@agntk/agent-harness 0.1.1

package/dist/intelligence-HJOCA4SJ.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/runtime/intelligence.ts"],"sourcesContent":["import { existsSync, readdirSync, readFileSync, statSync } from 'fs';\nimport { join, relative } from 'path';\nimport { loadDirectoryWithErrors, loadDirectory } from '../primitives/loader.js';\nimport { buildDependencyGraph } from './graph.js';\nimport { getPrimitiveDirs } from '../core/types.js';\nimport type { HarnessConfig, HarnessDocument } from '../core/types.js';\nimport { loadConfig } from '../core/config.js';\nimport type { InstinctCandidate } from './instinct-learner.js';\nimport { installInstinct } from './instinct-learner.js';\nimport { log } from '../core/logger.js';\nimport { checkRateLimit } from './rate-limiter.js';\nimport { buildRateLimits } from './guardrails.js';\nimport { checkBudget } from './cost-tracker.js';\nimport { validateHarness } from './validator.js';\n\n// --- Auto-Promote Instincts ---\n\nexport interface PatternOccurrence {\n  behavior: string;\n  journalDates: string[];\n  count: number;\n}\n\nexport interface AutoPromoteResult {\n  patterns: PatternOccurrence[];\n  promoted: string[];\n  skipped: string[];\n  journalsScanned: number;\n}\n\n/**\n * Scan all journals for instinct candidates that appear 3+ times.\n * These repeated patterns suggest strong behavioral signals worth auto-promoting.\n *\n * The function:\n * 1. Reads all journal files\n * 2. Extracts \"## Instinct Candidates\" sections\n * 3. Normalizes behavior text for fuzzy matching\n * 4. Groups by similar behavior (normalized string comparison)\n * 5. Returns patterns with 3+ occurrences across different journal dates\n * 6. Optionally auto-installs promoted instincts\n */\nexport function autoPromoteInstincts(\n  harnessDir: string,\n  options?: { threshold?: number; install?: boolean },\n): AutoPromoteResult {\n  const threshold = options?.threshold ?? 3;\n  const journalDir = join(harnessDir, 'memory', 'journal');\n\n  if (!existsSync(journalDir)) {\n    return { patterns: [], promoted: [], skipped: [], journalsScanned: 0 };\n  }\n\n  const files = readdirSync(journalDir)\n    .filter((f) => f.endsWith('.md') && /^\\d{4}-\\d{2}-\\d{2}/.test(f))\n    .sort();\n\n  // Collect all instinct candidate behaviors with their journal dates\n  const behaviorMap = new Map<string, { original: string; dates: Set<string> }>();\n\n  for (const file of files) {\n    const content = readFileSync(join(journalDir, file), 'utf-8');\n    const dateMatch = file.match(/^(\\d{4}-\\d{2}-\\d{2})/);\n    if (!dateMatch) continue;\n    const journalDate = dateMatch[1];\n\n    // Extract instinct candidates section\n    const sectionMatch = content.match(/## Instinct Candidates\\n([\\s\\S]*?)(?=\\n## |\\n*$)/);\n    if (!sectionMatch) continue;\n\n    const lines = sectionMatch[1]\n      .split('\\n')\n      .filter((l) => l.startsWith('- '))\n      .map((l) => l.slice(2).trim().replace(/^INSTINCT:\\s*/i, ''));\n\n    for (const line of lines) {\n      if (!line) continue;\n      const normalized = normalizeBehavior(line);\n      if (!normalized) continue;\n\n      const existing = behaviorMap.get(normalized);\n      if (existing) {\n        existing.dates.add(journalDate);\n      } else {\n        behaviorMap.set(normalized, { original: line, dates: new Set([journalDate]) });\n      }\n    }\n  }\n\n  // Filter to patterns with threshold+ occurrences across different dates\n  const patterns: PatternOccurrence[] = [];\n  for (const [, value] of behaviorMap) {\n    if (value.dates.size >= threshold) {\n      patterns.push({\n        behavior: value.original,\n        journalDates: [...value.dates].sort(),\n        count: value.dates.size,\n      });\n    }\n  }\n\n  // Sort by count descending\n  patterns.sort((a, b) => b.count - a.count);\n\n  // Deduplicate against existing instincts\n  const existingIds = new Set<string>();\n  const existingBehaviors = new Set<string>();\n  const instinctsDir = join(harnessDir, 'instincts');\n  if (existsSync(instinctsDir)) {\n    const docs = loadDirectory(instinctsDir);\n    for (const doc of docs) {\n      existingIds.add(doc.frontmatter.id);\n      if (doc.l0) existingBehaviors.add(normalizeBehavior(doc.l0));\n    }\n  }\n\n  const promoted: string[] = [];\n  const skipped: string[] = [];\n\n  for (const pattern of patterns) {\n    const normalized = normalizeBehavior(pattern.behavior);\n    const id = behaviorToId(pattern.behavior);\n\n    if (existingIds.has(id) || existingBehaviors.has(normalized)) {\n      skipped.push(id);\n      continue;\n    }\n\n    if (options?.install) {\n      const candidate: InstinctCandidate = {\n        id,\n        behavior: pattern.behavior,\n        provenance: `auto-promote:${pattern.journalDates.length}x across ${pattern.journalDates[0]} to ${pattern.journalDates[pattern.journalDates.length - 1]}`,\n        confidence: Math.min(0.9, 0.5 + pattern.count * 0.1),\n      };\n\n      const path = installInstinct(harnessDir, candidate);\n      if (path) {\n        promoted.push(id);\n      } else {\n        skipped.push(id);\n      }\n    }\n  }\n\n  return { patterns, promoted, skipped, journalsScanned: files.length };\n}\n\n/**\n * Normalize behavior text for fuzzy matching.\n * Lowercases, strips punctuation, collapses whitespace.\n */\nfunction normalizeBehavior(text: string): string {\n  return text\n    .toLowerCase()\n    .replace(/[^a-z0-9\\s]/g, '')\n    .replace(/\\s+/g, ' ')\n    .trim();\n}\n\n/**\n * Convert a behavior string to a kebab-case ID.\n */\nfunction behaviorToId(behavior: string): string {\n  return behavior\n    .toLowerCase()\n    .replace(/[^a-z0-9\\s-]/g, '')\n    .replace(/\\s+/g, '-')\n    .slice(0, 50)\n    .replace(/-+$/, '');\n}\n\n// --- Dead Primitive Detection ---\n\nexport interface DeadPrimitive {\n  id: string;\n  path: string;\n  directory: string;\n  lastModified: string;\n  daysSinceModified: number;\n  reason: string;\n}\n\nexport interface DeadPrimitiveResult {\n  dead: DeadPrimitive[];\n  totalScanned: number;\n  thresholdDays: number;\n}\n\n/**\n * Detect \"dead\" primitives — files that are:\n * 1. Orphaned (no incoming or outgoing references via related:/with:)\n * 2. Not modified in the last N days (default 30)\n *\n * Excludes session and journal directories (memory files).\n * Does NOT flag recently created primitives even if orphaned.\n */\nexport function detectDeadPrimitives(\n  harnessDir: string,\n  config?: HarnessConfig,\n  options?: { thresholdDays?: number },\n): DeadPrimitiveResult {\n  const thresholdDays = options?.thresholdDays ?? 30;\n  const now = Date.now();\n  const thresholdMs = thresholdDays * 24 * 60 * 60 * 1000;\n\n  // Build dependency graph to find orphans\n  const graph = buildDependencyGraph(harnessDir, config);\n  const orphanIds = new Set(graph.orphans);\n\n  // Also find nodes with only broken refs (effectively orphaned)\n  const connectedIds = new Set<string>();\n  for (const edge of graph.edges) {\n    connectedIds.add(edge.from);\n    connectedIds.add(edge.to);\n  }\n\n  const dead: DeadPrimitive[] = [];\n  let totalScanned = 0;\n\n  for (const node of graph.nodes) {\n    totalScanned++;\n\n    // Skip non-orphans\n    if (!orphanIds.has(node.id)) continue;\n\n    // Check file modification time\n    const absPath = join(harnessDir, node.path);\n    if (!existsSync(absPath)) continue;\n\n    try {\n      const stat = statSync(absPath);\n      const mtime = stat.mtime.getTime();\n      const daysSince = Math.floor((now - mtime) / (24 * 60 * 60 * 1000));\n\n      if (daysSince >= thresholdDays) {\n        dead.push({\n          id: node.id,\n          path: node.path,\n          directory: node.directory,\n          lastModified: stat.mtime.toISOString().split('T')[0],\n          daysSinceModified: daysSince,\n          reason: `Orphaned (no references) and not modified in ${daysSince} days`,\n        });\n      }\n    } catch (err) {\n      log.warn(`Failed to stat ${absPath}: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  // Sort by days since modified (most stale first)\n  dead.sort((a, b) => b.daysSinceModified - a.daysSinceModified);\n\n  return { dead, totalScanned, thresholdDays };\n}\n\n// --- Contradiction Detection ---\n\nexport interface Contradiction {\n  primitiveA: { id: string; path: string; type: string; text: string };\n  primitiveB: { id: string; path: string; type: string; text: string };\n  reason: string;\n  severity: 'low' | 'medium' | 'high';\n}\n\nexport interface ContradictionResult {\n  contradictions: Contradiction[];\n  rulesChecked: number;\n  instinctsChecked: number;\n}\n\n/**\n * Detect contradictions between rules and instincts.