codecortex-ai 0.4.2 → 0.4.4

package/dist/chunk-4N3T43UG.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/mcp/server.ts","../src/mcp/tools/read.ts","../src/utils/files.ts","../src/utils/yaml.ts","../src/core/manifest.ts","../src/core/graph.ts","../src/utils/markdown.ts","../src/core/modules.ts","../src/core/sessions.ts","../src/core/decisions.ts","../src/core/search.ts","../src/git/diff.ts","../src/git/history.ts","../src/core/freshness.ts","../src/mcp/tools/write.ts","../src/types/schema.ts","../src/core/patterns.ts"],"sourcesContent":["/**\n * CodeCortex MCP Server\n *\n * Serves codebase knowledge to AI agents via Model Context Protocol.\n * 15 tools: 10 read (knowledge retrieval) + 5 write (knowledge creation).\n *\n * Usage:\n *   codecortex serve\n *\n * Config for Claude Code / Claude Desktop:\n *   {\n *     \"mcpServers\": {\n *       \"codecortex\": {\n *         \"command\": \"codecortex\",\n *         \"args\": [\"serve\"],\n *         \"cwd\": \"/path/to/your-project\"\n *       }\n *     }\n *   }\n */\n\nimport { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js'\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'\nimport { registerReadTools } from './tools/read.js'\nimport { registerWriteTools } from './tools/write.js'\n\nexport function createServer(projectRoot: string): McpServer {\n  const server = new McpServer({\n    name: 'codecortex',\n    version: '0.4.4',\n    description: 'Persistent codebase knowledge layer. Pre-digested architecture, symbols, coupling, and patterns served to AI agents.',\n  })\n\n  registerReadTools(server, projectRoot)\n  registerWriteTools(server, projectRoot)\n\n  return server\n}\n\nexport async function startServer(projectRoot: string): Promise<void> {\n  const server = createServer(projectRoot)\n  const transport = new StdioServerTransport()\n  await server.connect(transport)\n  console.error(`CodeCortex MCP server running on stdio (root: ${projectRoot})`)\n}\n\n// Direct execution\nif (import.meta.url === `file://${process.argv[1]}`) {\n  const root = process.cwd()\n  startServer(root).catch((err) => {\n    console.error('Fatal error:', err)\n    process.exit(1)\n  })\n}\n","import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js'\nimport { z } from 'zod'\nimport { readFile, cortexPath } from '../../utils/files.js'\nimport { readManifest } from '../../core/manifest.js'\nimport { readGraph, getModuleDependencies, getMostImportedFiles, getFileImporters } from '../../core/graph.js'\nimport { readModuleDoc, listModuleDocs } from '../../core/modules.js'\nimport { listSessions, readSession, getLatestSession } from '../../core/sessions.js'\nimport { listDecisions, readDecision } from '../../core/decisions.js'\nimport { searchKnowledge } from '../../core/search.js'\nimport { computeFreshness } from '../../core/freshness.js'\nimport type { TemporalData, SymbolIndex, FreshnessInfo } from '../../types/index.js'\n\nfunction textResult(data: unknown) {\n  return { content: [{ type: 'text' as const, text: JSON.stringify(data, null, 2) }] }\n}\n\n/** Attach freshness metadata to any response object. */\nfunction withFreshness<T extends object>(data: T, freshness: FreshnessInfo | null): T & { _freshness?: FreshnessInfo } {\n  if (!freshness) return data\n  return { ...data, _freshness: freshness }\n}\n\nexport function registerReadTools(server: McpServer, projectRoot: string): void {\n  // Cache freshness per MCP session to avoid repeated git calls.\n  // Invalidated when null (first call) or after 60 seconds.\n  let cachedFreshness: { info: FreshnessInfo | null; timestamp: number } | null = null\n  const FRESHNESS_TTL_MS = 60_000\n\n  async function getFreshness(): Promise<FreshnessInfo | null> {\n    const now = Date.now()\n    if (cachedFreshness && (now - cachedFreshness.timestamp) < FRESHNESS_TTL_MS) {\n      return cachedFreshness.info\n    }\n    const info = await computeFreshness(projectRoot)\n    cachedFreshness = { info, timestamp: now }\n    return info\n  }\n\n  // --- Tool 1: get_project_overview ---\n  server.registerTool(\n    'get_project_overview',\n    {\n      description: 'Get the full project overview: constitution (architecture, risk map, available knowledge), overview narrative, and dependency graph summary. This is the starting point for understanding any codebase. Always call this first.',\n      inputSchema: {},\n    },\n    async () => {\n      const constitution = await readFile(cortexPath(projectRoot, 'constitution.md'))\n      const overview = await readFile(cortexPath(projectRoot, 'overview.md'))\n      const manifest = await readManifest(projectRoot)\n\n      const graph = await readGraph(projectRoot)\n      let graphSummary = null\n      if (graph) {\n        graphSummary = {\n          modules: graph.modules.length,\n          imports: graph.imports.length,\n          entryPoints: graph.entryPoints,\n          mostImported: getMostImportedFiles(graph, 5),\n        }\n      }\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        constitution,\n        overview,\n        manifest,\n        graphSummary,\n      }, freshness))\n    }\n  )\n\n  // --- Tool 2: get_module_context ---\n  server.registerTool(\n    'get_module_context',\n    {\n      description: 'Get deep context for a specific module: purpose, data flow, public API, gotchas, dependencies, and temporal signals (churn, coupling, bug history). Use after get_project_overview when you need to work on a specific module.',\n      inputSchema: {\n        name: z.string().describe('Module name (e.g., \"scoring\", \"api\", \"indexer\")'),\n      },\n    },\n    async ({ name }) => {\n      const doc = await readModuleDoc(projectRoot, name)\n      if (!doc) {\n        const available = await listModuleDocs(projectRoot)\n        return textResult({ found: false, name, available, message: `Module \"${name}\" not found. Available modules: ${available.join(', ')}` })\n      }\n\n      // Get graph info for this module\n      const graph = await readGraph(projectRoot)\n      let deps = null\n      if (graph) {\n        deps = getModuleDependencies(graph, name)\n      }\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({ found: true, name, doc, dependencies: deps }, freshness))\n    }\n  )\n\n  // --- Tool 3: get_session_briefing ---\n  server.registerTool(\n    'get_session_briefing',\n    {\n      description: 'Get a briefing of what changed since the last session. Shows files changed, modules affected, and decisions recorded. Use at the start of a new session to catch up.',\n      inputSchema: {},\n    },\n    async () => {\n      const latestId = await getLatestSession(projectRoot)\n      if (!latestId) {\n        return textResult({ hasSession: false, message: 'No previous sessions recorded.' })\n      }\n\n      const session = await readSession(projectRoot, latestId)\n      const allSessions = await listSessions(projectRoot)\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        hasSession: true,\n        latest: session,\n        totalSessions: allSessions.length,\n        recentSessionIds: allSessions.slice(0, 5),\n      }, freshness))\n    }\n  )\n\n  // --- Tool 4: search_knowledge ---\n  server.registerTool(\n    'search_knowledge',\n    {\n      description: 'Search across all CodeCortex knowledge files (modules, decisions, patterns, sessions, constitution) for a keyword or phrase. Returns matching lines with context.',\n      inputSchema: {\n        query: z.string().describe('Search term or phrase'),\n      },\n    },\n    async ({ query }) => {\n      const results = await searchKnowledge(projectRoot, query)\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        query,\n        totalResults: results.length,\n        results: results.slice(0, 20),\n      }, freshness))\n    }\n  )\n\n  // --- Tool 5: get_decision_history ---\n  server.registerTool(\n    'get_decision_history',\n    {\n      description: 'Get architectural decision records. Shows WHY the codebase is built the way it is. Filter by topic keyword.',\n      inputSchema: {\n        topic: z.string().optional().describe('Optional keyword to filter decisions'),\n      },\n    },\n    async ({ topic }) => {\n      const