded(files: string[]): Promise<void> {\n    await this.adjustPatterns(files, 'positive');\n  }\n\n  async onWarningIgnored(files: string[]): Promise<void> {\n    await this.adjustPatterns(files, 'negative');\n  }\n\n  async onIncidentReported(incidentId: string, files: string[]): Promise<void> {\n    const incident = await this.graph.getNode('incident', incidentId);\n    if (incident && incident.type === 'incident') {\n      this.incidentIndex.addIncidentToTrie(incident as IncidentNode, files);\n    }\n    await this.discoverAndStorePatterns();\n  }\n\n  async onFeedback(helpful: boolean, files: string[] = []): Promise<void> {\n    await this.adjustPatterns(files, helpful ? 'positive' : 'negative');\n  }\n\n  private async adjustPatterns(files: string[], outcome: 'positive' | 'negative'): Promise<void> {\n    if (!files.length) return;\n    for (const file of files) {\n      const patterns = await this.graph.getPatternsForFile(file);\n      await Promise.all(patterns.map((p) => this.updatePatternConfidence(p, outcome)));\n    }\n  }\n\n  private async updatePatternConfidence(pattern: PatternNode, outcome: 'positive' | 'negative'): Promise<void> {\n    const current = pattern.data.confidence ?? 0.5;\n    const updated = adjustConfidence(current, outcome, 0.05);\n    await this.graph.updateNode('pattern', pattern.id, { confidence: updated, lastSeen: new Date().toISOString() });\n  }\n\n  private async discoverAndStorePatterns(): Promise<void> {\n    const hotPatterns = this.discovery.discoverHotPatterns();\n    for (const hot of hotPatterns) {\n      await this.graph.addNode('pattern', {\n        description: `${hot.type === 'directory' ? 'Directory' : 'File'} hot zone: ${hot.path}`,\n        appliesTo: [hot.path],\n        confidence: hot.confidence,\n        occurrences: hot.incidentCount,\n        firstSeen: new Date().toISOString(),\n        lastSeen: new Date().toISOString(),\n        isAntiPattern: true,\n        source: 'local'\n      });\n    }\n  }\n}\n","import { getRecentCommits, getDiff } from '../agent/git.js';\nimport { storeIssues } from '../memory/issue-store.js';\nimport { scanForVulnerabilities } from '../trie/vulnerability-signatures.js';\nimport { scanForVibeCodeIssues } from '../trie/vibe-code-signatures.js';\nimport type { Issue } from '../types/index.js';\nimport { ContextGraph } from '../context/graph.js';\nimport type { DecisionNodeData } from '../context/nodes.js';\nimport { LearningSystem } from '../agent/learning.js';\nimport path from 'node:path';\n\nexport interface LearningResult {\n  learned: number;\n  source: 'git-history' | 'manual-feedback';\n}\n\nexport class LearningEngine {\n  private readonly projectPath: string;\n  private readonly graph: ContextGraph;\n  private readonly learningSystem: LearningSystem;\n\n  constructor(projectPath: string, graph?: ContextGraph) {\n    this.projectPath = projectPath;\n    this.graph = graph || new ContextGraph(projectPath);\n    this.learningSystem = new LearningSystem(this.graph, projectPath);\n  }\n\n  /**\n   * Unified learning method: Scans history AND processes manual feedback\n   */\n  async learn(options: { \n    limit?: number; \n    manualFeedback?: { helpful: boolean; files: string[]; note?: string } \n  } = {}): Promise<LearningResult[]> {\n    const results: LearningResult[] = [];\n\n    // 1. Implicit Learning from Git History\n    if (!options.manualFeedback) {\n      const implicitCount = await this.learnFromHistory(options.limit || 20);\n      results.push({ learned: implicitCount, source: 'git-history' });\n    }\n\n    // 2. Manual Feedback Learning\n    if (options.manualFeedback) {\n      await this.recordManualFeedback(\n        options.manualFeedback.helpful, \n        options.manualFeedback.files, \n        options.manualFeedback.note\n      );\n      results.push({ learned: options.manualFeedback.files.length || 1, source: 'manual-feedback' });\n    }\n\n    return results;\n  }\n\n  /**\n   * Scan recent commits for implicit failure signals (reverts, fixes)\n   */\n  private async learnFromHistory(limit: number = 20): Promise<number> {\n    const commits = await getRecentCommits(this.projectPath, limit);\n    const issuesToStore: Issue[] = [];\n\n    for (const commit of commits) {\n      const isRevert = commit.message.toLowerCase().includes('revert') || commit.message.startsWith('Revert \"');\n      const isFix = /fix(es|ed)?