@dreamtree-org/graphify 1.0.0

package/dist/cli/index.cjs.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../../node_modules/tsup/assets/cjs_shims.js","../../src/security.ts","../../src/graphStore.ts","../../src/query.ts","../../src/mcp/server.ts","../../src/cli/index.ts","../../src/analyze.ts","../../src/cluster.ts","../../src/export.ts","../../src/pipeline.ts","../../src/build.ts","../../src/schema.ts","../../src/detect.ts","../../src/extract.ts","../../src/extractors/csharp.ts","../../src/extractors/common.ts","../../src/extractors/wasmLoader.ts","../../src/extractors/go.ts","../../src/extractors/java.ts","../../src/extractors/python.ts","../../src/extractors/ruby.ts","../../src/extractors/rust.ts","../../src/extractors/typescript.ts","../../src/report.ts","../../src/cli/commands/explain.ts","../../src/cli/commands/install.ts","../../src/cli/commands/path.ts","../../src/cli/commands/query.ts"],"sourcesContent":["// Shim globals in cjs bundle\n// There's a weird bug that esbuild will always inject importMetaUrl\n// if we export it as `const importMetaUrl = ... __filename ...`\n// But using a function will not cause this issue\n\nconst getImportMetaUrl = () => \n  typeof document === \"undefined\" \n    ? new URL(`file:${__filename}`).href \n    : (document.currentScript && document.currentScript.tagName.toUpperCase() === 'SCRIPT') \n      ? document.currentScript.src \n      : new URL(\"main.js\", document.baseURI).href;\n\nexport const importMetaUrl = /* @__PURE__ */ getImportMetaUrl()\n","/**\n * Security helpers — URL validation, SSRF-guarded fetch, path guards, label\n * sanitization, prompt-injection defenses. Every control listed in\n * SECURITY.md must have a corresponding function here and a unit test in\n * tests/security.test.ts. See the master prompt §5 for the full checklist.\n */\n\nimport { createHash } from 'node:crypto';\nimport * as dns from 'node:dns';\nimport * as http from 'node:http';\nimport * as https from 'node:https';\nimport * as fs from 'node:fs';\nimport * as net from 'node:net';\nimport * as nodePath from 'node:path';\n\nconst ALLOWED_SCHEMES = new Set(['http:', 'https:']);\nconst MAX_FETCH_BYTES = 50 * 1024 * 1024;\nconst MAX_TEXT_BYTES = 10 * 1024 * 1024;\nconst MAX_LABEL_LEN = 256;\nconst MAX_REDIRECTS = 5;\nconst REQUEST_TIMEOUT_MS = 15_000;\n\n/** Hostnames that must never be reachable, regardless of what they resolve to. */\nconst BLOCKED_HOSTNAMES = new Set([\n  'metadata.google.internal',\n  'metadata.internal',\n  'metadata',\n  'metadata.azure.com',\n  'instance-data',\n  'instance-data.ec2.internal',\n]);\n\n// ---------------------------------------------------------------------------\n// IP range checks (SSRF guard core). Implemented without extra dependencies.\n// ---------------------------------------------------------------------------\n\nfunction ipv4ToInt(ip: string): number | null {\n  const parts = ip.split('.');\n  if (parts.length !== 4) return null;\n  let result = 0;\n  for (const part of parts) {\n    if (!/^\\d{1,3}$/.test(part)) return null;\n    const n = Number(part);\n    if (n > 255) return null;\n    result = (result << 8) | n;\n  }\n  return result >>> 0;\n}\n\nfunction ipv4InCidr(ipInt: number, cidr: string): boolean {\n  const [base, prefixStr] = cidr.split('/');\n  const prefix = Number(prefixStr);\n  const baseInt = ipv4ToInt(base ?? '');\n  if (baseInt === null) return false;\n  const mask = prefix === 0 ? 0 : (~0 << (32 - prefix)) >>> 0;\n  return (ipInt & mask) >>> 0 === (baseInt & mask) >>> 0;\n}\n\n/** IPv4 ranges that must never be connected to from a server-side fetch. */\nconst BLOCKED_IPV4_CIDRS = [\n  '0.0.0.0/8', // \"this\" network\n  '10.0.0.0/8', // private\n  '100.64.0.0/10', // carrier-grade NAT (CGN)\n  '127.0.0.0/8', // loopback\n  '169.254.0.0/16', // link-local (covers 169.254.169.254 cloud metadata)\n  '172.16.0.0/12', // private\n  '192.0.0.0/24', // IETF protocol assignments\n  '192.0.2.0/24', // TEST-NET-1\n  '192.168.0.0/16', // private\n  '198.18.0.0/15', // benchmarking\n  '198.51.100.0/24', // TEST-NET-2\n  '203.0.113.0/24', // TEST-NET-3\n  '224.0.0.0/4', // multicast\n  '240.0.0.0/4', // reserved\n  '255.255.255.255/32', // broadcast\n];\n\nexport function isForbiddenIpv4(ip: string): boolean {\n  const ipInt = ipv4ToInt(ip);\n  if (ipInt === null) return true; // malformed -> treat as forbidden, fail closed\n  return BLOCKED_IPV4_CIDRS.some((cidr) => ipv4InCidr(ipInt, cidr));\n}\n\n/** Expand a (possibly `::`-compressed) IPv6 address into 8 16-bit groups. */\nfunction expandIpv6(ip: string): number[] | null {\n  const withoutZone = ip.split('%')[0] ?? '';\n  const parts = withoutZone.split('::');\n  if (parts.length > 2) return null;\n\n  const head = parts[0] ? parts[0].split(':').filter((s) => s.length > 0) : [];\n  const tail = parts.length === 2 && parts[1] ? parts[1].split(':').filter((s) => s.length > 0) : [];\n\n  let missing = 0;\n  if (parts.length === 2) {\n    missing = 8 - head.length - tail.length;\n    if (missing < 0) return null;\n  } else if (head.length + tail.length !== 8) {\n    return null;\n  }\n\n  const groupsHex = [...head, ...Array(missing).fill('0'), ...tail];\n  if (groupsHex.length !== 8) return null;\n\n  const groups: number[] = [];\n  for (const g of groupsHex) {\n    if (!/^[0-9a-fA-F]{1,4}$/.test(g)) return null;\n    groups.push(parseInt(g, 16));\n  }\n  return groups;\n}\n\nexport function isForbiddenIpv6(ip: string): boolean {\n  const lower = ip.toLowerCase();\n  if (lower === '::1' || lower === '::') return true;\n\n  const mapped = /^::ffff:(\\d+\\.\\d+\\.\\d+\\.\\d+)$/.exec(lower);\n  if (mapped) return isForbiddenIpv4(mapped[1] as string);\n\n  const groups = expandIpv6(lower);\n  if (groups === null) return true; // unparsable -> fail closed\n  const first = groups[0] as number;\n  if ((first & 0xffc0) === 0xfe80) return true; // fe80::/10 link-local\n  if ((first & 0xfe00) === 0xfc00) return true; // fc00::/7 unique local\n  if ((first & 0xff00) === 0xff00) return true; // ff00::/8 multicast\n  if (groups.every((g) => g === 0)) return true; // unspecified/all-zero\n  return false;\n}\n\nexport function isForbiddenIp(ip: string): boolean {\n  return net.isIPv6(ip) ? isForbiddenIpv6(ip) : isForbiddenIpv4(ip);\n}\n\n// ---------------------------------------------------------------------------\n// URL validation\n// ---------------------------------------------------------------------------\n\n/**\n * Validate a URL is http/https and, when the hostname is itself a literal\n * IP or a known cloud-metadata hostname, reject it synchronously. DNS-bound\n * hostnames are re-validated at connect time by safeFetch() (see below) —\n * this function alone cannot rule out DNS rebinding for a hostname that\n * currently resolves to a public IP.\n */\nexport function validateUrl(url: string): string {\n  let parsed: URL;\n  try {\n    parsed = new URL(url);\n  } catch {\n    throw new Error(`Invalid URL: ${url}`);\n  }\n\n  if (!ALLOWED_SCHEMES.has(parsed.protocol)) {\n    throw new Error(\n      `URL scheme not allowed: \"${parsed.protocol}\" (allowed: ${[...ALLOWED_SCHEMES].join(', ')})`,\n    );\n  }\n\n  const hostname = parsed.hostname.toLowerCase();\n  if (BLOCKED_HOSTNAMES.has(hostname)) {\n    throw new Error(`URL targets a blocked host: ${hostname}`);\n  }\n\n  // WHATWG URL keeps the brackets on an IPv6 literal host (e.g. \"[::1]\") —\n  // strip them before checking net.isIP()/isForbiddenIp().\n  const bareHost =\n    hostname.startsWith('[') && hostname.endsWith(']') ? hostname.slice(1, -1) : hostname;\n  if (net.isIP(bareHost) && isForbiddenIp(bareHost)) {\n    throw new Error(`URL targets a forbidden IP address: ${bareHost}`);\n  }\n\n  return parsed.toString();\n}\n\n// ---------------------------------------------------------------------------\n// safeFetch — SSRF-guarded, size-capped, redirect-revalidating fetch\n// ---------------------------------------------------------------------------\n\nexport type LookupFn = (hostname: string) => Promise<{ address: string; family: number }>;\n\n/**\n * Resolve a hostname (or pass through a literal IP) and validate the\n * result. `lookup` defaults to the real `dns.promises.lookup` — tests\n * substitute a fake to exercise the rebind guard deterministically without\n * making a real DNS query.