\n *\n * Checks for:\n * 1. Direct negation patterns (\"always X\" vs \"never X\", \"do X\" vs \"don't X\")\n * 2. Conflicting tag overlap with opposing behavioral signals\n * 3. Same topic with contradictory directives\n *\n * This is a heuristic-based detector (no LLM needed).\n * Returns candidate contradictions for human review.\n */\nexport function detectContradictions(\n  harnessDir: string,\n): ContradictionResult {\n  const rulesDir = join(harnessDir, 'rules');\n  const instinctsDir = join(harnessDir, 'instincts');\n\n  const rules: HarnessDocument[] = existsSync(rulesDir) ? loadDirectory(rulesDir) : [];\n  const instincts: HarnessDocument[] = existsSync(instinctsDir) ? loadDirectory(instinctsDir) : [];\n\n  const contradictions: Contradiction[] = [];\n\n  // Build a lookup of behavioral directives from each document\n  const ruleDirectives = rules.map((doc) => ({\n    doc,\n    directives: extractDirectives(doc),\n    topics: extractTopics(doc),\n  }));\n\n  const instinctDirectives = instincts.map((doc) => ({\n    doc,\n    directives: extractDirectives(doc),\n    topics: extractTopics(doc),\n  }));\n\n  // Cross-check rules vs instincts\n  for (const rule of ruleDirectives) {\n    for (const instinct of instinctDirectives) {\n      // Check directive negation patterns\n      for (const rd of rule.directives) {\n        for (const id of instinct.directives) {\n          const negation = checkNegation(rd, id);\n          if (negation) {\n            contradictions.push({\n              primitiveA: {\n                id: rule.doc.frontmatter.id,\n                path: relative(harnessDir, rule.doc.path),\n                type: 'rule',\n                text: rd.raw,\n              },\n              primitiveB: {\n                id: instinct.doc.frontmatter.id,\n                path: relative(harnessDir, instinct.doc.path),\n                type: 'instinct',\n                text: id.raw,\n              },\n              reason: negation,\n              severity: 'high',\n            });\n          }\n        }\n      }\n\n      // Check topic conflicts (same topic, opposing signals)\n      const sharedTopics = rule.topics.filter((t) => instinct.topics.includes(t));\n      if (sharedTopics.length > 0) {\n        // Check if one says \"always\" and other says \"never\" about shared topic\n        const ruleText = (rule.doc.l0 + ' ' + rule.doc.body).toLowerCase();\n        const instinctText = (instinct.doc.l0 + ' ' + instinct.doc.body).toLowerCase();\n\n        for (const topic of sharedTopics) {\n          const ruleHasAlways = hasPositiveDirective(ruleText, topic);\n          const instinctHasNever = hasNegativeDirective(instinctText, topic);\n          const ruleHasNever = hasNegativeDirective(ruleText, topic);\n          const instinctHasAlways = hasPositiveDirective(instinctText, topic);\n\n          if ((ruleHasAlways && instinctHasNever) || (ruleHasNever && instinctHasAlways)) {\n            // Avoid duplicate if already caught by directive check\n            const alreadyCaught = contradictions.some(\n              (c) =>\n                c.primitiveA.id === rule.doc.frontmatter.id &&\n                c.primitiveB.id === instinct.doc.frontmatter.id,\n            );\n            if (!alreadyCaught) {\n              contradictions.push({\n                primitiveA: {\n                  id: rule.doc.frontmatter.id,\n                  path: relative(harnessDir, rule.doc.path),\n                  type: 'rule',\n                  text: rule.doc.l0 || rule.doc.frontmatter.id,\n                },\n                primitiveB: {\n                  id: instinct.doc.frontmatter.id,\n                  path: relative(harnessDir, instinct.doc.path),\n                  type: 'instinct',\n                  text: instinct.doc.l0 || instinct.doc.frontmatter.id,\n                },\n                reason: `Conflicting directives about \"${topic}\"`,\n                severity: 'medium',\n              });\n            }\n          }\n        }\n      }\n    }\n  }\n\n  // Also check rules vs rules and instincts vs instincts\n  checkIntraGroupContradictions(ruleDirectives, 'rule', harnessDir, contradictions);\n  checkIntraGroupContradictions(instinctDirectives, 'instinct', harnessDir, contradictions);\n\n  return {\n    contradictions,\n    rulesChecked: rules.length,\n    instinctsChecked: instincts.length,\n  };\n}\n\ninterface Directive {\n  action: 'positive' | 'negative';\n  verb: string;\n  subject: string;\n  raw: string;\n}\n\n/**\n * Extract behavioral directives from a document.\n * Looks for patterns like \"always X\", \"never Y\", \"do X\", \"don't Y\", \"avoid X\", \"prefer Y\".\n */\nfunction extractDirectives(doc: HarnessDocument): Directive[] {\n  const directives: Directive[] = [];\n  const text = (doc.l0 + '\\n' + doc.body).trim();\n\n  // Process line by line\n  for (const line of text.split('\\n')) {\n    const trimmed = line.trim().toLowerCase();\n    if (!trimmed || trimmed.startsWith('#')) continue;\n\n    // Strip list markers\n    const cleaned = trimmed.replace(/^[-*]\\s+/, '').replace(/^\\d+\\.\\s+/, '');\n\n    // Positive patterns\n    const positiveMatch = cleaned.match(\n      /^(always|must|should|prefer|ensure|require|use)\\s+(.+)/,\n    );\n    if (positiveMatch) {\n      directives.push({\n        action: 'positive',\n        verb: positiveMatch[1],\n        subject: positiveMatch[2].replace(/[.!]$/, ''),\n        raw: cleaned,\n      });\n      continue;\n    }\n\n    // Negative patterns\n    const negativeMatch = cleaned.match(\n      /^(never|don'?t|avoid|do not|must not|should not|shouldn'?t)\\s+(.+)/,\n    );\n    if (negativeMatch) {\n      directives.push({\n        action: 'negative',\n        verb: negativeMatch[1],\n        subject: negativeMatch[2].replace(/[.!]$/, ''),\n        raw: cleaned,\n      });\n    }\n  }\n\n  return directives;\n}\n\n/**\n * Extract topic keywords from a document (from tags, ID, and L0).\n */\nfunction extractTopics(doc: HarnessDocument): string[] {\n  const topics: string[] = [];\n\n  // Tags as topics\n  for (const tag of doc.frontmatter.tags) {\n    topics.push(tag.toLowerCase());\n  }\n\n  // ID words as topics\n  const idParts = doc.frontmatter.id.split('-').filter((p) => p.length > 2);\n  topics.push(...idParts.map((p) => p.toLowerCase()));\n\n  return [...new Set(topics)];\n}\n\n/**\n * Check if two directives are negations of each other.\n */\nfunction checkNegation(a: Directive, b: Directive): string | null {\n  // One positive, one negative\n  if (a.action === b.action) return null;\n\n  // Normalize subjects for comparison\n  const subA = a.subject.toLowerCase().replace(/\\s+/g, ' ').trim();\n  const subB = b.subject.toLowerCase().replace(/\\s+/g, ' ').trim();\n\n  // Direct subject match\n  if (subA === subB) {\n    return `Direct contradiction: \"${a.raw}\" vs \"${b.raw}\"`;\n  }\n\n  // Fuzzy match: check if one subject is a substring of the other (with word boundaries)\n  const wordsA = subA.split(' ').filter((w) => w.length > 3);\n  const wordsB = subB.split(' ').filter((w) => w.length > 3);\n  const overlap = wordsA.filter((w) => wordsB.includes(w));\n\n  if (overlap.length >= 2 && overlap.length >= Math.min(wordsA.length, wordsB.length) * 0.6) {\n    return `Likely contradiction (shared terms: ${overlap.join(', ')}): \"${a.raw}\" vs \"${b.raw}\"`;\n  }\n\n  return null;\n}\n\nfunction hasPositiveDirective(text: string, topic: string): boolean {\n  const patterns = [\n    new RegExp(`always\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`must\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`should\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`prefer\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`use\\\\s+\\\\w*${topic}`, 'i'),\n  ];\n  return patterns.some((p) => p.test(text));\n}\n\nfunction hasNegativeDirective(text: string, topic: string): boolean {\n  const