@triedotdev/mcp 1.0.138 → 1.0.140

package/dist/chunk-EDDT4ZIH.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/cli/checkpoint.ts","../src/utils/trie-init.ts","../src/context/sync.ts","../src/utils/errors.ts","../src/skills/audit-logger.ts","../src/agent/git.ts","../src/utils/command-runner.ts","../src/agent/confidence.ts","../src/agent/learning.ts","../src/agent/learning-engine.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"],"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 { existsSync } from 'fs';\nimport { join } from 'path';\nimport { getWorkingDirectory, getTrieDirectory } from './workspace.js';\n\nconst INIT_MARKERS = [\n  'PROJECT.md',\n  'RULES.md',\n  'TEAM.md',\n  'BOOTSTRAP.md',\n  'AGENTS.md',\n  'config.json',\n];\n\nexport function isTrieInitialized(workDir?: string): boolean {\n  const dir = workDir || getWorkingDirectory(undefined, true);\n  const trieDir = getTrieDirectory(dir);\n  return INIT_MARKERS.some((marker) => existsSync(join(trieDir, marker)));\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","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","/**\n * Audit logger stub\n * Audit functionality has been integrated into decision ledger\n */\n\nexport interface AuditStatistics {\n  totalScans: number;\n  totalIssues: number;\n  criticalCount: number;\n  seriousCount: number;\n  moderateCount: number;\n  lowCount: number;\n  totalExecutions: number;\n  successfulExecutions: number;\n  failedExecutions: number;\n  uniqueSkills: number;\n  totalCommands: number;\n  blockedCommands: number;\n  totalNetworkCalls: number;\n  blockedNetworkCalls: number;\n}\n\nexport interface AuditEntry {\n  id: string;\n  timestamp: string;\n  command: string;\n  status: string;\n  commands?: ExecutedCommand[];\n}\n\nexport interface ExecutedCommand {\n  command: string;\n  timestamp: string;\n  exitCode?: number;\n  duration?: number;\n  stdout?: string;\n  stderr?: string;\n}\n\nexport interface SkillExecution {\n  skillName: string;\n  skillSource: string;\n  triggeredBy: 'scan' | 'mcp' | 'cli' | 'watch' | 'manual';\n  targetPath: string;\n  startedAt: string;\n  completedAt?: string;\n  success?: boolean;\n  error?: string;\n  commands?: ExecutedCommand[];\n}\n\nexport function formatAuditLog(_entry: AuditEntry): string {\n  return 'Audit logging has been integrated into the decision ledger';\n}\n\nexport function getAuditStatistics(): AuditStatistics {\n  return {\n    totalScans: 0,\n    totalIssues: 0,\n    criticalCount: 0,\n    seriousCount: 0,\n    moderateCount: 0,\n    lowCount: 0,\n    totalExecutions: 0,\n    successfulExecutions: 0,\n    failedExecutions: 0,\n    uniqueSkills: 0,\n    totalCommands: 0,\n    blockedCommands: 0,\n    totalNetworkCalls: 0,\n    blockedNetworkCalls: 0,\n  };\n}\n\nexport function createAuditEntry(\n  skillName: string, \n  skillSource: string, \n  triggeredBy: SkillExecution['triggeredBy'], \n  targetPath: string\n): SkillExecution {\n  return {\n    skillName,\n    skillSource,\n    triggeredBy,\n    targetPath,\n    startedAt: new Date().toISOString(),\n    commands: [],\n  };\n}\n\nexport function completeAuditEntry(\n  entry: SkillExecution, \n  success: boolean, \n  error?: string\n): SkillExecution {\n  const result: SkillExecution = {\n    ...entry,\n    completedAt: new Date().toISOString(),\n    success,\n  };\n  if (error !== undefined) {\n    result.error = error;\n  }\n  return result;\n}\n\nexport async function logSkillExecution(_execution: SkillExecution): Promise<void> {\n  // Stub - no-op\n}\n\nexport async function getRecentAuditLogs(_limit: number = 10): Promise<AuditEntry[]> {\n  return [];\n}\n\nexport async function getSkillAuditLogs(_skillName: string): Promise<AuditEntry[]> {\n  return [];\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","/**\n * Command Runner (with audit logging)\n *\n * Goal: Whenever Trie runs a shell command, record:\n * - command string\n * - exit code\n * - duration\n * - optional (redacted) stdout/stderr\n */\nimport { exec, execFile, execSync, type ExecException } from 'node:child_process';\nimport { promisify } from 'node:util';\n\nimport {\n  createAuditEntry,\n  completeAuditEntry,\n  logSkillExecution,\n  type ExecutedCommand,\n  type SkillExecution,\n} from '../skills/audit-logger.js';\n\nconst execAsync = promisify(exec);\nconst execFileAsync = promisify(execFile);\n\nexport type { ExecutedCommand, SkillExecution };\nexport type AuditTriggeredBy = SkillExecution['triggeredBy'];\n\nexport interface CommandAuditContext {\n  /** Shown as `skillName` in audit logs; use something like `tool:pr-review` */\n  actor: string;\n  /** Where this came from in the product flow */\n  triggeredBy: AuditTriggeredBy;\n  /** Usually the working directory / repo path */\n  targetPath: string;\n  /** Optional string for `skillSource` */\n  source?: string;\n}\n\nexport interface RunCommandOptions {\n  cwd?: string;\n  timeoutMs?: number;\n  maxBuffer?: number;\n\n  /** Capture stdout/stderr in the audit log */\n  captureOutput?: boolean;\n  /** Redact obvious secrets from captured output */\n  redactOutput?: boolean;\n  /** Max chars to keep per output stream */\n  maxOutputChars?: number;\n}\n\nfunction redact(text: string): string {\n  // Keep this conservative to avoid false redaction and avoid expensive processing.