\n */\nexport async function resolveAndValidate(\n  hostname: string,\n  lookup: LookupFn = dns.promises.lookup,\n): Promise<{ address: string; family: number }> {\n  if (net.isIP(hostname)) {\n    if (isForbiddenIp(hostname)) {\n      throw new Error(`Refusing to connect to forbidden IP: ${hostname}`);\n    }\n    return { address: hostname, family: net.isIPv6(hostname) ? 6 : 4 };\n  }\n  const result = await lookup(hostname);\n  if (isForbiddenIp(result.address)) {\n    throw new Error(`Refusing to connect to forbidden IP: ${hostname} -> ${result.address}`);\n  }\n  return result;\n}\n\nexport interface RawResponse {\n  statusCode: number;\n  headers: http.IncomingHttpHeaders;\n  body: Buffer;\n}\n\n/** Minimal shape of the `http`/`https` modules that requestOnce() needs — narrow on purpose so tests can substitute a fake transport instead of mocking network I/O. */\nexport type RequestTransport = Pick<typeof http, 'request'>;\n\n/**\n * Issue a single HTTP(S) request, connecting to `resolvedAddress` directly\n * (via a `lookup` override) rather than re-resolving DNS at connect time —\n * this is what prevents a DNS-rebind attacker from swapping the target\n * between validation and connection (TOCTOU). Streams the body and aborts\n * once it exceeds the byte cap for its declared content type.\n */\nexport function requestOnce(\n  target: URL,\n  resolvedAddress: string,\n  resolvedFamily: number,\n  transport: RequestTransport = target.protocol === 'https:' ? https : http,\n): Promise<RawResponse> {\n  return new Promise((resolve, reject) => {\n    const req = transport.request(\n      {\n        protocol: target.protocol,\n        hostname: target.hostname,\n        host: target.hostname,\n        port: target.port || (target.protocol === 'https:' ? 443 : 80),\n        path: `${target.pathname}${target.search}`,\n        method: 'GET',\n        timeout: REQUEST_TIMEOUT_MS,\n        headers: { 'user-agent': 'graphify/0.1', accept: '*/*' },\n        // Force the connection to the address we already validated — do not\n        // let Node re-resolve `target.hostname` at connect time.\n        lookup: (\n          _hostname: string,\n          options: unknown,\n          callback: (err: NodeJS.ErrnoException | null, address: string, family: number) => void,\n        ) => {\n          callback(null, resolvedAddress, resolvedFamily);\n        },\n      } as http.RequestOptions,\n      (res) => {\n        const statusCode = res.statusCode ?? 0;\n        const contentType = String(res.headers['content-type'] ?? '');\n        const isTextual = /^text\\/|json|xml|html|charset=/i.test(contentType);\n        const cap = isTextual ? MAX_TEXT_BYTES : MAX_FETCH_BYTES;\n\n        const chunks: Buffer[] = [];\n        let total = 0;\n        let aborted = false;\n\n        res.on('data', (chunk: Buffer) => {\n          total += chunk.length;\n          if (total > cap) {\n            aborted = true;\n            res.destroy();\n            req.destroy();\n            reject(new Error(`Response exceeded ${cap} byte cap (content-type: ${contentType})`));\n            return;\n          }\n          chunks.push(chunk);\n        });\n        res.on('end', () => {\n          if (aborted) return;\n          resolve({ statusCode, headers: res.headers, body: Buffer.concat(chunks) });\n        });\n        res.on('error', (err) => {\n          if (!aborted) reject(err);\n        });\n      },\n    );\n\n    req.on('timeout', () => {\n      req.destroy(new Error(`Request timed out after ${REQUEST_TIMEOUT_MS}ms`));\n    });\n    req.on('error', reject);\n    req.end();\n  });\n}\n\nexport interface SafeFetchDeps {\n  /** Override DNS resolution + IP validation (default: resolveAndValidate). */\n  resolve?: (hostname: string) => Promise<{ address: string; family: number }>;\n  /** Override the actual request (default: requestOnce against real http/https). */\n  request?: (target: URL, address: string, family: number) => Promise<RawResponse>;\n}\n\n/**\n * Fetch a URL with the SSRF guards from validateUrl() plus streaming size\n * caps (MAX_FETCH_BYTES / MAX_TEXT_BYTES) and a hard error on non-2xx\n * status. Every redirect hop is independently validated and re-resolved —\n * a redirect to a private/loopback/metadata address is rejected exactly\n * like a direct request would be.\n *\n * `deps` exists so tests can substitute the DNS/network collaborators with\n * deterministic fakes (see tests/security.test.ts) instead of mocking\n * Node's core modules or hitting real sockets — production callers should\n * never need to pass it.\n */\nexport async function safeFetch(url: string, deps: SafeFetchDeps = {}): Promise<Buffer> {\n  const resolve = deps.resolve ?? resolveAndValidate;\n  const doRequest = deps.request ?? requestOnce;\n\n  let current = validateUrl(url);\n  for (let hop = 0; hop <= MAX_REDIRECTS; hop++) {\n    const target = new URL(current);\n    const { address, family } = await resolve(target.hostname);\n    const response = await doRequest(target, address, family);\n\n    if (response.statusCode >= 300 && response.statusCode < 400) {\n      const location = response.headers.location;\n      if (!location) {\n        throw new Error(`Redirect response (${response.statusCode}) missing Location header`);\n      }\n      const next = new URL(location, target).toString();\n      current = validateUrl(next);\n      continue;\n    }\n\n    if (response.statusCode < 200 || response.statusCode >= 300) {\n      throw new Error(`Non-2xx response: ${response.statusCode}`);\n    }\n\n    return response.body;\n  }\n  throw new Error(`Too many redirects (> ${MAX_REDIRECTS}) while fetching ${url}`);\n}\n\n// ---------------------------------------------------------------------------\n// Path traversal guard\n// ---------------------------------------------------------------------------\n\n/**\n * Resolve `path` and require it stays inside `base` (defaults to\n * `<cwd>/graphify-out`). `base` must already exist. Throws on traversal\n * attempts (`../`, absolute escapes, symlink-resolved escapes).\n */\nexport function validateGraphPath(path: string, base?: string): string {\n  const baseDir = base ?? nodePath.join(process.cwd(), 'graphify-out');\n\n  let resolvedBase: string;\n  try {\n    resolvedBase = fs.realpathSync(baseDir);\n  } catch {\n    throw new Error(`Base directory does not exist: ${baseDir}`);\n  }\n\n  const candidate = nodePath.isAbsolute(path) ? path : nodePath.join(resolvedBase, path);\n  const resolvedCandidate = nodePath.resolve(candidate);\n\n  // Resolve symlinks for whichever is the deepest existing ancestor, so a\n  // symlink inside an otherwise-valid path can't escape the base dir either.\n  let realCandidate = resolvedCandidate;\n  try {\n    realCandidate = fs.realpathSync(resolvedCandidate);\n  } catch {\n    // Path (or part of it) may not exist yet (e.g. a file we're about to\n    // write) — fall back to the lexically-resolved path for the check.\n  }\n\n  const relative = nodePath.relative(resolvedBase, realCandidate);\n  const escapes = relative === '..' || relative.startsWith(`..${nodePath.sep}`) || nodePath.isAbsolute(relative);\n  if (escapes) {\n    throw new Error(`Path escapes graphify-out/: ${path}`);\n  }\n\n  return realCandidate;\n}\n\n// ---------------------------------------------------------------------------\n// Label sanitization (unchanged reference implementation) + HTML escaping\n// ---------------------------------------------------------------------------\n\n/** Strip control characters, cap length. Apply to every node/edge label. */\nexport function sanitizeLabel(text: string | null | undefined): string {\n  if (text == null) return '';\n  // eslint-disable-next-line no-control-regex -- intentional: stripping raw control chars\n  const stripped = String(text).replace(/[\\x00-\\x1f\\x7f]/g, '');\n  return stripped.slice(0, MAX_LABEL_LEN);\n}\n\n/**\n * HTML-escape a string. Callers must run sanitizeLabel() first for\n * length/control-char stripping, then escapeHtml() immediately before\n * embedding into graph.html (XSS control, see SECURITY.md).