ids = await listDecisions(projectRoot)\n      const decisions: string[] = []\n\n      for (const id of ids) {\n        const content = await readDecision(projectRoot, id)\n        if (content) {\n          if (!topic || content.toLowerCase().includes(topic.toLowerCase())) {\n            decisions.push(content)\n          }\n        }\n      }\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        total: decisions.length,\n        topic: topic || 'all',\n        decisions,\n      }, freshness))\n    }\n  )\n\n  // --- Tool 6: get_dependency_graph ---\n  server.registerTool(\n    'get_dependency_graph',\n    {\n      description: 'Get the import/export dependency graph. Shows which files import which, external dependencies, and entry points. Optionally filter to a specific file or module.',\n      inputSchema: {\n        file: z.string().optional().describe('Filter to edges involving this file path'),\n        module: z.string().optional().describe('Filter to edges involving this module name'),\n      },\n    },\n    async ({ file, module }) => {\n      const graph = await readGraph(projectRoot)\n      if (!graph) return textResult({ found: false, message: 'No graph data. Run codecortex init first.' })\n\n      const freshness = await getFreshness()\n\n      if (module) {\n        const deps = getModuleDependencies(graph, module)\n        return textResult(withFreshness({ module, ...deps }, freshness))\n      }\n\n      if (file) {\n        const imports = graph.imports.filter(e => e.source.includes(file) || e.target.includes(file))\n        const calls = graph.calls.filter(e => e.file.includes(file))\n        return textResult(withFreshness({ file, imports, calls }, freshness))\n      }\n\n      return textResult(withFreshness(graph, freshness))\n    }\n  )\n\n  // --- Tool 7: lookup_symbol ---\n  server.registerTool(\n    'lookup_symbol',\n    {\n      description: 'Look up a symbol (function, class, type, interface, const) by name. Returns file path, line numbers, signature, and whether it\\'s exported. Use to find where something is defined.',\n      inputSchema: {\n        name: z.string().describe('Symbol name to search for'),\n        kind: z.enum(['function', 'class', 'interface', 'type', 'const', 'enum', 'method', 'property', 'variable']).optional().describe('Filter by symbol kind'),\n        file: z.string().optional().describe('Filter by file path (partial match)'),\n      },\n    },\n    async ({ name, kind, file }) => {\n      const content = await readFile(cortexPath(projectRoot, 'symbols.json'))\n      if (!content) return textResult({ found: false, message: 'No symbol index. Run codecortex init first.' })\n\n      const index: SymbolIndex = JSON.parse(content)\n      let matches = index.symbols.filter(s =>\n        s.name.toLowerCase().includes(name.toLowerCase())\n      )\n\n      if (kind) matches = matches.filter(s => s.kind === kind)\n      if (file) matches = matches.filter(s => s.file.includes(file))\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        query: { name, kind, file },\n        totalMatches: matches.length,\n        symbols: matches.slice(0, 30),\n      }, freshness))\n    }\n  )\n\n  // --- Tool 8: get_change_coupling ---\n  server.registerTool(\n    'get_change_coupling',\n    {\n      description: 'CRITICAL: Call this BEFORE editing any file. Shows files that historically change together. If file A is coupled with file B, editing A without B will likely cause a bug. Hidden couplings (no import between files) are especially dangerous.',\n      inputSchema: {\n        file: z.string().optional().describe('Show coupling for this specific file'),\n        minStrength: z.number().min(0).max(1).default(0.3).describe('Minimum coupling strength (0-1). Default 0.3.'),\n      },\n    },\n    async ({ file, minStrength }) => {\n      const content = await readFile(cortexPath(projectRoot, 'temporal.json'))\n      if (!content) return textResult({ found: false, message: 'No temporal data. Run codecortex init first.' })\n\n      const temporal: TemporalData = JSON.parse(content)\n      let coupling = temporal.coupling.filter(c => c.strength >= minStrength)\n\n      if (file) {\n        coupling = coupling.filter(c =>\n          c.fileA.includes(file) || c.fileB.includes(file)\n        )\n      }\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        file: file || 'all',\n        minStrength,\n        couplings: coupling,\n        warning: coupling.filter(c => !c.hasImport).length > 0\n          ? 'HIDDEN DEPENDENCIES FOUND — some coupled files have NO import between them'\n          : null,\n      }, freshness))\n    }\n  )\n\n  // --- Tool 9: get_hotspots ---\n  server.registerTool(\n    'get_hotspots',\n    {\n      description: 'Get files ranked by risk: change frequency (churn), coupling count, and bug history. Volatile files with many couplings need extra care when editing.',\n      inputSchema: {\n        limit: z.number().int().min(1).max(50).default(10).describe('Number of files to return'),\n      },\n    },\n    async ({ limit }) => {\n      const content = await readFile(cortexPath(projectRoot, 'temporal.json'))\n      if (!content) return textResult({ found: false, message: 'No temporal data. Run codecortex init first.' })\n\n      const temporal: TemporalData = JSON.parse(content)\n\n      // Calculate risk score: churn + coupling count + bug count\n      const riskMap = new Map<string, { churn: number; couplings: number; bugs: number; risk: number }>()\n\n      for (const h of temporal.hotspots) {\n        riskMap.set(h.file, { churn: h.changes, couplings: 0, bugs: 0, risk: h.changes })\n      }\n\n      for (const c of temporal.coupling) {\n        for (const f of [c.fileA, c.fileB]) {\n          const entry = riskMap.get(f) || { churn: 0, couplings: 0, bugs: 0, risk: 0 }\n          entry.couplings++\n          entry.risk += c.strength * 2\n          riskMap.set(f, entry)\n        }\n      }\n\n      for (const b of temporal.bugHistory) {\n        const entry = riskMap.get(b.file) || { churn: 0, couplings: 0, bugs: 0, risk: 0 }\n        entry.bugs = b.fixCommits\n        entry.risk += b.fixCommits * 3\n        riskMap.set(b.file, entry)\n      }\n\n      const ranked = [...riskMap.entries()]\n        .sort((a, b) => b[1].risk - a[1].risk)\n        .slice(0, limit)\n        .map(([file, data]) => ({ file, ...data, risk: Math.round(data.risk * 100) / 100 }))\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        period: `${temporal.periodDays} days`,\n        totalCommits: temporal.totalCommits,\n        hotspots: ranked,\n      }, freshness))\n    }\n  )\n\n  // --- Tool 10: get_edit_briefing ---\n  server.registerTool(\n    'get_edit_briefing',\n    {\n      description: 'CALL THIS BEFORE EDITING FILES. Takes a list of files you plan to edit and returns everything you need to know: co-change warnings (files you must also update), risk assessment, who imports these files, relevant patterns, and recent change history. Prevents bugs from hidden dependencies.',\n      inputSchema: {\n        files: z.array(z.string()).min(1).describe('File paths you plan to edit (relative to project root)'),\n      },\n    },\n    async ({ files }) => {\n      const temporalContent = await readFile(cortexPath(projectRoot, 'temporal.json'))\n      if (!temporalContent) return textResult({ found: false, message: 'No temporal data. Run codecortex init first.' })\n\n      const temporal: TemporalData = JSON.parse(temporalContent)\n      const graph = await readGraph(projectRoot)\n      const patternsContent = await readFile(cortexPath(projectRoot, 'patterns.md'))\n\n      const briefings = files.map(file => {\n        // 1. Co-change warnings\n        const couplings = temporal.coupling\n          .filter(c => c.fileA.includes(file) || c.fileB.includes(file))\n          .map(c => {\n            const other = c.fileA.includes(file) ? c.fileB : c.fileA\n            return {\n              file: other,\n              cochanges: c.cochanges,\n              strength: c.strength,\n              hasImport: c.hasImport,\n              warning: c.warning || null,\n            }\n          })\n          .sort((a, b) => b.strength - a.strength)\n\n        // 2. Risk assessment\n        const hotspot = temporal.hotspots.find(h => h.file.includes(file))\n        const bugs = temporal.bugHistory.find(b => b.file.includes(file))\n        const couplingCount = couplings.length\n        const hiddenDeps = couplings.filter(c => !c.hasImport).length\n\n        let riskLevel: 'LOW' | 'MEDIUM' | 'HIGH' | 'CRITICAL' = 'LOW'\n        const riskScore = (hotspot?.changes || 0) + (couplingCount * 2) + ((bugs?.fixCommits || 0) * 3) + (hiddenDeps * 4)\n\n        if (riskScore >= 20) riskLevel = 'CRITICAL'\n        else if (riskScore >= 12) riskLevel = 'HIGH'\n        else if (riskScore >= 6) riskLevel = 'MEDIUM'\n\n        // 3. Who imports this file\n        let importedBy: string[] = []\n        if (graph) {\n          importedBy = getFileImporters(graph, file)\n        }\n\n        // 4. Recent changes\n        const recentChange = hotspot ? {\n          lastChanged: hotspot.lastChanged,\n          daysSinceChange: hotspot.daysSinceChange,\n          totalChanges: hotspot.changes,\n          stability: hotspot.stability,\n        } : null\n\n        // 5. Bug history\n        const bugHistory = bugs ? {\n          fixCommits: bugs.fixCommits,\n          lessons: bugs.lessons,\n        } : null\n\n        return {\n          file,\n          risk: {\n            level: riskLevel,\n            score: Math.round(riskScore * 100) / 100,\n            reason: buildRiskReason(riskLevel, hotspot, couplingCount, hiddenDeps, bugs),\n          },\n          cochangeWarnings: couplings,\n          importedBy,\n          recentChange,\n          bugHistory,\n        }\n      })\n\n      // Files you should also consider editing (coupled but not in the input list)\n      const inputSet = new Set(files)\n      const alsoConsider = new Set<string>()\n      for (const b of briefings) {\n        for (const c of b.cochangeWarnings) {\n          // Check if coupled file is NOT in the files being edited\n          const coupledFile = c.file\n          const isInInput = files.some(f => coupledFile.includes(f) || f.includes(coupledFile))\n          if (!isInInput && c.strength >= 0.5) {\n            alsoConsider.add(`${coupledFile} (${Math.round(c.strength * 100)}% co-change with ${b.file}${c.hasImport ? '' : ', NO import — hidden dep'})`)\n          }\n        }\n      }\n\n      const freshness = await getFreshness()\n\n      return textResult(withFreshness({\n        briefings,\n        alsoConsiderEditing: [...alsoConsider],\n        patterns: patternsContent || null,\n      }, freshness))\n    }\n  )\n}\n\nfunction buildRiskReason(\n  level: string,\n  hotspot: { changes: number; stability: string } | undefined,\n  couplings: number,\n  hiddenDeps: number,\n  bugs: { fixCommits: number } | undefined,\n): string {\n  if (level === 'LOW') return 'Low change frequency, few couplings.'\n  const parts: string[] = []\n  if (hotspot && hotspot.changes >= 5) parts.push(`${hotspot.changes} changes (${hotspot.stability})`)\n  if (couplings > 0) parts.push(`${couplings} coupled file${couplings === 1 ? '' : 's'}`)\n  if (hiddenDeps > 0) parts.push(`${hiddenDeps} hidden dep${hiddenDeps === 1 ? '' : 's'}`)\n  if (bugs && bugs.fixCommits > 0) parts.push(`${bugs.fixCommits} bug-fix commit${bugs.fixCommits === 1 ? '' : 's'}`)\n  return parts.join(', ') + '.'\n}\n","import { readFile as fsRead, writeFile as fsWrite, mkdir, readdir, stat } from 'node:fs/promises'\nimport { existsSync, createWriteStream } from 'node:fs'\nimport { join, dirname } from 'node:path'\n\nexport async function readFile(path: string): Promise<string | null> {\n  try {\n    return await fsRead(path, 'utf-8')\n  } catch {\n    return null\n  }\n}\n\nexport async function writeFile(path: string, content: string): Promise<void> {\n  await ensureDir(dirname(path))\n  await fsWrite(path, content, 'utf-8')\n}\n\nexport async function ensureDir(dir: string): Promise<void> {\n  if (!existsSync(dir)) {\n    await mkdir(dir, { recursive: true })\n  }\n}\n\nexport async function listFiles(dir: string, extension?: string): Promise<string[]> {\n  if (!existsSync(dir)) return []\n  const entries = await readdir(dir, { withFileTypes: true })\n  const files: string[] = []\n  for (const entry of entries) {\n    if (entry.isFile()) {\n      if (!extension || entry.name.endsWith(extension)) {\n        files.push(join(dir, entry.name))\n      }\n    }\n  }\n  return files\n}\n\nexport async function fileExists(path: string): Promise<boolean> {\n  try {\n    await stat(path)\n    return true\n  } catch {\n    return false\n  }\n}\n\nexport function cortexDir(projectRoot: string): string {\n  return join(projectRoot, '.codecortex')\n}\n\nexport function cortexPath(projectRoot: string, ...segments: string[]): string {\n  return join(projectRoot, '.codecortex', ...segments)\n}\n\nexport async function countLines(path: string): Promise<number> {\n  const content = await readFile(path)\n  if (!content) return 0\n  return content.split('\\n').length\n}\n\n/** Stream-write a large array-based JSON object to avoid V8 string length limits. */\nexport async function writeJsonStream<T extends object>(path: string, obj: T, arrayKey: string & keyof T): Promise<void> {\n  await ensureDir(dirname(path))\n  const arr = obj[arrayKey] as unknown[]\n  const stream = createWriteStream(path)\n  stream.setMaxListeners(0)\n\n  // Single error handler for the entire operation\n  let streamError: Error | null = null\n  stream.on('error', (err) => { streamError = err })\n\n  function waitDrain(): Promise<void> {\n    return new Promise((resolve) => stream.once('drain', resolve))\n  }\n\n  // Write non-array fields as header\n  const header: Record<string, unknown> = {}\n  for (const [k, v] of Object.entries(obj)) {\n    if (k !== arrayKey) header[k] = v\n  }\n  const headerJson = JSON.stringify(header)\n  stream.write(headerJson.slice(0, -1) + `,\"${arrayKey}\":[`)\n\n  // Write array elements in batches to reduce await overhead\n  const BATCH_SIZE = 1000\n  for (let i = 0; i < arr.length; i += BATCH_SIZE) {\n    if (streamError) throw streamError\n    const end = Math.min(i + BATCH_SIZE, arr.length)\n    const chunks: string[] = []\n    for (let j = i; j < end; j++) {\n      chunks.push((j > 0 ? ',' : '') + JSON.stringify(arr[j]))\n    }\n    if (!stream.write(chunks.join(''))) {\n      await waitDrain()\n    }\n  }\n\n  stream.write(']}')\n\n  return new Promise((resolve, reject) => {\n    if (streamError) { reject(streamError); return }\n    stream.on('finish', resolve)\n    stream.on('error', reject)\n    stream.end()\n  })\n}\n\nexport async function fileSize(path: string): Promise<number> {\n  try {\n    const s = await stat(path)\n    return s.size\n  } catch {\n    return 0\n  }\n}\n","import { parse, stringify } from 'yaml'\n\nexport function parseYaml<T = unknown>(content: string): T {\n  return parse(content) as T\n}\n\nexport function stringifyYaml(data: unknown): string {\n  return stringify(data, { lineWidth: 120 })\n}\n","import type { CortexManifest } from '../types/index.js'\nimport { readFile, writeFile, cortexPath } from '../utils/files.js'\nimport { parseYaml, stringifyYaml } from '../utils/yaml.js'\n\nexport async function readManifest(projectRoot: string): Promise<CortexManifest | null> {\n  const content = await readFile(cortexPath(projectRoot, 'cortex.yaml'))\n  if (!content) return null\n  return parseYaml<CortexManifest>(content)\n}\n\nexport async function writeManifest(projectRoot: string, manifest: CortexManifest): Promise<void> {\n  const content = stringifyYaml(manifest)\n  await writeFile(cortexPath(projectRoot, 'cortex.yaml'), content)\n}\n\nexport function createManifest(opts: {\n  project: string\n  root: string\n  languages: string[]\n  totalFiles: number\n  totalSymbols: number\n  totalModules: number\n}): CortexManifest {\n  const now = new Date().toISOString()\n  return {\n    version: '1.0.0',\n    project: opts.project,\n    root: opts.root,\n    generated: now,\n    lastUpdated: now,\n    languages: opts.languages,\n    totalFiles: opts.totalFiles,\n    totalSymbols: opts.totalSymbols,\n    totalModules: opts.totalModules,\n    tiers: {\n      