harness-evolve 1.0.0

package/dist/cli.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/cli.ts","../src/cli/init.ts","../src/cli/utils.ts","../src/scan/context-builder.ts","../src/scan/schemas.ts","../src/scan/scanners/redundancy.ts","../src/scan/scanners/mechanization.ts","../src/scan/scanners/staleness.ts","../src/scan/scanners/index.ts","../src/scan/index.ts","../src/commands/evolve-scan.ts","../src/commands/evolve-apply.ts","../src/storage/counter.ts","../src/schemas/counter.ts","../src/storage/dirs.ts","../src/delivery/state.ts","../src/schemas/delivery.ts","../src/cli/status.ts","../src/cli/uninstall.ts","../src/cli/scan.ts","../src/cli/apply.ts","../src/schemas/recommendation.ts","../src/delivery/auto-apply.ts","../src/storage/config.ts","../src/schemas/config.ts","../src/delivery/appliers/index.ts","../src/delivery/appliers/settings-applier.ts","../src/delivery/appliers/rule-applier.ts","../src/delivery/appliers/hook-applier.ts","../src/generators/schemas.ts","../src/generators/hook-generator.ts","../src/delivery/appliers/claude-md-applier.ts"],"sourcesContent":["#!/usr/bin/env node\n// CLI entry point -- Commander.js program with init, status, and uninstall subcommands\n\nimport { Command } from '@commander-js/extra-typings';\nimport { readFileSync } from 'node:fs';\nimport { join } from 'node:path';\nimport { registerInitCommand } from './cli/init.js';\nimport { registerStatusCommand } from './cli/status.js';\nimport { registerUninstallCommand } from './cli/uninstall.js';\nimport { registerScanCommand } from './cli/scan.js';\nimport { registerPendingCommand, registerApplyOneCommand, registerDismissCommand } from './cli/apply.js';\n\n// Read version from package.json at runtime\n// import.meta.dirname = dist/ (where cli.js lives after build)\nconst pkg = JSON.parse(\n  readFileSync(join(import.meta.dirname, '..', 'package.json'), 'utf-8'),\n);\n\nconst program = new Command()\n  .name('harness-evolve')\n  .description('Self-iteration engine for Claude Code')\n  .version(pkg.version);\n\n// Register all subcommands\nregisterInitCommand(program);\nregisterStatusCommand(program);\nregisterUninstallCommand(program);\nregisterScanCommand(program);\nregisterPendingCommand(program);\nregisterApplyOneCommand(program);\nregisterDismissCommand(program);\n\nprogram.parse();\n","// Init command implementation -- registers harness-evolve hooks in Claude Code settings.json\n// and runs a deep scan of existing configuration for quality issues.\n\nimport { copyFile, mkdir, access, writeFile } from 'node:fs/promises';\nimport { dirname, join } from 'node:path';\nimport type { Command } from '@commander-js/extra-typings';\nimport {\n  HOOK_REGISTRATIONS,\n  SETTINGS_PATH,\n  resolveHookPath,\n  readSettings,\n  writeSettings,\n  mergeHooks,\n  confirm,\n} from './utils.js';\nimport { runDeepScan } from '../scan/index.js';\nimport { generateScanCommand } from '../commands/evolve-scan.js';\nimport { generateApplyCommand } from '../commands/evolve-apply.js';\n\n/**\n * Options for runInit, with test overrides.\n */\nexport interface InitOptions {\n  yes: boolean;\n  settingsPath?: string;\n  baseDirOverride?: string;\n  projectDir?: string;\n}\n\n/**\n * Check if a file exists by attempting to access it.\n */\nasync function fileExists(path: string): Promise<boolean> {\n  try {\n    await access(path);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Install slash command Markdown files into the project's .claude/commands/evolve/ directory.\n * Creates the directory if it doesn't exist. Skips files that already exist (create-only guard).\n */\nasync function installSlashCommands(projectDir: string): Promise<void> {\n  const commandsDir = join(projectDir, '.claude', 'commands', 'evolve');\n  await mkdir(commandsDir, { recursive: true });\n\n  const commands = [\n    { name: 'scan', generate: generateScanCommand, path: join(commandsDir, 'scan.md') },\n    { name: 'apply', generate: generateApplyCommand, path: join(commandsDir, 'apply.md') },\n  ];\n\n  for (const cmd of commands) {\n    if (await fileExists(cmd.path)) {\n      console.log(`  /evolve:${cmd.name} already installed, skipping`);\n    } else {\n      await writeFile(cmd.path, cmd.generate(), 'utf-8');\n      console.log(`  /evolve:${cmd.name} installed`);\n    }\n  }\n}\n\n/**\n * Core init logic -- exported for testing.\n *\n * 1. Resolve hook paths for all 6 events\n * 2. Display planned registrations\n * 3. Detect npx install and warn about ephemeral paths\n * 4. Confirm with user (unless --yes)\n * 5. Ensure directory exists, backup existing settings, merge, write\n */\nexport async function runInit(options: InitOptions): Promise<void> {\n  const settingsPath = options.settingsPath ?? SETTINGS_PATH;\n\n  // Build hook commands with resolved absolute paths\n  const hookCommands = HOOK_REGISTRATIONS.map((reg) => {\n    const absolutePath = resolveHookPath(reg.hookFile, options.baseDirOverride);\n    return {\n      event: reg.event,\n      command: `node \"${absolutePath}\"`,\n      timeout: reg.timeout,\n      async: reg.async,\n      description: reg.description,\n    };\n  });\n\n  // Display planned registrations\n  console.log('\\nPlanned hook registrations:\\n');\n  for (const hc of hookCommands) {\n    const asyncLabel = hc.async ? ' (async)' : '';\n    console.log(`  ${hc.event}${asyncLabel} -- ${hc.description}`);\n    console.log(`    -> ${hc.command}`);\n  }\n  console.log('');\n\n  // Detect npx ephemeral paths\n  const samplePath = hookCommands[0].command;\n  if (samplePath.includes('.npm/_npx/')) {\n    console.log(\n      'WARNING: Detected npx installation. Hook paths may break when the',\n    );\n    console.log(\n      'npx cache is cleared. For persistent installation, use: npm i -g harness-evolve\\n',\n    );\n  }\n\n  // Confirm unless --yes\n  if (!options.yes) {\n    const accepted = await confirm('Register hooks in settings.json?');\n    if (!accepted) {\n      console.log('Aborted.');\n      return;\n    }\n  }\n\n  // Ensure settings directory exists\n  await mkdir(dirname(settingsPath), { recursive: true });\n\n  // Backup existing settings.json if it exists\n  const exists = await fileExists(settingsPath);\n  if (exists) {\n    await copyFile(settingsPath, settingsPath + '.backup');\n    console.log(`Backup created: ${settingsPath}.backup`);\n  }\n\n  // Read existing settings (returns {} if file missing)\n  const settings = await readSettings(settingsPath);\n\n  // Merge hooks\n  const merged = mergeHooks(settings, hookCommands);\n\n  // Write merged settings\n  await writeSettings(merged, settingsPath);\n\n  console.log(\n    `Hooks registered successfully! (${hookCommands.length} events)`,\n  );\n\n  // Install slash commands\n  console.log('\\nInstalling slash commands...\\n');\n  await installSlashCommands(options.projectDir ?? process.cwd());\n\n  // Deep scan: analyze existing configuration for quality issues\n  try {\n    console.log('\\nScanning configuration...\\n');\n    const scanResult = await runDeepScan(process.cwd());\n    if (scanResult.recommendations.length > 0) {\n      console.log(\n        `Found ${scanResult.recommendations.length} configuration suggestion(s):\\n`,\n      );\n      for (const rec of scanResult.recommendations) {\n        console.log(`  [${rec.confidence}] ${rec.title}`);\n        console.log(`    ${rec.description}`);\n        console.log(`    Suggested: ${rec.suggested_action}\\n`);\n      }\n    } else {\n      console.log('Configuration looks clean -- no issues detected.\\n');\n    }\n  } catch (err) {\n    // Scan is advisory -- don't block init on scan failures\n    console.error(\n      `Warning: Configuration scan failed: ${err instanceof Error ? err.message : String(err)}`,\n    );\n  }\n}\n\n/**\n * Register the init subcommand on a Commander.js program.\n */\nexport function registerInitCommand(program: Command): void {\n  program\n    .command('init')\n    .description('Register harness-evolve hooks in Claude Code settings')\n    .option('--yes', 'Skip confirmation prompt')\n    .action(async (opts) => {\n      await runInit({ yes: opts.yes ?? false });\n    });\n}\n","// Shared CLI utilities: hook definitions, settings I/O, path resolution, confirm prompt\n\nimport { readFile } from 'node:fs/promises';\nimport { dirname, join } from 'node:path';\nimport { createInterface } from 'node:readline/promises';\nimport writeFileAtomic from 'write-file-atomic';\n\n/**\n * Marker string used to identify harness-evolve hook entries in settings.json.\n * When scanning existing hooks, any command containing this string is ours.\n */\nexport const HARNESS_EVOLVE_MARKER = 'harness-evolve';\n\n/**\n * Default path to Claude Code user-scope settings.json.\n */\nexport const SETTINGS_PATH = join(\n  process.env.HOME ?? '',\n  '.claude',\n  'settings.json',\n);\n\n/**\n * Hook registration definition.\n */\nexport interface HookRegistration {\n  event: string;\n  hookFile: string;\n  timeout: number;\n  async: boolean;\n  description: string;\n}\n\n/**\n * All 6 hook events that harness-evolve registers.\n * Each entry maps an event name to the compiled JS hook file.\n */\nexport const HOOK_REGISTRATIONS: HookRegistration[] = [\n  {\n    event: 'UserPromptSubmit',\n    hookFile: 'user-prompt-submit.js',\n    timeout: 10,\n    async: false,\n    description: 'Captures prompts and delivers optimization notifications',\n  },\n  {\n    event: 'PreToolUse',\n    hookFile: 'pre-tool-use.js',\n    timeout: 10,\n    async: true,\n    description: 'Tracks tool usage patterns before execution',\n  },\n  {\n    event: 'PostToolUse',\n    hookFile: 'post-tool-use.js',\n    timeout: 10,\n    async: true,\n    description: 'Records tool outcomes for pattern analysis',\n  },\n  {\n    event: 'PostToolUseFailure',\n    hookFile: 'post-tool-use-failure.js',\n    timeout: 10,\n    async: true,\n    description: 'Logs tool failures to detect correction patterns',\n  },\n  {\n    event: 'PermissionRequest',\n    hookFile: 'permission-request.js',\n    timeout: 10,\n    async: true,\n    description: 'Monitors permission decisions for auto-approval suggestions',\n  },\n  {\n    event: 'Stop',\n    hookFile: 'stop.js',\n    timeout: 10,\n    async: true,\n    description: 'Triggers analysis when interaction threshold is reached',\n  },\n];\n\n/**\n * Resolve absolute path to a hook JS file.\n *\n * In production, import.meta.dirname of the compiled dist/cli/utils.js\n * points to <install>/dist/cli/. We go up one level to <install>/dist/,\n * then into hooks/<hookFile>.\n *\n * @param hookFile - The hook filename (e.g., 'user-prompt-submit.js')\n * @param baseDirOverride - Override for import.meta.dirname (for testing)\n */\nexport function resolveHookPath(\n  hookFile: string,\n  baseDirOverride?: string,\n): string {\n  const baseDir = baseDirOverride ?? import.meta.dirname;\n  return join(baseDir, 'hooks', hookFile);\n}\n\n/**\n * Read and parse Claude Code settings.json.\n * Returns empty object if file does not exist or JSON is invalid.\n */\nexport async function readSettings(\n  settingsPath?: string,\n): Promise<Record<string, unknown>> {\n  const filePath = settingsPath ?? SETTINGS_PATH;\n  try {\n    const raw = await readFile(filePath, 'utf-8');\n    return JSON.parse(raw) as Record<string, unknown>;\n  } catch {\n    // ENOENT (file missing) or SyntaxError (invalid JSON)\n    return {};\n  }\n}\n\n/**\n * Write settings.json atomically with 2-space indentation.\n */\nexport async function writeSettings(\n  settings: Record<string, unknown>,\n  settingsPath?: string,\n): Promise<void> {\n  const filePath = settingsPath ?? SETTINGS_PATH;\n  await writeFileAtomic(filePath, JSON.stringify(settings, null, 2));\n}\n\n/**\n * Hook command entry for merge logic.