\n  return text\n    // Common key=value secrets\n    .replace(/\\b(AWS|ANTHROPIC|OPENAI|GITHUB)_[A-Z0-9_]*\\s*=\\s*([^\\s\"'`]+)/gi, '$1_<REDACTED>=<REDACTED>')\n    // Bearer tokens\n    .replace(/\\bBearer\\s+[A-Za-z0-9\\-._~+/]+=*\\b/g, 'Bearer <REDACTED>')\n    // GitHub tokens / generic tokens\n    .replace(/\\bghp_[A-Za-z0-9]{20,}\\b/g, 'ghp_<REDACTED>')\n    .replace(/\\b(?:xox[baprs]-)[A-Za-z0-9-]{10,}\\b/g, '<REDACTED_SLACK_TOKEN>')\n    // AWS access key id (best-effort)\n    .replace(/\\bAKIA[0-9A-Z]{16}\\b/g, 'AKIA<REDACTED>');\n}\n\nfunction clampOutput(text: string, maxChars: number): string {\n  if (text.length <= maxChars) return text;\n  return text.slice(0, maxChars) + `\\n…(truncated ${text.length - maxChars} chars)`;\n}\n\nfunction buildCommandRecord(command: string): ExecutedCommand {\n  return {\n    command,\n    timestamp: new Date().toISOString(),\n  };\n}\n\nasync function finalizeAndWrite(\n  entry: SkillExecution,\n  cmd: ExecutedCommand,\n  outcome: { success: boolean; exitCode?: number; stdout?: string; stderr?: string; error?: string; startedAt: number },\n  options?: Pick<RunCommandOptions, 'captureOutput' | 'redactOutput' | 'maxOutputChars'>\n): Promise<void> {\n  const duration = Date.now() - outcome.startedAt;\n  cmd.duration = duration;\n  if (outcome.exitCode !== undefined) {\n    cmd.exitCode = outcome.exitCode;\n  }\n\n  const captureOutput = options?.captureOutput ?? false;\n  const redactOutput = options?.redactOutput ?? true;\n  const maxOutputChars = options?.maxOutputChars ?? 2000;\n\n  if (captureOutput) {\n    const out = outcome.stdout ?? '';\n    const err = outcome.stderr ?? '';\n    cmd.stdout = redactOutput ? redact(clampOutput(out, maxOutputChars)) : clampOutput(out, maxOutputChars);\n    cmd.stderr = redactOutput ? redact(clampOutput(err, maxOutputChars)) : clampOutput(err, maxOutputChars);\n  }\n\n  const completed = completeAuditEntry(entry, outcome.success, outcome.error);\n  await logSkillExecution(completed);\n}\n\nexport async function runShellCommand(\n  command: string,\n  audit: CommandAuditContext,\n  options?: RunCommandOptions\n): Promise<{ stdout: string; stderr: string; exitCode: number }> {\n  const startedAt = Date.now();\n  const entry = createAuditEntry(audit.actor, audit.source ?? 'trie', audit.triggeredBy, audit.targetPath);\n  const cmd = buildCommandRecord(command);\n  entry.commands?.push(cmd);\n\n  try {\n    const { stdout, stderr } = await execAsync(command, {\n      cwd: options?.cwd,\n      timeout: options?.timeoutMs,\n      maxBuffer: options?.maxBuffer,\n    });\n\n    await finalizeAndWrite(entry, cmd, { success: true, exitCode: 0, stdout, stderr, startedAt }, options);\n    return { stdout: stdout ?? '', stderr: stderr ?? '', exitCode: 0 };\n  } catch (e) {\n    const err = e as ExecException & { stdout?: unknown; stderr?: unknown; code?: unknown };\n    const stdout = typeof err.stdout === 'string' ? err.stdout : '';\n    const stderr = typeof err.stderr === 'string' ? err.stderr : '';\n    const exitCode = typeof err.code === 'number' ? err.code : 1;\n\n    await finalizeAndWrite(\n      entry,\n      cmd,\n      { success: false, exitCode, stdout, stderr, error: err.message, startedAt },\n      // Capture output for failures by default (so audits are useful)\n      { ...options, captureOutput: options?.captureOutput ?? true }\n    );\n\n    return { stdout, stderr, exitCode };\n  }\n}\n\nexport function runShellCommandSync(\n  command: string,\n  audit: CommandAuditContext,\n  options?: Omit<RunCommandOptions, 'timeoutMs'> & { timeoutMs?: number }\n): { stdout: string; exitCode: number } {\n  const startedAt = Date.now();\n  const entry = createAuditEntry(audit.actor, audit.source ?? 'trie', audit.triggeredBy, audit.targetPath);\n  const cmd = buildCommandRecord(command);\n  entry.commands?.push(cmd);\n\n  try {\n    const stdout = execSync(command, {\n      cwd: options?.cwd,\n      timeout: options?.timeoutMs,\n      maxBuffer: options?.maxBuffer,\n      encoding: 'utf-8',\n      stdio: ['pipe', 'pipe', 'pipe'],\n    });\n\n    // Fire-and-forget write; sync APIs can’t await.\n    void finalizeAndWrite(entry, cmd, { success: true, exitCode: 0, stdout, stderr: '', startedAt }, options);\n    return { stdout: stdout ?? '', exitCode: 0 };\n  } catch (e) {\n    const err = e as ExecException & { stdout?: unknown; stderr?: unknown; status?: unknown };\n    const stdout = typeof err.stdout === 'string' ? err.stdout : '';\n    const stderr = typeof err.stderr === 'string' ? err.stderr : '';\n    const exitCode = typeof err.status === 'number' ? err.status : 1;\n\n    void finalizeAndWrite(\n      entry,\n      cmd,\n      { success: false, exitCode, stdout, stderr, error: err.message, startedAt },\n      { ...options, captureOutput: options?.captureOutput ?? true }\n    );\n\n    return { stdout, exitCode };\n  }\n}\n\nexport async function runExecFile(\n  file: string,\n  args: string[],\n  audit: CommandAuditContext,\n  options?: Omit<RunCommandOptions, 'timeoutMs'> & { timeoutMs?: number }\n): Promise<{ stdout: string; stderr: string; exitCode: number }> {\n  const startedAt = Date.now();\n  const command = [file, ...args].join(' ');\n  const entry = createAuditEntry(audit.actor, audit.source ?? 'trie', audit.triggeredBy, audit.targetPath);\n  const cmd = buildCommandRecord(command);\n  entry.commands?.push(cmd);\n\n  try {\n    const { stdout, stderr } = await execFileAsync(file, args, {\n      cwd: options?.cwd,\n      timeout: options?.timeoutMs,\n      maxBuffer: options?.maxBuffer,\n    });\n\n    await finalizeAndWrite(entry, cmd, { success: true, exitCode: 0, stdout: String(stdout ?? ''), stderr: String(stderr ?? ''), startedAt }, options);\n    return { stdout: String(stdout ?? ''), stderr: String(stderr ?? ''), exitCode: 0 };\n  } catch (e) {\n    const err = e as ExecException & { stdout?: unknown; stderr?: unknown; code?: unknown };\n    const stdout = typeof err.stdout === 'string' ? err.stdout : '';\n    const stderr = typeof err.stderr === 'string' ? err.stderr : '';\n    const exitCode = typeof err.code === 'number' ? err.code : 1;\n\n    await finalizeAndWrite(\n      entry,\n      cmd,\n      { success: false, exitCode, stdout, stderr, error: err.message, startedAt },\n      { ...options, captureOutput: options?.captureOutput ?? true }\n    );\n    return { stdout, stderr, exitCode };\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 { 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 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 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package/dist/chunk-GFFUDJMK.