patterns = [\n    new RegExp(`never\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`avoid\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`don'?t\\\\s+\\\\w*${topic}`, 'i'),\n    new RegExp(`do not\\\\s+\\\\w*${topic}`, 'i'),\n  ];\n  return patterns.some((p) => p.test(text));\n}\n\nfunction checkIntraGroupContradictions(\n  group: Array<{ doc: HarnessDocument; directives: Directive[]; topics: string[] }>,\n  type: string,\n  harnessDir: string,\n  contradictions: Contradiction[],\n): void {\n  for (let i = 0; i < group.length; i++) {\n    for (let j = i + 1; j < group.length; j++) {\n      const a = group[i];\n      const b = group[j];\n\n      for (const da of a.directives) {\n        for (const db of b.directives) {\n          const negation = checkNegation(da, db);\n          if (negation) {\n            contradictions.push({\n              primitiveA: {\n                id: a.doc.frontmatter.id,\n                path: relative(harnessDir, a.doc.path),\n                type,\n                text: da.raw,\n              },\n              primitiveB: {\n                id: b.doc.frontmatter.id,\n                path: relative(harnessDir, b.doc.path),\n                type,\n                text: db.raw,\n              },\n              reason: negation,\n              severity: 'medium',\n            });\n          }\n        }\n      }\n    }\n  }\n}\n\n// --- Session Enrichment ---\n\nexport interface SessionEnrichment {\n  sessionId: string;\n  topics: string[];\n  tokenCount: number;\n  stepCount: number;\n  model: string;\n  toolsUsed: string[];\n  primitivesReferenced: string[];\n  duration: string;\n}\n\nexport interface EnrichmentResult {\n  enriched: SessionEnrichment[];\n  sessionsScanned: number;\n}\n\n/**\n * Enrich sessions with extracted metadata.\n *\n * Scans session files and extracts:\n * - Topics (from prompt text, frequent nouns, matched primitive IDs)\n * - Token/step counts (from frontmatter or markdown body)\n * - Model used\n * - Tools used (from tool call sections)\n * - Referenced primitives (IDs mentioned in session text)\n * - Duration\n */\nexport function enrichSessions(\n  harnessDir: string,\n  config?: HarnessConfig,\n  options?: { from?: string; to?: string },\n): EnrichmentResult {\n  const sessionsDir = join(harnessDir, 'memory', 'sessions');\n  if (!existsSync(sessionsDir)) {\n    return { enriched: [], sessionsScanned: 0 };\n  }\n\n  // Load all primitive IDs for cross-reference\n  const primitiveIds = new Set<string>();\n  const dirs = getPrimitiveDirs(config);\n  for (const dir of dirs) {\n    const fullPath = join(harnessDir, dir);\n    if (!existsSync(fullPath)) continue;\n    const { docs } = loadDirectoryWithErrors(fullPath);\n    for (const doc of docs) {\n      primitiveIds.add(doc.frontmatter.id);\n    }\n  }\n\n  const files = readdirSync(sessionsDir)\n    .filter((f) => f.endsWith('.md') && !f.startsWith('.') && !f.startsWith('_'))\n    .sort();\n\n  // Filter by date range\n  const filtered = files.filter((f) => {\n    if (!options?.from && !options?.to) return true;\n    const dateMatch = f.match(/^(\\d{4}-\\d{2}-\\d{2})/);\n    if (!dateMatch) return false;\n    const d = dateMatch[1];\n    if (options?.from && d < options.from) return false;\n    if (options?.to && d > options.to) return false;\n    return true;\n  });\n\n  const enriched: SessionEnrichment[] = [];\n\n  for (const file of filtered) {\n    const content = readFileSync(join(sessionsDir, file), 'utf-8');\n    const sessionId = file.replace(/\\.md$/, '');\n\n    const enrichment = enrichSession(content, sessionId, primitiveIds);\n    enriched.push(enrichment);\n  }\n\n  return { enriched, sessionsScanned: filtered.length };\n}\n\nfunction enrichSession(\n  content: string,\n  sessionId: string,\n  primitiveIds: Set<string>,\n): SessionEnrichment {\n  // Extract metadata from frontmatter/body\n  const tokensMatch = content.match(/[Tt]okens?[:\\s]+(\\d[\\d,]*)/);\n  const tokenCount = tokensMatch ? parseInt(tokensMatch[1].replace(/,/g, ''), 10) : 0;\n\n  const stepsMatch = content.match(/[Ss]teps?[:\\s]+(\\d+)/);\n  const stepCount = stepsMatch ? parseInt(stepsMatch[1], 10) : 0;\n\n  const modelMatch = content.match(/[Mm]odel[:\\s]+([^\\n]+)/);\n  const model = modelMatch ? modelMatch[1].trim() : 'unknown';\n\n  const durationMatch = content.match(/[Dd]uration[:\\s]+([^\\n]+)/);\n  const duration = durationMatch ? durationMatch[1].trim() : '';\n\n  // Extract tools used from tool call sections\n  const toolsUsed: string[] = [];\n  const toolMatches = content.matchAll(/### Tool(?:\\s+Call)?:\\s*(\\S+)/g);\n  for (const match of toolMatches) {\n    const toolName = match[1];\n    if (!toolsUsed.includes(toolName)) {\n      toolsUsed.push(toolName);\n    }\n  }\n\n  // Also check for tool_calls in frontmatter-style sections\n  const toolCallMatches = content.matchAll(/toolName[:\\s]+[\"']?(\\S+)[\"']?/g);\n  for (const match of toolCallMatches) {\n    const toolName = match[1];\n    if (!toolsUsed.includes(toolName)) {\n      toolsUsed.push(toolName);\n    }\n  }\n\n  // Find referenced primitives (any primitive ID that appears in text)\n  const primitivesReferenced: string[] = [];\n  for (const id of primitiveIds) {\n    if (id.length < 3) continue; // Skip very short IDs to avoid false positives\n    if (content.includes(id)) {\n      primitivesReferenced.push(id);\n    }\n  }\n\n  // Extract topics from prompt section\n  const topics = extractSessionTopics(content);\n\n  return {\n    sessionId,\n    topics,\n    tokenCount,\n    stepCount,\n    model,\n    toolsUsed,\n    primitivesReferenced,\n    duration,\n  };\n}\n\n/**\n * Extract topic keywords from session content.\n * Uses a simple frequency-based approach on meaningful words.\n */\nfunction extractSessionTopics(content: string): string[] {\n  // Extract prompt section specifically\n  const promptMatch = content.match(/## Prompt\\n([\\s\\S]*?)(?=\\n## |$)/);\n  const promptText = promptMatch ? promptMatch[1] : '';\n\n  // Also include summary\n  const summaryMatch = content.match(/## Summary\\n([\\s\\S]*?)(?=\\n## |$)/);\n  const summaryText = summaryMatch ? summaryMatch[1] : '';\n\n  const text = (promptText + ' ' + summaryText).toLowerCase();\n\n  // Common stop words to filter out\n  const stopWords = new Set([\n    'the', 'a', 'an', 'is', 'are', 'was', 'were', 'be', 'been', 'being',\n    'have', 'has', 'had', 'do', 'does', 'did', 'will', 'would', 'could',\n    'should', 'may', 'might', 'shall', 'can', 'need', 'must', 'to', 'of',\n    'in', 'for', 'on', 'with', 'at', 'by', 'from', 'as', 'into', 'about',\n    'like', 'through', 'after', 'before', 'between', 'under', 'during',\n    'and', 'or', 'but', 'not', 'no', 'nor', 'so', 'yet', 'both', 'either',\n    'neither', 'each', 'every', 'all', 'any', 'few', 'more', 'most', 'other',\n    'some', 'such', 'than', 'too', 'very', 'just', 'also', 'this', 'that',\n    'these', 'those', 'it', 'its', 'i', 'me', 'my', 'we', 'our', 'you',\n    'your', 'he', 'she', 'they', 'them', 'their', 'what', 'which', 'who',\n    'when', 'where', 'how', 'why', 'if', 'then', 'else', 'while', 'up',\n    'out', 'off', 'over', 'only', 'own', 'same', 'get', 'got', 'make',\n    'made', 'use', 'used', 'using', 'one', 'two', 'new',\n  ]);\n\n  // Count word frequencies\n  const words = text\n    .replace(/[^a-z0-9\\s-]/g, '')\n    .split(/\\s+/)\n    .filter((w) => w.length > 3 && !stopWords.has(w));\n\n  const freq = new Map<string, number>();\n  for (const word of words) {\n    freq.set(word, (freq.get(word) ?? 0) + 1);\n  }\n\n  // Return top 5 most frequent meaningful words\n  return Array.from(freq.entries())\n    .filter(([, count]) => count >= 1)\n    .sort((a, b) => b[1] - a[1])\n    .slice(0, 5)\n    .map(([word]) => word);\n}\n\n// --- Capability Suggestions ---\n\nexport interface CapabilitySuggestion {\n  topic: string;\n  frequency: number;\n  sessionDates: string[];\n  suggestion: string;\n  suggestedType: 'skill' | 'playbook';\n}\n\nexport interface CapabilitySuggestionResult {\n  suggestions: CapabilitySuggestion[];\n  topicsAnalyzed: number;\n  sessionsScanned: number;\n}\n\n/**\n * Suggest capabilities (skills/playbooks) for frequent session topics\n * that don't have existing coverage.