\n */\ninterface HookCommand {\n  event: string;\n  command: string;\n  timeout: number;\n  async: boolean;\n}\n\n/**\n * Merge harness-evolve hooks into existing settings without destroying user hooks.\n *\n * For each hook command:\n * - If the event already has a harness-evolve entry (identified by HARNESS_EVOLVE_MARKER\n *   in the command string), skip it.\n * - Otherwise, append a new matcher entry to the event array.\n *\n * User hooks are preserved untouched.\n */\nexport function mergeHooks(\n  existing: Record<string, unknown>,\n  hookCommands: HookCommand[],\n): Record<string, unknown> {\n  const hooks = (\n    existing.hooks != null ? { ...(existing.hooks as Record<string, unknown>) } : {}\n  ) as Record<string, unknown[]>;\n\n  for (const hc of hookCommands) {\n    const eventArray = (\n      Array.isArray(hooks[hc.event]) ? [...hooks[hc.event]] : []\n    ) as Array<Record<string, unknown>>;\n\n    // Check if harness-evolve hook already registered for this event\n    const alreadyRegistered = eventArray.some((entry) => {\n      const innerHooks = entry.hooks as\n        | Array<Record<string, unknown>>\n        | undefined;\n      if (!Array.isArray(innerHooks)) return false;\n      return innerHooks.some((h) =>\n        String(h.command ?? '').includes(HARNESS_EVOLVE_MARKER),\n      );\n    });\n\n    if (!alreadyRegistered) {\n      const hookEntry: Record<string, unknown> = {\n        type: 'command',\n        command: hc.command,\n        timeout: hc.timeout,\n      };\n      if (hc.async) {\n        hookEntry.async = true;\n      }\n\n      eventArray.push({\n        matcher: '*',\n        hooks: [hookEntry],\n      });\n    }\n\n    hooks[hc.event] = eventArray;\n  }\n\n  return { ...existing, hooks };\n}\n\n/**\n * Interactive confirmation prompt.\n * Returns true if user answers 'y' or 'yes' (case-insensitive).\n */\nexport async function confirm(message: string): Promise<boolean> {\n  const rl = createInterface({\n    input: process.stdin,\n    output: process.stdout,\n  });\n\n  try {\n    const answer = await rl.question(`${message} [y/N] `);\n    return /^y(es)?$/i.test(answer.trim());\n  } finally {\n    rl.close();\n  }\n}\n","// Context builder for deep scan module.\n// Reads all Claude Code configuration sources (CLAUDE.md files, rules,\n// settings, commands, hooks) from the filesystem and produces a validated\n// ScanContext object for scanner analysis.\n\nimport { readFile, readdir } from 'node:fs/promises';\nimport { join, basename } from 'node:path';\nimport { scanContextSchema, type ScanContext } from './schemas.js';\n\n/**\n * Safely read a file, returning its content or null if it cannot be read.\n */\nasync function readFileSafe(path: string): Promise<string | null> {\n  try {\n    return await readFile(path, 'utf-8');\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Extract markdown headings (# through ######) from content.\n */\nexport function extractHeadings(content: string): string[] {\n  const headings: string[] = [];\n  const regex = /^#{1,6}\\s+(.+)$/gm;\n  let match: RegExpExecArray | null;\n  while ((match = regex.exec(content)) !== null) {\n    headings.push(match[1].trim());\n  }\n  return headings;\n}\n\n/**\n * Extract @-reference paths from content (e.g., @docs/guide.md).\n * Filters out email-like patterns (user@domain).\n */\nexport function extractReferences(content: string): string[] {\n  const refs: string[] = [];\n  const regex = /@([\\w./-]+)/g;\n  let match: RegExpExecArray | null;\n  while ((match = regex.exec(content)) !== null) {\n    const ref = match[1];\n    // Filter out email-like patterns: if preceded by a word char, skip\n    const idx = match.index;\n    if (idx > 0 && /\\w/.test(content[idx - 1])) {\n      continue;\n    }\n    // Strip trailing dots only if they don't look like file extensions\n    // e.g., \"file.ts.\" -> \"file.ts\", but \"file.md\" stays as-is\n    const cleaned = ref.replace(/\\.$/, '');\n    refs.push(cleaned);\n  }\n  return refs;\n}\n\n/**\n * Read CLAUDE.md files from the 3 standard locations.\n */\nasync function readClaudeMdFiles(\n  cwd: string,\n  home: string,\n): Promise<ScanContext['claude_md_files']> {\n  const locations: Array<{ path: string; scope: 'user' | 'project' | 'local' }> = [\n    { path: join(cwd, 'CLAUDE.md'), scope: 'project' },\n    { path: join(cwd, '.claude', 'CLAUDE.md'), scope: 'local' },\n    { path: join(home, '.claude', 'CLAUDE.md'), scope: 'user' },\n  ];\n\n  const files: ScanContext['claude_md_files'] = [];\n\n  for (const loc of locations) {\n    const content = await readFileSafe(loc.path);\n    if (content !== null) {\n      files.push({\n        path: loc.path,\n        scope: loc.scope,\n        content,\n        line_count: content.split('\\n').length,\n        headings: extractHeadings(content),\n        references: extractReferences(content),\n      });\n    }\n  }\n\n  return files;\n}\n\n/**\n * Recursively collect all .md files from a directory.\n */\nasync function collectMdFiles(dir: string): Promise<string[]> {\n  const results: string[] = [];\n  try {\n    const entries = await readdir(dir, { withFileTypes: true });\n    for (const entry of entries) {\n      const fullPath = join(dir, entry.name);\n      if (entry.isDirectory()) {\n        const nested = await collectMdFiles(fullPath);\n        results.push(...nested);\n      } else if (entry.isFile() && entry.name.endsWith('.md')) {\n        results.push(fullPath);\n      }\n    }\n  } catch {\n    // Directory does not exist or is unreadable\n  }\n  return results;\n}\n\n/**\n * Parse simple YAML frontmatter from markdown content.\n * Looks for --- delimiters and extracts paths array if present.\n */\nfunction parseFrontmatter(\n  content: string,\n): { paths?: string[] } | undefined {\n  const match = content.match(/^---\\n([\\s\\S]*?)\\n---/);\n  if (!match) return undefined;\n\n  const frontmatter = match[1];\n  const pathsMatch = frontmatter.match(\n    /paths:\\s*\\n((?:\\s*-\\s*.+\\n?)*)/,\n  );\n  if (!pathsMatch) return {};\n\n  const paths = pathsMatch[1]\n    .split('\\n')\n    .map((line) => line.replace(/^\\s*-\\s*/, '').trim())\n    .filter((line) => line.length > 0);\n\n  return paths.length > 0 ? { paths } : {};\n}\n\n/**\n * Read all rule files from .claude/rules/ recursively.\n */\nasync function readRuleFiles(cwd: string): Promise<ScanContext['rules']> {\n  const rulesDir = join(cwd, '.claude', 'rules');\n  const mdFiles = await collectMdFiles(rulesDir);\n\n  const rules: ScanContext['rules'] = [];\n  for (const filePath of mdFiles) {\n    const content = await readFileSafe(filePath);\n    if (content !== null) {\n      rules.push({\n        path: filePath,\n        filename: basename(filePath),\n        content,\n        frontmatter: parseFrontmatter(content),\n        headings: extractHeadings(content),\n      });\n    }\n  }\n\n  return rules;\n}\n\n/**\n * Read settings.json from all 3 scopes (user, project, local).\n */\nasync function readAllSettings(\n  cwd: string,\n  home: string,\n): Promise<ScanContext['settings']> {\n  const settingsPaths = {\n    user: join(home, '.claude', 'settings.json'),\n    project: join(cwd, '.claude', 'settings.json'),\n    local: join(cwd, '.claude', 'settings.local.json'),\n  };\n\n  const readJsonSafe = async (path: string): Promise<unknown | null> => {\n    try {\n      const raw = await readFile(path, 'utf-8');\n      return JSON.parse(raw) as unknown;\n    } catch {\n      return null;\n    }\n  };\n\n  const [user, project, local] = await Promise.all([\n    readJsonSafe(settingsPaths.user),\n    readJsonSafe(settingsPaths.project),\n    readJsonSafe(settingsPaths.local),\n  ]);\n\n  return { user, project, local };\n}\n\n/**\n * Read command files from .claude/commands/ directory.\n */\nasync function readCommandFiles(\n  cwd: string,\n): Promise<ScanContext['commands']> {\n  const commandsDir = join(cwd, '.claude', 'commands');\n  const commands: ScanContext['commands'] = [];\n\n  try {\n    const entries = await readdir(commandsDir, { withFileTypes: true });\n    for (const entry of entries) {\n      if (entry.isFile() && entry.name.endsWith('.md')) {\n        const filePath = join(commandsDir, entry.name);\n        const content = await readFileSafe(filePath);\n        if (content !== null) {\n          commands.push({\n            path: filePath,\n            name: entry.name.replace(/\\.md$/, ''),\n            content,\n          });\n        }\n      }\n    }\n  } catch {\n    // Directory does not exist\n  }\n\n  return commands;\n}\n\n/**\n * Extract hook registrations from all settings scopes.\n */\nfunction extractHooksFromAllSettings(\n  settings: ScanContext['settings'],\n): ScanContext['hooks_registered'] {\n  const hooks: ScanContext['hooks_registered'] = [];\n\n  const extractFromScope = (\n    settingsObj: unknown,\n    scope: 'user' | 'project' | 'local',\n  ): void => {\n    if (!settingsObj || typeof settingsObj !== 'object') return;\n    const obj = settingsObj as Record<string, unknown>;\n    if (!obj.hooks || typeof obj.hooks !== 'object') return;\n\n    const hooksConfig = obj.hooks as Record<string, unknown>;\n    for (const [event, defs] of Object.entries(hooksConfig)) {\n      if (!Array.isArray(defs)) continue;\n      for (const def of defs) {\n        if (!def || typeof def !== 'object') continue;\n        const hookDef = def as Record<string, unknown>;\n        const type = String(hookDef.type ?? 'command');\n        const command =\n          typeof hookDef.command === 'string' ? hookDef.command : undefined;\n        hooks.push({ event, scope, type, command });\n      }\n    }\n  };\n\n  extractFromScope(settings.user, 'user');\n  extractFromScope(settings.project, 'project');\n  extractFromScope(settings.local, 'local');\n\n  return hooks;\n}\n\n/**\n * Build a complete ScanContext by reading all configuration sources.\n * Returns a validated ScanContext or throws if validation fails.\n *\n * @param cwd  - Project root directory\n * @param home - User home directory (defaults to process.env.HOME)\n */\nexport async function buildScanContext(\n  cwd: string,\n  home?: string,\n): Promise<ScanContext> {\n  const homeDir = home ?? process.env.HOME ?? '';\n\n  const [claudeMdFiles, rules, settings, commands] = await Promise.all([\n    readClaudeMdFiles(cwd, homeDir),\n    readRuleFiles(cwd),\n    readAllSettings(cwd, homeDir),\n    readCommandFiles(cwd),\n  ]);\n\n  const hooksRegistered = extractHooksFromAllSettings(settings);\n\n  const ctx = {\n    generated_at: new Date().toISOString(),\n    project_root: cwd,\n    claude_md_files: claudeMdFiles,\n    rules,\n    settings,\n    commands,\n    hooks_registered: hooksRegistered,\n  };\n\n  return scanContextSchema.parse(ctx);\n}\n","// Scan module schemas.\n// Defines the ScanContext shape that captures all Claude Code configuration\n// sources (CLAUDE.md, rules, settings, commands, hooks) for deep analysis.\n\nimport { z } from 'zod/v4';\n\nexport const scanContextSchema = z.object({\n  generated_at: z.iso.datetime(),\n  project_root: z.string(),\n  claude_md_files: z.array(\n    z.object({\n      path: z.string(),\n      scope: z.enum(['user', 'project', 'local']),\n      content: z.string(),\n      line_count: z.number(),\n      headings: z.array(z.string()),\n      references: z.array(z.string()),\n    }),\n  ),\n  rules: z.array(\n    z.object({\n      path: z.string(),\n      filename: z.string(),\n      content: z.string(),\n      frontmatter: z\n        .object({\n          paths: z.array(z.string()).optional(),\n        })\n        .optional(),\n      headings: z.array(z.string()),\n    }),\n  ),\n  settings: z.object({\n    user: z.unknown().nullable(),\n    project: z.unknown().nullable(),\n    local: z.unknown().nullable(),\n  }),\n  commands: z.array(\n    z.object({\n      path: z.string(),\n      name: z.string(),\n      content: z.string(),\n    }),\n  ),\n  hooks_registered: z.array(\n    z.object({\n      event: z.string(),\n      scope: z.enum(['user', 'project', 'local']),\n      type: z.string(),\n      command: z.string().optional(),\n    }),\n  ),\n});\nexport type ScanContext = z.infer<typeof scanContextSchema>;\n","// Redundancy scanner for deep scan module.