\n */\nexport function escapeHtml(text: string): string {\n  return text\n    .replace(/&/g, '&amp;')\n    .replace(/</g, '&lt;')\n    .replace(/>/g, '&gt;')\n    .replace(/\"/g, '&quot;')\n    .replace(/'/g, '&#39;');\n}\n\n// ---------------------------------------------------------------------------\n// Prompt-injection defenses for LLM-bound file content\n// ---------------------------------------------------------------------------\n\n/**\n * Known jailbreak / chat-template sentinels that must never reach a prompt\n * unescaped, whether they occur in source files or are forged to spoof our\n * own <untrusted_source> delimiter.\n */\nconst SENTINEL_PATTERNS: RegExp[] = [\n  /<\\|im_start\\|>/gi,\n  /<\\|im_end\\|>/gi,\n  /<\\|system\\|>/gi,\n  /\\[INST\\]/gi,\n  /\\[\\/INST\\]/gi,\n  /<<SYS>>/gi,\n  /<<\\/SYS>>/gi,\n  /<\\/untrusted_source>/gi,\n  /<untrusted_source/gi,\n];\n\n/**\n * Render brackets as fullwidth lookalikes (＜ ＞ ［ ］) so the defanged\n * echo is human-visible but no longer byte-identical to the original\n * sentinel — a naive downstream scan for the literal delimiter/sentinel\n * text will not re-match our own \"we found one\" marker.\n */\nfunction toFullwidthBrackets(text: string): string {\n  return text\n    .replace(/</g, '＜')\n    .replace(/>/g, '＞')\n    .replace(/\\[/g, '［')\n    .replace(/\\]/g, '］');\n}\n\n/**\n * Replace known jailbreak/chat-template sentinels with a visibly defanged\n * form — never silently stripped (silent stripping can itself be an\n * injection vector if it changes meaning unexpectedly).\n */\nfunction defangSentinels(content: string): string {\n  let result = content;\n  for (const pattern of SENTINEL_PATTERNS) {\n    result = result.replace(pattern, (match) => `[DEFANGED:${toFullwidthBrackets(match)}]`);\n  }\n  return result;\n}\n\n/**\n * Wrap file content for LLM prompts in a hash-stamped untrusted-source\n * delimiter and neutralize known jailbreak/chat-template sentinels. This\n * raises the bar against prompt injection; it does not eliminate it —\n * document that plainly wherever this is referenced.\n */\nexport function wrapUntrustedSource(path: string, content: string): string {\n  const sha256 = createHash('sha256').update(content, 'utf8').digest('hex');\n  const safePath = escapeHtml(sanitizeLabel(path));\n  const defanged = defangSentinels(content);\n  return `<untrusted_source path=\"${safePath}\" sha256=\"${sha256}\">\\n${defanged}\\n</untrusted_source>`;\n}\n","import * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport Graph from 'graphology';\nimport { validateGraphPath } from './security.js';\n\n/**\n * Load a previously-exported graph.json back into a graphology Graph.\n * Always goes through security.validateGraphPath() (path-traversal guard —\n * see SECURITY.md) so a caller-supplied `outDir`/CLI arg can never make\n * this read outside the graphify-out/ directory it resolves to.\n */\nexport async function loadGraph(outDir: string = path.join(process.cwd(), 'graphify-out')): Promise<Graph> {\n  const jsonPath = validateGraphPath('graph.json', outDir);\n  const raw = await fs.readFile(jsonPath, 'utf-8');\n  const data: unknown = JSON.parse(raw);\n  return Graph.from(data as Parameters<typeof Graph.from>[0]);\n}\n","import type Graph from 'graphology';\n\n/**\n * Library-level graph queries shared by the CLI (`graphify query/path/\n * explain`) and the MCP server tools of the same name. None of this is an\n * LLM call — it's lexical node matching + graph traversal, so it works\n * fully offline and deterministically.\n */\n\nconst STOPWORDS = new Set([\n  'a', 'an', 'the', 'is', 'are', 'was', 'were', 'do', 'does', 'did', 'how',\n  'what', 'where', 'when', 'why', 'who', 'which', 'to', 'of', 'in', 'on',\n  'for', 'and', 'or', 'this', 'that', 'it', 'does', 'that\\'s',\n]);\n\nfunction tokenize(text: string): string[] {\n  return text\n    .toLowerCase()\n    .split(/[^a-z0-9_.]+/)\n    .filter((token) => token.length > 1 && !STOPWORDS.has(token));\n}\n\nexport interface NodeMatch {\n  id: string;\n  label: string;\n  score: number;\n}\n\n/** Score every node by how many query tokens appear in its label or id. */\nexport function scoreNodes(graph: Graph, query: string): NodeMatch[] {\n  const tokens = tokenize(query);\n  const matches: NodeMatch[] = [];\n\n  graph.forEachNode((id, attributes) => {\n    const label = (attributes.label as string | undefined) ?? id;\n    const haystack = `${label} ${id}`.toLowerCase();\n    let score = 0;\n    for (const token of tokens) {\n      if (haystack.includes(token)) score += 1;\n    }\n    if (score > 0) matches.push({ id, label, score });\n  });\n\n  matches.sort((a, b) => b.score - a.score || a.id.localeCompare(b.id));\n  return matches;\n}\n\n/**\n * Best-effort single-node resolution: the highest-scoring lexical match,\n * or null if nothing in the graph matches at all. Deliberately does *not*\n * fall back to \"the most connected node\" — path/explain name a specific\n * node by intent, and silently substituting an unrelated one would be\n * more misleading than clearly saying \"no match\".\n */\nexport function resolveNode(graph: Graph, query: string): NodeMatch | null {\n  const matches = scoreNodes(graph, query);\n  return matches[0] ?? null;\n}\n\nexport interface VisitedNode {\n  id: string;\n  label: string;\n  sourceFile: string;\n  sourceLocation: string;\n  depth: number;\n}\n\nexport interface TraversalEdge {\n  source: string;\n  target: string;\n  relation: string;\n  confidence: string;\n}\n\nexport interface QueryResult {\n  seeds: NodeMatch[];\n  visited: VisitedNode[];\n  edges: TraversalEdge[];\n}\n\nexport interface QueryOptions {\n  dfs?: boolean;\n  /** Approximate cap on how many nodes to include (a stand-in for a true token budget — see docs). */\n  budget?: number;\n  maxDepth?: number;\n  maxSeeds?: number;\n}\n\nconst DEFAULT_MAX_DEPTH = 2;\nconst DEFAULT_MAX_SEEDS = 5;\nconst DEFAULT_BUDGET = 40;\n\n/**\n * BFS (default, broad context) or DFS (--dfs, trace a specific path)\n * traversal from the nodes whose label best matches `question`'s\n * keywords. This is lexical retrieval, not natural-language\n * understanding — it surfaces the neighborhood of the graph an agent (or\n * a human) should look at to answer the question, it does not itself\n * compose an answer.\n */\nexport function queryGraph(graph: Graph, question: string, options: QueryOptions = {}): QueryResult {\n  const maxDepth = options.maxDepth ?? DEFAULT_MAX_DEPTH;\n  const maxSeeds = options.maxSeeds ?? DEFAULT_MAX_SEEDS;\n  const budget = options.budget ?? DEFAULT_BUDGET;\n\n  const allMatches = scoreNodes(graph, question);\n  const seeds = allMatches.length > 0 ? allMatches.slice(0, maxSeeds) : [];\n\n  const visited = new Map<string, number>(); // id -> depth\n  const frontier: Array<{ id: string; depth: number }> = seeds.map((s) => ({ id: s.id, depth: 0 }));\n  for (const seed of seeds) visited.set(seed.id, 0);\n\n  while (frontier.length > 0 && visited.size < budget) {\n    const current = options.dfs ? (frontier.pop() as { id: string; depth: number }) : (frontier.shift() as { id: string; depth: number });\n    if (current.depth >= maxDepth) continue;\n\n    const neighbors = [...graph.neighbors(current.id)].sort((a, b) => a.localeCompare(b));\n    for (const neighbor of neighbors) {\n      if (visited.has(neighbor) || visited.size >= budget) continue;\n      visited.set(neighbor, current.depth + 1);\n      frontier.push({ id: neighbor, depth: current.depth + 1 });\n    }\n  }\n\n  const visitedNodes: VisitedNode[] = [...visited.entries()]\n    .map(([id, depth]) => {\n      const attrs = graph.getNodeAttributes(id);\n      return {\n        id,\n        label: (attrs.label as string | undefined) ?? id,\n        sourceFile: (attrs.sourceFile as string | undefined) ?? '',\n        sourceLocation: (attrs.sourceLocation as string | undefined) ?? '',\n        depth,\n      };\n    })\n    .sort((a, b) => a.depth - b.depth || a.id.localeCompare(b.id));\n\n  const edges: TraversalEdge[] = [];\n  graph.forEachEdge((_edge, attrs, source, target) => {\n    if (visited.has(source) && visited.has(target)) {\n      edges.push({\n        source,\n        target,\n        relation: String(attrs.relation),\n        confidence: String(attrs.confidence),\n      });\n    }\n  });\n  edges.sort(\n    (a, b) => a.source.localeCompare(b.source) || a.target.localeCompare(b.target) || a.relation.localeCompare(b.relation),\n  );\n\n  return { seeds, visited: visitedNodes, edges };\n}\n\nexport interface PathResult {\n  from: NodeMatch;\n  to: NodeMatch;\n  found: boolean;\n  path: string[];\n  edges: TraversalEdge[];\n}\n\n/** Shortest path between the nodes that best match `fromQuery` and `toQuery` (undirected BFS — connectivity, not call direction). */\nexport function shortestPath(graph: Graph, fromQuery: string, toQuery: string): PathResult | null {\n  const from = resolveNode(graph, fromQuery);\n  const to = resolveNode(graph, toQuery);\n  if (!from || !to) return null;\n\n  if (from.id === to.id) {\n    return { from, to, found: true, path: [from.id], edges: [] };\n  }\n\n  const predecessor = new Map<string, string>();\n  const visited = new Set<string>([from.id]);\n  const queue: string[] = [from.id];\n\n  while (queue.length > 0) {\n    const current = queue.shift() as string;\n    if (current === to.id) break;\n    const neighbors = [...graph.neighbors(current)].sort((a, b) => a.localeCompare(b));\n    for (const neighbor of neighbors) {\n      if (visited.has(neighbor)) continue;\n      visited.add(neighbor);\n      predecessor.set(neighbor, current);\n      queue.push(neighbor);\n    }\n  }\n\n  if (!visited.has(to.id)) {\n    return { from, to, found: false, path: [], edges: [] };\n  }\n\n  const path: string[] = [to.id];\n  let cursor = to.id;\n  while (cursor !== from.id) {\n    const prev = predecessor.get(cursor);\n    if (!prev) break;\n    path.unshift(prev);\n    cursor = prev;\n  }\n\n  const edges: TraversalEdge[] = [];\n  for (let i = 0; i < path.length - 1; i++) {\n    const a = path[i] as string;\n    const b = path[i + 1] as string;\n    const key = graph.edges(a, b)[0] ?? graph.edges(b, a)[0];\n    if (key) {\n      const attrs = graph.getEdgeAttributes(key);\n      edges.push({ source: a, target: b, relation: String(attrs.relation), confidence: String(attrs.confidence) });\n    }\n  }\n\n  return { from, to, found: true, path, edges };\n}\n\nexport interface ExplainResult {\n  id: string;\n  label: string;\n  sourceFile: string;\n  sourceLocation: string;\n  communityLabel?: string;\n  outgoing: TraversalEdge[];\n  incoming: TraversalEdge[];\n}\n\n/** Plain-language-ready explanation of the node that best matches `query`. */\nexport function explainNode(graph: Graph, query: string): ExplainResult | null {\n  const match = resolveNode(graph, query);\n  if (!match) return null;\n\n  const attrs = graph.getNodeAttributes(match.id);\n  const outgoing: TraversalEdge[] = [];\n  const incoming: TraversalEdge[] = [];\n\n  graph.forEachOutEdge(match.id, (_edge, edgeAttrs, source, target) => {\n    outgoing.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n  });\n  graph.forEachInEdge(match.id, (_edge, edgeAttrs, source, target) => {\n    incoming.push({ source, target, relation: String(edgeAttrs.relation), confidence: String(edgeAttrs.confidence) });\n  });\n\n  outgoing.sort((a, b) => a.target.localeCompare(b.target) || a.relation.localeCompare(b.relation));\n  incoming.sort((a, b) => a.source.localeCompare(b.source) || a.relation.localeCompare(b.relation));\n\n  return {\n    id: match.id,\n    label: match.label,\n    sourceFile: (attrs.sourceFile as string | undefined) ?? '',\n    sourceLocation: (attrs.sourceLocation as string | undefined) ?? '',\n    communityLabel: attrs.communityLabel as string | undefined,\n    outgoing,\n    incoming,\n  };\n}\n","/**\n * MCP stdio server exposing query/path/explain as tools against an existing\n * graphify-out/graph.json. Stdio only — never opens a network listener.\n * All graph file paths go through security.validateGraphPath().\n *\n * This module is a pure library: importing it has no side effects (it does\n * not read argv or start a server on import). `startServer()` is called\n * explicitly by `bin/graphify-mcp.js` (the standalone `graphify-mcp` CLI\n * entry point) and by `graphify --mcp` (see src/cli/index.ts).\n */\nimport * as path from 'node:path';\nimport { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';\nimport { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';\nimport type { Transport } from '@modelcontextprotocol/sdk/shared/transport.js';\nimport { z } from 'zod';\nimport { loadGraph } from '../graphStore.js';\nimport { explainNode, queryGraph, shortestPath } from '../query.js';\nimport { validateGraphPath } from '../security.js';\n\nfunction textResult(text: string): { content: Array<{ type: 'text'; text: string }> } {\n  return { content: [{ type: 'text', text }] };\n}\n\n/**\n * Build the McpServer instance (tools registered, nothing connected yet).\n * Split out from startServer() so tests can connect it to an in-memory\n * transport instead of real stdio (see tests/mcp/server.test.ts).\n */\nexport function createGraphifyMcpServer(outDir: string): McpServer {\n  const server = new McpServer({ name: 'graphify', version: '0.1.0' });\n\n  server.registerTool(\n    'query',\n    {\n      description:\n        'BFS (default) or DFS traversal of the graphify knowledge graph, seeded from nodes ' +\n        'whose label matches the question. Returns the matched seeds, the visited node ' +\n        'context, and the edges among them — broad context for answering a structural question.',\n      inputSchema: {\n        question: z.string().describe('Natural-language question or keywords to search the graph for.'),\n        dfs: z.boolean().optional().describe('Use depth-first traversal instead of the default breadth-first.'),\n        budget: z.number().int().positive().optional().describe('Approximate cap on how many nodes to include.'),\n      },\n    },\n    async ({ question, dfs, budget }) => {\n      const graph = await loadGraph(outDir);\n      const result = queryGraph(graph, question, { dfs, budget });\n      return textResult(JSON.stringify(result, null, 2));\n    },\n  );\n\n  server.registerTool(\n    'path',\n    {\n      description: 'Shortest path between two named nodes in the graphify knowledge graph.',\n      inputSchema: {\n        from: z.string().describe('Name/label of the starting node.'),\n        to: z.string().describe('Name/label of the destination node.'),\n      },\n    },\n    async ({ from, to }) => {\n      const graph = await loadGraph(outDir);\n      const result = shortestPath(graph, from, to);\n      if (!result) {\n        return textResult(`Could not resolve \"${from}\" and/or \"${to}\" to a node in the graph.`);\n      }\n      return textResult(JSON.stringify(result, null, 2));\n    },\n  );\n\n  server.registerTool(\n    'explain',\n    {\n      description:\n        'Plain-language-ready explanation of a single node: its source location, community, ' +\n        'and incoming/outgoing edges.',\n      inputSchema: {\n        node: z.string().describe('Name/label (or id) of the node to explain.'),\n      },\n    },\n    async ({ node }) => {\n      const graph = await loadGraph(outDir);\n      const result = explainNode(graph, node);\n      if (!result) {\n        return textResult(`No node matched \"${node}\".`);\n      }\n      return textResult(JSON.stringify(result, null, 2));\n    },\n  );\n\n  return server;\n}\n\n/**\n * Start the MCP server, serving `query`/`path`/`explain` tools against the\n * graph.json found in `graphPath`'s directory. `graphPath` is validated\n * (via security.validateGraphPath()) up front so a bad path fails\n * immediately with a clear error instead of the first time a client calls\n * a tool. `transport` defaults to real stdio; tests substitute an\n * in-memory transport.\n */\nexport async function startServer(graphPath: string, transport: Transport = new StdioServerTransport()): Promise<void> {\n  const outDir = path.dirname(path.resolve(graphPath));\n  const fileName = path.basename(graphPath);\n  // Fail fast (and clearly) if the graph path escapes/doesn't exist, rather\n  // than only surfacing that the first time a tool is called.\n  validateGraphPath(fileName, outDir);\n\n  const server = createGraphifyMcpServer(outDir);\n  await server.connect(transport);\n}\n\n/** Entry point used by bin/graphify-mcp.js. */\nexport async function main(argv: string[] = process.argv): Promise<void> {\n  const graphPath = argv[2] ?? path.join(process.cwd(), 'graphify-out', 'graph.json');\n  await startServer(graphPath);\n}\n","#!