hot: ['cortex.yaml', 'constitution.md', 'overview.md', 'graph.json', 'symbols.json', 'temporal.json'],\n      warm: ['modules/'],\n      cold: ['decisions/', 'sessions/', 'patterns.md'],\n    },\n  }\n}\n\nexport async function updateManifest(\n  projectRoot: string,\n  updates: Partial<Pick<CortexManifest, 'totalFiles' | 'totalSymbols' | 'totalModules' | 'languages'>>\n): Promise<CortexManifest | null> {\n  const manifest = await readManifest(projectRoot)\n  if (!manifest) return null\n\n  const updated: CortexManifest = {\n    ...manifest,\n    ...updates,\n    lastUpdated: new Date().toISOString(),\n  }\n\n  await writeManifest(projectRoot, updated)\n  return updated\n}\n","import type { DependencyGraph, ImportEdge, CallEdge, ModuleNode, ChangeCoupling } from '../types/index.js'\nimport { readFile, writeFile, ensureDir, cortexPath } from '../utils/files.js'\nimport { createWriteStream } from 'node:fs'\nimport { dirname } from 'node:path'\n\nexport async function readGraph(projectRoot: string): Promise<DependencyGraph | null> {\n  const content = await readFile(cortexPath(projectRoot, 'graph.json'))\n  if (!content) return null\n  return JSON.parse(content) as DependencyGraph\n}\n\nexport async function writeGraph(projectRoot: string, graph: DependencyGraph): Promise<void> {\n  const path = cortexPath(projectRoot, 'graph.json')\n  await ensureDir(dirname(path))\n  const stream = createWriteStream(path)\n  stream.setMaxListeners(0)\n\n  function waitDrain(): Promise<void> {\n    return new Promise((resolve) => stream.once('drain', resolve))\n  }\n\n  async function writeArray(arr: unknown[]): Promise<void> {\n    stream.write('[')\n    const BATCH = 1000\n    for (let i = 0; i < arr.length; i += BATCH) {\n      const end = Math.min(i + BATCH, arr.length)\n      const chunks: string[] = []\n      for (let j = i; j < end; j++) {\n        chunks.push((j > 0 ? ',' : '') + JSON.stringify(arr[j]))\n      }\n      if (!stream.write(chunks.join(''))) await waitDrain()\n    }\n    stream.write(']')\n  }\n\n  // Write scalar fields\n  stream.write(`{\"generated\":${JSON.stringify(graph.generated)},\"modules\":`)\n  await writeArray(graph.modules)\n  stream.write(',\"imports\":')\n  await writeArray(graph.imports)\n  stream.write(',\"calls\":')\n  await writeArray(graph.calls)\n  stream.write(`,\"entryPoints\":${JSON.stringify(graph.entryPoints)}`)\n  stream.write(`,\"externalDeps\":${JSON.stringify(graph.externalDeps)}`)\n  stream.write('}')\n\n  return new Promise((resolve, reject) => {\n    stream.on('finish', resolve)\n    stream.on('error', reject)\n    stream.end()\n  })\n}\n\nexport function buildGraph(opts: {\n  modules: ModuleNode[]\n  imports: ImportEdge[]\n  calls: CallEdge[]\n  entryPoints: string[]\n  externalDeps: Record<string, string[]>\n}): DependencyGraph {\n  return {\n    generated: new Date().toISOString(),\n    modules: opts.modules,\n    imports: opts.imports,\n    calls: opts.calls,\n    entryPoints: opts.entryPoints,\n    externalDeps: opts.externalDeps,\n  }\n}\n\nexport function getModuleDependencies(graph: DependencyGraph, moduleName: string): {\n  imports: ImportEdge[]\n  importedBy: ImportEdge[]\n  calls: CallEdge[]\n} {\n  const moduleFiles = new Set(\n    graph.modules.find(m => m.name === moduleName)?.files || []\n  )\n\n  return {\n    imports: graph.imports.filter(e => moduleFiles.has(e.source)),\n    importedBy: graph.imports.filter(e => moduleFiles.has(e.target)),\n    calls: graph.calls.filter(e => moduleFiles.has(e.file)),\n  }\n}\n\nexport function getFileImporters(graph: DependencyGraph, file: string): string[] {\n  return graph.imports\n    .filter(e => e.target.includes(file))\n    .map(e => e.source)\n}\n\nexport function getMostImportedFiles(graph: DependencyGraph, limit: number = 10): { file: string; importCount: number }[] {\n  const counts = new Map<string, number>()\n  for (const edge of graph.imports) {\n    counts.set(edge.target, (counts.get(edge.target) || 0) + 1)\n  }\n\n  return [...counts.entries()]\n    .sort((a, b) => b[1] - a[1])\n    .slice(0, limit)\n    .map(([file, importCount]) => ({ file, importCount }))\n}\n\nexport function enrichCouplingWithImports(\n  graph: DependencyGraph,\n  coupling: ChangeCoupling[]\n): void {\n  const importPairs = new Set<string>()\n  for (const edge of graph.imports) {\n    importPairs.add([edge.source, edge.target].sort().join('|'))\n  }\n\n  for (const pair of coupling) {\n    const key = [pair.fileA, pair.fileB].sort().join('|')\n    pair.hasImport = importPairs.has(key)\n    if (pair.strength >= 0.7 && !pair.hasImport) {\n      pair.warning = `HIDDEN DEPENDENCY — ${Math.round(pair.strength * 100)}% co-change rate`\n    }\n  }\n}\n","import type { ModuleAnalysis, DecisionRecord, CodingPattern } from '../types/index.js'\n\nexport function generateModuleDoc(analysis: ModuleAnalysis): string {\n  const lines: string[] = [\n    `# Module: ${analysis.name}`,\n    '',\n    `## Purpose`,\n    analysis.purpose,\n    '',\n    `## Data Flow`,\n    analysis.dataFlow,\n    '',\n    `## Public API`,\n    ...analysis.publicApi.map(api => `- \\`${api}\\``),\n    '',\n    `## Dependencies`,\n    ...analysis.dependencies.map(dep => `- ${dep}`),\n  ]\n\n  if (analysis.gotchas.length > 0) {\n    lines.push('', `## Gotchas`, ...analysis.gotchas.map(g => `- ${g}`))\n  }\n\n  if (analysis.temporalSignals) {\n    const t = analysis.temporalSignals\n    lines.push(\n      '',\n      `## Temporal Signals`,\n      `- **Churn:** ${t.churn}`,\n      `- **Coupled with:** ${t.coupledWith.join(', ') || 'none'}`,\n      `- **Stability:** ${t.stability}`,\n    )\n    if (t.bugHistory.length > 0) {\n      lines.push(`- **Bug history:** ${t.bugHistory.join('; ')}`)\n    }\n    lines.push(`- **Last changed:** ${t.lastChanged}`)\n  }\n\n  return lines.join('\\n') + '\\n'\n}\n\nexport function generateDecisionDoc(decision: DecisionRecord): string {\n  const lines: string[] = [\n    `# Decision: ${decision.title}`,\n    '',\n    `**Date:** ${decision.date}`,\n    `**Status:** ${decision.status}`,\n    '',\n    `## Context`,\n    decision.context,\n    '',\n    `## Decision`,\n    decision.decision,\n  ]\n\n  if (decision.alternatives.length > 0) {\n    lines.push('', `## Alternatives Considered`, ...decision.alternatives.map(a => `- ${a}`))\n  }\n\n  if (decision.consequences.length > 0) {\n    lines.push('', `## Consequences`, ...decision.consequences.map(c => `- ${c}`))\n  }\n\n  return lines.join('\\n') + '\\n'\n}\n\nexport function generatePatternEntry(pattern: CodingPattern): string {\n  const lines: string[] = [\n    `### ${pattern.name}`,\n    '',\n    pattern.description,\n    '',\n    '```',\n    pattern.example,\n    '```',\n  ]\n\n  if (pattern.files.length > 0) {\n    lines.push('', `Files: ${pattern.files.map(f => `\\`${f}\\``).join(', ')}`)\n  }\n\n  return lines.join('\\n')\n}\n","import type { ModuleAnalysis } from '../types/index.js'\nimport { readFile, writeFile, listFiles, cortexPath, ensureDir } from '../utils/files.js'\nimport { generateModuleDoc } from '../utils/markdown.js'\n\nexport async function readModuleDoc(projectRoot: string, moduleName: string): Promise<string | null> {\n  return readFile(cortexPath(projectRoot, 'modules', `${moduleName}.md`))\n}\n\nexport async function writeModuleDoc(projectRoot: string, analysis: ModuleAnalysis): Promise<void> {\n  const dir = cortexPath(projectRoot, 'modules')\n  await ensureDir(dir)\n  const content = generateModuleDoc(analysis)\n  await writeFile(cortexPath(projectRoot, 'modules', `${analysis.name}.md`), content)\n}\n\nexport async function listModuleDocs(projectRoot: string): Promise<string[]> {\n  const dir = cortexPath(projectRoot, 'modules')\n  const files = await listFiles(dir, '.md')\n  return files.map(f => {\n    const name = f.split('/').pop() || ''\n    return name.replace('.md', '')\n  })\n}\n\nexport function buildAnalysisPrompt(moduleName: string, sourceFiles: { path: string; content: string }[]): string {\n  const fileList = sourceFiles.map(f => `### ${f.path}\\n\\`\\`\\`\\n${f.content}\\n\\`\\`\\``).join('\\n\\n')\n\n  return `Analyze the \"${moduleName}\" module. Return a JSON object with this exact structure:\n\n{\n  \"name\": \"${moduleName}\",\n  \"purpose\": \"One paragraph describing what this module does and why it exists\",\n  \"dataFlow\": \"How data flows through this module — inputs, transformations, outputs\",\n  \"publicApi\": [\"list\", \"of\", \"exported\", \"functions\", \"and\", \"types\"],\n  \"gotchas\": [\"Things that are surprising or could cause bugs\"],\n  \"dependencies\": [\"What this module depends on and why\"]\n}\n\nSource files:\n\n${fileList}`\n}\n","import type { SessionLog } from '../types/index.js'\nimport { readFile, writeFile, listFiles, cortexPath, ensureDir } from '../utils/files.js'\n\nexport async function writeSession(projectRoot: string, session: SessionLog): Promise<void> {\n  const dir = cortexPath(projectRoot, 'sessions')\n  await ensureDir(dir)\n\n  const lines = [\n    `# Session: ${session.date}`,\n    '',\n    `**ID:** ${session.id}`,\n    session.previousSession ? `**Previous:** ${session.previousSession}` : null,\n    '',\n    `## Summary`,\n    session.summary,\n    '',\n    `## Files Changed`,\n    ...session.filesChanged.map(f => `- \\`${f}\\``),\n    '',\n    `## Modules Affected`,\n    ...session.modulesAffected.map(m => `- ${m}`),\n  ].filter(Boolean) as string[]\n\n  if (session.decisionsRecorded.length > 0) {\n    lines.push('', `## Decisions Recorded`, ...session.decisionsRecorded.map(d => `- ${d}`))\n  }\n\n  await writeFile(cortexPath(projectRoot, 'sessions', `${session.id}.md`), lines.join('\\n') + '\\n')\n}\n\nexport async function readSession(projectRoot: string, id: string): Promise<string | null> {\n  return readFile(cortexPath(projectRoot, 'sessions', `${id}.md`))\n}\n\nexport async function listSessions(projectRoot: string): Promise<string[]> {\n  const dir = cortexPath(projectRoot, 'sessions')\n  const files = await listFiles(dir, '.md')\n  return files\n    .map(f => (f.split('/').pop() || '').replace('.md', ''))\n    .sort()\n    .reverse()\n}\n\nexport async function getLatestSession(projectRoot: string): Promise<string | null> {\n  const sessions = await listSessions(projectRoot)\n  return sessions[0] ?? null\n}\n\nexport function createSession(opts: {\n  filesChanged: string[]\n  modulesAffected: string[]\n  decisionsRecorded?: string[]\n  summary: string\n  previousSession?: string\n}): SessionLog {\n  const now = new Date()\n  const id = now.toISOString().replace(/[:.]/g, '-').slice(0, 19)\n\n  return {\n    id,\n    date: now.toISOString(),\n    previousSession: opts.previousSession,\n    filesChanged: opts.filesChanged,\n    modulesAffected: opts.modulesAffected,\n    decisionsRecorded: opts.decisionsRecorded || [],\n    summary: opts.summary,\n  }\n}\n","import type { DecisionRecord } from '../types/index.js'\nimport { readFile, writeFile, listFiles, cortexPath, ensureDir } from '../utils/files.js'\nimport { generateDecisionDoc } from '../utils/markdown.js'\n\nexport async function readDecision(projectRoot: string, id: string): Promise<string | null> {\n  return readFile(cortexPath(projectRoot, 'decisions', `${id}.md`))\n}\n\nexport async function writeDecision(projectRoot: string, decision: DecisionRecord): Promise<void> {\n  const dir = cortexPath(projectRoot, 'decisions')\n  await ensureDir(dir)\n  const content = generateDecisionDoc(decision)\n  await writeFile(cortexPath(projectRoot, 'decisions', `${decision.id}.md`), content)\n}\n\nexport async function listDecisions(projectRoot: string): Promise<string[]> {\n  const dir = cortexPath(projectRoot, 'decisions')\n  const files = await listFiles(dir, '.md')\n  return files.map(f => {\n    const name = f.split('/').pop() || ''\n    return name.replace('.md', '')\n  })\n}\n\nexport function createDecision(input: {\n  title: string\n  context: string\n  decision: string\n  alternatives?: string[]\n  consequences?: string[]\n}): DecisionRecord {\n  const id = input.title\n    .toLowerCase()\n    .replace(/[^a-z0-9]+/g, '-')\n    .replace(/^-|-$/g, '')\n    .slice(0, 60)\n\n  return {\n    id,\n    date: new Date().toISOString().split('T')[0] ?? '',\n    title: input.title,\n    context: input.context,\n    decision: input.decision,\n    alternatives: input.alternatives || [],\n    consequences: input.consequences || [],\n    status: 'accepted',\n  }\n}\n","import { readFile, listFiles, cortexPath } from '../utils/files.js'\nimport { readdir } from 'node:fs/promises'\nimport { join } from 'node:path'\nimport { existsSync } from 'node:fs'\n\nexport interface SearchResult {\n  file: string\n  line: number\n  content: string\n  context: string\n}\n\nexport async function searchKnowledge(projectRoot: string, query: string): Promise<SearchResult[]> {\n  const cortexRoot = cortexPath(projectRoot)\n  if (!existsSync(cortexRoot)) return []\n\n  const results: SearchResult[] = []\n  const queryLower = query.toLowerCase()\n\n  const allFiles = await getAllCortexFiles(cortexRoot)\n\n  for (const filePath of allFiles) {\n    const content = await readFile(filePath)\n    if (!content) continue\n\n    const lines = content.split('\\n')\n    for (let i = 0; i < lines.length; i++) {\n      const line = lines[i]\n      if (line?.toLowerCase().includes(queryLower)) {\n        // Get surrounding context (2 lines before and after)\n        const start = Math.max(0, i - 2)\n        const end = Math.min(lines.length - 1, i + 2)\n        const context = lines.slice(start, end + 1).join('\\n')\n\n        results.push({\n          file: filePath.replace(cortexRoot + '/', ''),\n          line: i + 1,\n          content: line.trim(),\n          context,\n        })\n      }\n    }\n  }\n\n  return results\n}\n\nasync function getAllCortexFiles(dir: string): Promise<string[]> {\n  const files: string[] = []\n\n  if (!existsSync(dir)) return files\n\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 subFiles = await getAllCortexFiles(fullPath)\n      files.push(...subFiles)\n    } else if (entry.isFile() && (entry.name.endsWith('.md') || entry.name.endsWith('.json') || entry.name.endsWith('.yaml'))) {\n      files.push(fullPath)\n    }\n  }\n\n  return files\n}\n","import simpleGit from 'simple-git'\n\nexport interface DiffResult {\n  filesChanged: string[]\n  insertions: number\n  deletions: number\n  summary: string\n}\n\nexport async function getUncommittedDiff(root: string): Promise<DiffResult> {\n  const git = simpleGit(root)\n  const diff = await git.diffSummary()\n\n  return {\n    filesChanged: diff.files.map(f => f.file),\n    insertions: diff.insertions,\n    deletions: diff.deletions,\n    summary: `${diff.files.length} files changed, +${diff.insertions} -${diff.deletions}`,\n  }\n}\n\nexport async function getDiffSinceCommit(root: string, commitHash: string): Promise<DiffResult> {\n  const git = simpleGit(root)\n  const diff = await git.diffSummary([commitHash, 'HEAD'])\n\n  return {\n    filesChanged: diff.files.map(f => f.file),\n    insertions: diff.insertions,\n    deletions: diff.deletions,\n    summary: `${diff.files.length} files changed since ${commitHash.slice(0, 7)}, +${diff.insertions} -${diff.deletions}`,\n  }\n}\n\nexport async function getChangedFilesSinceDate(root: string, sinceDate: string): Promise<string[]> {\n  const git = simpleGit(root)\n  const log = await git.log({ '--since': sinceDate, '--name-only': null })\n\n  const files = new Set<string>()\n  for (const commit of log.all) {\n    const diff = commit.diff\n    if (diff) {\n      for (const file of diff.files) {\n        files.add(file.file)\n      }\n    }\n  }\n\n  return [...files]\n}\n\nexport function mapFilesToModules(files: string[]): Map<string, string[]> {\n  const moduleMap = new Map<string, string[]>()\n\n  for (const file of files) {\n    const parts = file.split('/')\n    let module = 'root'\n\n    if (parts[0] === 'src' && parts.length >= 3 && parts[1]) {\n      module = parts[1]\n    } else if (parts[0] === 'lib' && parts.length >= 3 && parts[1]) {\n      module = parts[1]\n    }\n\n    const existing = moduleMap.get(module) || []\n    existing.push(file)\n    moduleMap.set(module, existing)\n  }\n\n  return moduleMap\n}\n","import simpleGit from 'simple-git'\n\nexport interface CommitInfo {\n  hash: string\n  date: string\n  message: string\n  author: string\n  filesChanged: string[]\n}\n\nexport async function getCommitHistory(root: string, days: number = 90): Promise<CommitInfo[]> {\n  const git = simpleGit(root)\n  const since = new Date(Date.now() - days * 24 * 60 * 60 * 1000).toISOString().split('T')[0]\n\n  const log = await git.log({\n    '--since': since,\n    '--stat': null,\n    maxCount: 500,\n  })\n\n  return log.all.map(commit => ({\n    hash: commit.hash,\n    date: commit.date,\n    message: commit.message,\n    author: commit.author_name,\n    filesChanged: parseStatFiles(commit.diff),\n  }))\n}\n\nfunction parseStatFiles(diff: { files?: { file: string }[] } | null | undefined): string[] {\n  if (!diff || !diff.files) return []\n  return diff.files.map((f) => f.file)\n}\n\nexport async function getLastCommitDate(root: string, file: string): Promise<string | null> {\n  const git = simpleGit(root)\n  try {\n    const log = await git.log({ file, maxCount: 1 })\n    return log.latest?.date || null\n  } catch {\n    return null\n  }\n}\n\nexport async function isGitRepo(root: string): Promise<boolean> {\n  const git = simpleGit(root)\n  try {\n    await git.status()\n    return true\n  } catch {\n    return false\n  }\n}\n\nexport async function getHeadCommit(root: string): Promise<string | null> {\n  const git = simpleGit(root)\n  try {\n    const log = await git.log({ maxCount: 1 })\n    return log.latest?.hash || null\n  } catch {\n    return null\n  }\n}\n","import { readManifest } from './manifest.js'\nimport { getChangedFilesSinceDate } from '../git/diff.js'\nimport { isGitRepo } from '../git/history.js'\n\nexport type FreshnessStatus = 'fresh' | 'slightly_stale' | 'stale' | 'very_stale'\n\nexport interface FreshnessInfo {\n  status: FreshnessStatus\n  lastAnalyzed: string\n  daysSinceAnalysis: number\n  filesChangedSince: number\n  changedFiles: string[]\n  message: string\n}\n\n/**\n * Compute freshness of .codecortex/ knowledge relative to the actual codebase.\n * Compares manifest.lastUpdated against git changes since that date.\n */\nexport async function computeFreshness(projectRoot: string): Promise<FreshnessInfo | null> {\n  const manifest = await readManifest(projectRoot)\n  if (!manifest) return null\n\n  const lastUpdated = manifest.lastUpdated\n  if (!lastUpdated) return null\n\n  const isRepo = await isGitRepo(projectRoot)\n  let changedFiles: string[] = []\n\n  if (isRepo) {\n    try {\n      changedFiles = await getChangedFilesSinceDate(projectRoot, lastUpdated)\n      // Filter out noise files that don't affect knowledge quality\n      changedFiles = changedFiles.filter(f => {\n        const base = f.split('/').pop() ?? ''\n        return !base.endsWith('.lock') &&\n          base !== 'package-lock.json' &&\n          base !== 'yarn.lock' &&\n          base !== 'pnpm-lock.yaml' &&\n          base !== 'CHANGELOG.md' &&\n          !f.startsWith('.codecortex/')\n      })\n    } catch {\n      // Git operation failed — can't determine freshness from git\n      changedFiles = []\n    }\n  }\n\n  const now = new Date()\n  const analyzed = new Date(lastUpdated)\n  const daysSinceAnalysis = Math.floor((now.getTime() - analyzed.getTime()) / (1000 * 60 * 60 * 24))\n\n  const count = changedFiles.length\n  let status: FreshnessStatus\n  let message: string\n\n  if (count === 0 && daysSinceAnalysis <= 7) {\n    status = 'fresh'\n    message = 'Knowledge is up to date.'\n  } else if (count <= 2 && daysSinceAnalysis <= 7) {\n    status = 'slightly_stale'\n    message = `${count} file${count === 1 ? '' : 's'} changed since last analysis. Minor drift.`\n  } else if (count <= 5 || daysSinceAnalysis <= 14) {\n    status = 'stale'\n    message = `${count} file${count === 1 ? '' : 's'} changed since last analysis. Consider running \\`codecortex update\\`.`\n  } else {\n    status = 'very_stale'\n    message = `${count} files changed over ${daysSinceAnalysis} days since last analysis. Run \\`codecortex update\\` before trusting this knowledge.`\n  }\n\n  return {\n    status,\n    lastAnalyzed: lastUpdated,\n    daysSinceAnalysis,\n    filesChangedSince: count,\n    changedFiles: changedFiles.slice(0, 20), // Cap to avoid bloating response\n    message,\n  }\n}\n","import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js'\nimport { z } from 'zod'\nimport { readFile as readFileUtil, cortexPath } from '../../utils/files.js'\nimport { ModuleAnalysisSchema, DecisionInputSchema, PatternInputSchema, FeedbackInputSchema } from '../../types/schema.js'\nimport { writeModuleDoc, buildAnalysisPrompt, listModuleDocs } from '../../core/modules.js'\nimport { writeDecision, createDecision } from '../../core/decisions.js'\nimport { addPattern } from '../../core/patterns.js'\nimport { writeFile, ensureDir } from '../../utils/files.js'\nimport { readGraph } from '../../core/graph.js'\nimport type { ModuleAnalysis, TemporalData, Hotspot, ChangeCoupling, BugRecord } from '../../types/index.js'\nimport { readFile } from 'node:fs/promises'\nimport { join } from 'node:path'\n\nfunction textResult(data: unknown) {\n  return { content: [{ type: 'text' as const, text: JSON.stringify(data, null, 2) }] }\n}\n\nexport function registerWriteTools(server: McpServer, projectRoot: string): void {\n  // --- Tool 10: analyze_module ---\n  server.registerTool(\n    'analyze_module',\n    {\n      description: 'Prepares a module for analysis. Returns the source files and a structured prompt. You should read the source files, analyze them, then call save_module_analysis with the result.',\n      inputSchema: {\n        name: z.string().describe('Module name (e.g., \"scoring\", \"api\")'),\n      },\n    },\n    async ({ name }) => {\n      const graph = await readGraph(projectRoot)\n      if (!graph) {\n        return textResult({ error: 'No graph data. Run codecortex init first.' })\n      }\n\n      const module = graph.modules.find(m => m.name === name)\n      if (!module) {\n        const available = graph.modules.map(m => m.name)\n        return textResult({ error: `Module \"${name}\" not found`, available })\n      }\n\n      // Read source files for this module\n      const sourceFiles: { path: string; content: string }[] = []\n      for (const filePath of module.files) {\n        try {\n          const content = await readFile(join(projectRoot, filePath), 'utf-8')\n          sourceFiles.push({ path: filePath, content })\n        } catch {\n          // Skip files that can't be read\n        }\n      }\n\n      const prompt = buildAnalysisPrompt(name, sourceFiles)\n\n      return textResult({\n        module: name,\n        files: module.files,\n        prompt,\n        instruction: 'Analyze the source files above and call save_module_analysis with the JSON result.',\n      })\n    }\n  )\n\n  // --- Tool 11: save_module_analysis ---\n  server.registerTool(\n    'save_module_analysis',\n    {\n      description: 'Save the result of a module analysis. Provide the structured analysis (purpose, dataFlow, publicApi, gotchas, dependencies) and it will be persisted to modules/*.md.',\n      inputSchema: {\n        analysis: ModuleAnalysisSchema.describe('The structured module analysis'),\n      },\n    },\n    async ({ analysis }) => {\n      const moduleAnalysis: ModuleAnalysis = {\n        ...analysis,\n      }\n\n      // Enrich with temporal data if available\n      const temporalContent = await readFileUtil(cortexPath(projectRoot, 'temporal.json'))\n      if (temporalContent) {\n        const temporal: TemporalData = JSON.parse(temporalContent)\n        const hotspot = temporal.hotspots?.find((h: Hotspot) =>\n          h.file.includes(`/${analysis.name}/`) || h.file.includes(`${analysis.name}.