\n// Detects duplicate headings across CLAUDE.md and rule files, and\n// duplicate rule files with highly similar heading sets.\n\nimport type { ScanContext } from '../schemas.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\n\n/**\n * Normalize text for comparison: lowercase, trim, collapse whitespace.\n */\nexport function normalizeText(text: string): string {\n  return text.toLowerCase().trim().replace(/\\s+/g, ' ');\n}\n\n/**\n * Scan for redundant configuration: duplicate headings across CLAUDE.md\n * and rules, and duplicate rule files with matching heading sets.\n */\nexport function scanRedundancy(context: ScanContext): Recommendation[] {\n  const recommendations: Recommendation[] = [];\n  let index = 0;\n\n  // Check 1: CLAUDE.md headings vs rule headings\n  const claudeMdHeadings = context.claude_md_files.flatMap(f =>\n    f.headings.map(h => ({ heading: normalizeText(h), source: f.path })),\n  );\n  const ruleHeadings = context.rules.flatMap(r =>\n    r.headings.map(h => ({ heading: normalizeText(h), source: r.path })),\n  );\n\n  for (const cmdH of claudeMdHeadings) {\n    const match = ruleHeadings.find(rH => rH.heading === cmdH.heading);\n    if (match) {\n      recommendations.push({\n        id: `rec-scan-redundancy-${index++}`,\n        target: 'RULE',\n        confidence: 'MEDIUM',\n        pattern_type: 'scan_redundancy',\n        title: `Redundant section: \"${cmdH.heading}\"`,\n        description:\n          `The heading \"${cmdH.heading}\" appears in both ` +\n          `${cmdH.source} and ${match.source}. ` +\n          `This may indicate duplicated instructions.`,\n        evidence: {\n          count: 2,\n          examples: [cmdH.source, match.source],\n        },\n        suggested_action:\n          'Consolidate into one location. If it belongs in rules, ' +\n          'remove from CLAUDE.md. If it belongs in CLAUDE.md, remove the rule file.',\n      });\n    }\n  }\n\n  // Check 2: Duplicate rule files (same heading set in 2+ rule files)\n  const rulesByHeadingSet = new Map<string, string[]>();\n  for (const rule of context.rules) {\n    const key = rule.headings\n      .map(h => normalizeText(h))\n      .sort()\n      .join('||');\n    if (!key) continue; // Skip rules with no headings\n    const existing = rulesByHeadingSet.get(key) ?? [];\n    existing.push(rule.path);\n    rulesByHeadingSet.set(key, existing);\n  }\n\n  for (const [, paths] of rulesByHeadingSet) {\n    if (paths.length < 2) continue;\n    recommendations.push({\n      id: `rec-scan-redundancy-${index++}`,\n      target: 'RULE',\n      confidence: 'MEDIUM',\n      pattern_type: 'scan_redundancy',\n      title: `Duplicate rule files detected (${paths.length} files with same headings)`,\n      description:\n        `${paths.length} rule files share the same heading structure: ` +\n        `${paths.join(', ')}. They may contain redundant content.`,\n      evidence: {\n        count: paths.length,\n        examples: paths.slice(0, 3),\n      },\n      suggested_action:\n        'Review these rule files and merge them into a single file, ' +\n        'or differentiate their content.',\n    });\n  }\n\n  return recommendations;\n}\n","// Mechanization scanner for deep scan module.\n// Detects operations described in rules/CLAUDE.md text that should be\n// enforced via hooks for 100% reliable execution.\n\nimport type { ScanContext } from '../schemas.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\n\n/**\n * Patterns in rule/CLAUDE.md text that suggest hookable operations.\n * Each indicator maps a text pattern to the hook event that could enforce it.\n */\nexport const MECHANIZATION_INDICATORS = [\n  { regex: /always\\s+run\\s+[\"`']?(\\S+)/i, hookEvent: 'PreToolUse', label: 'always run' },\n  {\n    regex: /before\\s+committing?,?\\s+run\\s+[\"`']?(\\S+)/i,\n    hookEvent: 'PreToolUse',\n    label: 'pre-commit check',\n  },\n  {\n    regex: /after\\s+every\\s+(?:edit|change|write)/i,\n    hookEvent: 'PostToolUse',\n    label: 'post-edit action',\n  },\n  {\n    regex: /must\\s+(?:always\\s+)?check\\s+[\"`']?(\\S+)/i,\n    hookEvent: 'PreToolUse',\n    label: 'mandatory check',\n  },\n  {\n    regex: /never\\s+(?:allow|permit|run)\\s+[\"`']?(\\S+)/i,\n    hookEvent: 'PreToolUse',\n    label: 'forbidden operation',\n  },\n  {\n    regex: /forbidden.*(?:rm\\s+-rf|drop\\s+|delete\\s+|truncate)/i,\n    hookEvent: 'PreToolUse',\n    label: 'dangerous command guard',\n  },\n] as const;\n\n/**\n * Scan for operations described in text that should be enforced via hooks.\n * Skips patterns that are already covered by a registered hook for the\n * corresponding event type.\n */\nexport function scanMechanization(context: ScanContext): Recommendation[] {\n  const recommendations: Recommendation[] = [];\n  let index = 0;\n\n  // Collect all text sources: CLAUDE.md files and rule files\n  const allTextSources = [\n    ...context.claude_md_files.map(f => ({ content: f.content, source: f.path })),\n    ...context.rules.map(r => ({ content: r.content, source: r.path })),\n  ];\n\n  for (const source of allTextSources) {\n    for (const indicator of MECHANIZATION_INDICATORS) {\n      const match = source.content.match(indicator.regex);\n      if (!match) continue;\n\n      // Check if a hook already covers this event\n      const alreadyCovered = context.hooks_registered.some(\n        h => h.event === indicator.hookEvent,\n      );\n      if (alreadyCovered) continue;\n\n      recommendations.push({\n        id: `rec-scan-mechanize-${index++}`,\n        target: 'HOOK',\n        confidence: 'MEDIUM',\n        pattern_type: 'scan_missing_mechanization',\n        title: `Mechanizable rule: \"${match[0].substring(0, 60)}\"`,\n        description:\n          `Found a rule in ${source.source} that describes an operation ` +\n          `suitable for a ${indicator.hookEvent} hook: \"${match[0]}\". ` +\n          'Hooks provide 100% reliable execution, while rules depend on ' +\n          \"Claude's probabilistic compliance.\",\n        evidence: {\n          count: 1,\n          examples: [match[0].substring(0, 100)],\n        },\n        suggested_action:\n          `Create a ${indicator.hookEvent} hook to enforce this rule ` +\n          `automatically. See Claude Code hooks docs for ${indicator.hookEvent} event.`,\n      });\n    }\n  }\n\n  return recommendations;\n}\n","// Staleness scanner for deep scan module.\n// Detects broken @references in CLAUDE.md files and hook commands\n// pointing to non-existent scripts.\n\nimport type { ScanContext } from '../schemas.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport { access } from 'node:fs/promises';\nimport { constants } from 'node:fs';\nimport { resolve, dirname } from 'node:path';\n\n/**\n * Check if a file exists on disk.\n */\nasync function fileExistsOnDisk(filePath: string): Promise<boolean> {\n  try {\n    await access(filePath, constants.F_OK);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Extract a file path from a hook command string.\n * Handles patterns like:\n *   node \"path/to/script.js\"\n *   node 'path/to/script.js'\n *   node path/to/script.js\n *   sh /path/to/script.sh\n *   /usr/bin/node /path/to/file.js\n */\nfunction extractPathFromCommand(command: string): string | null {\n  // Match quoted path: node \"path\" or node 'path'\n  const quotedMatch = command.match(/(?:node|sh|bash|python)\\s+[\"']([^\"']+)[\"']/i);\n  if (quotedMatch) return quotedMatch[1];\n\n  // Match unquoted path after common interpreters\n  const unquotedMatch = command.match(\n    /(?:node|sh|bash|python)\\s+(\\S+\\.(?:js|ts|sh|py|mjs|cjs))/i,\n  );\n  if (unquotedMatch) return unquotedMatch[1];\n\n  return null;\n}\n\n/**\n * Scan for stale references: broken @references in CLAUDE.md files and\n * hook commands pointing to non-existent scripts.\n *\n * This scanner is async because it needs to check the filesystem for\n * reference targets not present in the ScanContext.\n */\nexport async function scanStaleness(context: ScanContext): Promise<Recommendation[]> {\n  const recommendations: Recommendation[] = [];\n  let index = 0;\n\n  // Check 1: Stale @references in CLAUDE.md files\n  for (const claudeMd of context.claude_md_files) {\n    for (const ref of claudeMd.references) {\n      const resolved = resolve(dirname(claudeMd.path), ref);\n\n      // Check if referenced path exists in context data\n      const inContext =\n        context.rules.some(r => r.path === resolved) ||\n        context.claude_md_files.some(f => f.path === resolved) ||\n        context.commands.some(c => c.path === resolved);\n\n      if (inContext) continue;\n\n      // Check filesystem as fallback\n      const existsOnDisk = await fileExistsOnDisk(resolved);\n      if (existsOnDisk) continue;\n\n      recommendations.push({\n        id: `rec-scan-stale-${index++}`,\n        target: 'CLAUDE_MD',\n        confidence: 'HIGH',\n        pattern_type: 'scan_stale_reference',\n        title: `Stale reference: @${ref}`,\n        description: `${claudeMd.path} references @${ref}, but this file does not exist.`,\n        evidence: {\n          count: 1,\n          examples: [`@${ref} in ${claudeMd.path}`],\n        },\n        suggested_action:\n          `Remove the @${ref} reference from ${claudeMd.path}, ` +\n          'or create the missing file.',\n      });\n    }\n  }\n\n  // Check 2: Hook commands pointing to non-existent scripts\n  for (const hook of context.hooks_registered) {\n    if (!hook.command) continue;\n\n    const scriptPath = extractPathFromCommand(hook.command);\n    if (!scriptPath) continue;\n\n    const exists = await fileExistsOnDisk(scriptPath);\n    if (exists) continue;\n\n    recommendations.push({\n      id: `rec-scan-stale-${index++}`,\n      target: 'SETTINGS',\n      confidence: 'HIGH',\n      pattern_type: 'scan_stale_reference',\n      title: `Stale hook script: ${scriptPath}`,\n      description:\n        `Hook (${hook.event}, ${hook.scope}) references script \"${scriptPath}\", ` +\n        'but this file does not exist. The hook will fail when triggered.',\n      evidence: {\n        count: 1,\n        examples: [`${hook.event} hook command: ${hook.command}`],\n      },\n      suggested_action:\n        `Create the missing script at \"${scriptPath}\", ` +\n        'or update the hook command in settings.json.',\n    });\n  }\n\n  return recommendations;\n}\n","// Scanner registry for deep scan module.\n// Defines the Scanner type signature and holds all registered scanner\n// functions. Supports both sync and async scanners.\n\nimport type { ScanContext } from '../schemas.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport { scanRedundancy } from './redundancy.js';\nimport { scanMechanization } from './mechanization.js';\nimport { scanStaleness } from './staleness.js';\n\nexport type Scanner = (context: ScanContext) => Recommendation[] | Promise<Recommendation[]>;\n\n// Scanner registry -- all 3 scanners registered\nexport const scanners: Scanner[] = [scanRedundancy, scanMechanization, scanStaleness];\n","// Deep scan orchestrator: builds context from config files and runs all scanners.\n// Entry point for the scan module -- coordinates context building with scanner\n// execution and returns merged recommendations.