/usr/bin/env node\nimport { execFile } from 'node:child_process';\nimport * as fs from 'node:fs/promises';\nimport * as os from 'node:os';\nimport * as path from 'node:path';\nimport { promisify } from 'node:util';\nimport { watch as watchFiles } from 'chokidar';\nimport { Command } from 'commander';\nimport { analyze } from '../analyze.js';\nimport { cluster } from '../cluster.js';\nimport { exportGraph } from '../export.js';\nimport { loadGraph } from '../graphStore.js';\nimport { runPipeline } from '../pipeline.js';\nimport { renderReport } from '../report.js';\nimport { validateUrl } from '../security.js';\nimport { runExplain } from './commands/explain.js';\nimport { runInstall } from './commands/install.js';\nimport { runPath } from './commands/path.js';\nimport { runQuery } from './commands/query.js';\n\nconst execFileAsync = promisify(execFile);\n\ninterface DefaultCommandOptions {\n  mode?: string;\n  update?: boolean;\n  watch?: boolean;\n  clusterOnly?: boolean;\n  viz: boolean; // commander negatable --no-viz -> options.viz\n  svg?: boolean;\n  graphml?: boolean;\n  neo4j?: boolean;\n  mcp?: boolean;\n  leiden?: boolean;\n  maxIterations?: number;\n}\n\nfunction looksLikeGitUrl(value: string): boolean {\n  if (!/^https?:\\/\\//i.test(value)) return false;\n  return /github\\.com|gitlab\\.com|bitbucket\\.org/i.test(value) || value.endsWith('.git');\n}\n\n/** Clone `url` into a fresh temp directory using an argv-array child_process call (never shell: true, never a shell string built from input). */\nasync function cloneRepo(url: string): Promise<string> {\n  const validated = validateUrl(url);\n  const dest = await fs.mkdtemp(path.join(os.tmpdir(), 'graphify-clone-'));\n  await execFileAsync('git', ['clone', '--depth', '1', validated, dest]);\n  return dest;\n}\n\nfunction exportOptionsFrom(options: DefaultCommandOptions) {\n  return { html: options.viz, svg: options.svg, graphml: options.graphml, neo4j: options.neo4j };\n}\n\nfunction clusterOptionsFrom(options: DefaultCommandOptions) {\n  return {\n    algorithm: options.leiden ? ('leiden' as const) : ('louvain' as const),\n    maxIterations: options.maxIterations,\n  };\n}\n\nasync function runClusterOnly(root: string, options: DefaultCommandOptions): Promise<void> {\n  const outDir = path.join(root, 'graphify-out');\n  const graph = await loadGraph(outDir);\n  cluster(graph, clusterOptionsFrom(options));\n  const analysis = analyze(graph);\n  const report = renderReport(graph, analysis);\n  await exportGraph(graph, { outDir, ...exportOptionsFrom(options) }, report);\n  console.error(`Re-clustered the existing graph (${clusterOptionsFrom(options).algorithm}).`);\n}\n\n/** Watch `root` (ignoring graphify-out/, node_modules/, .git/) and re-run `runOnce` on any change, debounced. Never resolves — the process stays alive until interrupted, matching normal watch-mode CLI behavior. */\nasync function watchAndRebuild(root: string, runOnce: () => Promise<unknown>): Promise<void> {\n  const watcher = watchFiles(root, {\n    ignored: (filePath: string) => /(^|[/\\\\])(node_modules|\\.git|graphify-out)([/\\\\]|$)/.test(filePath),\n    ignoreInitial: true,\n  });\n\n  let timer: ReturnType<typeof setTimeout> | null = null;\n  let running = false;\n  const schedule = (): void => {\n    if (timer) clearTimeout(timer);\n    timer = setTimeout(() => {\n      if (running) return;\n      running = true;\n      console.error('Change detected, rebuilding...');\n      runOnce()\n        .catch((error: unknown) => console.error(`graphify --watch: rebuild failed: ${(error as Error).message}`))\n        .finally(() => {\n          running = false;\n        });\n    }, 300);\n  };\n\n  watcher.on('add', schedule).on('change', schedule).on('unlink', schedule);\n\n  await new Promise<never>(() => {\n    /* keep the process alive until the user interrupts it (Ctrl+C) */\n  });\n}\n\nconst program = new Command();\n\nprogram\n  .name('graphify')\n  .description('Turn a folder of code/docs/papers into a queryable knowledge graph.')\n  .argument('[path]', 'path to scan, or a GitHub URL', '.')\n  .option('--mode <mode>', 'extraction mode (deep for richer INFERRED edges — reserved, no-op in v1)')\n  .option('--update', 'incremental re-extract of changed files only (not implemented in v1 — runs full pipeline)')\n  .option('--watch', 'rebuild on file change')\n  .option('--cluster-only', 'rerun clustering on an existing graph')\n  .option('--leiden', 'use Leiden instead of Louvain for community detection (v2 — better community quality)')\n  .option('--max-iterations <n>', 'Leiden only: cap on outer iterations for very large graphs', Number)\n  .option('--no-viz', 'skip graph.html')\n  .option('--svg', 'also export graph.svg (not implemented in v1)')\n  .option('--graphml', 'also export graph.graphml (not implemented in v1)')\n  .option('--neo4j', 'generate graphify-out/cypher.txt for Neo4j (not implemented in v1)')\n  .option('--mcp', 'start MCP stdio server instead of running the pipeline')\n  .action(async (targetArg: string, options: DefaultCommandOptions) => {\n    try {\n      if (options.mcp) {\n        const outDir = path.resolve(targetArg === '.' ? process.cwd() : targetArg, 'graphify-out');\n        const { startServer } = await import('../mcp/server.js');\n        await startServer(path.join(outDir, 'graph.json'));\n        return;\n      }\n\n      let root = targetArg;\n      if (looksLikeGitUrl(targetArg)) {\n        console.error(`Cloning ${targetArg} ...`);\n        root = await cloneRepo(targetArg);\n      }\n      root = path.resolve(root);\n\n      if (options.update) {\n        console.error(\n          '--update (incremental re-extract) is not implemented yet in v1 — running the full pipeline instead.',\n        );\n      }\n      if (options.mode) {\n        console.error(`--mode ${options.mode} is reserved for a future richer-INFERRED-edges pass — currently a no-op.`);\n      }\n\n      if (options.clusterOnly) {\n        await runClusterOnly(root, options);\n        return;\n      }\n\n      const runOnce = () =>\n        runPipeline(root, {\n          ...exportOptionsFrom(options),\n          ...clusterOptionsFrom(options),\n          onProgress: (m) => console.error(m),\n        });\n      await runOnce();\n\n      if (options.watch) {\n        console.error(`Watching ${root} for changes (Ctrl+C to stop) ...`);\n        await watchAndRebuild(root, runOnce);\n      }\n    } catch (error) {\n      console.error(`graphify: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('query <question>')\n  .description('BFS (default) or DFS traversal answering a question against the existing graph')\n  .option('--dfs', 'depth-first traversal (trace a specific path)')\n  .option('--budget <tokens>', 'cap answer at N tokens', Number)\n  .action(async (question: string, options: { dfs?: boolean; budget?: number }) => {\n    try {\n      await runQuery(question, options);\n    } catch (error) {\n      console.error(`graphify query: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('path <from> <to>')\n  .description('shortest path between two named nodes')\n  .action(async (from: string, to: string) => {\n    try {\n      await runPath(from, to);\n    } catch (error) {\n      console.error(`graphify path: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('explain <node>')\n  .description('plain-language explanation of a node')\n  .action(async (node: string) => {\n    try {\n      await runExplain(node);\n    } catch (error) {\n      console.error(`graphify explain: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram\n  .command('install')\n  .description('install the skill files into the local agent(s)')\n  .action(async () => {\n    try {\n      await runInstall();\n    } catch (error) {\n      console.error(`graphify install: ${(error as Error).message}`);\n      process.exitCode = 1;\n    }\n  });\n\nprogram.parseAsync(process.argv);\n","import type Graph from 'graphology';\nimport type { Analysis, Confidence } from './types.js';\n\n/** A node needs at least this many total connections to ever be a \"god node\", regardless of graph size. */\nconst ABSOLUTE_DEGREE_FLOOR = 10;\n/** ...and needs to be at least this many times the graph's mean degree. */\nconst MEAN_DEGREE_MULTIPLIER = 3;\n/** Cap how many items of a given kind get spelled out in a single message. */\nconst MAX_LISTED = 10;\n\nfunction truncatedList(items: string[]): string {\n  const shown = items.slice(0, MAX_LISTED).join(', ');\n  return items.length > MAX_LISTED ? `${shown}, ...