\n *\n * Scans sessions for recurring topics, cross-references against existing\n * skills/playbooks, and suggests new ones for uncovered topics.\n */\nexport function suggestCapabilities(\n  harnessDir: string,\n  config?: HarnessConfig,\n  options?: { minFrequency?: number },\n): CapabilitySuggestionResult {\n  const minFrequency = options?.minFrequency ?? 3;\n\n  // Enrich sessions to get topics\n  const { enriched, sessionsScanned } = enrichSessions(harnessDir, config);\n\n  // Collect topic frequency across sessions\n  const topicOccurrences = new Map<string, Set<string>>();\n  for (const session of enriched) {\n    const dateMatch = session.sessionId.match(/^(\\d{4}-\\d{2}-\\d{2})/);\n    const date = dateMatch ? dateMatch[1] : session.sessionId;\n\n    for (const topic of session.topics) {\n      if (!topicOccurrences.has(topic)) {\n        topicOccurrences.set(topic, new Set());\n      }\n      topicOccurrences.get(topic)!.add(date);\n    }\n  }\n\n  // Load existing skills and playbooks\n  const coveredTopics = new Set<string>();\n  const skillsDir = join(harnessDir, 'skills');\n  const playbooksDir = join(harnessDir, 'playbooks');\n\n  for (const dir of [skillsDir, playbooksDir]) {\n    if (!existsSync(dir)) continue;\n    const docs = loadDirectory(dir);\n    for (const doc of docs) {\n      // Add ID parts as covered topics\n      for (const part of doc.frontmatter.id.split('-')) {\n        if (part.length > 2) coveredTopics.add(part.toLowerCase());\n      }\n      // Add tags as covered topics\n      for (const tag of doc.frontmatter.tags) {\n        coveredTopics.add(tag.toLowerCase());\n      }\n    }\n  }\n\n  // Find frequent uncovered topics\n  const suggestions: CapabilitySuggestion[] = [];\n\n  for (const [topic, dates] of topicOccurrences) {\n    if (dates.size < minFrequency) continue;\n    if (coveredTopics.has(topic)) continue;\n\n    const suggestedType = dates.size >= 5 ? 'playbook' : 'skill';\n    suggestions.push({\n      topic,\n      frequency: dates.size,\n      sessionDates: [...dates].sort(),\n      suggestion: `Create a ${suggestedType} for \"${topic}\" — appeared in ${dates.size} session(s)`,\n      suggestedType,\n    });\n  }\n\n  // Sort by frequency\n  suggestions.sort((a, b) => b.frequency - a.frequency);\n\n  return {\n    suggestions,\n    topicsAnalyzed: topicOccurrences.size,\n    sessionsScanned,\n  };\n}\n\n// --- Failure Taxonomy ---\n\n/**\n * Named failure modes with recovery strategies.\n * Based on common agent failure patterns (context overflow, tool errors,\n * budget exhaustion, hallucination, stale primitives, circular delegation).\n */\nexport type FailureMode =\n  | 'context_overflow'\n  | 'tool_execution_error'\n  | 'budget_exhausted'\n  | 'rate_limited'\n  | 'llm_timeout'\n  | 'llm_error'\n  | 'hallucination_detected'\n  | 'stale_primitive'\n  | 'circular_delegation'\n  | 'missing_dependency'\n  | 'parse_error'\n  | 'config_invalid'\n  | 'mcp_connection_failed'\n  | 'state_corruption'\n  | 'unknown';\n\nexport interface FailureRecord {\n  mode: FailureMode;\n  timestamp: string;\n  sessionId?: string;\n  message: string;\n  context?: Record<string, unknown>;\n  recoveryAttempted?: string;\n  recovered: boolean;\n}\n\nexport interface FailureTaxonomy {\n  modes: Record<FailureMode, {\n    description: string;\n    severity: 'low' | 'medium' | 'high' | 'critical';\n    recoveryStrategies: string[];\n    autoRecoverable: boolean;\n  }>;\n}\n\n/**\n * The canonical failure taxonomy for agent-harness.\n * Each mode has a description, severity level, recovery strategies,\n * and whether automatic recovery is possible.\n */\nexport const FAILURE_TAXONOMY: FailureTaxonomy = {\n  modes: {\n    context_overflow: {\n      description: 'System prompt + conversation exceeds model context window',\n      severity: 'high',\n      recoveryStrategies: [\n        'Trim oldest messages from conversation history',\n        'Reduce primitive loading level (L2 → L1 → L0)',\n        'Archive old sessions to free memory budget',\n        'Split into sub-conversations with summarized context',\n      ],\n      autoRecoverable: true,\n    },\n    tool_execution_error: {\n      description: 'An MCP or HTTP tool call failed during execution',\n      severity: 'medium',\n      recoveryStrategies: [\n        'Retry with exponential backoff',\n        'Fall back to alternative tool if available',\n        'Report error to LLM and ask for alternative approach',\n        'Skip tool and proceed with available context',\n      ],\n      autoRecoverable: true,\n    },\n    budget_exhausted: {\n      description: 'Daily or monthly spending limit has been reached',\n      severity: 'critical',\n      recoveryStrategies: [\n        'Wait until next budget period',\n        'Switch to cheaper model (fast_model or summary_model)',\n        'Queue non-urgent tasks for later execution',\n        'Alert operator to increase budget',\n      ],\n      autoRecoverable: false,\n    },\n    rate_limited: {\n      description: 'LLM API rate limit hit (per-minute/hour/day)',\n      severity: 'medium',\n      recoveryStrategies: [\n        'Wait for retryAfterMs from rate limiter',\n        'Reduce request frequency',\n        'Queue and batch requests',\n      ],\n      autoRecoverable: true,\n    },\n    llm_timeout: {\n      description: 'LLM API call timed out without response',\n      severity: 'medium',\n      recoveryStrategies: [\n        'Retry with same prompt',\n        'Retry with shorter prompt (reduce context)',\n        'Switch to faster model',\n        'Increase timeout_ms in config',\n      ],\n      autoRecoverable: true,\n    },\n    llm_error: {\n      description: 'LLM API returned an error response (4xx/5xx)',\n      severity: 'high',\n      recoveryStrategies: [\n        'Retry with exponential backoff (max_retries in config)',\n        'Switch to fallback model',\n        'Check API key validity',\n        'Log error details for debugging',\n      ],\n      autoRecoverable: true,\n    },\n    hallucination_detected: {\n      description: 'LLM output contains fabricated facts or references to non-existent primitives',\n      severity: 'medium',\n      recoveryStrategies: [\n        'Re-prompt with explicit grounding: \"Only reference primitives that exist\"',\n        'Validate output against known primitive IDs',\n        'Add validation step before acting on LLM output',\n        'Record in journal for future training',\n      ],\n      autoRecoverable: false,\n    },\n    stale_primitive: {\n      description: 'A referenced primitive is outdated, deprecated, or orphaned',\n      severity: 'low',\n      recoveryStrategies: [\n        'Run detectDeadPrimitives() to identify stale files',\n        'Archive deprecated primitives',\n        'Update references to point to current versions',\n        'Auto-flag via validator',\n      ],\n      autoRecoverable: true,\n    },\n    circular_delegation: {\n      description: 'Agent delegation loop detected (A delegates to B delegates to A)',\n      severity: 'high',\n      recoveryStrategies: [\n        'Track delegation chain and break on cycle detection',\n        'Set max delegation depth (default: 3)',\n        'Return partial result from last agent in chain',\n        'Log delegation graph for debugging',\n      ],\n      autoRecoverable: true,\n    },\n    missing_dependency: {\n      description: 'A required dependency (primitive, MCP server, API key) is missing',\n      severity: 'high',\n      recoveryStrategies: [\n        'Run doctorHarness() to auto-fix missing files',\n        'Check .env for required API keys',\n        'Install missing MCP servers',\n        'Prompt user to install missing bundle',\n      ],\n      autoRecoverable: false,\n    },\n    parse_error: {\n      description: 'A primitive file has invalid YAML frontmatter or malformed content',\n      severity: 'medium',\n      recoveryStrategies: [\n        'Run fixCapability() to auto-repair frontmatter',\n        'Skip the malformed file and log a warning',\n        'Use default frontmatter values',\n        'Report to user for manual fix',\n      ],\n      autoRecoverable: true,\n    },\n    config_invalid: {\n      description: 'config.yaml fails schema validation',\n      severity: 'critical',\n      recoveryStrategies: [\n        'Fall back to CONFIG_DEFAULTS',\n        