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/agent/goal-validator.ts"],"sourcesContent":["/**\n * Goal Validator - Helpers for goal tracking\n * \n * Goal detection is handled entirely by the AI watcher in watch.ts.\n * The AI (Anthropic) checks every changed file against user-defined goals,\n * using the Trie's priority scoring for cost control.\n * \n * This module provides:\n * - getActiveGoals: loads active goals for the AI prompt\n * - recordGoalViolationCaught: tracks when a violation is detected\n * - recordGoalViolationFixed: tracks when a violation is auto-fixed\n * - measureInitialGoalValue: measures current state for new goals\n */\n\nimport type { Goal } from './project-state.js';\nimport { getProjectState } from './project-state.js';\nimport { searchIssues } from '../memory/issue-store.js';\n\n/**\n * Get active goals for a project (used by the AI watcher)\n */\nexport async function getActiveGoals(projectPath: string): Promise<Goal[]> {\n  const projectState = getProjectState(projectPath);\n  await projectState.load();\n  return projectState.getAllGoals().filter(g => g.status === 'active');\n}\n\nexport async function recordGoalViolationCaught(\n  goal: Goal,\n  file: string,\n  projectPath: string\n): Promise<void> {\n  const projectState = getProjectState(projectPath);\n  await projectState.load();\n  \n  const metadata = goal.metadata || {};\n  const caughtCount = (metadata.caughtCount || 0) + 1;\n  \n  await projectState.updateGoal(goal.id, {\n    metadata: {\n      ...metadata,\n      caughtCount,\n      lastCaught: new Date().toISOString(),\n      lastCaughtFile: file,\n    },\n  });\n}\n\nexport async function recordGoalViolationFixed(\n  goal: Goal,\n  file: string,\n  projectPath: string\n): Promise<void> {\n  const projectState = getProjectState(projectPath);\n  await projectState.load();\n  \n  const metadata = goal.metadata || {};\n  const fixedCount = (metadata.fixedCount || 0) + 1;\n  \n  await projectState.updateGoal(goal.id, {\n    metadata: {\n      ...metadata,\n      fixedCount,\n      lastFixed: new Date().toISOString(),\n      lastFixedFile: file,\n    },\n  });\n  \n  // Resolve the goal-violation issue in the issue store\n  // This is the source of truth - measureGoalMetric() will query from here\n  const { resolveGoalViolation } = await import('../memory/issue-store.js');\n  await resolveGoalViolation(file, goal.description, projectPath);\n  \n  // Trigger immediate progress update so UI reflects the fix\n  const { getGoalManager } = await import('./goal-manager.js');\n  const goalManager = getGoalManager(projectPath);\n  await goalManager.updateGoalProgress();\n}\n\n/**\n * Measure the initial value for a new goal based on existing issues.\n * This sets a proper baseline so progress calculation works correctly.\n * \n * For reduction goals (like \"no emojis\"), we count current violations.\n * For other goals, we use semantic matching against existing issues.\n * \n * Returns the count to use as both startValue and currentValue.\n */\nexport async function measureInitialGoalValue(\n  description: string,\n  projectPath: string\n): Promise<number> {\n  try {\n    const issues = await searchIssues('', {\n      workDir: projectPath,\n      limit: 1000,\n      includeResolved: false,\n    });\n    \n    if (issues.length === 0) {\n      return 0;\n    }\n    \n    const desc = description.toLowerCase();\n    \n    // Check for goal-violation issues that might already exist for similar goals\n    const goalViolations = issues.filter(r => \n      r.issue.agent === 'goal-violation' &&\n      r.issue.issue.toLowerCase().includes(desc.slice(0, 30))\n    );\n    if (goalViolations.length > 0) {\n      return goalViolations.length;\n    }\n    \n    // Security goals\n    if (desc.includes('security') || desc.includes('vulnerab')) {\n      return issues.filter(r => \n        r.issue.agent === 'security' || r.issue.severity === 'critical'\n      ).length;\n    }\n    \n    // Type safety goals\n    if (desc.includes('type') || desc.includes('typescript') || desc.includes('any type')) {\n      return issues.filter(r => \n        r.issue.agent === 'typecheck' ||\n        r.issue.issue.toLowerCase().includes('type')\n      ).length;\n    }\n    \n    // Bug-related goals\n    if (desc.includes('bug') || desc.includes('error')) {\n      return issues.filter(r => \n        r.issue.agent === 'bug-finding' ||\n        r.issue.severity === 'critical' ||\n        r.issue.severity === 'serious'\n      ).length;\n    }\n    \n    // Dead code / unused code goals\n    if (desc.includes('dead code') || desc.includes('unused')) {\n      return issues.filter(r => {\n        const msg = r.issue.issue.toLowerCase();\n        return msg.includes('unused') || msg.includes('dead code') || msg.includes('never used');\n      }).length;\n    }\n    \n    // For custom goals like \"no emojis\", we start at 0 and let the AI scanner find violations\n    // This is