\n\nimport { buildScanContext } from './context-builder.js';\nimport { scanners } from './scanners/index.js';\nimport type { ScanContext } from './schemas.js';\nimport type { Recommendation } from '../schemas/recommendation.js';\nimport type { Scanner } from './scanners/index.js';\n\nexport interface ScanResult {\n  generated_at: string;\n  scan_context: ScanContext;\n  recommendations: Recommendation[];\n}\n\n/**\n * Run a deep scan of Claude Code configuration at the given directory.\n * Reads all config files into a ScanContext, then runs all registered\n * scanners to detect quality issues. Returns merged recommendations.\n *\n * Errors in individual scanners are caught and logged, not propagated.\n * An empty recommendations array means no issues detected.\n */\nexport async function runDeepScan(\n  cwd: string,\n  home?: string,\n): Promise<ScanResult> {\n  const scanContext = await buildScanContext(cwd, home);\n  const recommendations: Recommendation[] = [];\n\n  for (const scanner of scanners) {\n    try {\n      const result = await scanner(scanContext);\n      recommendations.push(...result);\n    } catch (err) {\n      // Log but don't propagate -- scan is advisory, not critical\n      console.error(\n        `Scanner error: ${err instanceof Error ? err.message : String(err)}`,\n      );\n    }\n  }\n\n  return {\n    generated_at: new Date().toISOString(),\n    scan_context: scanContext,\n    recommendations,\n  };\n}\n\n// Re-export key types for consumers\nexport type { ScanContext } from './schemas.js';\nexport type { Scanner } from './scanners/index.js';\n","// Slash command template generator for /evolve:scan\n\n/**\n * Generate the Markdown content for the /evolve:scan slash command.\n *\n * This command instructs Claude Code to run a deep configuration scan\n * using the harness-evolve CLI and present results grouped by confidence.\n */\nexport function generateScanCommand(): string {\n  return `---\nname: scan\ndescription: Run a deep harness-evolve configuration scan to detect quality issues\ndisable-model-invocation: true\n---\n\n# Evolve Scan\n\nRun a deep scan of the current project's Claude Code configuration to detect quality issues and optimization opportunities.\n\n## What This Does\n\nAnalyzes your Claude Code configuration files to detect:\n- **Redundant rules** -- same constraint defined in multiple files (CLAUDE.md, .claude/rules/, settings.json)\n- **Missing mechanization** -- operations in rules or CLAUDE.md that should be hooks for 100% reliability\n- **Stale config** -- references to non-existent files, outdated commands, or unused settings\n- **Configuration drift** -- inconsistencies between .claude/commands/, rules, and settings\n\nFiles scanned: CLAUDE.md, .claude/rules/, settings.json, .claude/commands/\n\n## Instructions\n\nRun the scan CLI command:\n\n\\`\\`\\`bash\nnpx harness-evolve scan\n\\`\\`\\`\n\nOr if globally installed:\n\n\\`\\`\\`bash\nharness-evolve scan\n\\`\\`\\`\n\n## Presenting Results\n\nPresent the results grouped by confidence level (HIGH first, then MEDIUM, then LOW):\n\n1. **HIGH confidence** -- Issues that are very likely real problems. Recommend immediate action.\n2. **MEDIUM confidence** -- Probable issues worth reviewing. Present with context for user to decide.\n3. **LOW confidence** -- Possible improvements. Mention briefly and let user prioritize.\n\nFor each issue, show:\n- Confidence level and category\n- Description of the problem\n- Affected file(s)\n- Suggested fix\n\nIf issues are found, suggest running \\`/evolve:apply\\` to review and apply the recommendations interactively.\n\nIf no issues are found, congratulate the user on a clean configuration.\n`;\n}\n","// Slash command template generator for /evolve:apply\n\n/**\n * Generate the Markdown content for the /evolve:apply slash command.\n *\n * This command instructs Claude Code to read pending recommendations,\n * present them interactively, and let the user apply, skip, or ignore each one.\n */\nexport function generateApplyCommand(): string {\n  return `---\nname: apply\ndescription: Review and apply pending harness-evolve recommendations one by one\ndisable-model-invocation: true\nargument-hint: \"[filter: all|high|medium|low]\"\n---\n\n# Evolve Apply\n\nReview pending harness-evolve recommendations interactively. For each recommendation, you can choose to apply it, skip it for later, or permanently dismiss it.\n\n## Arguments\n\nIf \\`$ARGUMENTS\\` is provided (e.g., \"high\", \"medium\", or \"low\"), filter recommendations to only show that confidence level. If empty or \"all\", show all pending recommendations.\n\n## Instructions\n\n### Step 1: Read Pending Recommendations\n\n\\`\\`\\`bash\nnpx harness-evolve pending\n\\`\\`\\`\n\nIf the command outputs no pending recommendations, inform the user:\n> No pending recommendations. Run \\`/evolve:scan\\` to analyze your configuration and generate new recommendations.\n\n### Step 2: Present Each Recommendation\n\nFor each pending recommendation, present the following:\n\n- **Confidence level** (HIGH / MEDIUM / LOW)\n- **Title** -- what the recommendation is about\n- **Description** -- detailed explanation of the issue\n- **Evidence** -- what data or pattern triggered this recommendation\n- **Suggested action** -- what change is proposed\n\n### Step 3: Ask User to Choose\n\nFor each recommendation, ask the user to choose one of three actions:\n\n1. **Apply** -- Execute the recommendation. Run:\n   \\`\\`\\`bash\n   npx harness-evolve apply-one <id>\n   \\`\\`\\`\n   Report the result (success or failure) and show what changed.\n\n2. **Skip** -- Do nothing for now. The recommendation stays pending for future review. No command needed.\n\n3. **Ignore** -- Permanently dismiss this recommendation. Run:\n   \\`\\`\\`bash\n   npx harness-evolve dismiss <id>\n   \\`\\`\\`\n   Confirm the recommendation has been dismissed.\n\n### Step 4: Continue or Finish\n\nAfter processing each recommendation, move to the next one. When all recommendations have been processed, summarize what was done:\n- How many applied\n- How many skipped\n- How many ignored\n\n## Notes\n\n- Recommendations are generated by \\`harness-evolve scan\\` or automatic background analysis\n- Applied recommendations modify configuration files (settings.json, CLAUDE.md, .claude/rules/, etc.)\n- Ignored recommendations will not appear in future \\`/evolve:apply\\` sessions\n- Skipped recommendations remain pending and will reappear next time\n`;\n}\n","import { readFile } from 'node:fs/promises';\nimport { lock } from 'proper-lockfile';\nimport writeFileAtomic from 'write-file-atomic';\nimport { counterSchema, type Counter } from '../schemas/counter.js';\nimport { paths, ensureInit } from './dirs.js';\n\n/**\n * Read the current counter state from disk.\n * Returns defaults (total=0, session={}) if no counter file exists.\n */\nexport async function readCounter(): Promise<Counter> {\n  await ensureInit();\n  try {\n    const raw = await readFile(paths.counter, 'utf-8');\n    return counterSchema.parse(JSON.parse(raw));\n  } catch {\n    // File doesn't exist or invalid -- return defaults\n    return {\n      total: 0,\n      session: {},\n      last_updated: new Date().toISOString(),\n    };\n  }\n}\n\n/**\n * Atomically increment the interaction counter with cross-process safety.\n *\n * Uses proper-lockfile (mkdir-based, macOS-safe) for cross-process locking\n * and write-file-atomic for crash-safe writes inside the lock.\n *\n * Pattern: ensure-file -> lock -> read -> increment -> atomic-write -> unlock\n */\nexport async function incrementCounter(sessionId: string): Promise<number> {\n  await ensureInit();\n\n  // Ensure counter file exists before locking (proper-lockfile requires existing file)\n  try {\n    await readFile(paths.counter, 'utf-8');\n  } catch {\n    const initial: Counter = {\n      total: 0,\n      session: {},\n      last_updated: new Date().toISOString(),\n    };\n    await writeFileAtomic(paths.counter, JSON.stringify(initial, null, 2));\n  }\n\n  const release = await lock(paths.counter, {\n    retries: { retries: 50, minTimeout: 20, maxTimeout: 1000, randomize: true },\n    stale: 10000, // Consider lock stale after 10 seconds\n  });\n\n  try {\n    const raw = await readFile(paths.counter, 'utf-8');\n    const data = counterSchema.parse(JSON.parse(raw));\n    data.total += 1;\n    data.session[sessionId] = (data.session[sessionId] ?? 0) + 1;\n    data.last_updated = new Date().toISOString();\n    await writeFileAtomic(paths.counter, JSON.stringify(data, null, 2));\n    return data.total;\n  } finally {\n    await release();\n  }\n}\n\n/**\n * Reset the counter to zero. Used for testing and post-analysis reset.\n */\nexport async function resetCounter(): Promise<void> {\n  await ensureInit();\n  const data: Counter = {\n    total: 0,\n    session: {},\n    last_updated: new Date().toISOString(),\n  };\n  await writeFileAtomic(paths.counter, JSON.stringify(data, null, 2));\n}\n","import { z } from 'zod/v4';\n\nexport const counterSchema = z.object({\n  total: z.number().default(0),\n  session: z.record(z.string(), z.number()).default({}),\n  last_analysis: z.iso.datetime().optional(),\n  last_updated: z.iso.datetime(),\n});\nexport type Counter = z.infer<typeof counterSchema>;\n","import { mkdir } from 'node:fs/promises';\nimport { join } from 'node:path';\n\nconst BASE_DIR = join(process.env.HOME ?? '', '.harness-evolve');\n\nexport const paths = {\n  base: BASE_DIR,\n  logs: {\n    prompts: join(BASE_DIR, 'logs', 'prompts'),\n    tools: join(BASE_DIR, 'logs', 'tools'),\n    permissions: join(BASE_DIR, 'logs', 'permissions'),\n    sessions: join(BASE_DIR, 'logs', 'sessions'),\n  },\n  analysis: join(BASE_DIR, 'analysis'),\n  analysisPreProcessed: join(BASE_DIR, 'analysis', 'pre-processed'),\n  summary: join(BASE_DIR, 'analysis', 'pre-processed', 'summary.json'),\n  environmentSnapshot: join(BASE_DIR, 'analysis', 'environment-snapshot.json'),\n  analysisResult: join(BASE_DIR, 'analysis', 'analysis-result.json'),\n  pending: join(BASE_DIR, 'pending'),\n  config: join(BASE_DIR, 'config.json'),\n  counter: join(BASE_DIR, 'counter.json'),\n  recommendations: join(BASE_DIR, 'recommendations.md'),\n  recommendationState: join(BASE_DIR, 'analysis', 'recommendation-state.json'),\n  recommendationArchive: join(BASE_DIR, 'analysis', 'recommendations-archive'),\n  notificationFlag: join(BASE_DIR, 'analysis', 'has-pending-notifications'),\n  autoApplyLog: join(BASE_DIR, 'analysis', 'auto-apply-log.jsonl'),\n  outcomeHistory: join(BASE_DIR, 'analysis', 'outcome-history.jsonl'),\n} as const;\n\nlet initialized = false;\n\nexport async function ensureInit(): Promise<void> {\n  if (initialized) return;\n  await mkdir(paths.logs.prompts, { recursive: true });\n  await mkdir(paths.logs.tools, { recursive: true });\n  await mkdir(paths.logs.permissions, { recursive: true });\n  await mkdir(paths.logs.sessions, { recursive: true });\n  await mkdir(paths.analysis, { recursive: true });\n  await mkdir(paths.analysisPreProcessed, { recursive: true });\n  await mkdir(paths.pending, { recursive: true });\n  await mkdir(paths.recommendationArchive, { recursive: true });\n  initialized = true;\n}\n\n// For testing: reset the initialized flag\nexport function resetInit(): void {\n  initialized = false;\n}\n","// Recommendation state lifecycle management.\n// Tracks recommendation statuses (pending/applied/dismissed) in a JSON file\n// that survives across analysis re-runs and sessions.\n\nimport { readFile } from 'node:fs/promises';\nimport writeFileAtomic from 'write-file-atomic';\nimport { paths } from '../storage/dirs.js';\nimport {\n  recommendationStateSchema,\n  type RecommendationState,\n  type RecommendationStatus,\n} from '../schemas/delivery.js';\n\n/**\n * Load the recommendation state from disk.