'Report specific validation errors to user',\n        'Run harness doctor to attempt repair',\n      ],\n      autoRecoverable: false,\n    },\n    mcp_connection_failed: {\n      description: 'Failed to connect to an MCP server (process spawn or HTTP)',\n      severity: 'medium',\n      recoveryStrategies: [\n        'Retry connection with backoff',\n        'Disable the server and continue without its tools',\n        'Check command/URL/env configuration',\n        'Fall back to built-in tools only',\n      ],\n      autoRecoverable: true,\n    },\n    state_corruption: {\n      description: 'state.md is unreadable or contains invalid data',\n      severity: 'high',\n      recoveryStrategies: [\n        'Fall back to DEFAULT_STATE',\n        'Rebuild state from session history',\n        'Reset state.md and log the event',\n      ],\n      autoRecoverable: true,\n    },\n    unknown: {\n      description: 'An unclassified error occurred',\n      severity: 'high',\n      recoveryStrategies: [\n        'Log full error with stack trace',\n        'Record in health.json failure counter',\n        'Alert operator',\n        'Graceful shutdown if critical path',\n      ],\n      autoRecoverable: false,\n    },\n  },\n};\n\nexport interface FailureAnalysis {\n  recentFailures: FailureRecord[];\n  modeFrequency: Record<string, number>;\n  mostCommonMode: FailureMode | null;\n  suggestedRecovery: string[];\n  healthImplication: 'healthy' | 'degraded' | 'unhealthy';\n}\n\n/**\n * Classify an error into a failure mode.\n */\nexport function classifyFailure(error: Error | string, context?: Record<string, unknown>): FailureMode {\n  const msg = typeof error === 'string' ? error.toLowerCase() : error.message.toLowerCase();\n\n  if (msg.includes('context') && (msg.includes('overflow') || msg.includes('too long') || msg.includes('exceed'))) {\n    return 'context_overflow';\n  }\n  if (msg.includes('tool') && (msg.includes('fail') || msg.includes('error') || msg.includes('timeout'))) {\n    return 'tool_execution_error';\n  }\n  if (msg.includes('budget') || msg.includes('spending') || msg.includes('limit exceeded')) {\n    return 'budget_exhausted';\n  }\n  if (msg.includes('rate limit') || msg.includes('429') || msg.includes('too many requests')) {\n    return 'rate_limited';\n  }\n  if (msg.includes('timeout') || msg.includes('timed out') || msg.includes('ETIMEDOUT')) {\n    return 'llm_timeout';\n  }\n  if (msg.includes('mcp') && (msg.includes('connect') || msg.includes('spawn') || msg.includes('failed'))) {\n    return 'mcp_connection_failed';\n  }\n  if (msg.includes('parse') || msg.includes('yaml') || msg.includes('frontmatter') || msg.includes('malformed')) {\n    return 'parse_error';\n  }\n  if (msg.includes('config') && (msg.includes('invalid') || msg.includes('validation'))) {\n    return 'config_invalid';\n  }\n  if (msg.includes('state') && (msg.includes('corrupt') || msg.includes('invalid') || msg.includes('unreadable'))) {\n    return 'state_corruption';\n  }\n  if (msg.includes('circular') || msg.includes('delegation loop') || msg.includes('cycle')) {\n    return 'circular_delegation';\n  }\n  if (msg.includes('missing') || msg.includes('not found') || msg.includes('dependency')) {\n    return 'missing_dependency';\n  }\n  if (msg.includes('401') || msg.includes('403') || msg.includes('500') || msg.includes('502') || msg.includes('503')) {\n    return 'llm_error';\n  }\n\n  return 'unknown';\n}\n\n/**\n * Get recovery strategies for a failure mode.\n */\nexport function getRecoveryStrategies(mode: FailureMode): string[] {\n  return FAILURE_TAXONOMY.modes[mode]?.recoveryStrategies ?? ['Log error and alert operator'];\n}\n\n/**\n * Analyze failure patterns from session history and health data.\n * Returns frequency analysis and recovery suggestions.\n */\nexport function analyzeFailures(\n  harnessDir: string,\n  options?: { days?: number },\n): FailureAnalysis {\n  const days = options?.days ?? 7;\n  const now = Date.now();\n  const cutoffMs = days * 24 * 60 * 60 * 1000;\n\n  const recentFailures: FailureRecord[] = [];\n\n  // Scan health.json for failures\n  const healthPath = join(harnessDir, 'memory', 'health.json');\n  if (existsSync(healthPath)) {\n    try {\n      const health = JSON.parse(readFileSync(healthPath, 'utf-8'));\n      if (health.lastError) {\n        const mode = classifyFailure(health.lastError);\n        recentFailures.push({\n          mode,\n          timestamp: health.lastFailure || new Date().toISOString(),\n          message: health.lastError,\n          recovered: health.consecutiveFailures === 0,\n        });\n      }\n    } catch {\n      // Malformed health.json\n    }\n  }\n\n  // Scan sessions for error indicators\n  const sessionsDir = join(harnessDir, 'memory', 'sessions');\n  if (existsSync(sessionsDir)) {\n    const files = readdirSync(sessionsDir)\n      .filter((f) => f.endsWith('.md') && !f.startsWith('.'))\n      .sort()\n      .reverse();\n\n    for (const file of files) {\n      const dateMatch = file.match(/^(\\d{4}-\\d{2}-\\d{2})/);\n      if (dateMatch) {\n        const fileDate = new Date(dateMatch[1]).getTime();\n        if (now - fileDate > cutoffMs) break;\n      }\n\n      try {\n        const content = readFileSync(join(sessionsDir, file), 'utf-8');\n        // Look for error patterns in session content\n        const errorLines = content.split('\\n').filter((l) =>\n          l.toLowerCase().includes('error') ||\n          l.toLowerCase().includes('failed') ||\n          l.toLowerCase().includes('timeout'),\n        );\n\n        for (const line of errorLines.slice(0, 3)) {\n          const mode = classifyFailure(line);\n          if (mode !== 'unknown') {\n            recentFailures.push({\n              mode,\n              timestamp: dateMatch?.[1] ?? 'unknown',\n              sessionId: file.replace('.md', ''),\n              message: line.trim().slice(0, 200),\n              recovered: true,\n            });\n          }\n        }\n      } catch {\n        // Skip unreadable sessions\n      }\n    }\n  }\n\n  // Calculate frequency\n  const modeFrequency: Record<string, number> = {};\n  for (const f of recentFailures) {\n    modeFrequency[f.mode] = (modeFrequency[f.mode] ?? 0) + 1;\n  }\n\n  // Find most common mode\n  let mostCommonMode: FailureMode | null = null;\n  let maxFreq = 0;\n  for (const [mode, count] of Object.entries(modeFrequency)) {\n    if (count > maxFreq) {\n      maxFreq = count;\n      mostCommonMode = mode as FailureMode;\n    }\n  }\n\n  // Suggest recovery\n  const suggestedRecovery = mostCommonMode\n    ? getRecoveryStrategies(mostCommonMode)\n    : [];\n\n  // Determine health implication\n  let healthImplication: 'healthy' | 'degraded' | 'unhealthy' = 'healthy';\n  if (recentFailures.length > 5) {\n    healthImplication = 'unhealthy';\n  } else if (recentFailures.length > 0) {\n    healthImplication = 'degraded';\n  }\n\n  return {\n    recentFailures: recentFailures.slice(0, 20),\n    modeFrequency,\n    mostCommonMode,\n    suggestedRecovery,\n    healthImplication,\n  };\n}\n\n// --- Verification Gates ---\n\nexport type GateStatus = 'pass' | 'fail' | 'warn' | 'skip';\n\nexport interface GateCheck {\n  name: string;\n  description: string;\n  status: GateStatus;\n  message: string;\n  details?: Record<string, unknown>;\n}\n\nexport interface VerificationGateResult {\n  gateName: string;\n  passed: boolean;\n  checks: GateCheck[];\n  summary: string;\n}\n\nexport type GateDefinition = {\n  name: string;\n  description: string;\n  check: (harnessDir: string, config?: HarnessConfig) => GateCheck[];\n};\n\n/**\n * Built-in verification gates for the harness.\n * Each gate is a set of checks that must pass at a specific stage.\n */\nexport const BUILTIN_GATES: GateDefinition[] = [\n  {\n    name: 'pre-boot',\n    description: 'Checks before agent boot: config valid, CORE.md exists, API key available',\n    check: (harnessDir: string) => {\n      const checks: GateCheck[] = [];\n\n      // CORE.md exists\n      checks.push(existsSync(join(harnessDir, 'CORE.md'))\n        ? { name: 'core-md', description: 'CORE.md exists', status: 'pass', message: 'CORE.md present' }\n        : { name: 'core-md', description: 'CORE.md exists', status: 'fail', message: 'Missing CORE.md — required for agent identity' });\n\n      // Config valid\n      try {\n        loadConfig(harnessDir);\n        checks.push({ name: 'config-valid', description: 'config.yaml valid', status: 'pass', message: 'Config parsed successfully' });\n      } catch (err) {\n        checks.push({ name: 'config-valid', description: 'config.yaml valid', status: 'fail', message: `Config error: ${err instanceof Error ? err.message : String(err)}` });\n      }\n\n      // API key available\n      const hasKey = !!