` : shown;\n}\n\n/** Connected components treating the (directed) graph as undirected — reachability via any edge direction. */\nfunction connectedComponents(graph: Graph): string[][] {\n  const visited = new Set<string>();\n  const components: string[][] = [];\n  const sortedNodes = [...graph.nodes()].sort((a, b) => a.localeCompare(b));\n\n  for (const start of sortedNodes) {\n    if (visited.has(start)) continue;\n    const component: string[] = [];\n    const queue: string[] = [start];\n    visited.add(start);\n\n    while (queue.length > 0) {\n      const current = queue.shift() as string;\n      component.push(current);\n      const neighbors = [...graph.neighbors(current)].sort((a, b) => a.localeCompare(b));\n      for (const neighbor of neighbors) {\n        if (!visited.has(neighbor)) {\n          visited.add(neighbor);\n          queue.push(neighbor);\n        }\n      }\n    }\n\n    component.sort((a, b) => a.localeCompare(b));\n    components.push(component);\n  }\n\n  components.sort((a, b) => b.length - a.length || (a[0] ?? '').localeCompare(b[0] ?? ''));\n  return components;\n}\n\nfunction labelOf(graph: Graph, id: string): string {\n  return (graph.getNodeAttribute(id, 'label') as string | undefined) ?? id;\n}\n\n/**\n * Surface god-nodes (excessive fan-in/out), structural surprises (self\n * references, AMBIGUOUS edges), and open questions (isolated nodes,\n * disconnected components) for a human to review in GRAPH_REPORT.md.\n */\nexport function analyze(graph: Graph): Analysis {\n  const godNodes: string[] = [];\n  const surprises: string[] = [];\n  const openQuestions: string[] = [];\n\n  if (graph.order === 0) {\n    openQuestions.push(\n      'The graph is empty — no nodes were extracted. Check detect()/extract() coverage for this codebase.',\n    );\n    return { godNodes, surprises, openQuestions };\n  }\n\n  const degreeEntries = [...graph.nodes()]\n    .map((id) => ({ id, degree: graph.degree(id) }))\n    .sort((a, b) => a.id.localeCompare(b.id));\n  const meanDegree = degreeEntries.reduce((sum, e) => sum + e.degree, 0) / degreeEntries.length;\n  const threshold = Math.max(ABSOLUTE_DEGREE_FLOOR, meanDegree * MEAN_DEGREE_MULTIPLIER);\n\n  for (const { id, degree } of degreeEntries) {\n    if (degree > 0 && degree >= threshold) {\n      godNodes.push(id);\n      surprises.push(\n        `${labelOf(graph, id)} has ${degree} connections (fan-in + fan-out) — well above the graph ` +\n          `average of ${meanDegree.toFixed(1)}. Likely a god node / hotspot worth reviewing for ` +\n          'excessive coupling.',\n      );\n    }\n  }\n\n  graph.forEachEdge((_edge, attributes, source, target) => {\n    if (source === target) {\n      surprises.push(`${labelOf(graph, source)} has a self-referential \"${String(attributes.relation)}\" edge.`);\n    }\n  });\n\n  const ambiguousEdges: string[] = [];\n  graph.forEachEdge((_edge, attributes, source, target) => {\n    if ((attributes.confidence as Confidence) === 'AMBIGUOUS') {\n      ambiguousEdges.push(\n        `${labelOf(graph, source)} --${String(attributes.relation)}--> ${labelOf(graph, target)}`,\n      );\n    }\n  });\n  if (ambiguousEdges.length > 0) {\n    ambiguousEdges.sort((a, b) => a.localeCompare(b));\n    openQuestions.push(\n      `${ambiguousEdges.length} edge(s) are marked AMBIGUOUS and need human review: ` +\n        truncatedList(ambiguousEdges),\n    );\n  }\n\n  const isolated = degreeEntries.filter((e) => e.degree === 0).map((e) => e.id);\n  if (isolated.length > 0) {\n    openQuestions.push(\n      `${isolated.length} node(s) have no incoming or outgoing edges (${truncatedList(isolated)}) — ` +\n        'dead code, an entry point, or a gap in extraction?',\n    );\n  }\n\n  const components = connectedComponents(graph);\n  if (components.length > 1) {\n    const largest = components[0] as string[];\n    openQuestions.push(\n      `The graph has ${components.length} disconnected components — the largest has ${largest.length} ` +\n        'node(s). Confirm this reflects real module boundaries rather than missed cross-file edges.',\n    );\n  }\n\n  return { godNodes, surprises, openQuestions };\n}\n","import { createHash } from 'node:crypto';\nimport Graph from 'graphology';\n// A pure-JS, graphology-native Leiden implementation — extracted from the\n// upstream graphology monorepo's own (never separately published)\n// src/communities-leiden, repackaged with an optional `maxIterations` cap.\n// No native compilation (no .node bindings) — same \"no native\n// compilation\" constraint as the rest of this package. See v2 notes below.\nimport leiden from '@aflsolutions/graphology-communities-leiden';\nimport louvain from 'graphology-communities-louvain';\n\n/** Fixed seed so repeated runs on the same graph explore ties identically. */\nconst FIXED_SEED = 0x5eed_1234;\n\n/** mulberry32 — small, dependency-free, deterministic PRNG. */\nfunction mulberry32(seed: number): () => number {\n  let a = seed >>> 0;\n  return function next(): number {\n    a = (a + 0x6d2b79f5) | 0;\n    let t = Math.imul(a ^ (a >>> 15), 1 | a);\n    t = (t + Math.imul(t ^ (t >>> 7), 61 | t)) ^ t;\n    return ((t ^ (t >>> 14)) >>> 0) / 4294967296;\n  };\n}\n\ninterface EdgeEntry {\n  key: string;\n  source: string;\n  target: string;\n  attributes: Record<string, unknown>;\n}\n\n/**\n * Build a copy of `graph` with nodes and edges (re-)inserted in sorted\n * order, so the clustering algorithm's own internal iteration — and\n * therefore its tie-breaking — is fed a canonical order regardless of how\n * the input graph happened to be constructed (master prompt §4: \"sort\n * nodes/edges before feeding the algorithm\").\n */\nfunction sortedWorkingCopy(graph: Graph): Graph {\n  const copy = new Graph({ type: graph.type, multi: graph.multi, allowSelfLoops: graph.allowSelfLoops });\n\n  const nodeIds = graph.nodes().sort((a, b) => a.localeCompare(b));\n  for (const id of nodeIds) {\n    copy.addNode(id, { ...graph.getNodeAttributes(id) });\n  }\n\n  const edgeEntries: EdgeEntry[] = [];\n  graph.forEachEdge((edge, attributes, source, target) => {\n    edgeEntries.push({ key: edge, source, target, attributes });\n  });\n  edgeEntries.sort(\n    (a, b) =>\n      a.source.localeCompare(b.source) ||\n      a.target.localeCompare(b.target) ||\n      String(a.attributes.relation).localeCompare(String(b.attributes.relation)),\n  );\n  for (const entry of edgeEntries) {\n    copy.addEdgeWithKey(entry.key, entry.source, entry.target, { ...entry.attributes });\n  }\n\n  return copy;\n}\n\nexport type ClusterAlgorithm = 'louvain' | 'leiden';\n\nexport interface ClusterOptions {\n  /**\n   * `louvain` (default, v1 behavior, unchanged) or `leiden` (v2: better\n   * community quality / guaranteed well-connectedness, via\n   * `@aflsolutions/graphology-communities-leiden` — see master prompt's\n   * v2 upgrade ideas, \"Real Leiden clustering\"). Both run deterministically\n   * against a sorted working copy with the same fixed-seed PRNG.\n   */\n  algorithm?: ClusterAlgorithm;\n  /**\n   * Leiden-only: hard cap on outer iterations, for very large graphs where\n   * full convergence is expensive and the last iterations buy little\n   * additional modularity. Ignored for `algorithm: 'louvain'`.\n   */\n  maxIterations?: number;\n}\n\n/**\n * @aflsolutions/graphology-communities-leiden (like upstream graphology's\n * own Leiden) only implements the undirected case — it throws on a graph\n * whose edges are all directed. Community detection is inherently an\n * undirected-connectivity notion anyway (classic Louvain/Leiden\n * modularity is defined over undirected graphs), so we run Leiden against\n * an undirected copy and copy the resulting `community` assignment back\n * onto `working` by node id.\n */\nfunction toUndirectedCopy(graph: Graph): Graph {\n  const copy = new Graph({ type: 'undirected', multi: true, allowSelfLoops: graph.allowSelfLoops });\n  graph.forEachNode((nodeId, attributes) => copy.addNode(nodeId, { ...attributes }));\n  graph.forEachEdge((edgeKey, attributes, source, target) => {\n    copy.addEdgeWithKey(edgeKey, source, target, { ...attributes });\n  });\n  return copy;\n}\n\nfunction runAlgorithm(working: Graph, options: ClusterOptions): void {\n  const rng = mulberry32(FIXED_SEED);\n  if (options.algorithm === 'leiden') {\n    const undirected = toUndirectedCopy(working);\n    leiden.assign(undirected, { rng, maxIterations: options.maxIterations ?? 