correct because we don't know the count until a scan runs\n    return 0;\n  } catch {\n    return 0;\n  }\n}\n\n/**\n * Manually check files against goals\n * Returns violations found\n * \n * NOW WITH CACHING: Uses CodebaseIndex to avoid re-scanning unchanged files\n */\nexport async function checkFilesForGoalViolations(\n  goals: Goal[],\n  projectPath: string,\n  filesToCheck?: string[],\n  onProgress?: (message: string) => void\n): Promise<Array<{ file: string; message: string; severity: 'critical' | 'warning' | 'info' }>> {\n  // Import AI client and codebase index\n  const { isAIAvailable, runAIAnalysis } = await import('../ai/client.js');\n  const { CodebaseIndex } = await import('../context/codebase-index.js');\n  \n  if (!isAIAvailable()) {\n    throw new Error('AI not available - ANTHROPIC_API_KEY not set');\n  }\n  \n  // Initialize codebase index for caching\n  const codebaseIndex = new CodebaseIndex(projectPath);\n  \n  // Check if index needs to be built\n  if (codebaseIndex.isEmpty()) {\n    onProgress?.('Building codebase index (first-time, may take a minute)...');\n    console.error('[Goal Check] Codebase index is empty - building index first...');\n    console.error('[Goal Check] This is a one-time operation. Future checks will be much faster.');\n    \n    // Auto-index using same file selection as checks (most recently modified) so cache overlaps\n    const { glob } = await import('glob');\n    const { stat } = await import('fs/promises');\n    const indexPattern = `${projectPath}/**/*.{ts,tsx,js,jsx,mjs,vue,svelte,astro,py,go,rs,java,c,cpp,h,hpp,cs,rb,php,css,scss,html}`;\n    const indexFiles = await glob(indexPattern, {\n      ignore: ['**/node_modules/**', '**/dist/**', '**/build/**', '**/.git/**', '**/.trie/**', '**/coverage/**'],\n      nodir: true,\n    });\n    \n    const withStats = await Promise.all(\n      indexFiles.map(async (f) => {\n        try {\n          const stats = await stat(f);\n          return { file: f, mtime: stats.mtime.getTime() };\n        } catch {\n          return null;\n        }\n      })\n    );\n    const toIndex = withStats\n      .filter((f): f is { file: string; mtime: number } => f !== null)\n      .sort((a, b) => b.mtime - a.mtime)\n      .slice(0, 500)\n      .map((f) => f.file);\n    \n    let indexed = 0;\n    for (const filePath of toIndex) {\n      let relativePath = filePath;\n      if (filePath.toLowerCase().startsWith(projectPath.toLowerCase() + '/')) {\n        relativePath = filePath.slice(projectPath.length + 1);\n      }\n      const result = await codebaseIndex.indexFile(relativePath);\n      if (result) indexed++;\n      if (indexed % 50 === 0) {\n        onProgress?.(`Indexing files (${indexed}/${toIndex.length})...`);\n      }\n    }\n    \n    await codebaseIndex.save();\n    console.error(`[Goal Check] Index built: ${indexed} files indexed`);\n  }\n  \n  // Get files to check\n  let files: string[] = [];\n  if (filesToCheck && filesToCheck.length > 0) {\n    files = filesToCheck;\n  } else {\n    // MANUAL CHECK MODE: Scan ALL relevant files, not just recently modified\n    const { glob } = await import('glob');\n    \n    const pattern = `${projectPath}/**/*.{ts,tsx,js,jsx,py,go,rs,java,c,cpp,h,hpp,cs,rb,php,css,scss,html,vue,svelte}`;\n    const allFiles = await glob(pattern, {\n      ignore: ['**/node_modules/**', '**/dist/**', '**/build/**', '**/.git/**', '**/.trie/**', '**/coverage/**'],\n      nodir: true,\n    });\n    \n    // For manual checks, use more files but still reasonable limit\n    // Sort by modification time to prioritize recently modified\n    const { stat } = await import('fs/promises');\n    const withStats = await Promise.all(\n      allFiles.map(async (f) => {\n        try {\n          const stats = await stat(f);\n          return { file: f, mtime: stats.mtime.getTime() };\n        } catch {\n          return null;\n        }\n      })\n    );\n    \n    files = withStats\n      .filter((f): f is { file: string; mtime: number } => f !== null)\n      .sort((a, b) => b.mtime - a.mtime)\n      .slice(0, 100) // Check up to 100 files for manual scans\n      .map(f => f.file);\n  }\n  \n  if (files.length === 0) {\n    throw new Error('No files found to check');\n  }\n\n  // Pre-index the files we're about to check so cache lookups work.\n  // The initial index may have indexed different files (first 500 from glob), while we check\n  // the 100 most recently modified - these can have zero overlap, causing every run to scan.\n  for (const filePath of files) {\n    let rel = filePath;\n    if (filePath.toLowerCase().startsWith(projectPath.toLowerCase() + '/')) {\n      rel = filePath.slice(projectPath.length + 1);\n    } else if (filePath.startsWith('/') && !filePath.toLowerCase().startsWith(projectPath.toLowerCase())) {\n      continue;\n    }\n    await codebaseIndex.indexFile(rel);\n  }\n  \n  // Check which files need scanning vs can use cached results\n  const filesToScan: string[] = [];\n  const cachedViolations: Array<{ file: string; message: string; severity: 'critical' | 'warning' | 'info' }> = [];\n  \n  for (const filePath of files) {\n    // Handle case-insensitive filesystems (macOS) and ensure we get a proper relative path\n    let relativePath = filePath;\n    if (filePath.toLowerCase().startsWith(projectPath.toLowerCase() + '/')) {\n      relativePath = filePath.slice(projectPath.length + 1);\n    } else if (filePath.startsWith('/')) {\n      // Already absolute but doesn't match projectPath - skip this file\n      // This can happen with stale cache entries from different projects\n      continue;\n    }\n    const hasChanged = await