(process.env.OPENROUTER_API_KEY || process.env.OPENAI_API_KEY || process.env.ANTHROPIC_API_KEY);\n      checks.push(hasKey\n        ? { name: 'api-key', description: 'API key available', status: 'pass', message: 'API key found in environment' }\n        : { name: 'api-key', description: 'API key available', status: 'warn', message: 'No API key in environment — will need --api-key flag' });\n\n      // Memory directory\n      const memDir = join(harnessDir, 'memory');\n      checks.push(existsSync(memDir)\n        ? { name: 'memory-dir', description: 'Memory directory exists', status: 'pass', message: 'memory/ directory present' }\n        : { name: 'memory-dir', description: 'Memory directory exists', status: 'warn', message: 'memory/ directory missing — will be created on first run' });\n\n      return checks;\n    },\n  },\n  {\n    name: 'pre-run',\n    description: 'Checks before each LLM call: budget, rate limits, context budget',\n    check: (harnessDir: string) => {\n      const checks: GateCheck[] = [];\n\n      let config: HarnessConfig;\n      try {\n        config = loadConfig(harnessDir);\n      } catch {\n        checks.push({ name: 'config-load', description: 'Config loadable', status: 'fail', message: 'Cannot load config' });\n        return checks;\n      }\n\n      // Budget check\n      try {\n        const budgetStatus = checkBudget(harnessDir, config.budget);\n        const exceeded = (budgetStatus.daily_remaining_usd !== null && budgetStatus.daily_remaining_usd <= 0) ||\n          (budgetStatus.monthly_remaining_usd !== null && budgetStatus.monthly_remaining_usd <= 0);\n        if (exceeded) {\n          checks.push({ name: 'budget', description: 'Budget not exceeded', status: 'fail', message: 'Budget limit exceeded', details: { ...budgetStatus } });\n        } else {\n          checks.push({ name: 'budget', description: 'Budget not exceeded', status: 'pass', message: 'Within budget' });\n        }\n      } catch (err) {\n        checks.push({ name: 'budget', description: 'Budget not exceeded', status: 'skip', message: `Budget check unavailable: ${err instanceof Error ? err.message : String(err)}` });\n      }\n\n      // Rate limit check\n      try {\n        const limits = buildRateLimits(config);\n        if (limits.length === 0) {\n          checks.push({ name: 'rate-limit', description: 'Rate limit not hit', status: 'pass', message: 'No rate limits configured' });\n        } else {\n          let blocked = false;\n          for (const limit of limits) {\n            const rateCheck = checkRateLimit(harnessDir, limit);\n            if (!rateCheck.allowed) {\n              const windowLabel = limit.window_ms <= 60_000 ? 'minute' : limit.window_ms <= 3_600_000 ? 'hour' : 'day';\n              checks.push({ name: 'rate-limit', description: 'Rate limit not hit', status: 'fail', message: `Rate limited (${windowLabel}): ${rateCheck.current}/${rateCheck.max}. Retry after ${Math.ceil(rateCheck.retry_after_ms / 1000)}s` });\n              blocked = true;\n              break;\n            }\n          }\n          if (!blocked) {\n            checks.push({ name: 'rate-limit', description: 'Rate limit not hit', status: 'pass', message: 'Within rate limits' });\n          }\n        }\n      } catch (err) {\n        checks.push({ name: 'rate-limit', description: 'Rate limit not hit', status: 'skip', message: `Rate limit check unavailable: ${err instanceof Error ? err.message : String(err)}` });\n      }\n\n      // Health check\n      const healthPath = join(harnessDir, 'memory', 'health.json');\n      if (existsSync(healthPath)) {\n        try {\n          const health = JSON.parse(readFileSync(healthPath, 'utf-8'));\n          if (health.consecutiveFailures >= 3) {\n            checks.push({ name: 'health', description: 'Agent healthy', status: 'warn', message: `${health.consecutiveFailures} consecutive failures detected` });\n          } else {\n            checks.push({ name: 'health', description: 'Agent healthy', status: 'pass', message: 'No recent failure pattern' });\n          }\n        } catch {\n          checks.push({ name: 'health', description: 'Agent healthy', status: 'skip', message: 'Health data unavailable' });\n        }\n      }\n\n      return checks;\n    },\n  },\n  {\n    name: 'post-session',\n    description: 'Checks after a session: session recorded, no parse errors, primitives intact',\n    check: (harnessDir: string) => {\n      const checks: GateCheck[] = [];\n\n      // Sessions directory exists and has files\n      const sessionsDir = join(harnessDir, 'memory', 'sessions');\n      if (existsSync(sessionsDir)) {\n        const files = readdirSync(sessionsDir).filter((f) => f.endsWith('.md') && !f.startsWith('.'));\n        checks.push({\n          name: 'sessions-recorded',\n          description: 'Sessions being recorded',\n          status: files.length > 0 ? 'pass' : 'warn',\n          message: `${files.length} session file(s) in memory`,\n        });\n      } else {\n        checks.push({ name: 'sessions-recorded', description: 'Sessions being recorded', status: 'warn', message: 'No sessions directory' });\n      }\n\n      // Check for parse errors in primitives\n      const dirs = getPrimitiveDirs();\n      let totalParseErrors = 0;\n      for (const dir of dirs) {\n        const fullPath = join(harnessDir, dir);\n        if (!existsSync(fullPath)) continue;\n        const { errors } = loadDirectoryWithErrors(fullPath);\n        totalParseErrors += errors.length;\n      }\n\n      checks.push(totalParseErrors === 0\n        ? { name: 'parse-errors', description: 'No primitive parse errors', status: 'pass', message: 'All primitives parse cleanly' }\n        : { name: 'parse-errors', description: 'No primitive parse errors', status: 'warn', message: `${totalParseErrors} parse error(s) in primitives` });\n\n      return checks;\n    },\n  },\n  {\n    name: 'pre-deploy',\n    description: 'Checks before deployment: validator passes, no dead primitives, no contradictions',\n    check: (harnessDir: string, config?: HarnessConfig) => {\n      const checks: GateCheck[] = [];\n\n      // Run validator\n      try {\n        const validation = validateHarness(harnessDir);\n        if (validation.errors.length > 0) {\n          checks.push({ name: 'validator', description: 'Validator passes', status: 'fail', message: `${validation.errors.length} error(s)`, details: { errors: validation.errors } });\n        } else if (validation.warnings.length > 0) {\n          checks.push({ name: 'validator', description: 'Validator passes', status: 'warn', message: `${validation.warnings.length} warning(s)` });\n        } else {\n          checks.push({ name: 'validator', description: 'Validator passes', status: 'pass', message: 'Validation clean' });\n        }\n      } catch (err) {\n        checks.push({ name: 'validator', description: 'Validator passes', status: 'fail', message: `Validator error: ${err instanceof Error ? err.message : String(err)}` });\n      }\n\n      // Check for dead primitives\n      const deadResult = detectDeadPrimitives(harnessDir, config);\n      checks.push(deadResult.dead.length === 0\n        ? { name: 'dead-primitives', description: 'No dead primitives', status: 'pass', message: 'All primitives referenced or recently modified' }\n        : { name: 'dead-primitives', description: 'No dead primitives', status: 'warn', message: `${deadResult.dead.length} dead primitive(s) found`, details: { dead: deadResult.dead.map((d) => d.id) } });\n\n      // Check for contradictions\n      const contradictionResult = detectContradictions(harnessDir);\n      checks.push(contradictionResult.contradictions.length === 0\n        ? { name: 'contradictions', description: 'No contradictions', status: 'pass', message: 'No conflicting rules/instincts' }\n        : { name: 'contradictions', description: 'No contradictions', status: 'warn', message: `${contradictionResult.contradictions.length} potential contradiction(s)` });\n\n      return checks;\n    },\n  },\n];\n\n/**\n * Run a verification gate by name.