0 });\n    undirected.forEachNode((nodeId, attributes) => {\n      working.setNodeAttribute(nodeId, 'community', attributes.community);\n    });\n    return;\n  }\n  louvain.assign(working, { rng });\n}\n\n/**\n * Community detection — Louvain by default (v1, unchanged), or Leiden\n * (v2, `{ algorithm: 'leiden' }`) for better-quality, guaranteed\n * well-connected communities on the same graph. Deterministic: runs\n * against a sorted working copy with a fixed RNG seed, then copies the\n * resulting `community` assignment back onto the original graph by node id\n * (so `cluster()` still mutates and returns the graph instance it was\n * given). Labels each community after its highest-degree (\"hub\") member;\n * no LLM required for a usable baseline. Also stamps a `communityHash`\n * (sha256 of the community's sorted member ids) so `--cluster-only` can\n * tell which communities actually changed vs. merely being relabeled with\n * a different arbitrary index next run.\n */\nexport function cluster(graph: Graph, options: ClusterOptions = {}): Graph {\n  if (graph.order === 0) return graph;\n\n  const working = sortedWorkingCopy(graph);\n  runAlgorithm(working, options);\n\n  // Highest-degree member per community, computed on the sorted copy so\n  // ties break on node id deterministically.\n  const hubs = new Map<number, { id: string; degree: number }>();\n  working.forEachNode((nodeId) => {\n    const community = working.getNodeAttribute(nodeId, 'community') as number;\n    const degree = working.degree(nodeId);\n    const current = hubs.get(community);\n    if (!current || degree > current.degree) {\n      hubs.set(community, { id: nodeId, degree });\n    }\n  });\n\n  const membersByCommunity = new Map<number, string[]>();\n  working.forEachNode((nodeId) => {\n    const community = working.getNodeAttribute(nodeId, 'community') as number;\n    const list = membersByCommunity.get(community);\n    if (list) list.push(nodeId);\n    else membersByCommunity.set(community, [nodeId]);\n  });\n\n  const labelByCommunity = new Map<number, string>();\n  const hashByCommunity = new Map<number, string>();\n  for (const [community, members] of membersByCommunity) {\n    members.sort((a, b) => a.localeCompare(b));\n    hashByCommunity.set(community, createHash('sha256').update(members.join('\\n')).digest('hex'));\n\n    const hub = hubs.get(community);\n    const hubLabel = hub ? (working.getNodeAttribute(hub.id, 'label') as string) : undefined;\n    labelByCommunity.set(community, hubLabel && hubLabel.length > 0 ? hubLabel : `community-${community}`);\n  }\n\n  working.forEachNode((nodeId) => {\n    const community = working.getNodeAttribute(nodeId, 'community') as number;\n    graph.mergeNodeAttributes(nodeId, {\n      community,\n      communityLabel: labelByCommunity.get(community),\n      communityHash: hashByCommunity.get(community),\n    });\n  });\n\n  return graph;\n}\n","import { createRequire } from 'node:module';\nimport * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport type Graph from 'graphology';\nimport { escapeHtml, sanitizeLabel, validateGraphPath } from './security.js';\nimport type { ExportOptions } from './types.js';\n\nconst require = createRequire(import.meta.url);\n\n/** Locate the bundled, self-contained vis-network assets (no CDN, works fully offline). */\nfunction resolveVisNetworkAssets(): { jsPath: string; cssPath: string } {\n  const packageJsonPath = require.resolve('vis-network/package.json');\n  const root = path.dirname(packageJsonPath);\n  return {\n    jsPath: path.join(root, 'standalone', 'umd', 'vis-network.min.js'),\n    cssPath: path.join(root, 'styles', 'vis-network.min.css'),\n  };\n}\n\n/** A small, deterministic categorical palette, cycled by community index. */\nconst COMMUNITY_PALETTE = [\n  '#4e79a7',\n  '#f28e2b',\n  '#e15759',\n  '#76b7b2',\n  '#59a14f',\n  '#edc948',\n  '#b07aa1',\n  '#ff9da7',\n  '#9c755f',\n  '#bab0ac',\n];\n\nfunction colorForCommunity(community: number | undefined): string {\n  if (community === undefined) return '#8ab4f8';\n  const index = ((community % COMMUNITY_PALETTE.length) + COMMUNITY_PALETTE.length) % COMMUNITY_PALETTE.length;\n  return COMMUNITY_PALETTE[index] as string;\n}\n\n/**\n * Embedding untrusted-derived strings (node labels ultimately come from\n * source file content) inside an inline <script> tag has one extra XSS\n * vector JSON.stringify() alone doesn't cover: a literal `</script>`\n * substring in the JSON text would close our script tag early and let the\n * rest be parsed as raw HTML. Escape the forward slash so that can't happen.\n */\nfunction safeInlineJson(value: unknown): string {\n  return JSON.stringify(value, null, 2).replace(/<\\/(script)/gi, '<\\\\/$1');\n}\n\nfunction buildVisNodesAndEdges(graph: Graph): { nodes: unknown[]; edges: unknown[] } {\n  const nodes = graph.nodes().map((id) => {\n    const attributes = graph.getNodeAttributes(id);\n    const rawLabel = (attributes.label as string | undefined) ?? id;\n    const label = escapeHtml(sanitizeLabel(rawLabel));\n    const sourceFile = escapeHtml(sanitizeLabel((attributes.sourceFile as string | undefined) ?? ''));\n    const sourceLocation = escapeHtml(sanitizeLabel((attributes.sourceLocation as string | undefined) ?? ''));\n    const communityLabel = escapeHtml(sanitizeLabel((attributes.communityLabel as string | undefined) ?? ''));\n    return {\n      id,\n      label,\n      title: `${label}\\n${sourceFile}${sourceLocation ? `:${sourceLocation}` : ''}${\n        communityLabel ? `\\ncommunity: ${communityLabel}` : ''\n      }`,\n      color: colorForCommunity(attributes.community as number | undefined),\n    };\n  });\n\n  const edges: unknown[] = [];\n  graph.forEachEdge((edgeKey, attributes, source, target) => {\n    const relation = escapeHtml(sanitizeLabel(String(attributes.relation ?? '')));\n    const confidence = escapeHtml(sanitizeLabel(String(attributes.confidence ?? '')));\n    edges.push({\n      id: edgeKey,\n      from: source,\n      to: target,\n      label: relation,\n      title: `${relation} (${confidence})`,\n      dashes: confidence === 'INFERRED' || confidence === 'AMBIGUOUS',\n      arrows: 'to',\n    });\n  });\n\n  return { nodes, edges };\n}\n\nasync function renderHtml(graph: Graph): Promise<string> {\n  const { jsPath, cssPath } = resolveVisNetworkAssets();\n  const [visJs, visCss] = await Promise.all([\n    fs.readFile(jsPath, 'utf-8'),\n    fs.readFile(cssPath, 'utf-8'),\n  ]);\n\n  const { nodes, edges } = buildVisNodesAndEdges(graph);\n  const dataJson = safeInlineJson({ nodes, edges });\n\n  return `<!doctype html>\n<html lang=\"en\">\n<head>\n<meta charset=\"utf-8\">\n<title>graphify — graph.html</title>\n<style>\n  html, body { margin: 0; padding: 0; height: 100%; font-family: system-ui, sans-serif; }\n  #graph { width: 100%; height: 100vh; }\n  ${visCss}\n</style>\n</head>\n<body>\n<div id=\"graph\"></div>\n<script>\n${visJs}\n</script>\n<script>\n(function () {\n  var data = ${dataJson};\n  var nodes = new vis.DataSet(data.nodes);\n  var edges = new vis.DataSet(data.edges);\n  var container = document.getElementById('graph');\n  var network = new vis.Network(container, { nodes: nodes, edges: edges }, {\n    nodes: { shape: 'dot', size: 12, font: { size: 14 } },\n    edges: { smooth: { type: 'continuous' }, font: { size: 10, align: 'middle' } },\n    physics: { stabilization: true },\n    interaction: { hover: true, tooltipDelay: 150 },\n  });\n  window.__graphifyNetwork = network;\n})();\n</script>\n</body>\n</html>\n`;\n}\n\n/**\n * Write graph.json (graphology's node-link serialization, GraphRAG-ready)\n * and, per options, graph.html (vis-network, bundled inline — no CDN, works\n * fully offline) and GRAPH_REPORT.md. Every label/title embedded in\n * graph.html is passed through security.sanitizeLabel() + escapeHtml()\n * first (XSS control, see SECURITY.md).\n *\n * Obsidian vault / .graphml / Neo4j cypher export are NOT implemented in\n * v1 — if requested, exportGraph logs a clear warning and skips them\n * rather than silently doing nothing or faking output.