codebaseIndex.hasChanged(relativePath);\n    \n    if (hasChanged) {\n      // File changed or not indexed - needs scanning\n      // Try to index the file first; skip if it doesn't exist\n      const indexed = await codebaseIndex.indexFile(relativePath);\n      if (indexed) {\n        filesToScan.push(filePath);\n      }\n      // If indexFile returns null, file doesn't exist - skip it silently\n    } else {\n      // File unchanged - check cache for each goal\n      for (const goal of goals) {\n        const cached = codebaseIndex.getCachedViolations(relativePath, goal.id);\n        if (cached && cached.length > 0) {\n          const violation = cached[0];\n          if (violation && violation.found) {\n            cachedViolations.push({\n              file: relativePath,\n              message: `Goal \"${goal.description}\" violated in ${relativePath}: ${violation.details || 'Violation found'} [${violation.confidence || 90}% confidence] (cached)`,\n              severity: 'warning',\n            });\n          }\n        } else {\n          // No cache for this goal - needs scanning\n          if (!filesToScan.includes(filePath)) {\n            filesToScan.push(filePath);\n          }\n        }\n      }\n    }\n  }\n  \n  onProgress?.(`Checking ${filesToScan.length} files for violations...`);\n  console.error(`[Goal Check] ${files.length} files total, ${filesToScan.length} need scanning, ${files.length - filesToScan.length} using cache`);\n  \n  // Process files that need scanning in batches\n  const allViolations: Array<{ file: string; message: string; severity: 'critical' | 'warning' | 'info' }> = [...cachedViolations];\n  \n  if (filesToScan.length === 0) {\n    // All results from cache!\n    await codebaseIndex.save();\n    return allViolations;\n  }\n  \n  // For large file sets, process in batches to avoid token limits\n  const BATCH_SIZE = 25; // Process 25 files at a time\n  \n  const totalBatches = Math.ceil(filesToScan.length / BATCH_SIZE);\n  for (let batchStart = 0; batchStart < filesToScan.length; batchStart += BATCH_SIZE) {\n    const batchNum = Math.floor(batchStart / BATCH_SIZE) + 1;\n    onProgress?.(`Analyzing files (batch ${batchNum}/${totalBatches})...`);\n    const batchFiles = filesToScan.slice(batchStart, batchStart + BATCH_SIZE);\n    \n    // Read file contents for this batch\n    const { readFile } = await import('fs/promises');\n    const fileContents = await Promise.all(\n      batchFiles.map(async (filePath) => {\n        try {\n          const content = await readFile(filePath, 'utf-8');\n          const relativePath = filePath.replace(projectPath + '/', '');\n          return {\n            path: relativePath,\n            content: content.slice(0, 10000), // Increased limit for manual checks\n          };\n        } catch {\n          return null;\n        }\n      })\n    );\n    \n    const validFiles = fileContents.filter((f): f is { path: string; content: string } => f !== null);\n    \n    if (validFiles.length === 0) continue;\n    \n    // Build files block for AI\n    const filesBlock = validFiles\n      .map(f => `--- ${f.path} ---\\n${f.content}`)\n      .join('\\n\\n');\n    \n    // Build goals section\n    const goalsSection = `\nUSER-DEFINED GOALS (check EVERY file against ALL goals):\n${goals.map((g, i) => `  ${i + 1}. \"${g.description}\"`).join('\\n')}\n\nThis is a MANUAL CHECK requested by the user. Report ALL goal violations you find.\nFor emoji detection, look for Unicode emoji characters.\n`;\n  \n    // Run AI analysis\n    const result = await runAIAnalysis({\n      systemPrompt: `You are checking code for GOAL VIOLATIONS ONLY.\n${goalsSection}\nReply ONLY with a JSON array. Each element must have:\n- \"file\": relative file path\n- \"severity\": \"critical\" | \"major\" | \"minor\"\n- \"description\": 1-sentence description of the goal violation with specific examples\n- \"confidence\": number 0-100, how confident you are this is a violation\n- \"isGoalViolation\": true (always true for this scan)\n- \"goalIndex\": 0-based index of the violated goal\n\nCRITICAL DETECTION RULES:\n\n**EMOJIS**: Any Unicode emoji characters including but not limited to:\n- Emoticons: 😀😃😄😊🙂🙃😉😇🥰😍🤩😘😗☺️😚😙🥲\n- Symbols: ⚡️⚠️✅❌➜→←↑↓►◄▲▼★☆●○◆◇■□▪️▫️\n- Objects: 📊📈📉💻🖥️📱⌨️🖱️💾💿📀🔧🔨⚙️🛠️\n- Actions: 🔥💪👍👎👏🙌🤝✊👊🎯🎉🎊🚀\n- Weather: ☀️🌤️⛅☁️🌦️🌧️⛈️🌩️🌨️❄️\n- ALL OTHER Unicode emoji in ranges U+1F300-U+1F9FF, U+2600-U+27BF, U+2B00-U+2BFF\n\n**COLORS**: For \"purple\" or \"gradient\" goals, check:\n- CSS: purple, #purple, hsl(purple), rgb(purple), violet, #8B00FF, #9B59D6, etc.\n- Gradients: linear-gradient, radial-gradient, conic-gradient, background-image with gradients\n- Tailwind: purple-*, violet-*, bg-gradient-*\n- Styled components or CSS-in-JS with purple/violet/gradient\n\nBe EXTREMELY thorough. Check:\n1. String literals and template literals\n2. JSX/HTML content\n3. CSS files and style blocks\n4. Comments (emojis in comments still violate \"no emojis\")\n5. console.log statements\n6. Component names, variable names (if they contain emojis)\n\nIf a goal says \"no emojis\" and you see ANY emoji ANYWHERE in the file, report it.\nIf a goal says \"no console.log\" and you see console.log ANYWHERE, report it.\nIf a goal says \"no purple/gradient\" and you see ANY purple color or gradient, report it.\n\nIf no violations found, reply with: []\nOutput ONLY the JSON array, no markdown fences, no commentary.