`)\n        )\n        const couplings = temporal.coupling?.filter((c: ChangeCoupling) =>\n          c.fileA.includes(`/${analysis.name}/`) || c.fileB.includes(`/${analysis.name}/`)\n        ) || []\n        const bugs = temporal.bugHistory?.filter((b: BugRecord) =>\n          b.file.includes(`/${analysis.name}/`)\n        ) || []\n\n        if (hotspot || couplings.length > 0 || bugs.length > 0) {\n          moduleAnalysis.temporalSignals = {\n            churn: hotspot ? `${hotspot.changes} changes (${hotspot.stability})` : 'unknown',\n            coupledWith: couplings.map((c: ChangeCoupling) => {\n              const other = c.fileA.includes(`/${analysis.name}/`) ? c.fileB : c.fileA\n              return `${other} (${c.cochanges} co-changes)`\n            }),\n            stability: hotspot?.stability || 'unknown',\n            bugHistory: bugs.flatMap((b: BugRecord) => b.lessons),\n            lastChanged: hotspot?.lastChanged || 'unknown',\n          }\n        }\n      }\n\n      await writeModuleDoc(projectRoot, moduleAnalysis)\n\n      return textResult({\n        saved: true,\n        module: analysis.name,\n        path: `.codecortex/modules/${analysis.name}.md`,\n      })\n    }\n  )\n\n  // --- Tool 12: record_decision ---\n  server.registerTool(\n    'record_decision',\n    {\n      description: 'Record an architectural decision. Documents WHY something is built a certain way, what alternatives were considered, and consequences. Use whenever a non-obvious technical choice is made.',\n      inputSchema: {\n        title: z.string().describe('Decision title (e.g., \"Use tree-sitter for parsing\")'),\n        context: z.string().describe('What situation led to this decision'),\n        decision: z.string().describe('What was decided'),\n        alternatives: z.array(z.string()).default([]).describe('What other options were considered'),\n        consequences: z.array(z.string()).default([]).describe('Expected consequences of this decision'),\n      },\n    },\n    async ({ title, context, decision, alternatives, consequences }) => {\n      const record = createDecision({ title, context, decision, alternatives, consequences })\n      await writeDecision(projectRoot, record)\n\n      return textResult({\n        recorded: true,\n        id: record.id,\n        path: `.codecortex/decisions/${record.id}.md`,\n      })\n    }\n  )\n\n  // --- Tool 13: update_patterns ---\n  server.registerTool(\n    'update_patterns',\n    {\n      description: 'Add or update a coding pattern. Patterns document HOW code is written in this project (naming conventions, error handling, testing approaches). Returns \"added\", \"updated\", or \"noop\".',\n      inputSchema: {\n        name: z.string().describe('Pattern name (e.g., \"Error handling in API routes\")'),\n        description: z.string().describe('What the pattern is and when to use it'),\n        example: z.string().describe('Code example showing the pattern'),\n        files: z.array(z.string()).default([]).describe('Files where this pattern is used'),\n      },\n    },\n    async ({ name, description, example, files }) => {\n      const result = await addPattern(projectRoot, { name, description, example, files })\n\n      return textResult({\n        action: result,\n        pattern: name,\n        path: '.codecortex/patterns.md',\n      })\n    }\n  )\n\n  // --- Tool 14: report_feedback ---\n  server.registerTool(\n    'report_feedback',\n    {\n      description: 'Report incorrect or outdated knowledge. If you discover that a module doc, decision, or pattern is wrong, report it here. The feedback will be stored and used in the next analysis cycle.',\n      inputSchema: {\n        file: z.string().describe('Which knowledge file is incorrect (e.g., \"modules/scoring.md\")'),\n        issue: z.string().describe('What is wrong or outdated'),\n        reporter: z.string().default('agent').describe('Who is reporting (default: agent)'),\n      },\n    },\n    async ({ file, issue, reporter }) => {\n      const dir = cortexPath(projectRoot, 'feedback')\n      await ensureDir(dir)\n\n      const entry = {\n        date: new Date().toISOString(),\n        file,\n        issue,\n        reporter,\n      }\n\n      // Append to feedback log\n      const feedbackPath = cortexPath(projectRoot, 'feedback', 'log.json')\n      const existing = await readFileUtil(feedbackPath)\n      const entries = existing ? JSON.parse(existing) : []\n      entries.push(entry)\n      await writeFile(feedbackPath, JSON.stringify(entries, null, 2))\n\n      return textResult({\n        recorded: true,\n        totalFeedback: entries.length,\n        message: 'Feedback recorded. Will be addressed in next codecortex update.',\n      })\n    }\n  )\n}\n","import { z } from 'zod'\n\nexport const ModuleAnalysisSchema = z.object({\n  name: z.string(),\n  purpose: z.string(),\n  dataFlow: z.string(),\n  publicApi: z.array(z.string()),\n  gotchas: z.array(z.string()),\n  dependencies: z.array(z.string()),\n})\n\nexport const DecisionInputSchema = z.object({\n  title: z.string(),\n  context: z.string(),\n  decision: z.string(),\n  alternatives: z.array(z.string()).default([]),\n  consequences: z.array(z.string()).default([]),\n})\n\nexport const PatternInputSchema = z.object({\n  name: z.string(),\n  description: z.string(),\n  example: z.string(),\n  files: z.array(z.string()).default([]),\n})\n\nexport const FeedbackInputSchema = z.object({\n  file: z.string(),\n  issue: z.string(),\n  reporter: z.string().default('agent'),\n})\n","import type { CodingPattern } from '../types/index.js'\nimport { readFile, writeFile, cortexPath } from '../utils/files.js'\nimport { generatePatternEntry } from '../utils/markdown.js'\n\nexport async function readPatterns(projectRoot: string): Promise<string | null> {\n  return readFile(cortexPath(projectRoot, 'patterns.md'))\n}\n\nexport async function addPattern(projectRoot: string, pattern: CodingPattern): Promise<'added' | 'updated' | 'noop'> {\n  const existing = await readPatterns(projectRoot) || '# Coding Patterns\\n'\n\n  // Check if pattern with same name already exists\n  const nameRegex = new RegExp(`### ${escapeRegex(pattern.name)}`, 'i')\n  if (nameRegex.test(existing)) {\n    // Update: replace the existing pattern section\n    const entry = generatePatternEntry(pattern)\n    const sectionRegex = new RegExp(\n      `### ${escapeRegex(pattern.name)}[\\\\s\\\\S]*?(?=### |$)`,\n      'i'\n    )\n    const updated = existing.replace(sectionRegex, entry + '\\n\\n')\n    await writeFile(cortexPath(projectRoot, 'patterns.md'), updated)\n    return 'updated'\n  }\n\n  // Add new pattern\n  const entry = generatePatternEntry(pattern)\n  const content = existing.trimEnd() + '\\n\\n' + entry + '\\n'\n  await writeFile(cortexPath(projectRoot, 'patterns.md'), content)\n  return 'added'\n}\n\nfunction escapeRegex(str: string): string {\n  return str.replace(/[.*+?^${}()|[\\]\\\\]/g, 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package/dist/cli/index.js

@@ -6,11 +6,16 @@ import {
   createSession,
   enrichCouplingWithImports,
   ensureDir,
+  getCommitHistory,
+  getHeadCommit,
   getLatestSession,
   getModuleDependencies,
+  getUncommittedDiff,
+  isGitRepo,
   listDecisions,
   listModuleDocs,
   listSessions,
+  mapFilesToModules,
   readFile,
   readGraph,
   readManifest,
@@ -24,7 +29,7 @@ import {
   writeManifest,
   writeModuleDoc,
   writeSession
-} from "../chunk-PBYRGMCK.js";
+} from "../chunk-4N3T43UG.js";
 
 // src/cli/index.ts
 import { createRequire as createRequire2 } from "module";
@@ -37,7 +42,7 @@ import { resolve } from "path";
 import { execSync } from "child_process";
 import { readFile as fsRead2, stat } from "fs/promises";
 import { join, relative, basename, extname } from "path";
-import { existsSync } from "fs";
+import { existsSync, readFileSync as readFileSyncFs } from "fs";
 
 // src/extraction/parser.ts
 import { createRequire } from "module";
@@ -218,7 +223,7 @@ function detectProjectName(root) {
   const pkgPath = join(root, "package.json");
   if (existsSync(pkgPath)) {
     try {
-      const pkg = JSON.parse(execSync(`cat "${pkgPath}"`, { encoding: "utf-8" }));
+      const pkg = JSON.parse(readFileSyncFs(pkgPath, "utf-8"));
       if (pkg.name) return pkg.name;
     } catch {
     }
@@ -226,7 +231,7 @@ function detectProjectName(root) {
   const cargoPath = join(root, "Cargo.toml");
   if (existsSync(cargoPath)) {
     try {
-      const cargo = execSync(`cat "${cargoPath}"`, { encoding: "utf-8" });
+      const cargo = readFileSyncFs(cargoPath, "utf-8");
       const match = cargo.match(/name\s*=\s*"(.+?)"/);
       if (match?.[1]) return match[1];
     } catch {