\n * Returns all check results and an overall pass/fail status.\n */\nexport function runGate(\n  gateName: string,\n  harnessDir: string,\n  config?: HarnessConfig,\n): VerificationGateResult {\n  const gate = BUILTIN_GATES.find((g) => g.name === gateName);\n  if (!gate) {\n    return {\n      gateName,\n      passed: false,\n      checks: [{ name: 'gate-not-found', description: 'Gate exists', status: 'fail', message: `Unknown gate: ${gateName}` }],\n      summary: `Gate \"${gateName}\" not found. Available: ${BUILTIN_GATES.map((g) => g.name).join(', ')}`,\n    };\n  }\n\n  const checks = gate.check(harnessDir, config);\n  const hasFails = checks.some((c) => c.status === 'fail');\n  const hasWarns = checks.some((c) => c.status === 'warn');\n\n  const passed = !hasFails;\n  const passCount = checks.filter((c) => c.status === 'pass').length;\n  const failCount = checks.filter((c) => c.status === 'fail').length;\n  const warnCount = checks.filter((c) => c.status === 'warn').length;\n\n  let summary = `${gate.name}: ${passCount} passed`;\n  if (failCount > 0) summary += `, ${failCount} failed`;\n  if (warnCount > 0) summary += `, ${warnCount} warnings`;\n\n  return { gateName, passed, checks, summary };\n}\n\n/**\n * Run all built-in verification gates.\n */\nexport function runAllGates(\n  harnessDir: string,\n  config?: HarnessConfig,\n): VerificationGateResult[] {\n  return BUILTIN_GATES.map((gate) => runGate(gate.name, harnessDir, config));\n}\n\n/**\n * List available gate names and descriptions.\n */\nexport function listGates(): Array<{ name: string; description: string }> {\n  return BUILTIN_GATES.map((g) => ({ name: g.name, description: g.description 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package/dist/journal-WANJL3MI.js

@@ -0,0 +1,24 @@
+#!/usr/bin/env node
+
+import {
+  compressJournals,
+  listJournals,
+  listUnjournaled,
+  parseJournalSynthesis,
+  synthesizeJournal,
+  synthesizeJournalRange
+} from "./chunk-CSL3ERUI.js";
+import "./chunk-UPLBF4RZ.js";
+import "./chunk-IZ6UZ3ZL.js";
+import "./chunk-CHJ5GNZC.js";
+import "./chunk-4CWAGBNS.js";
+import "./chunk-ZZJOFKAT.js";
+export {
+  compressJournals,
+  listJournals,
+  listUnjournaled,
+  parseJournalSynthesis,
+  synthesizeJournal,
+  synthesizeJournalRange
+};
+//# sourceMappingURL=journal-WANJL3MI.js.map

package/dist/journal-WANJL3MI.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/dist/loader-C3TKIKZR.js

@@ -0,0 +1,23 @@
+#!/usr/bin/env node
+
+import {
+  estimateTokens,
+  getAtLevel,
+  loadAllPrimitives,
+  loadAllPrimitivesWithErrors,
+  loadDirectory,
+  loadDirectoryWithErrors,
+  parseHarnessDocument
+} from "./chunk-UPLBF4RZ.js";
+import "./chunk-4CWAGBNS.js";
+import "./chunk-ZZJOFKAT.js";
+export {
+  estimateTokens,
+  getAtLevel,
+  loadAllPrimitives,
+  loadAllPrimitivesWithErrors,
+  loadDirectory,
+  loadDirectoryWithErrors,
+  parseHarnessDocument
+};
+//# sourceMappingURL=loader-C3TKIKZR.js.map

package/dist/loader-C3TKIKZR.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/dist/mcp-WTQJJZAO.js

@@ -0,0 +1,15 @@
+#!/usr/bin/env node
+
+import {
+  createMcpManager,
+  loadMcpTools,
+  validateMcpConfig
+} from "./chunk-5H34JPMB.js";
+import "./chunk-BSKDOFRT.js";
+import "./chunk-ZZJOFKAT.js";
+export {
+  createMcpManager,
+  loadMcpTools,
+  validateMcpConfig
+};
+//# sourceMappingURL=mcp-WTQJJZAO.js.map

package/dist/mcp-WTQJJZAO.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":[],"sourcesContent":[],"mappings":"","names":[]}

package/dist/mcp-discovery-WPAQFL6S.js

@@ -0,0 +1,377 @@
+#!/usr/bin/env node
+
+import "./chunk-ZZJOFKAT.js";
+
+// src/runtime/mcp-discovery.ts
+import { existsSync, readFileSync } from "fs";
+import { join } from "path";
+import { homedir, platform } from "os";
+function vscodeGlobalStoragePath(h, mac, extensionId) {
+  if (mac) {
+    return join(h, "Library", "Application Support", "Code", "User", "globalStorage", extensionId);
+  }
+  return join(h, ".config", "Code", "User", "globalStorage", extensionId);
+}
+function extractClaudeCodeServers(root) {
+  const merged = {};
+  const topLevel = root.mcpServers;
+  if (topLevel && typeof topLevel === "object" && !Array.isArray(topLevel)) {
+    Object.assign(merged, topLevel);
+  }
+  const projects = root.projects;
+  if (projects && typeof projects === "object" && !Array.isArray(projects)) {
+    for (const projectData of Object.values(projects)) {
+      if (!projectData || typeof projectData !== "object" || Array.isArray(projectData)) continue;
+      const proj = projectData;
+      const projServers = proj.mcpServers;
+      if (projServers && typeof projServers === "object" && !Array.isArray(projServers)) {
+        for (const [name, config] of Object.entries(projServers)) {
+          if (!(name in merged)) {
+            merged[name] = config;
+          }
+        }
+      }
+    }
+  }
+  return merged;
+}
+function buildToolConfigs(h, mac) {
+  return [
+    {
+      tool: "Claude Desktop",
+      path: () => mac ? join(h, "Library", "Application Support", "Claude", "claude_desktop_config.json") : join(h, ".config", "Claude", "claude_desktop_config.json"),
+      rootKey: "mcpServers"
+    },
+    {
+      tool: "Claude Code",
+      path: () => join(h, ".claude.json"),
+      rootKey: "mcpServers",
+      usesTypeField: true,
+      extractServers: extractClaudeCodeServers
+    },
+    {
+      tool: "Cursor",
+      path: () => join(h, ".cursor", "mcp.json"),
+      rootKey: "mcpServers"
+    },
+    {
+      tool: "Windsurf",
+      path: () => join(h, ".codeium", "windsurf", "mcp_config.json"),
+      rootKey: "mcpServers"
+    },
+    {
+      tool: "Copilot CLI",
+      path: () => join(h, ".copilot", "mcp-config.json"),
+      rootKey: "mcpServers"
+    },
+    {
+      tool: "Cline",
+      path: () => join(vscodeGlobalStoragePath(h, mac, "saoudrizwan.claude-dev"), "settings", "cline_mcp_settings.json"),
+      rootKey: "mcpServers"
+    },
+    {
+      tool: "Roo Code",
+      path: () => join(vscodeGlobalStoragePath(h, mac, "rooveterinaryinc.roo-cline"), "settings", "mcp_settings.json"),
+      rootKey: "mcpServers"
+    },
+    {
+      tool: "VS Code",
+      path: () => mac ? join(h, "Library", "Application Support", "Code", "User", "mcp.json") : join(h, ".config", "Code", "User", "mcp.json"),
+      rootKey: "servers",
+      usesTypeField: true
+    },
+    {
+      tool: "Zed",
+      path: () => join(h, ".config", "zed", "settings.json"),
+      rootKey: "context_servers"
+    }
+  ];
+}
+function inferTransport(serverObj, usesTypeField) {
+  if (usesTypeField && typeof serverObj.type === "string") {
+    const t = serverObj.type.toLowerCase();
+    if (t === "sse") return "sse";
+    if (t === "http") return "http";
+    if (t === "stdio") return "stdio";
+  }
+  if (typeof serverObj.command === "string") return "stdio";
+  if (typeof serverObj.url === "string" || typeof serverObj.serverUrl === "string") {
+    const url = serverObj.url ?? serverObj.serverUrl;
+    if (url.includes("/sse") || serverObj.type === "sse") return "sse";
+    return "http";
+  }
+  return "stdio";
+}
+function parseServer(name, serverObj, usesTypeField) {
+  const transport = inferTransport(serverObj, usesTypeField);
+  const server = { name, transport };
+  if (transport === "stdio") {
+    if (typeof serverObj.command === "string") server.command = serverObj.command;
+    if (Array.isArray(serverObj.args)) {
+      server.args = serverObj.args.filter((a) => typeof a === "string").map((a) => redactArgValue(a));
+    }
+    if (serverObj.env && typeof serverObj.env === "object" && !Array.isArray(serverObj.env)) {
+      server.env = redactEnv(filterStringRecord(serverObj.env));
+    }
+    if (typeof serverObj.cwd === "string") server.cwd = serverObj.cwd;
+  } else {
+    const url = serverObj.url ?? serverObj.serverUrl;
+    if (typeof url === "string") server.url = url;
+    if (serverObj.headers && typeof serverObj.headers === "object" && !Array.isArray(serverObj.headers)) {