`,\n      userPrompt: `Check these ${validFiles.length} files for goal violations:\\n\\n${filesBlock}`,\n      maxTokens: 8192, // Increased for larger codebases\n      temperature: 0.1,\n    });\n    \n    // Parse response\n    let issues: Array<{\n      file: string;\n      severity: 'critical' | 'major' | 'minor';\n      description: string;\n      confidence: number;\n      isGoalViolation: boolean;\n      goalIndex?: number;\n    }> = [];\n    \n    try {\n      const cleaned = result.content.replace(/```json?\\n?|\\n?```/g, '').trim();\n      issues = JSON.parse(cleaned);\n      if (!Array.isArray(issues)) issues = [];\n    } catch (err) {\n      // Parse failed - continue to next batch\n      console.debug('[Goal Check] Batch parse failed:', err);\n      continue;\n    }\n    \n    // Convert to violation format and record\n    for (const issue of issues) {\n      if (!issue.isGoalViolation || issue.confidence < 50) continue;\n      if (issue.goalIndex == null || issue.goalIndex < 0 || issue.goalIndex >= goals.length) continue;\n      \n      const goal = goals[issue.goalIndex];\n      if (!goal) continue; // Defensive check\n      const severity = issue.severity === 'critical' ? 'critical' : 'warning';\n      const message = `Goal \"${goal.description}\" violated in ${issue.file}: ${issue.description} [${issue.confidence}% confidence]`;\n      \n      allViolations.push({\n        file: issue.file,\n        message,\n        severity,\n      });\n      \n      // Cache the result in codebase index\n      codebaseIndex.recordViolation(\n        issue.file,\n        goal.id,\n        goal.description,\n        true, // found\n        issue.description,\n        issue.confidence\n      );\n      \n      // Record violation\n      await recordGoalViolationCaught(goal, issue.file, projectPath);\n    }\n    \n    // Also record \"no violation\" for scanned files\n    for (const file of validFiles) {\n      for (let goalIdx = 0; goalIdx < goals.length; goalIdx++) {\n        const goal = goals[goalIdx];\n        if (!goal) continue;\n        const hasViolation = issues.some(i => i.file === file.path && i.goalIndex === goalIdx);\n        if (!hasViolation) {\n          codebaseIndex.recordViolation(\n            file.path,\n            goal.id,\n            goal.description,\n            false, // not found\n            undefined,\n            100\n          );\n        }\n      }\n    }\n  }\n  \n  // Save updated index\n  await codebaseIndex.save();\n  \n  return 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package/dist/chunk-J5EMP4XW.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/utils/autonomy-config.ts","../src/types/autonomy.ts"],"sourcesContent":["/**\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    aiWatcher: {\n      ...DEFAULT_AUTONOMY_CONFIG.aiWatcher,\n      ...(partial.aiWatcher || {}),\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 * AI Watcher configuration -- controls the Claude-powered file watcher\n */\nexport interface AIWatcherConfig {\n  /** Enable AI-powered file watching */\n  enabled: boolean;\n  /** Max tokens to spend per hour on AI scans */\n  hourlyTokenLimit: number;\n  /** Minimum seconds between AI scans */\n  scanCooldownSec: number;\n  /** Seconds before re-scanning a file that was clean */\n  cleanFileCooldownSec: number;\n  /** Max files to include in a single AI scan */\n  maxFilesPerScan: number;\n  /** Max characters to send per file */\n  maxCharsPerFile: 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  /** AI watcher settings (Claude-powered file scanning) */\n  aiWatcher: AIWatcherConfig;\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-debugger',\n      'remove-emoji',\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  aiWatcher: {\n    enabled: true,\n    hourlyTokenLimit: 50_000,\n    scanCooldownSec: 30,\n    cleanFileCooldownSec: 300,\n    maxFilesPerScan: 5,\n    maxCharsPerFile: 4000,\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: 'remove-console-log' | 'remove-debugger' | 'remove-emoji' | 'remove-unused-import' | \n        'add-missing-await' | 'fix-typo' | 'goal-violation' | 'custom' | string;\n  /** Category of fix */\n  category: 'trivial' | 'safe' | 'moderate' | 'risky' | 'goal-violation';\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?: 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package/dist/chunk-QSWUPSLK.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/context/graph.ts","../src/context/store.ts"],"sourcesContent":["import crypto from 'node:crypto';\nimport path from 'node:path';\n\nimport type { RiskLevel } from '../types/index.js';\nimport { ContextStore } from './store.js';\nimport type {\n  ChangeNode,\n  ChangeNodeData,\n  ContextSnapshot,\n  DecisionNode,\n  DecisionNodeData,\n  Edge,\n  EdgeDirection,\n  EdgeType,\n  FileNode,\n  FileNodeData,\n  FixNode,\n  FixNodeData,\n  IncidentNode,\n  IncidentNodeData,\n  IssueNode,\n  IssueNodeData,\n  LinearTicketNode,\n  LinearTicketNodeData,\n  Node,\n  NodeData,\n  NodeType,\n  PatternNode,\n  PatternNodeData\n} from './types.js';\n\nexport class ContextGraph {\n  private readonly store: ContextStore;\n  private readonly projectPath: string;\n\n  constructor(projectPath: string, dbPath?: string, store?: ContextStore) {\n    this.projectPath = projectPath;\n    this.store = store ?? new ContextStore(projectPath, dbPath);\n  }\n\n  get projectRoot(): string {\n    return this.projectPath;\n  }\n\n  async addNode(type: 'file', data: FileNodeData): Promise<FileNode>;\n  async addNode(type: 'change', data: ChangeNodeData): Promise<ChangeNode>;\n  async addNode(type: 'incident', data: IncidentNodeData): Promise<IncidentNode>;\n  async addNode(type: 'issue', data: IssueNodeData): Promise<IssueNode>;\n  async addNode(type: 'pattern', data: PatternNodeData): Promise<PatternNode>;\n  async addNode(type: 