\\s+#\\d+/i.test(commit.message) || commit.message.toLowerCase().includes('bugfix');\n\n      if (isRevert || isFix) {\n        const type = isRevert ? 'revert' : 'fix';\n        const diff = await getDiff(this.projectPath, commit.hash);\n        const files = this.extractFilesFromDiff(diff);\n        \n        for (const file of files) {\n          const learnedIssues = await this.extractIssuesFromDiff(diff, file, type, commit.message);\n          issuesToStore.push(...learnedIssues);\n        }\n      }\n    }\n\n    if (issuesToStore.length > 0) {\n      const result = await storeIssues(issuesToStore, path.basename(this.projectPath), this.projectPath);\n      return result.stored;\n    }\n\n    return 0;\n  }\n\n  /**\n   * Record manual feedback (trie ok/bad) and adjust pattern confidence\n   */\n  private async recordManualFeedback(helpful: boolean, files: string[], note?: string): Promise<void> {\n    const context = files[0] ?? 'unspecified';\n    const decision = await this.graph.addNode('decision', {\n      context,\n      decision: helpful ? 'helpful' : 'not helpful',\n      reasoning: note ?? null,\n      outcome: helpful ? 'good' : 'bad',\n      timestamp: new Date().toISOString(),\n    } satisfies DecisionNodeData);\n\n    if (files.length > 0) {\n      for (const file of files) {\n        const fileNode = await this.graph.getNode('file', file);\n        if (fileNode) {\n          await this.graph.addEdge(decision.id, fileNode.id, 'affects');\n        }\n      }\n      await this.learningSystem.onFeedback(helpful, files);\n    }\n  }\n\n  private extractFilesFromDiff(diff: string): string[] {\n    const files = new Set<string>();\n    const lines = diff.split('\\n');\n    for (const line of lines) {\n      if (line.startsWith('+++ b/')) {\n        files.add(line.slice(6));\n      }\n    }\n    return Array.from(files);\n  }\n\n  private async extractIssuesFromDiff(diff: string, file: string, type: 'revert' | 'fix', message: string): Promise<Issue[]> {\n    const issues: Issue[] = [];\n    const badLines = this.getBadLinesFromDiff(diff, file, type);\n    const content = badLines.join('\\n');\n\n    if (!content) return [];\n\n    const vulnerabilities = await scanForVulnerabilities(content, file);\n    const vibeIssues = await scanForVibeCodeIssues(content, file);\n\n    const allMatches = [...vulnerabilities, ...vibeIssues];\n\n    for (const match of allMatches) {\n      issues.push({\n        id: `implicit-${type}-${Date.now()}-${Math.random().toString(36).slice(2, 7)}`,\n        severity: 'serious',\n        issue: `Implicit failure detected via ${type}: ${message}. Linked to pattern: ${match.category}`,\n        fix: `Review the ${type} commit and avoid this pattern in ${file}.`,\n        file: file,\n        confidence: 0.7,\n        autoFixable: false,\n        agent: 'implicit-learning',\n        category: match.category\n      });\n    }\n\n    if (issues.length === 0) {\n      issues.push({\n        id: `implicit-${type}-${Date.now()}`,\n        severity: 'moderate',\n        issue: `Historical ${type} detected: ${message}`,\n        fix: `Review the changes in ${file} from this commit to avoid regression.`,\n        file: file,\n        confidence: 0.5,\n        autoFixable: false,\n        agent: 'implicit-learning'\n      });\n    }\n\n    return issues;\n  }\n\n  private getBadLinesFromDiff(diff: string, file: string, type: 'revert' | 'fix'): string[] {\n    const badLines: string[] = [];\n    const lines = diff.split('\\n');\n    let inTargetFile = false;\n\n    for (const line of lines) {\n      if (line.startsWith('+++ b/') || line.startsWith('--- a/')) {\n        inTargetFile = line.includes(file);\n        continue;\n      }\n\n      if (!inTargetFile) continue;\n\n      if (type === 'fix' && line.startsWith('-') && !line.startsWith('---')) {\n        badLines.push(line.slice(1));\n      } else if (type === 'revert' && line.startsWith('+') && !line.startsWith('+++')) {\n        badLines.push(line.slice(1));\n      }\n    }\n\n    return badLines;\n  }\n}\n","import { loadConfig } from '../config/loader.js';\nimport { ContextGraph } from '../context/graph.js';\nimport type { LinearTicketNodeData } from '../context/nodes.js';\n\nexport interface LinearTicket {\n  id: string;\n  identifier: string;\n  title: string;\n  description: string;\n  priority: number;\n  status: { name: string };\n  assignee?: { name: string };\n  labels: { nodes: { name: string }[] };\n  createdAt: string;\n  updatedAt: string;\n}\n\nexport