\n * Returns an empty state when the file does not exist.\n */\nexport async function loadState(): Promise<RecommendationState> {\n  try {\n    const raw = await readFile(paths.recommendationState, 'utf-8');\n    return recommendationStateSchema.parse(JSON.parse(raw));\n  } catch (err: unknown) {\n    // File not found or invalid JSON: return empty state\n    if (isNodeError(err) && err.code === 'ENOENT') {\n      return { entries: [], last_updated: new Date().toISOString() };\n    }\n    // Re-throw unexpected errors\n    throw err;\n  }\n}\n\n/**\n * Save the recommendation state atomically to disk.\n */\nexport async function saveState(state: RecommendationState): Promise<void> {\n  await writeFileAtomic(\n    paths.recommendationState,\n    JSON.stringify(state, null, 2),\n  );\n}\n\n/**\n * Update the status of a recommendation by ID.\n * Creates a new entry if the ID is not found.\n */\nexport async function updateStatus(\n  id: string,\n  status: RecommendationStatus,\n  details?: string,\n): Promise<void> {\n  const state = await loadState();\n  const now = new Date().toISOString();\n\n  const existing = state.entries.find((e) => e.id === id);\n  if (existing) {\n    existing.status = status;\n    existing.updated_at = now;\n    if (status === 'applied' && details !== undefined) {\n      existing.applied_details = details;\n    } else if (status !== 'applied') {\n      // Clear applied_details when not in applied status\n      existing.applied_details = undefined;\n    }\n  } else {\n    state.entries.push({\n      id,\n      status,\n      updated_at: now,\n      ...(status === 'applied' && details !== undefined\n        ? { applied_details: details }\n        : {}),\n    });\n  }\n\n  state.last_updated = now;\n  await saveState(state);\n}\n\n/**\n * Get a Map of recommendation ID to status for quick lookups.\n */\nexport async function getStatusMap(): Promise<Map<string, RecommendationStatus>> {\n  const state = await loadState();\n  return new Map(state.entries.map((e) => [e.id, e.status]));\n}\n\n// Type guard for Node.js errors with code property\nfunction isNodeError(err: unknown): err is NodeJS.ErrnoException {\n  return err instanceof Error && 'code' in err;\n}\n","// Delivery schemas for recommendation state tracking and auto-apply logging.\n// Defines: recommendation status lifecycle (pending/applied/dismissed),\n// state entries persisted in JSON, and auto-apply audit log entries.\n\nimport { z } from 'zod/v4';\n\nexport const recommendationStatusSchema = z.enum(['pending', 'applied', 'dismissed']);\nexport type RecommendationStatus = z.infer<typeof recommendationStatusSchema>;\n\nexport const recommendationStateEntrySchema = z.object({\n  id: z.string(),\n  status: recommendationStatusSchema,\n  updated_at: z.iso.datetime(),\n  applied_details: z.string().optional(),\n});\nexport type RecommendationStateEntry = z.infer<typeof recommendationStateEntrySchema>;\n\nexport const recommendationStateSchema = z.object({\n  entries: z.array(recommendationStateEntrySchema),\n  last_updated: z.iso.datetime(),\n});\nexport type RecommendationState = z.infer<typeof recommendationStateSchema>;\n\nexport const autoApplyLogEntrySchema = z.object({\n  timestamp: z.iso.datetime(),\n  recommendation_id: z.string(),\n  target: z.string(),\n  action: z.string(),\n  success: z.boolean(),\n  details: z.string().optional(),\n  backup_path: z.string().optional(),\n});\nexport type AutoApplyLogEntry = z.infer<typeof autoApplyLogEntrySchema>;\n","// Status command implementation -- shows harness-evolve status and statistics\n\nimport type { Command } from '@commander-js/extra-typings';\nimport { readCounter } from '../storage/counter.js';\nimport { loadState } from '../delivery/state.js';\nimport { readSettings, HARNESS_EVOLVE_MARKER, SETTINGS_PATH } from './utils.js';\n\n/**\n * Options for runStatus, with test overrides.\n */\nexport interface StatusOptions {\n  settingsPath?: string;\n}\n\n/**\n * Core status logic -- exported for testing.\n *\n * Reads counter, recommendation state, and settings to display:\n * - Total interaction count\n * - Last analysis timestamp\n * - Pending recommendations count\n * - Hook registration status\n */\nexport async function runStatus(options: StatusOptions): Promise<void> {\n  const settingsPath = options.settingsPath ?? SETTINGS_PATH;\n\n  // Read counter data (returns defaults if counter.json missing)\n  const counter = await readCounter();\n\n  // Read recommendation state (returns empty entries if file missing)\n  const state = await loadState();\n\n  // Count pending recommendations\n  const pendingCount = state.entries.filter(\n    (e) => e.status === 'pending',\n  ).length;\n\n  // Check hook registration in settings.json\n  const settings = await readSettings(settingsPath);\n  const hooksRegistered = JSON.stringify(settings.hooks ?? {}).includes(\n    HARNESS_EVOLVE_MARKER,\n  );\n\n  // Display status\n  console.log('');\n  console.log('harness-evolve status');\n  console.log('=====================');\n  console.log(`Interactions:     ${counter.total}`);\n  console.log(`Last analysis:    ${counter.last_analysis ?? 'never'}`);\n  console.log(`Pending recs:     ${pendingCount}`);\n  console.log(`Hooks registered: ${hooksRegistered ? 'Yes' : 'No'}`);\n  console.log('');\n}\n\n/**\n * Register the status subcommand on a Commander.js program.\n */\nexport function registerStatusCommand(program: Command): void {\n  program\n    .command('status')\n    .description('Show harness-evolve status and statistics')\n    .action(async () => {\n      await runStatus({});\n    });\n}\n","// Uninstall command implementation -- removes harness-evolve hooks and optionally deletes data\n\nimport { copyFile, rm, rmdir, access } from 'node:fs/promises';\nimport { constants } from 'node:fs';\nimport { join } from 'node:path';\nimport type { Command } from '@commander-js/extra-typings';\nimport {\n  readSettings,\n  writeSettings,\n  HARNESS_EVOLVE_MARKER,\n  SETTINGS_PATH,\n  confirm,\n} from './utils.js';\nimport { paths } from '../storage/dirs.js';\n\n/**\n * Options for runUninstall, with test overrides.\n */\nexport interface UninstallOptions {\n  purge: boolean;\n  yes: boolean;\n  settingsPath?: string;\n  projectDir?: string;\n}\n\n/**\n * Remove slash command files from the project's .claude/commands/evolve/ directory.\n * Handles missing files gracefully. Attempts to remove the evolve/ directory if empty.\n */\nasync function removeSlashCommands(projectDir: string): Promise<void> {\n  const commandsDir = join(projectDir, '.claude', 'commands', 'evolve');\n\n  for (const file of ['scan.md', 'apply.md']) {\n    try {\n      await rm(join(commandsDir, file));\n      console.log(`  Removed /evolve:${file.replace('.md', '')}`);\n    } catch {\n      // File doesn't exist -- nothing to remove\n    }\n  }\n\n  // Try to remove empty directory\n  try {\n    await rmdir(commandsDir);\n  } catch {\n    // Directory not empty (user added files) or doesn't exist\n  }\n}\n\n/**\n * Core uninstall logic -- exported for testing.\n *\n * 1. Remove harness-evolve hook entries from settings.json (preserve user hooks)\n * 2. Optionally delete ~/.harness-evolve/ data directory with --purge\n */\nexport async function runUninstall(options: UninstallOptions): Promise<void> {\n  const settingsPath = options.settingsPath ?? SETTINGS_PATH;\n\n  // --- Remove hooks from settings.json ---\n  const settings = await readSettings(settingsPath);\n  const hooks = settings.hooks as Record<string, unknown[]> | undefined;\n\n  if (!hooks || Object.keys(hooks).length === 0) {\n    console.log('No harness-evolve hooks found in settings.json');\n  } else {\n    let removedCount = 0;\n    const filteredHooks: Record<string, unknown[]> = {};\n\n    for (const [event, entries] of Object.entries(hooks)) {\n      if (!Array.isArray(entries)) {\n        filteredHooks[event] = entries;\n        continue;\n      }\n\n      // Filter out entries whose hooks sub-array contains harness-evolve\n      const kept = entries.filter((entry) => {\n        const innerHooks = (entry as Record<string, unknown>).hooks as\n          | Array<Record<string, unknown>>\n          | undefined;\n        if (!Array.isArray(innerHooks)) return true;\n        const isHarnessEvolve = innerHooks.some((h) =>\n          String(h.command ?? '').includes(HARNESS_EVOLVE_MARKER),\n        );\n        if (isHarnessEvolve) removedCount++;\n        return !isHarnessEvolve;\n      });\n\n      // Only keep the event key if there are remaining entries\n      if (kept.length > 0) {\n        filteredHooks[event] = kept;\n      }\n    }\n\n    if (removedCount > 0) {\n      // Backup before modification\n      await copyFile(settingsPath, settingsPath + '.backup');\n      console.log(`Backup created: ${settingsPath}.backup`);\n\n      // Write filtered settings\n      settings.hooks = filteredHooks;\n      await writeSettings(settings, settingsPath);\n      console.log('Removed harness-evolve hooks from settings.json');\n    } else {\n      console.log('No harness-evolve hooks found in settings.json');\n    }\n  }\n\n  // --- Remove slash commands ---\n  console.log('\\nRemoving slash commands...');\n  await removeSlashCommands(options.projectDir ?? process.cwd());\n\n  // --- Optionally delete data directory ---\n  if (options.purge) {\n    if (!options.yes) {\n      const accepted = await confirm(\n        'Delete all harness-evolve data (~/.harness-evolve/)?',\n      );\n      if (!accepted) {\n        console.log('Data directory preserved.');\n        return;\n      }\n    }\n\n    try {\n      await access(paths.base, constants.F_OK);\n      await rm(paths.base, { recursive: true, force: true });\n      console.log(`Deleted data directory: ${paths.base}`);\n    } catch {\n      console.log(`Data directory not found: ${paths.base}`);\n    }\n  }\n}\n\n/**\n * Register the uninstall subcommand on a Commander.js program.\n */\nexport function registerUninstallCommand(program: Command): void {\n  program\n    .command('uninstall')\n    .description('Remove harness-evolve hooks and optionally delete data')\n    .option('--purge', 'Also delete ~/.harness-evolve/ data directory')\n    .option('--yes', 'Skip confirmation prompt')\n    .action(async (opts) => {\n      await runUninstall({\n        purge: opts.purge ?? false,\n        yes: opts.yes ?? false,\n      });\n    });\n}\n","// Scan CLI subcommand -- triggers deep configuration scan and outputs JSON results.\n// Used by the /evolve:scan slash command to programmatically invoke scanning.\n\nimport type { Command } from '@commander-js/extra-typings';\nimport { runDeepScan } from '../scan/index.js';\n\n/** Confidence tier ordering: HIGH (0) -> MEDIUM (1) -> LOW (2) */\nconst CONFIDENCE_ORDER: Record<string, number> = { HIGH: 0, MEDIUM: 1, LOW: 2 };\n\n/**\n * Register the 'scan' subcommand on a Commander.js program.\n *\n * Runs a full deep configuration scan (CLAUDE.md, rules, settings, hooks)\n * and outputs the results as structured JSON to stdout. The output omits\n * scan_context to keep it concise for slash command consumers.\n */\nexport function registerScanCommand(program: Command): void {\n  program\n    .command('scan')\n    .description('Run deep configuration scan and output results as JSON')\n    .action(async () => {\n      try {\n        const result = await runDeepScan(process.cwd());\n        // Sort recommendations by confidence: HIGH -> MEDIUM -> LOW\n        const sorted = [...result.recommendations].sort((a, b) =>\n          (CONFIDENCE_ORDER[a.confidence] ?? 3) - (CONFIDENCE_ORDER[b.confidence] ?? 