'fix', data: FixNodeData): Promise<FixNode>;\n  async addNode(type: 'decision', data: DecisionNodeData): Promise<DecisionNode>;\n  async addNode(type: 'linear-ticket', data: LinearTicketNodeData): Promise<LinearTicketNode>;\n  async addNode(type: NodeType, data: NodeData): Promise<Node> {\n    const now = new Date().toISOString();\n    const id = this.generateNodeId(type, data);\n    const node = {\n      id,\n      type,\n      data,\n      created_at: now,\n      updated_at: now\n    } as Node;\n\n    this.store.addNode(node);\n    return 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const incident = this.store.getNodeByType('incident', ce.from_id);\n        if (incident) incidents.set(incident.id, incident as IncidentNode);\n      }\n    }\n\n    return Array.from(incidents.values());\n  }\n\n  async getPatternsForFile(filePath: string): Promise<PatternNode[]> {\n    const normalized = this.normalizePath(filePath);\n    const nodes = this.store.findNodesByType('pattern') as PatternNode[];\n\n    return nodes.filter((node) =>\n      node.data.appliesTo.some((pattern) => normalized.includes(pattern) || filePath.includes(pattern))\n    );\n  }\n\n  async getRecentChanges(limit: number): Promise<ChangeNode[]> {\n    const nodes = this.store.findNodesByType('change') as ChangeNode[];\n    return nodes\n      .sort((a, b) => new Date(b.data.timestamp).getTime() - new Date(a.data.timestamp).getTime())\n      .slice(0, limit);\n  }\n\n  async calculateFileRisk(filePath: string): Promise<RiskLevel> {\n    const fileNode = this.findFileNode(filePath);\n    if (!fileNode) return 'low';\n\n    // Simple heuristic based on incidents and changes\n    const incidentScore = Math.min(fileNode.data.incidentCount * 2, 6);\n    const changeScore = Math.min(fileNode.data.changeCount, 4);\n    const baseScore = this.riskLevelToScore(fileNode.data.riskLevel);\n    const total = baseScore + incidentScore + changeScore;\n\n    if (total >= 10) return 'critical';\n    if (total >= 7) return 'high';\n    if (total >= 4) return 'medium';\n    return 'low';\n  }\n\n  async listNodes(): Promise<Node[]> {\n    return this.store.listNodes();\n  }\n\n  async listEdges(): Promise<Edge[]> {\n    return this.store.listEdges();\n  }\n\n  async deleteEdge(id: string): Promise<void> {\n    this.store.deleteEdge(id);\n  }\n\n  async getSnapshot(): Promise<ContextSnapshot> {\n    return {\n      nodes: this.store.listNodes(),\n      edges: this.store.listEdges(),\n      exported_at: new Date().toISOString()\n    };\n  }\n\n  async applySnapshot(snapshot: ContextSnapshot): Promise<void> {\n    for (const node of snapshot.nodes) {\n      const existing = this.store.getNode(node.id);\n      if (!existing || this.isNewer(node.updated_at, existing.updated_at)) {\n        this.store.upsertNode(node);\n      }\n    }\n\n    for (const edge of snapshot.edges) {\n      const existing = this.store.getEdge(edge.id);\n      if (!existing) {\n        this.store.upsertEdge(edge);\n      }\n    }\n  }\n\n  private generateNodeId(type: NodeType, data: NodeData): string {\n    if (type === 'file') {\n      const fileData = data as FileNodeData;\n      return this.normalizePath(fileData.path);\n    }\n\n    if (type === 'change') {\n      const changeData = data as ChangeNodeData;\n      if (changeData.commitHash) {\n        return changeData.commitHash;\n      }\n    }\n\n    if (type === 'linear-ticket') {\n      const ticketData = data as LinearTicketNodeData;\n      return `linear:${ticketData.ticketId}`;\n    }\n\n    return crypto.randomUUID();\n  }\n\n  private findFileNode(filePath: string): FileNode | null {\n    const normalized = this.normalizePath(filePath);\n    const nodes = this.store.findNodesByType('file') as FileNode[];\n    return (\n      nodes.find(\n        (node) =>\n          node.id === normalized ||\n          this.normalizePath(node.data.path) === normalized ||\n          node.data.path === filePath\n      ) ?? null\n    );\n  }\n\n  private normalizePath(filePath: string): string {\n    return path.resolve(this.projectPath, filePath);\n  }\n\n  private riskLevelToScore(level: RiskLevel): number {\n    switch (level) {\n      case 'critical':\n        return 6;\n      case 'high':\n        return 4;\n      case 'medium':\n        return 2;\n      default:\n        return 0;\n    }\n  }\n\n  private isNewer(incoming: string, existing: string): boolean {\n    return new Date(incoming).getTime() >= new Date(existing).getTime();\n  }\n}\n","import Database, { type Database as DatabaseType } from 'better-sqlite3';\nimport fs from 'node:fs';\nimport path from 'node:path';\nimport { getTrieDirectory } from '../utils/workspace.js';\n\nimport type { Edge, EdgeDirection, EdgeType, Node, NodeData, NodeType } from './types.js';\n\ntype NodeRow = {\n  id: string;\n  type: NodeType;\n  data: string;\n  created_at: string;\n  updated_at: string;\n};\n\ntype EdgeRow = {\n  id: string;\n  from_id: string;\n  to_id: string;\n  type: EdgeType;\n  weight: number;\n  metadata: string | null;\n  created_at: string;\n};\n\nexport class ContextStore {\n  private db: DatabaseType;\n  private readonly dbFilePath: string;\n\n  constructor(projectPath: string, dbFilePath?: string) {\n    this.dbFilePath = dbFilePath ?? path.join(getTrieDirectory(projectPath), 'context.db');\n    this.ensureDirectory();\n\n    this.db = new Database(this.dbFilePath);\n    this.configure();\n    this.prepareSchema();\n  }\n\n  get databasePath(): string {\n    return this.dbFilePath;\n  }\n\n  addNode(node: Node): Node {\n    const stmt = 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FROM nodes WHERE id = ?').get(id) as NodeRow | undefined;\n    return row ? this.mapNodeRow(row) : null;\n  }\n\n  getNodeByType(type: NodeType, id: string): Node | null {\n    const row = this.db\n      .prepare('SELECT * FROM nodes WHERE id = ? AND type = ?')