class LinearIngester {\n  private readonly graph: ContextGraph;\n\n  constructor(_projectPath: string, graph: ContextGraph) {\n    this.graph = graph;\n  }\n\n  async syncTickets(): Promise<void> {\n    const apiKey = await this.getApiKey();\n    if (!apiKey) {\n      console.warn('Linear API key not found. Run \"trie linear auth <key>\" to enable ticket sync.');\n      return;\n    }\n\n    const tickets = await this.fetchActiveTickets(apiKey);\n    for (const ticket of tickets) {\n      await this.ingestTicket(ticket);\n    }\n  }\n\n  private async getApiKey(): Promise<string | null> {\n    const config = await loadConfig();\n    return (config.apiKeys as any)?.linear || process.env.LINEAR_API_KEY || null;\n  }\n\n  private async fetchActiveTickets(apiKey: string): Promise<LinearTicket[]> {\n    const query = `\n      query {\n        issues(filter: { state: { type: { in: [\"started\", \"unstarted\"] } } }) {\n          nodes {\n            id\n            identifier\n            title\n            description\n            priority\n            status {\n              name\n            }\n            assignee {\n              name\n            }\n            labels {\n              nodes {\n                name\n              }\n            }\n            createdAt\n            updatedAt\n          }\n        }\n      }\n    `;\n\n    const response = await fetch('https://api.linear.app/graphql', {\n      method: 'POST',\n      headers: {\n        'Content-Type': 'application/json',\n        'Authorization': apiKey,\n      },\n      body: JSON.stringify({ query }),\n    });\n\n    if (!response.ok) {\n      throw new Error(`Linear API error: ${response.statusText}`);\n    }\n\n    const data = (await response.json()) as any;\n    return data.data.issues.nodes as LinearTicket[];\n  }\n\n  private async ingestTicket(ticket: LinearTicket): Promise<void> {\n    const labels = ticket.labels.nodes.map(l => l.name);\n    const intentVibe = this.extractIntentVibes(ticket.title, ticket.description, labels);\n    \n    // Attempt to find linked files in description or via labels (heuristic)\n    const linkedFiles = this.extractLinkedFiles(ticket.description);\n\n    const data: LinearTicketNodeData = {\n      ticketId: ticket.identifier,\n      title: ticket.title,\n      description: ticket.description || '',\n      priority: this.mapPriority(ticket.priority),\n      labels,\n      intentVibe,\n      linkedFiles,\n      status: ticket.status.name,\n      assignee: ticket.assignee?.name || null,\n      createdAt: ticket.createdAt,\n      updatedAt: ticket.updatedAt,\n    };\n\n    await this.graph.addNode('linear-ticket', data);\n\n    // Link to files if found\n    for (const file of linkedFiles) {\n      const fileNode = await this.graph.getNode('file', file); // Use ID (path)\n      if (fileNode) {\n        await this.graph.addEdge(`linear:${ticket.identifier}`, fileNode.id, 'relatedTo');\n      }\n    }\n  }\n\n  private extractIntentVibes(title: string, description: string, labels: string[]): string[] {\n    const vibes = new Set<string>();\n    const text = (title + ' ' + (description || '') + ' ' + labels.join(' ')).toLowerCase();\n\n    if (text.includes('performance') || text.includes('slow') || text.includes('optimize')) vibes.add('performance');\n    if (text.includes('security') || text.includes('auth') || text.includes('vulnerability')) vibes.add('security');\n    if (text.includes('refactor') || text.includes('cleanup') || text.includes('debt')) vibes.add('refactor');\n    if (text.includes('feature') || text.includes('new')) vibes.add('feature');\n    if (text.includes('bug') || text.includes('fix') || text.includes('broken')) vibes.add('bug');\n    if (text.includes('breaking') || text.includes('major change')) vibes.add('breaking-change');\n\n    return Array.from(vibes);\n  }\n\n  private extractLinkedFiles(description: string): string[] {\n    if (!description) return [];\n    const matches = description.match(/[\\\\w./_-]+\\\\.(ts|tsx|js|jsx|mjs|cjs|py|go|rs)/gi);\n    if (!matches) return [];\n    return Array.from(new Set(matches.map(m => m.replace(/^\\.\\/+/, ''))));\n  }\n\n  private mapPriority(priority: number): string {\n    switch (priority) {\n      case 1: return 'urgent';\n      case 2: return 'high';\n      case 3: return 'medium';\n      case 4: return 'low';\n      default: return 'none';\n    }\n  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