+      const headers = filterStringRecord(serverObj.headers);
+      for (const [k, v] of Object.entries(headers)) {
+        if (SECRET_PATTERNS.test(k) || SECRET_PATTERNS.test(v)) {
+          headers[k] = `\${${k.toUpperCase().replace(/[^A-Z0-9]/g, "_")}}`;
+        }
+      }
+      server.headers = headers;
+    }
+  }
+  return server;
+}
+function filterStringRecord(obj) {
+  const result = {};
+  for (const [k, v] of Object.entries(obj)) {
+    if (typeof v === "string") result[k] = v;
+  }
+  return result;
+}
+var SECRET_PATTERNS = /(?:api[_-]?key|secret|token|password|bearer|auth)/i;
+var SAFE_ENV_KEYS = /^(?:PATH|HOME|NODE_ENV|NODE_OPTIONS|SHELL|LANG|LC_\w+|TZ|TERM|EDITOR)$/;
+var BEARER_PATTERN = /^(Authorization:\s*Bearer\s+)\S+$/i;
+var TOKEN_ARG_PATTERN = /^(--(?:token|api-key|secret|password)[=:])\S+$/i;
+function redactArgValue(arg) {
+  const bearerMatch = BEARER_PATTERN.exec(arg);
+  if (bearerMatch) return `${bearerMatch[1]}\${BEARER_TOKEN}`;
+  const tokenMatch = TOKEN_ARG_PATTERN.exec(arg);
+  if (tokenMatch) return `${tokenMatch[1]}\${TOKEN}`;
+  return arg;
+}
+function redactEnv(env) {
+  const result = {};
+  for (const [k, v] of Object.entries(env)) {
+    if (SAFE_ENV_KEYS.test(k)) {
+      result[k] = v;
+    } else if (SECRET_PATTERNS.test(k)) {
+      result[k] = `\${${k}}`;
+    } else {
+      result[k] = v;
+    }
+  }
+  return result;
+}
+function readJsonSafe(filePath) {
+  let raw = readFileSync(filePath, "utf-8");
+  raw = raw.replace(/[\x00-\x08\x0b\x0c\x0e-\x1f]/g, "");
+  let result = "";
+  let inString = false;
+  let escape = false;
+  let i = 0;
+  while (i < raw.length) {
+    const ch = raw[i];
+    if (escape) {
+      result += ch;
+      escape = false;
+      i++;
+      continue;
+    }
+    if (inString) {
+      if (ch === "\\") {
+        escape = true;
+        result += ch;
+      } else if (ch === '"') {
+        inString = false;
+        result += ch;
+      } else {
+        result += ch;
+      }
+      i++;
+      continue;
+    }
+    if (ch === '"') {
+      inString = true;
+      result += ch;
+      i++;
+    } else if (ch === "/" && i + 1 < raw.length && raw[i + 1] === "/") {
+      while (i < raw.length && raw[i] !== "\n") i++;
+    } else if (ch === "/" && i + 1 < raw.length && raw[i + 1] === "*") {
+      i += 2;
+      while (i + 1 < raw.length && !(raw[i] === "*" && raw[i + 1] === "/")) i++;
+      i += 2;
+    } else {
+      result += ch;
+      i++;
+    }
+  }
+  return JSON.parse(result);
+}
+function scanTool(toolConfig) {
+  const configPath = toolConfig.path();
+  const source = {
+    tool: toolConfig.tool,
+    configPath,
+    found: false,
+    servers: []
+  };
+  if (!existsSync(configPath)) {
+    return source;
+  }
+  source.found = true;
+  try {
+    const parsed = readJsonSafe(configPath);
+    if (!parsed || typeof parsed !== "object") {
+      source.error = "Config file is not a JSON object";
+      return source;
+    }
+    const root = parsed;
+    const serversObj = toolConfig.extractServers ? toolConfig.extractServers(root) : root[toolConfig.rootKey];
+    if (!serversObj || typeof serversObj !== "object" || Array.isArray(serversObj)) {
+      return source;
+    }
+    const entries = Object.entries(serversObj);
+    for (const [name, value] of entries) {
+      if (!value || typeof value !== "object" || Array.isArray(value)) continue;
+      const serverObj = value;
+      if (serverObj.disabled === true || serverObj.enabled === false) continue;
+      try {
+        const server = parseServer(name, serverObj, toolConfig.usesTypeField);
+        if (server.command || server.url) {
+          source.servers.push(server);
+        }
+      } catch {
+      }
+    }
+  } catch (err) {
+    source.error = err instanceof Error ? err.message : String(err);
+  }
+  return source;
+}
+function discoverMcpServers(options) {
+  const h = options?.homeDir ?? homedir();
+  const mac = options?.isMac ?? platform() === "darwin";
+  const toolConfigs = buildToolConfigs(h, mac);
+  const sources = [];
+  const seenNames = /* @__PURE__ */ new Set();
+  const uniqueServers = [];
+  for (const toolConfig of toolConfigs) {
+    const source = scanTool(toolConfig);
+    sources.push(source);
+    for (const server of source.servers) {
+      if (!seenNames.has(server.name)) {
+        seenNames.add(server.name);
+        uniqueServers.push(server);
+      }
+    }
+  }
+  return {
+    sources,
+    servers: uniqueServers,
+    sourcesFound: sources.filter((s) => s.found).length,
+    totalServers: uniqueServers.length
+  };
+}
+var NORMALIZABLE_BINARIES = /* @__PURE__ */ new Set(["npx", "node", "python", "python3"]);
+function normalizeCommand(command) {
+  if (!command.startsWith("/")) return command;
+  const base = command.substring(command.lastIndexOf("/") + 1);
+  if (NORMALIZABLE_BINARIES.has(base)) return base;
+  return command;
+}
+function hasAuthConfigured(server) {
+  if (server.headers) {
+    for (const k of Object.keys(server.headers)) {
+      if (k.toLowerCase() === "authorization") return true;
+    }
+  }
+  return false;
+}
+function findEnvPlaceholders(value) {
+  const matches = value.matchAll(/\$\{([A-Z_][A-Z0-9_]*)\}/gi);
+  return Array.from(matches, (m) => m[1]);
+}
+function filterUnsafeServers(servers) {
+  const result = [];
+  for (const server of servers) {
+    if (server.transport === "http" || server.transport === "sse") {
+      if (!hasAuthConfigured(server)) {
+        console.warn(`[mcp-discovery] skipping ${server.name}: ${server.transport} transport with no Authorization header`);
+        continue;
+      }
+    }
+    let missingVar;
+    if (server.env) {
+      for (const v of Object.values(server.env)) {
+        for (const varName of findEnvPlaceholders(v)) {
+          if (!(varName in process.env) || !process.env[varName]) {
+            missingVar = varName;
+            break;
+          }
+        }
+        if (missingVar) break;
+      }
+    }
+    if (!missingVar && server.headers) {
+      for (const v of Object.values(server.headers)) {
+        for (const varName of findEnvPlaceholders(v)) {
+          if (!(varName in process.env) || !process.env[varName]) {
+            missingVar = varName;
+            break;
+          }
+        }
+        if (missingVar) break;
+      }
+    }
+    if (missingVar) {
+      console.warn(`[mcp-discovery] skipping ${server.name}: required env var ${missingVar} not set`);
+      continue;
+    }
+    result.push(server);
+  }
+  return result;
+}
+function discoveredServersToYaml(servers) {
+  if (servers.length === 0) return "";
+  const lines = ["mcp:", "  servers:"];
+  for (const server of servers) {
+    lines.push(`    ${server.name}:`);
+    lines.push(`      transport: ${server.transport}`);
+    if (server.transport === "stdio") {
+      let normalizedCommand;
+      if (server.command) {
+        normalizedCommand = normalizeCommand(server.command);
+        lines.push(`      command: ${normalizedCommand}`);
+      }
+      const wasNormalized = !!server.command && normalizedCommand !== server.command;
+      if (server.args && server.args.length > 0) {
+        lines.push(`      args: [${server.args.map((a) => `"${a}"`).join(", ")}]`);
+      }
+      const filteredEnv = server.env ? Object.fromEntries(Object.entries(server.env).filter(([k]) => !(wasNormalized && k === "PATH"))) : void 0;
+      if (filteredEnv && Object.keys(filteredEnv).length > 0) {
+        lines.push("      env:");
+        for (const [k, v] of Object.entries(filteredEnv)) {
+          lines.push(`        ${k}: "${v}"`);
+        }
+      }
+      if (server.cwd) lines.push(`      cwd: "${server.cwd}"`);
+    } else {
+      if (server.url) lines.push(`      url: "${server.url}"`);
+      if (server.headers && Object.keys(server.headers).length > 0) {
+        lines.push("      headers:");
+        for (const [k, v] of Object.entries(server.headers)) {
+          lines.push(`        ${k}: "${v}"`);
+        }
+      }
+    }
+  }
+  return lines.join("\n");
+}
+function getScannedTools() {
+  return buildToolConfigs("", true).map((t) => t.tool);
+}
+export {
+  discoverMcpServers,
+  discoveredServersToYaml,
+  filterUnsafeServers,
+  getScannedTools
+};
+//# sourceMappingURL=mcp-discovery-WPAQFL6S.js.map