\n      .get(id, type) as NodeRow | undefined;\n    return row ? this.mapNodeRow(row) : null;\n  }\n\n  updateNode(id: string, updates: Partial<NodeData>, updatedAt: string): Node | null {\n    const existing = this.getNode(id);\n    if (!existing) {\n      return null;\n    }\n\n    const merged = {\n      ...existing,\n      data: { ...existing.data, ...updates },\n      updated_at: updatedAt\n    } as Node;\n\n    this.db\n      .prepare(\n        `UPDATE nodes SET data = @data, updated_at = @updated_at\n         WHERE id = @id`\n      )\n      .run({\n        id,\n        data: JSON.stringify(merged.data),\n        updated_at: merged.updated_at\n      });\n\n    return merged;\n  }\n\n  deleteNode(id: string): void {\n    const deleteEdges = this.db.prepare('DELETE FROM edges WHERE from_id = ? OR to_id = ?');\n    const deleteNodeStmt = this.db.prepare('DELETE FROM nodes WHERE id = ?');\n\n    const transaction = this.db.transaction((nodeId: string) => {\n      deleteEdges.run(nodeId, nodeId);\n      deleteNodeStmt.run(nodeId);\n    });\n\n    transaction(id);\n  }\n\n  listNodes(): Node[] {\n    const rows = this.db.prepare('SELECT * FROM nodes').all() as NodeRow[];\n    return rows.map((row) => this.mapNodeRow(row));\n  }\n\n  findNodesByType(type: NodeType): Node[] {\n    const rows = this.db.prepare('SELECT * FROM nodes WHERE type = ?').all(type) as NodeRow[];\n    return rows.map((row) => this.mapNodeRow(row));\n  }\n\n  addEdge(edge: Edge): Edge {\n    const stmt = this.db.prepare(\n      `INSERT INTO edges (id, from_id, to_id, type, weight, metadata, created_at)\n       VALUES (@id, @from_id, @to_id, @type, @weight, @metadata, @created_at)`\n    );\n\n    stmt.run({\n      id: edge.id,\n      from_id: edge.from_id,\n      to_id: edge.to_id,\n      type: edge.type,\n      weight: edge.weight,\n      metadata: JSON.stringify(edge.metadata ?? {}),\n      created_at: edge.created_at\n    });\n\n    return edge;\n  }\n\n  upsertEdge(edge: Edge): Edge {\n    const stmt = this.db.prepare(\n      `INSERT INTO edges (id, from_id, to_id, type, weight, metadata, created_at)\n       VALUES (@id, @from_id, @to_id, @type, @weight, @metadata, @created_at)\n       ON CONFLICT(id) DO UPDATE SET\n         from_id=excluded.from_id,\n         to_id=excluded.to_id,\n         type=excluded.type,\n         weight=excluded.weight,\n         metadata=excluded.metadata`\n    );\n\n    stmt.run({\n      id: edge.id,\n      from_id: edge.from_id,\n      to_id: edge.to_id,\n      type: edge.type,\n      weight: edge.weight,\n      metadata: JSON.stringify(edge.metadata ?? {}),\n      created_at: edge.created_at\n    });\n\n    return edge;\n  }\n\n  getEdge(id: string): Edge | null {\n    const row = this.db.prepare('SELECT * FROM edges WHERE id = ?').get(id) as EdgeRow | undefined;\n    return row ? this.mapEdgeRow(row) : null;\n  }\n\n  getEdges(nodeId: string, direction: EdgeDirection = 'both'): Edge[] {\n    let rows: EdgeRow[];\n\n    if (direction === 'in') {\n      rows = this.db.prepare('SELECT * FROM edges WHERE to_id = ?').all(nodeId) as EdgeRow[];\n    } else if (direction === 'out') {\n      rows = this.db.prepare('SELECT * FROM edges WHERE from_id = ?').all(nodeId) as EdgeRow[];\n    } else {\n      rows = this.db\n        .prepare('SELECT * FROM edges WHERE from_id = ? OR to_id = ?')\n        .all(nodeId, nodeId) as EdgeRow[];\n    }\n\n    return rows.map((row) => this.mapEdgeRow(row));\n  }\n\n  listEdges(): Edge[] {\n    const rows = this.db.prepare('SELECT * FROM edges').all() as EdgeRow[];\n    return rows.map((row) => this.mapEdgeRow(row));\n  }\n\n  deleteEdge(id: string): void {\n    this.db.prepare('DELETE FROM edges WHERE id = ?').run(id);\n  }\n\n  close(): void {\n    this.db.close();\n  }\n\n  private ensureDirectory(): void {\n    fs.mkdirSync(path.dirname(this.dbFilePath), { recursive: true });\n  }\n\n  private configure(): void {\n    this.db.pragma('journal_mode = WAL');\n    this.db.pragma('busy_timeout = 5000');\n    this.db.pragma('synchronous = NORMAL');\n  }\n\n  private prepareSchema(): void {\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS nodes (\n        id TEXT PRIMARY KEY,\n        type TEXT NOT NULL,\n        data TEXT NOT NULL,\n        created_at TEXT NOT NULL,\n        updated_at TEXT NOT NULL\n      );\n\n      CREATE TABLE IF NOT EXISTS edges (\n        id TEXT PRIMARY KEY,\n        from_id TEXT NOT NULL,\n        to_id TEXT NOT NULL,\n        type TEXT NOT NULL,\n        weight REAL NOT NULL DEFAULT 1,\n        metadata TEXT DEFAULT '{}',\n        created_at TEXT NOT NULL\n      );\n\n      CREATE INDEX IF NOT EXISTS idx_nodes_type ON nodes(type);\n      CREATE INDEX IF NOT EXISTS idx_edges_from ON edges(from_id);\n      CREATE INDEX IF NOT EXISTS idx_edges_to ON edges(to_id);\n      CREATE INDEX IF NOT EXISTS idx_edges_type ON edges(type);\n    `);\n  }\n\n  private mapNodeRow(row: NodeRow): Node {\n    return {\n      id: row.id,\n      type: row.type,\n      data: JSON.parse(row.data),\n      created_at: row.created_at,\n      updated_at: row.updated_at\n    } as Node;\n  }\n\n  private mapEdgeRow(row: EdgeRow): Edge {\n    return {\n      id: row.id,\n      from_id: row.from_id,\n      to_id: row.to_id,\n      type: row.type,\n      weight: row.weight,\n      created_at: row.created_at,\n      metadata: row.metadata ? 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