@@ -295,8 +300,8 @@ async function walkDirectory(root, baseRoot) {
   }
   return paths;
 }
+var MODULE_ROOTS = /* @__PURE__ */ new Set(["src", "lib", "pkg", "packages", "apps", "extensions", "crates", "internal", "cmd", "scripts", "tools", "rust"]);
 function detectModules(root, files) {
-  const MODULE_ROOTS = /* @__PURE__ */ new Set(["src", "lib", "pkg", "packages", "apps", "extensions", "crates", "internal", "cmd", "scripts", "tools", "rust"]);
   const srcDirs = /* @__PURE__ */ new Set();
   for (const file of files) {
     const parts = file.path.split("/");
@@ -311,13 +316,31 @@ function detectModules(root, files) {
   }
   return [...srcDirs].sort();
 }
+function buildModuleNodes(modules, files, symbols) {
+  return modules.map((modName) => {
+    const modFiles = files.filter((f) => {
+      const parts = f.path.split("/");
+      const topDir2 = parts[0] ?? "";
+      return MODULE_ROOTS.has(topDir2) && parts[1] === modName || parts[0] === modName;
+    });
+    const topDir = modFiles[0]?.path.split("/")[0] ?? "src";
+    return {
+      path: `${topDir}/${modName}`,
+      name: modName,
+      files: modFiles.map((f) => f.path),
+      language: modFiles[0]?.language || "unknown",
+      lines: modFiles.reduce((sum, f) => sum + f.lines, 0),
+      symbols: symbols.filter((s) => modFiles.some((f) => f.path === s.file)).length
+    };
+  });
+}
 function detectEntryPoints(root, files, type) {
   const entryPoints = [];
   if (type === "node") {
     const pkgPath = join(root, "package.json");
     if (existsSync(pkgPath)) {
       try {
-        const pkg = JSON.parse(execSync(`cat "${pkgPath}"`, { encoding: "utf-8" }));
+        const pkg = JSON.parse(readFileSyncFs(pkgPath, "utf-8"));
         if (pkg.main) entryPoints.push(pkg.main);
         if (pkg.bin) {
           const bins = typeof pkg.bin === "string" ? [pkg.bin] : Object.values(pkg.bin);
@@ -449,47 +472,6 @@ async function generateConstitution(projectRoot, data) {
   return content;
 }
 
-// src/git/history.ts
-import simpleGit from "simple-git";
-async function getCommitHistory(root, days = 90) {
-  const git = simpleGit(root);
-  const since = new Date(Date.now() - days * 24 * 60 * 60 * 1e3).toISOString().split("T")[0];
-  const log = await git.log({
-    "--since": since,
-    "--stat": null,
-    maxCount: 500
-  });
-  return log.all.map((commit) => ({
-    hash: commit.hash,
-    date: commit.date,
-    message: commit.message,
-    author: commit.author_name,
-    filesChanged: parseStatFiles(commit.diff)
-  }));
-}
-function parseStatFiles(diff) {
-  if (!diff || !diff.files) return [];
-  return diff.files.map((f) => f.file);
-}
-async function isGitRepo(root) {
-  const git = simpleGit(root);
-  try {
-    await git.status();
-    return true;
-  } catch {
-    return false;
-  }
-}
-async function getHeadCommit(root) {
-  const git = simpleGit(root);
-  try {
-    const log = await git.log({ maxCount: 1 });
-    return log.latest?.hash || null;
-  } catch {
-    return null;
-  }
-}
-
 // src/git/temporal.ts
 var TEMPORAL_NOISE_FILES = /* @__PURE__ */ new Set([
   "CHANGELOG.md",
@@ -583,18 +565,14 @@ function getChangeCoupling(commits) {
     const fileB = parts[1] ?? "";
     const maxChanges = Math.max(fileCounts.get(fileA) || 0, fileCounts.get(fileB) || 0);
     const strength = maxChanges > 0 ? cochanges / maxChanges : 0;
-    const coupling = {
+    results.push({
       fileA,
       fileB,
       cochanges,
       strength: Math.round(strength * 100) / 100,
       hasImport: false
       // Will be enriched by graph analysis
-    };
-    if (strength >= 0.7 && !coupling.hasImport) {
-      coupling.warning = `HIDDEN DEPENDENCY \u2014 ${Math.round(strength * 100)}% co-change rate`;
-    }
-    results.push(coupling);
+    });
   }
   return results.sort((a, b) => b.cochanges - a.cochanges);
 }
@@ -1615,23 +1593,7 @@ async function initCommand(opts) {
   }
   console.log("");
   console.log("Step 3/6: Building dependency graph...");
-  const MODULE_ROOTS = /* @__PURE__ */ new Set(["src", "lib", "pkg", "packages", "apps", "extensions", "crates", "internal", "cmd", "scripts", "tools", "rust"]);
-  const moduleNodes = project.modules.map((modName) => {
-    const modFiles = project.files.filter((f) => {
-      const parts = f.path.split("/");
-      const topDir2 = parts[0] ?? "";
-      return MODULE_ROOTS.has(topDir2) && parts[1] === modName || parts[0] === modName;
-    });
-    const topDir = modFiles[0]?.path.split("/")[0] ?? "src";
-    return {
-      path: `${topDir}/${modName}`,
-      name: modName,
-      files: modFiles.map((f) => f.path),
-      language: modFiles[0]?.language || "unknown",
-      lines: modFiles.reduce((sum, f) => sum + f.lines, 0),
-      symbols: allSymbols.filter((s) => modFiles.some((f) => f.path === s.file)).length
-    };
-  });
+  const moduleNodes = buildModuleNodes(project.modules, project.files, allSymbols);
   const externalDeps = {};
   for (const file of project.files) {
     try {
@@ -1785,37 +1747,6 @@ async function serveCommand(opts) {
 // src/cli/commands/update.ts
 import { resolve as resolve3 } from "path";
 import { existsSync as existsSync5 } from "fs";
-
-// src/git/diff.ts
-import simpleGit2 from "simple-git";
-async function getUncommittedDiff(root) {
-  const git = simpleGit2(root);
-  const diff = await git.diffSummary();
-  return {
-    filesChanged: diff.files.map((f) => f.file),
-    insertions: diff.insertions,
-    deletions: diff.deletions,
-    summary: `${diff.files.length} files changed, +${diff.insertions} -${diff.deletions}`
-  };
-}
-function mapFilesToModules(files) {
-  const moduleMap = /* @__PURE__ */ new Map();
-  for (const file of files) {
-    const parts = file.split("/");
-    let module = "root";
-    if (parts[0] === "src" && parts.length >= 3 && parts[1]) {
-      module = parts[1];
-    } else if (parts[0] === "lib" && parts.length >= 3 && parts[1]) {
-      module = parts[1];
-    }
-    const existing = moduleMap.get(module) || [];
-    existing.push(file);
-    moduleMap.set(module, existing);
-  }
-  return moduleMap;
-}
-
-// src/cli/commands/update.ts
 import { readFile as fsRead3 } from "fs/promises";
 async function updateCommand(opts) {
   const root = resolve3(opts.root);
@@ -1846,23 +1777,7 @@ async function updateCommand(opts) {
     }
   }
   console.log("Rebuilding dependency graph...");
-  const MODULE_ROOTS = /* @__PURE__ */ new Set(["src", "lib", "pkg", "packages", "apps", "extensions", "crates", "internal", "cmd", "scripts", "tools", "rust"]);
-  const moduleNodes = project.modules.map((modName) => {
-    const modFiles = project.files.filter((f) => {
-      const parts = f.path.split("/");
-      const topDir2 = parts[0] ?? "";
-      return MODULE_ROOTS.has(topDir2) && parts[1] === modName || parts[0] === modName;
-    });
-    const topDir = modFiles[0]?.path.split("/")[0] ?? "src";
-    return {
-      path: `${topDir}/${modName}`,
-      name: modName,
-      files: modFiles.map((f) => f.path),
-      language: modFiles[0]?.language || "unknown",
-      lines: modFiles.reduce((sum, f) => sum + f.lines, 0),
-      symbols: allSymbols.filter((s) => modFiles.some((f) => f.path === s.file)).length
-    };
-  });
+  const moduleNodes = buildModuleNodes(project.modules, project.files, allSymbols);
   const externalDeps = {};
   for (const file of project.files) {
     try {
@@ -2318,7 +2233,7 @@ function pad3(str, len) {
 import { resolve as resolve9, join as join3 } from "path";
 import { existsSync as existsSync11 } from "fs";
 import { readFile as readFile4, writeFile as writeFile2, chmod, unlink } from "fs/promises";
-import simpleGit3 from "simple-git";
+import simpleGit from "simple-git";
 var HOOK_START = "# --- codecortex-hook-start ---";
 var HOOK_END = "# --- codecortex-hook-end ---";
 var HOOK_TYPES = ["post-commit", "post-merge"];
@@ -2355,7 +2270,7 @@ function isEmptyHook(content) {
   return stripped.length === 0;
 }
 async function getGitHooksDir(root) {
-  const git = simpleGit3(root);
+  const git = simpleGit(root);
   const gitDir = (await git.revparse(["--git-dir"])).trim();
   const resolved = resolve9(root, gitDir);
   return join3(resolved, "hooks");