3)\n        );\n        // Output minimal JSON (no scan_context to keep output clean for slash command)\n        const output = {\n          generated_at: result.generated_at,\n          recommendation_count: sorted.length,\n          recommendations: sorted,\n        };\n        console.log(JSON.stringify(output, null, 2));\n      } catch (err) {\n        console.log(JSON.stringify({\n          error: err instanceof Error ? err.message : String(err),\n          recommendations: [],\n        }, null, 2));\n        process.exitCode = 1;\n      }\n    });\n}\n","// Apply CLI subcommands -- pending, apply-one, dismiss.\n// Used by the /evolve:apply slash command for interactive recommendation management.\n\nimport { readFile, appendFile } from 'node:fs/promises';\nimport type { Command } from '@commander-js/extra-typings';\nimport { loadState, updateStatus } from '../delivery/state.js';\nimport { paths } from '../storage/dirs.js';\nimport type { Recommendation } from '../schemas/recommendation.js';\nimport { analysisResultSchema } from '../schemas/recommendation.js';\n\n// Trigger applier registration by importing auto-apply (registers all 4 appliers as side effect)\nimport '../delivery/auto-apply.js';\nimport { getApplier } from '../delivery/appliers/index.js';\n\n/** Confidence tier ordering: HIGH (0) -> MEDIUM (1) -> LOW (2) */\nconst CONFIDENCE_ORDER: Record<string, number> = { HIGH: 0, MEDIUM: 1, LOW: 2 };\n\n/**\n * Load recommendations from the analysis result file.\n * Returns an empty array when the file does not exist or is invalid.\n */\nasync function loadAnalysisResult(): Promise<Recommendation[]> {\n  try {\n    const raw = await readFile(paths.analysisResult, 'utf-8');\n    const parsed = analysisResultSchema.parse(JSON.parse(raw));\n    return parsed.recommendations;\n  } catch {\n    return [];\n  }\n}\n\n/**\n * Register the 'pending' subcommand on a Commander.js program.\n *\n * Reads the analysis result and recommendation state, filters to\n * recommendations that are not yet applied or dismissed, and outputs\n * the pending list as structured JSON.\n */\nexport function registerPendingCommand(program: Command): void {\n  program\n    .command('pending')\n    .description('List pending recommendations as JSON')\n    .action(async () => {\n      const allRecs = await loadAnalysisResult();\n      const state = await loadState();\n      const statusMap = new Map(state.entries.map(e => [e.id, e.status]));\n\n      // Filter to pending: recommendations not in state, or explicitly pending\n      // Sort by confidence: HIGH -> MEDIUM -> LOW\n      const pending = allRecs\n        .filter(rec => {\n          const status = statusMap.get(rec.id);\n          return status === undefined || status === 'pending';\n        })\n        .sort((a, b) =>\n          (CONFIDENCE_ORDER[a.confidence] ?? 3) - (CONFIDENCE_ORDER[b.confidence] ?? 3)\n        );\n\n      console.log(JSON.stringify({ pending, count: pending.length }, null, 2));\n    });\n}\n\n/**\n * Register the 'apply-one' subcommand on a Commander.js program.\n *\n * Loads the recommendation by ID from analysis result, finds the correct\n * applier from the registry, applies the recommendation, logs the attempt,\n * and updates the recommendation status on success.\n */\nexport function registerApplyOneCommand(program: Command): void {\n  program\n    .command('apply-one')\n    .description('Apply a single recommendation by ID')\n    .argument('<id>', 'Recommendation ID to apply')\n    .action(async (id) => {\n      try {\n        const allRecs = await loadAnalysisResult();\n        const rec = allRecs.find(r => r.id === id);\n        if (!rec) {\n          console.log(JSON.stringify({\n            recommendation_id: id,\n            success: false,\n            details: `Recommendation '${id}' not found`,\n          }));\n          process.exitCode = 1;\n          return;\n        }\n\n        const applier = getApplier(rec.target);\n        if (!applier || !applier.canApply(rec)) {\n          console.log(JSON.stringify({\n            recommendation_id: id,\n            success: false,\n            details: `No applicable applier for target '${rec.target}'`,\n          }));\n          process.exitCode = 1;\n          return;\n        }\n\n        const result = await applier.apply(rec);\n\n        // Log the attempt (non-critical -- ignore write failures)\n        const logEntry = {\n          timestamp: new Date().toISOString(),\n          recommendation_id: rec.id,\n          target: rec.target,\n          action: rec.suggested_action,\n          success: result.success,\n          details: result.details,\n        };\n        try {\n          await appendFile(paths.autoApplyLog, JSON.stringify(logEntry) + '\\n', 'utf-8');\n        } catch {\n          // Log failure is non-critical\n        }\n\n        // Update status to applied on success\n        if (result.success) {\n          await updateStatus(id, 'applied', `Applied via /evolve:apply: ${result.details}`);\n        }\n\n        console.log(JSON.stringify(result, null, 2));\n      } catch (err) {\n        console.log(JSON.stringify({\n          recommendation_id: id,\n          success: false,\n          details: err instanceof Error ? err.message : String(err),\n        }));\n        process.exitCode = 1;\n      }\n    });\n}\n\n/**\n * Register the 'dismiss' subcommand on a Commander.js program.\n *\n * Permanently dismisses a recommendation by updating its status to 'dismissed'.\n * Outputs JSON confirmation with the recommendation ID and status.\n */\nexport function registerDismissCommand(program: Command): void {\n  program\n    .command('dismiss')\n    .description('Permanently dismiss a recommendation by ID')\n    .argument('<id>', 'Recommendation ID to dismiss')\n    .action(async (id) => {\n      try {\n        await updateStatus(id, 'dismissed', 'Dismissed by user via /evolve:apply');\n        console.log(JSON.stringify({ id, status: 'dismissed' }, null, 2));\n      } catch (err) {\n        console.log(JSON.stringify({\n          id,\n          error: err instanceof Error ? err.message : String(err),\n        }));\n        process.exitCode = 1;\n      }\n    });\n}\n","// Recommendation and analysis result schemas.\n// Defines the output contracts for the analysis engine: routing targets,\n// confidence tiers, recommendation structure, and analysis configuration.\n\nimport { z } from 'zod/v4';\n\nexport const routingTargetSchema = z.enum([\n  'HOOK',\n  'SKILL',\n  'RULE',\n  'CLAUDE_MD',\n  'MEMORY',\n  'SETTINGS',\n]);\nexport type RoutingTarget = z.infer<typeof routingTargetSchema>;\n\nexport const confidenceSchema = z.enum(['HIGH', 'MEDIUM', 'LOW']);\nexport type Confidence = z.infer<typeof confidenceSchema>;\n\nexport const patternTypeSchema = z.enum([\n  'repeated_prompt',\n  'long_prompt',\n  'permission-always-approved',\n  'code_correction',\n  'personal_info',\n  'config_drift',\n  'version_update',\n  'ecosystem_gsd',\n  'ecosystem_cog',\n  'onboarding_start_hooks',\n  'onboarding_start_rules',\n  'onboarding_start_claudemd',\n  'onboarding_optimize',\n  'scan_redundancy',\n  'scan_missing_mechanization',\n  'scan_stale_reference',\n]);\nexport type PatternType = z.infer<typeof patternTypeSchema>;\n\nexport const recommendationSchema = z.object({\n  id: z.string(),\n  target: routingTargetSchema,\n  confidence: confidenceSchema,\n  pattern_type: patternTypeSchema,\n  title: z.string(),\n  description: z.string(),\n  evidence: z.object({\n    count: z.number(),\n    sessions: z.number().optional(),\n    examples: z.array(z.string()).max(3),\n  }),\n  suggested_action: z.string(),\n  ecosystem_context: z.string().optional(),\n});\nexport type Recommendation = z.infer<typeof recommendationSchema>;\n\n// Default threshold values for classifiers\nconst DEFAULT_THRESHOLDS = {\n  repeated_prompt_min_count: 5,\n  repeated_prompt_high_count: 10,\n  repeated_prompt_high_sessions: 3,\n  repeated_prompt_medium_sessions: 2,\n  long_prompt_min_words: 200,\n  long_prompt_min_count: 2,\n  long_prompt_high_words: 300,\n  long_prompt_high_count: 3,\n  permission_approval_min_count: 10,\n  permission_approval_min_sessions: 3,\n  permission_approval_high_count: 15,\n  permission_approval_high_sessions: 4,\n  code_correction_min_failure_rate: 0.3,\n  code_correction_min_failures: 3,\n} as const;\n\nexport const analysisConfigSchema = z.object({\n  thresholds: z.object({\n    repeated_prompt_min_count: z.number().default(DEFAULT_THRESHOLDS.repeated_prompt_min_count),\n    repeated_prompt_high_count: z.number().default(DEFAULT_THRESHOLDS.repeated_prompt_high_count),\n    repeated_prompt_high_sessions: z.number().default(DEFAULT_THRESHOLDS.repeated_prompt_high_sessions),\n    repeated_prompt_medium_sessions: z.number().default(DEFAULT_THRESHOLDS.repeated_prompt_medium_sessions),\n    long_prompt_min_words: z.number().default(DEFAULT_THRESHOLDS.long_prompt_min_words),\n    long_prompt_min_count: z.number().default(DEFAULT_THRESHOLDS.long_prompt_min_count),\n    long_prompt_high_words: z.number().default(DEFAULT_THRESHOLDS.long_prompt_high_words),\n    long_prompt_high_count: z.number().default(DEFAULT_THRESHOLDS.long_prompt_high_count),\n    permission_approval_min_count: z.number().default(DEFAULT_THRESHOLDS.permission_approval_min_count),\n    permission_approval_min_sessions: z.number().default(DEFAULT_THRESHOLDS.permission_approval_min_sessions),\n    permission_approval_high_count: z.number().default(DEFAULT_THRESHOLDS.permission_approval_high_count),\n    permission_approval_high_sessions: z.number().default(DEFAULT_THRESHOLDS.permission_approval_high_sessions),\n    code_correction_min_failure_rate: z.number().default(DEFAULT_THRESHOLDS.code_correction_min_failure_rate),\n    code_correction_min_failures: z.number().default(DEFAULT_THRESHOLDS.code_correction_min_failures),\n  }).default(() => ({ ...DEFAULT_THRESHOLDS })),\n  max_recommendations: z.number().default(20),\n}).default(() => ({\n  thresholds: { ...DEFAULT_THRESHOLDS },\n  max_recommendations: 20,\n}));\nexport type AnalysisConfig = z.infer<typeof analysisConfigSchema>;\n\nexport const analysisResultSchema = z.object({\n  generated_at: z.iso.datetime(),\n  summary_period: z.object({\n    since: z.string(),\n    until: z.string(),\n    days: z.number(),\n  }),\n  recommendations: z.array(recommendationSchema),\n  metadata: z.object({\n    classifier_count: z.number(),\n    patterns_evaluated: z.number(),\n    environment_ecosystems: z.array(z.string()),\n    claude_code_version: z.string(),\n  }),\n});\nexport type AnalysisResult = z.infer<typeof analysisResultSchema>;\n","// Auto-apply module for high-confidence recommendations.\n// When fullAuto mode is enabled (config.delivery.fullAuto=true), this module\n// automatically applies HIGH-confidence recommendations that have a registered\n// applier. Dispatches to the correct applier via the strategy pattern registry.\n// v1 appliers: SettingsApplier (permission-always-approved), RuleApplier (create-only rules).\n// v2 appliers: HookApplier (hook script generation + settings registration), ClaudeMdApplier (CLAUDE.md append).\n\nimport { appendFile } from 'node:fs/promises';\nimport { paths, ensureInit } from '../storage/dirs.js';\nimport { loadConfig } from '../storage/config.js';\nimport { updateStatus, getStatusMap } from './state.js';\nimport {\n  registerApplier,\n  getApplier,\n  hasApplier,\n} from './appliers/index.js';\nimport { SettingsApplier } from './appliers/settings-applier.js';\nimport { RuleApplier } from './appliers/rule-applier.js';\nimport { HookApplier } from './appliers/hook-applier.js';\nimport { ClaudeMdApplier } from './appliers/claude-md-applier.js';\nimport type { Recommendation } from '../schemas/recommendation.js';\nimport type { AutoApplyLogEntry } from '../schemas/delivery.js';\nimport type { ApplierOptions } from './appliers/index.js';\n\nexport interface AutoApplyResult {\n  recommendation_id: string;\n  success: boolean;\n  details: string;\n}\n\nexport interface AutoApplyOptions extends ApplierOptions {}\n\n// Register all built-in appliers\nregisterApplier(new SettingsApplier());\nregisterApplier(new RuleApplier());\nregisterApplier(new HookApplier());\nregisterApplier(new ClaudeMdApplier());\n\n/**\n * Auto-apply HIGH-confidence recommendations when fullAuto is enabled.\n * Returns an empty array when fullAuto is false (default, per QUA-01).\n *\n * Dispatches to the appropriate Applier based on rec.target via the\n * applier registry. Only processes recommendations whose target has a\n * registered applier and whose applier.canApply() returns true.\n */\nexport async function autoApplyRecommendations(\n  recommendations: Recommendation[],\n  options?: AutoApplyOptions,\n): Promise<AutoApplyResult[]> {\n  const config = await loadConfig();\n  if (!config.delivery.fullAuto) return [];\n\n  await ensureInit();\n  const stateMap = await getStatusMap();\n  const results: AutoApplyResult[] = [];\n\n  // Filter: only HIGH confidence + has registered applier + pending status\n  const candidates = recommendations.filter(\n    (rec) =>\n      rec.confidence === 'HIGH' &&\n      hasApplier(rec.target) &&\n      (stateMap.get(rec.id) ?? 'pending') === 'pending',\n  );\n\n  for (const rec of candidates) {\n    const applier = getApplier(rec.target);\n    let result: AutoApplyResult;\n\n    if (!applier || !applier.canApply(rec)) {\n      result = {\n        recommendation_id: rec.id,\n        success: false,\n        details: `No applicable applier for target '${rec.target}' with pattern_type '${rec.pattern_type}'`,\n      };\n    } else {\n      result = await applier.apply(rec, options);\n    }\n\n    results.push(result);\n\n    // Log the attempt\n    const logEntry: AutoApplyLogEntry = {\n      timestamp: new Date().toISOString(),\n      recommendation_id: rec.id,\n      target: rec.target,\n      action: rec.suggested_action,\n      success: result.success,\n      details: result.details,\n      backup_path: undefined,\n    };\n    await appendFile(\n      paths.autoApplyLog,\n      JSON.stringify(logEntry) + '\\n',\n      'utf-8',\n    );\n\n    // Update status on success\n    if (result.success) {\n      await updateStatus(rec.id, 'applied', `Auto-applied: ${result.details}`);\n    }\n  }\n\n  return results;\n}\n","import { readFile } from 'node:fs/promises';\nimport writeFileAtomic from 'write-file-atomic';\nimport { configSchema, type Config } from '../schemas/config.js';\nimport { paths } from './dirs.js';\n\nexport async function loadConfig(): Promise<Config> {\n  try {\n    const raw = await readFile(paths.config, 'utf-8');\n    return configSchema.parse(JSON.parse(raw));\n  } catch {\n    // File doesn't exist, is invalid JSON, or fails strict validation\n    const defaults = configSchema.parse({});\n    await writeFileAtomic(paths.config, JSON.stringify(defaults, null, 2));\n    return defaults;\n  }\n}\n","import { z } from 'zod/v4';\n\nexport const configSchema = z.object({\n  version: z.number().default(1),\n  analysis: z.object({\n    threshold: z.number().min(1).default(50),\n    enabled: z.boolean().default(true),\n    classifierThresholds: z.record(z.string(), z.number()).default({}),\n  }).default({ threshold: 50, enabled: true, classifierThresholds: {} }),\n  hooks: z.object({\n    capturePrompts: z.boolean().default(true),\n    captureTools: z.boolean().default(true),\n    capturePermissions: z.boolean().default(true),\n    captureSessions: z.boolean().default(true),\n  }).default({\n    capturePrompts: true,\n    captureTools: true,\n    capturePermissions: true,\n    captureSessions: true,\n  }),\n  scrubbing: z.object({\n    enabled: z.boolean().default(true),\n    highEntropyDetection: z.boolean().default(false),\n    customPatterns: z.array(z.object({\n      name: z.string(),\n      regex: z.string(),\n      replacement: z.string(),\n    })).default([]),\n  }).default({\n    enabled: true,\n    highEntropyDetection: false,\n    customPatterns: [],\n  }),\n  delivery: z.object({\n    stdoutInjection: z.boolean().default(true),\n    maxTokens: z.number().default(200),\n    fullAuto: z.boolean().default(false),\n    maxRecommendationsInFile: z.number().default(20),\n    archiveAfterDays: z.number().default(7),\n  }).default({\n    stdoutInjection: true,\n    maxTokens: 200,\n    fullAuto: false,\n    maxRecommendationsInFile: 20,\n    archiveAfterDays: 7,\n  }),\n}).strict();\n\nexport type Config = z.infer<typeof configSchema>;\n","// Applier interface, options, and registry for auto-apply dispatch.\n// The registry maps routing targets (e.g. 'SETTINGS', 'RULE') to their\n// corresponding Applier implementations. Adding a new applier requires\n// only implementing the Applier interface and calling registerApplier().\n\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport type { AutoApplyResult } from '../auto-apply.js';\n\nexport interface ApplierOptions {\n  /** Override settings.json path (used in testing) */\n  settingsPath?: string;\n  /** Override rules directory (used in testing) */\n  rulesDir?: string;\n  /** Override hooks directory (used in testing) */\n  hooksDir?: string;\n  /** Override CLAUDE.md path (used in testing) */\n  claudeMdPath?: string;\n}\n\nexport interface Applier {\n  readonly target: string;\n  canApply(rec: Recommendation): boolean;\n  apply(rec: Recommendation, options?: ApplierOptions): Promise<AutoApplyResult>;\n}\n\nconst registry = new Map<string, Applier>();\n\nexport function registerApplier(applier: Applier): void {\n  registry.set(applier.target, applier);\n}\n\nexport function getApplier(target: string): Applier | undefined {\n  return registry.get(target);\n}\n\nexport function hasApplier(target: string): boolean {\n  return registry.has(target);\n}\n","// SettingsApplier: handles auto-apply for SETTINGS/permission-always-approved.\n// Extracted from auto-apply.ts — adds tools to allowedTools in settings.json\n// with atomic writes and backup creation before modification.\n\nimport { readFile, copyFile, mkdir } from 'node:fs/promises';\nimport { join, dirname } from 'node:path';\nimport writeFileAtomic from 'write-file-atomic';\nimport type { Applier, ApplierOptions } from './index.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport type { AutoApplyResult } from '../auto-apply.js';\nimport { paths } from '../../storage/dirs.js';\n\nexport class SettingsApplier implements Applier {\n  readonly target = 'SETTINGS';\n\n  canApply(rec: Recommendation): boolean {\n    return (\n      rec.confidence === 'HIGH' &&\n      rec.target === 'SETTINGS' &&\n      rec.pattern_type === 'permission-always-approved'\n    );\n  }\n\n  async apply(\n    rec: Recommendation,\n    options?: ApplierOptions,\n  ): Promise<AutoApplyResult> {\n    try {\n      // v1 scope: only handle permission-always-approved pattern\n      if (rec.pattern_type !== 'permission-always-approved') {\n        return {\n          recommendation_id: rec.id,\n          success: false,\n          details: `Skipped: pattern_type '${rec.pattern_type}' not supported for auto-apply in v1`,\n        };\n      }\n\n      const settingsFilePath =\n        options?.settingsPath ??\n        join(process.env.HOME ?? '', '.claude', 'settings.json');\n\n      // Read current settings\n      const raw = await readFile(settingsFilePath, 'utf-8');\n      const settings = JSON.parse(raw) as Record<string, unknown>;\n\n      // Create backup before modification\n      const backup = join(\n        paths.analysis,\n        'backups',\n        `settings-backup-${rec.id}.json`,\n      );\n      await mkdir(dirname(backup), { recursive: true });\n      await copyFile(settingsFilePath, backup);\n\n      // Extract tool name from evidence\n      const toolName = extractToolName(rec);\n      if (!toolName) {\n        return {\n          recommendation_id: rec.id,\n          success: false,\n          details:\n            'Could not extract tool name from recommendation evidence',\n        };\n      }\n\n      // Get or create allowedTools array\n      const allowedTools = Array.isArray(settings.allowedTools)\n        ? (settings.allowedTools as string[])\n        : [];\n\n      // Add tool if not already present\n      if (!allowedTools.includes(toolName)) {\n        allowedTools.push(toolName);\n      }\n      settings.allowedTools = allowedTools;\n\n      // Write modified settings atomically\n      await writeFileAtomic(\n        settingsFilePath,\n        JSON.stringify(settings, null, 2),\n      );\n\n      return {\n        recommendation_id: rec.id,\n        success: true,\n        details: `Added ${toolName} to allowedTools`,\n      };\n    } catch (err: unknown) {\n      const message = err instanceof Error ? err.message : String(err);\n      return {\n        recommendation_id: rec.id,\n        success: false,\n        details: message,\n      };\n    }\n  }\n}\n\n/**\n * Extract tool name from recommendation evidence examples.\n * Looks for patterns like \"Bash(npm test)\" -> \"Bash\"\n * or \"ToolName(args)\" -> \"ToolName\".\n */\nfunction extractToolName(rec: Recommendation): string | undefined {\n  for (const example of rec.evidence.examples) {\n    const match = example.match(/^(\\w+)\\(/);\n    if (match) return match[1];\n  }\n  return undefined;\n}\n","// RuleApplier: handles auto-apply for HIGH-confidence RULE recommendations.\n// Creates .claude/rules/evolve-{pattern_type}.md files with the recommendation\n// title, description, and suggested action. Create-only: never overwrites\n// existing rule files to respect user customizations (Pitfall 18).\n\nimport { writeFile, access, mkdir } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport type { Applier, ApplierOptions } from './index.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport type { AutoApplyResult } from '../auto-apply.js';\n\nexport class RuleApplier implements Applier {\n  readonly target = 'RULE';\n\n  canApply(rec: Recommendation): boolean {\n    return rec.confidence === 'HIGH' && rec.target === 'RULE';\n  }\n\n  async apply(\n    rec: Recommendation,\n    options?: ApplierOptions,\n  ): Promise<AutoApplyResult> {\n    const rulesDir =\n      options?.rulesDir ??\n      join(process.env.HOME ?? '', '.claude', 'rules');\n    const fileName = `evolve-${rec.pattern_type}.md`;\n    const filePath = join(rulesDir, fileName);\n\n    // Create-only guard: never overwrite existing files (Pitfall 18)\n    try {\n      await access(filePath);\n      return {\n        recommendation_id: rec.id,\n        success: false,\n        details: `Rule file already exists: ${fileName}`,\n      };\n    } catch {\n      // File does not exist — proceed to create\n    }\n\n    try {\n      await mkdir(rulesDir, { recursive: true });\n\n      const content = [\n        `# ${rec.title}`,\n        '',\n        rec.description,\n        '',\n        '## Action',\n        '',\n        rec.suggested_action,\n        '',\n        '---',\n        `*Auto-generated by harness-evolve (${rec.id})*`,\n      ].join('\\n');\n\n      await writeFile(filePath, content, 'utf-8');\n\n      return {\n        recommendation_id: rec.id,\n        success: true,\n        details: `Created rule file: ${fileName}`,\n      };\n    } catch (err: unknown) {\n      const message = err instanceof Error ? err.message : String(err);\n      return {\n        recommendation_id: rec.id,\n        success: false,\n        details: message,\n      };\n    }\n  }\n}\n","// HookApplier: handles auto-apply for HIGH-confidence HOOK recommendations.\n// Generates a bash hook script via generateHook(), writes it to disk with +x\n// permission, and registers the hook in settings.json via mergeHooks().\n// Create-only: never overwrites existing hook files.\n\nimport { writeFile, access, mkdir, chmod, copyFile } from 'node:fs/promises';\nimport { join, basename, dirname } from 'node:path';\nimport type { Applier, ApplierOptions } from './index.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport type { AutoApplyResult } from '../auto-apply.js';\nimport { generateHook } from '../../generators/hook-generator.js';\nimport {\n  readSettings,\n  writeSettings,\n  mergeHooks,\n} from '../../cli/utils.js';\nimport { paths } from '../../storage/dirs.js';\n\nexport class HookApplier implements Applier {\n  readonly target = 'HOOK';\n\n  canApply(rec: Recommendation): boolean {\n    return rec.confidence === 'HIGH' && rec.target === 'HOOK';\n  }\n\n  async apply(\n    rec: Recommendation,\n    options?: ApplierOptions,\n  ): Promise<AutoApplyResult> {\n    try {\n      // Generate hook script from recommendation\n      const artifact = generateHook(rec);\n      if (!artifact) {\n        return {\n          recommendation_id: rec.id,\n          success: false,\n          details: 'Generator returned null — recommendation not applicable for hook generation',\n        };\n      }\n\n      // Resolve hooks directory\n      const hooksDir =\n        options?.hooksDir ??\n        join(process.env.HOME ?? '', '.claude', 'hooks');\n\n      // Extract script filename from artifact path\n      const scriptFilename = basename(artifact.filename);\n      const scriptPath = join(hooksDir, scriptFilename);\n\n      // Create-only guard: never overwrite existing hook files\n      try {\n        await access(scriptPath);\n        return {\n          recommendation_id: rec.id,\n          success: false,\n          details: `Hook file already exists: ${scriptFilename}`,\n        };\n      } catch {\n        // File does not exist — proceed to create\n      }\n\n      // Create hooks directory\n      await mkdir(hooksDir, { recursive: true });\n\n      // Write hook script file\n      await writeFile(scriptPath, artifact.content, 'utf-8');\n\n      // Set executable permission\n      await chmod(scriptPath, 0o755);\n\n      // Resolve settings.json path\n      const settingsPath =\n        options?.settingsPath ??\n        join(process.env.HOME ?? '', '.claude', 'settings.json');\n\n      // Read current settings\n      const settings = await readSettings(settingsPath);\n\n      // Create backup before modification\n      const backupDir = join(paths.analysis, 'backups');\n      await mkdir(backupDir, { recursive: true });\n      const backupFile = join(backupDir, `settings-backup-${rec.id}.json`);\n      // Only backup if settings file exists and has content\n      try {\n        await copyFile(settingsPath, backupFile);\n      } catch {\n        // Settings file may not exist yet — write current state as backup\n        await writeFile(backupFile, JSON.stringify(settings, null, 2), 'utf-8');\n      }\n\n      // Extract hook event from generated content\n      const eventMatch = artifact.content.match(/# Hook event: (\\w+)/);\n      const hookEvent = eventMatch?.[1] ?? 'PreToolUse';\n\n      // Merge hook into settings\n      const merged = mergeHooks(settings, [\n        {\n          event: hookEvent,\n          command: `bash \"${scriptPath}\"`,\n          timeout: 10,\n          async: true,\n        },\n      ]);\n\n      // Write merged settings\n      await writeSettings(merged, settingsPath);\n\n      return {\n        recommendation_id: rec.id,\n        success: true,\n        details: `Created hook script: ${scriptFilename} and registered under ${hookEvent}`,\n      };\n    } catch (err: unknown) {\n      const message = err instanceof Error ? err.message : String(err);\n      return {\n        recommendation_id: rec.id,\n        success: false,\n        details: message,\n      };\n    }\n  }\n}\n","// Generator module schemas and shared utilities.\n// Defines the GeneratedArtifact output contract for all generators,\n// plus helper functions (toSlug, escapeYaml) used across generator implementations.\n\nimport { z } from 'zod/v4';\n\n// Version stamp embedded in every generated artifact\nexport const GENERATOR_VERSION = '1.0.0';\n\n// Return current time as ISO 8601 string\nexport function nowISO(): string {\n  return new Date().toISOString();\n}\n\n/**\n * Convert text to a URL/filename-safe slug.\n * Lowercases, replaces non-alphanumeric with hyphens,\n * collapses consecutive hyphens, strips leading/trailing hyphens,\n * and caps at 50 characters.\n */\nexport function toSlug(text: string): string {\n  if (!text) return '';\n  return text\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, '-')\n    .replace(/-+/g, '-')\n    .replace(/^-|-$/g, '')\n    .slice(0, 50);\n}\n\n// Characters that require quoting in YAML values\nconst YAML_SPECIAL = /[:\"'{}[\\]#&*!|>\\\\,\\n]/;\n\n/**\n * Escape a string for safe inclusion as a YAML frontmatter value.\n * Wraps in double quotes and escapes internal double quotes\n * when the text contains YAML-special characters.\n */\nexport function escapeYaml(text: string): string {\n  if (!YAML_SPECIAL.test(text)) return text;\n  return `\"${text.replace(/\"/g, '\\\\\"')}\"`;\n}\n\nexport const generatedArtifactSchema = z.object({\n  type: z.enum(['skill', 'hook', 'claude_md_patch']),\n  filename: z.string(),\n  content: z.string(),\n  source_recommendation_id: z.string(),\n  metadata: z.object({\n    generated_at: z.iso.datetime(),\n    generator_version: z.string(),\n    pattern_type: z.string(),\n  }),\n});\nexport type GeneratedArtifact = z.infer<typeof generatedArtifactSchema>;\n\nexport interface GeneratorOptions {\n  projectRoot?: string;\n}\n","// Hook generator: converts HOOK-targeted recommendations into bash hook\n// script drafts. Handles both scan_missing_mechanization and repeated_prompt\n// pattern types. Pure function -- no filesystem access, no side effects.\n// Returns null for non-applicable recommendations.\n\nimport type { Recommendation } from '../schemas/recommendation.js';\nimport type { GeneratedArtifact } from './schemas.js';\nimport { toSlug, GENERATOR_VERSION, nowISO } from './schemas.js';\n\n/**\n * Extract the hook event name from a recommendation's description\n * or suggested_action field.\n *\n * Tries these patterns in order:\n * 1. \"suitable for a <HookEvent> hook\" in description\n * 2. \"Create a <HookEvent> hook\" in suggested_action\n * 3. Falls back to 'PreToolUse' if no match\n */\nfunction extractHookEvent(rec: Recommendation): string {\n  const descMatch = rec.description.match(/suitable for a (\\w+) hook/i);\n  if (descMatch) return descMatch[1];\n\n  const actionMatch = rec.suggested_action.match(/Create a (\\w+) hook/i);\n  if (actionMatch) return actionMatch[1];\n\n  return 'PreToolUse';\n}\n\n/**\n * Generate a bash hook script draft from a HOOK-targeted recommendation.\n *\n * @param rec - A Recommendation object (from mechanization scanner or repeated-prompts classifier)\n * @returns GeneratedArtifact with type 'hook', or null if the recommendation\n *          is not applicable (wrong target)\n */\nexport function generateHook(rec: Recommendation): GeneratedArtifact | null {\n  if (rec.target !== 'HOOK') return null;\n\n  const hookEvent = extractHookEvent(rec);\n  const slugName = toSlug(rec.title);\n\n  const content = [\n    '#!/usr/bin/env bash',\n    `# Auto-generated hook for: ${rec.title}`,\n    `# Hook event: ${hookEvent}`,\n    `# Source: harness-evolve (${rec.id})`,\n    '#',\n    '# TODO: Review and customize this script before use.',\n    '',\n    '# Read hook input from stdin',\n    'INPUT=$(cat)',\n    '',\n    '# Extract relevant fields',\n    `# Adjust jq path based on your ${hookEvent} event schema`,\n    '',\n    `# ${rec.suggested_action}`,\n    '',\n    '# Exit 0 to allow, exit 2 to block',\n    'exit 0',\n  ].join('\\n');\n\n  return {\n    type: 'hook',\n    filename: `.claude/hooks/evolve-${slugName}.sh`,\n    content,\n    source_recommendation_id: rec.id,\n    metadata: {\n      generated_at: nowISO(),\n      generator_version: GENERATOR_VERSION,\n      pattern_type: rec.pattern_type,\n    },\n  };\n}\n","// ClaudeMdApplier: handles auto-apply for HIGH-confidence CLAUDE_MD recommendations.\n// Appends new sections to CLAUDE.md for generic pattern types. Refuses to\n// auto-apply destructive patterns (scan_stale_reference, scan_redundancy) that\n// require manual review. Uses write-file-atomic for safe writes.\n// Creates backup of original CLAUDE.md before modification.\n\nimport { readFile, mkdir } from 'node:fs/promises';\nimport { join, dirname } from 'node:path';\nimport writeFileAtomic from 'write-file-atomic';\nimport type { Applier, ApplierOptions } from './index.js';\nimport type { Recommendation } from '../../schemas/recommendation.js';\nimport type { AutoApplyResult } from '../auto-apply.js';\nimport { paths } from '../../storage/dirs.js';\n\n/** Pattern types that require manual review — no destructive auto-apply. */\nconst DESTRUCTIVE_PATTERNS = new Set([\n  'scan_stale_reference',\n  'scan_redundancy',\n]);\n\nexport class ClaudeMdApplier implements Applier {\n  readonly target = 'CLAUDE_MD';\n\n  canApply(rec: Recommendation): boolean {\n    return rec.confidence === 'HIGH' && rec.target === 'CLAUDE_MD';\n  }\n\n  async apply(\n    rec: Recommendation,\n    options?: ApplierOptions,\n  ): Promise<AutoApplyResult> {\n    try {\n      // Pattern-type guard: refuse destructive patterns\n      if (DESTRUCTIVE_PATTERNS.has(rec.pattern_type)) {\n        return {\n          recommendation_id: rec.id,\n          success: false,\n          details: `Pattern type '${rec.pattern_type}' requires manual review — cannot safely auto-apply`,\n        };\n      }\n\n      // Resolve CLAUDE.md path\n      const claudeMdPath =\n        options?.claudeMdPath ??\n        join(process.cwd(), 'CLAUDE.md');\n\n      // Read existing content (empty string if file doesn't exist)\n      let existingContent = '';\n      try {\n        existingContent = await readFile(claudeMdPath, 'utf-8');\n      } catch {\n        // File does not exist — will be created\n      }\n\n      // Create backup if content exists\n      if (existingContent) {\n        const backupDir = join(paths.analysis, 'backups');\n        await mkdir(backupDir, { recursive: true });\n        const backupFile = join(backupDir, `claudemd-backup-${rec.id}.md`);\n        await writeFileAtomic(backupFile, existingContent);\n      }\n\n      // Build new section to append\n      const newSection = [\n        '',\n        '',\n        `## ${rec.title}`,\n        '',\n        rec.suggested_action,\n        '',\n        '---',\n        `*Auto-generated by harness-evolve (${rec.id})*`,\n        '',\n      ].join('\\n');\n\n      // Append section to existing content\n      const updatedContent = existingContent + newSection;\n\n      // Ensure parent directory exists\n      await mkdir(dirname(claudeMdPath), { recursive: true });\n\n      // Write updated content atomically\n      await writeFileAtomic(claudeMdPath, updatedContent);\n\n      return {\n        recommendation_id: rec.id,\n        success: true,\n        details: `Appended section: ${rec.title}`,\n      };\n    } catch (err: unknown) {\n      const message = err instanceof Error ? err.message : String(err);\n      return {\n        recommendation_id: rec.id,\n        success: false,\n        details: message,\n      };\n    }\n  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package/dist/delivery/run-evolve.d.ts

@@ -0,0 +1,2 @@
+
+export {  }