\n */\nexport async function exportGraph(graph: Graph, options: ExportOptions, report?: string): Promise<void> {\n  const outDir = path.resolve(options.outDir);\n  await fs.mkdir(outDir, { recursive: true });\n\n  const jsonPath = validateGraphPath('graph.json', outDir);\n  await fs.writeFile(jsonPath, JSON.stringify(graph.toJSON(), null, 2), 'utf-8');\n\n  if (options.html !== false) {\n    const htmlPath = validateGraphPath('graph.html', outDir);\n    await fs.writeFile(htmlPath, await renderHtml(graph), 'utf-8');\n  }\n\n  if (report !== undefined) {\n    const reportPath = validateGraphPath('GRAPH_REPORT.md', outDir);\n    await fs.writeFile(reportPath, report, 'utf-8');\n  }\n\n  const notImplemented: string[] = [];\n  if (options.svg) notImplemented.push('--svg');\n  if (options.graphml) notImplemented.push('--graphml');\n  if (options.neo4j) notImplemented.push('--neo4j');\n  if (options.obsidian) notImplemented.push('--obsidian');\n  for (const flag of notImplemented) {\n    console.warn(`graphify: ${flag} export is not implemented yet in v1 — skipping.`);\n  }\n}\n","import * as path from 'node:path';\nimport type Graph from 'graphology';\nimport { analyze } from './analyze.js';\nimport { buildGraph } from './build.js';\nimport { cluster, type ClusterAlgorithm } from './cluster.js';\nimport { collectFiles } from './detect.js';\nimport { extract } from './extract.js';\nimport { exportGraph } from './export.js';\nimport { renderReport } from './report.js';\nimport type { Analysis, ExtractionResult, FileManifest } from './types.js';\n\nexport interface PipelineOptions {\n  /** Where to write graph.json/graph.html/GRAPH_REPORT.md. Defaults to `<root>/graphify-out`. */\n  outDir?: string;\n  html?: boolean;\n  svg?: boolean;\n  graphml?: boolean;\n  neo4j?: boolean;\n  obsidian?: boolean;\n  /** `louvain` (default, v1) or `leiden` (v2 — better community quality, see cluster.ts). */\n  algorithm?: ClusterAlgorithm;\n  /** Leiden-only: cap on outer iterations for very large graphs. */\n  maxIterations?: number;\n  /** Called with a short progress message after each stage (e.g. for CLI stderr output). */\n  onProgress?: (message: string) => void;\n}\n\nexport interface PipelineResult {\n  manifest: FileManifest;\n  graph: Graph;\n  analysis: Analysis;\n  report: string;\n}\n\n/**\n * The full `detect -> extract -> build -> cluster -> analyze -> report ->\n * export` pipeline as a single library call — the CLI's default command is\n * a thin wrapper over this. Every extension registered in\n * EXTRACTOR_REGISTRY (see extract.ts) is run; files with no registered\n * extractor are skipped (not an error — see extract()'s doc comment).\n */\nexport async function runPipeline(root: string, options: PipelineOptions = {}): Promise<PipelineResult> {\n  const progress = options.onProgress ?? (() => {});\n  const resolvedRoot = path.resolve(root);\n\n  progress(`Scanning ${resolvedRoot} ...`);\n  const manifest = collectFiles(resolvedRoot);\n  progress(\n    `Found ${manifest.totalFiles} file(s) (${manifest.files.code.length} code, ` +\n      `${manifest.skippedSensitive.length} skipped as sensitive).`,\n  );\n\n  progress('Extracting...');\n  const extractions: ExtractionResult[] = [];\n  for (const relFile of manifest.files.code.sort((a, b) => a.localeCompare(b))) {\n    // Relative to CWD (not necessarily to `resolvedRoot`) so fs reads inside\n    // the extractor resolve correctly, while still keeping sourceFile short\n    // and human-readable rather than a fully absolute path.\n    const filePath = path.relative(process.cwd(), path.join(resolvedRoot, relFile)) || relFile;\n    try {\n      const extraction = await extract(filePath);\n      extractions.push(extraction);\n    } catch (error) {\n      progress(`  extraction failed for ${relFile}: ${(error as Error).message}`);\n      throw error;\n    }\n  }\n\n  progress('Building graph...');\n  const graph = buildGraph(extractions);\n\n  progress(`Clustering (${options.algorithm ?? 'louvain'})...`);\n  cluster(graph, { algorithm: options.algorithm, maxIterations: options.maxIterations });\n\n  progress('Analyzing...');\n  const analysis = analyze(graph);\n\n  progress('Rendering report...');\n  const report = renderReport(graph, analysis);\n\n  const outDir = options.outDir ?? path.join(resolvedRoot, 'graphify-out');\n  progress(`Exporting to ${outDir} ...`);\n  await exportGraph(\n    graph,\n    {\n      outDir,\n      html: options.html,\n      svg: options.svg,\n      graphml: options.graphml,\n      neo4j: options.neo4j,\n      obsidian: options.obsidian,\n    },\n    report,\n  );\n\n  progress('Done.');\n  return { manifest, graph, analysis, report };\n}\n","import Graph from 'graphology';\nimport { validateExtraction } from './schema.js';\nimport type { Confidence, ExtractionResult } from './types.js';\n\nconst CONFIDENCE_RANK: Record<Confidence, number> = { EXTRACTED: 3, INFERRED: 2, AMBIGUOUS: 1 };\n\nfunction strongerConfidence(a: Confidence, b: Confidence): Confidence {\n  return CONFIDENCE_RANK[a] >= CONFIDENCE_RANK[b] ? a : b;\n}\n\nfunction ensureNode(graph: Graph, id: string): void {\n  if (graph.hasNode(id)) return;\n  // An edge endpoint that never appeared in any extraction's `nodes` array —\n  // shouldn't happen with a well-behaved extractor, but auto-vivify a\n  // minimal placeholder rather than let addEdge throw and abort the merge.\n  graph.addNode(id, { label: id, sourceFile: '<unknown>', sourceLocation: 'L0' });\n}\n\n/**\n * Merge per-file extraction results into one graphology graph.\n *\n * Every extraction is validated against the ExtractionResult schema before\n * anything is added to the graph — a single malformed extraction throws\n * (via validateExtraction()/ExtractionValidationError) before any node from\n * *any* extraction is merged, so a bad extractor can never silently\n * corrupt a graph that also contains good data.\n *\n * Nodes and edges are sorted before being added so the resulting graph (and\n * the graph.json ultimately exported from it) is deterministic regardless\n * of the order files were extracted in. Duplicate edges — same\n * source/target/relation, e.g. two different call sites resolving to the\n * same callee — are merged into a single edge, keeping the strongest\n * confidence seen (EXTRACTED > INFERRED > AMBIGUOUS) rather than being\n * counted as parallel edges (the schema has no call-count/weight field, so\n * \"A calls B\" is either true or it isn't). Multiple distinct relations\n * between the same pair (e.g. a file both `imports` and `imports_from` the\n * same module) are kept as separate edges.\n */\nexport function buildGraph(extractions: ExtractionResult[]): Graph {\n  const graph = new Graph({ type: 'directed', multi: true, allowSelfLoops: true });\n\n  const validated = extractions.map((extraction, index) =>\n    validateExtraction(extraction, `extraction #${index}`),\n  );\n\n  const allNodes = validated.flatMap((extraction) => extraction.nodes);\n  const allEdges = validated.flatMap((extraction) => extraction.edges);\n\n  const sortedNodes = [...allNodes].sort((a, b) => a.id.localeCompare(b.id));\n  for (const node of sortedNodes) {\n    if (graph.hasNode(node.id)) continue;\n    graph.addNode(node.id, {\n      label: node.label,\n      sourceFile: node.sourceFile,\n      sourceLocation: node.sourceLocation,\n    });\n  }\n\n  const sortedEdges = [...allEdges].sort(\n    (a, b) =>\n      a.source.localeCompare(b.source) ||\n      a.target.localeCompare(b.target) ||\n      a.relation.localeCompare(b.relation),\n  );\n\n  for (const edge of sortedEdges) {\n    ensureNode(graph, edge.source);\n    ensureNode(graph, edge.target);\n\n    const key = `${edge.source}|${edge.relation}|${edge.target}`;\n    if (graph.hasEdge(key)) {\n      const existing = graph.getEdgeAttribute(key, 'confidence') as Confidence;\n      graph.setEdgeAttribute(key, 'confidence', strongerConfidence(existing, edge.confidence));\n      continue;\n    }\n    graph.addEdgeWithKey(key, edge.source, edge.target, {\n      relation: edge.relation,\n      confidence: edge.confidence,\n    });\n  }\n\n  return graph;\n}\n","import { z } from 'zod';\nimport type { ExtractionResult } from './types.js';\n\n/**\n * Runtime schema for ExtractionResult (see types.ts + master prompt §2).\n * Every extractor's output is validated against this before buildGraph()\n * merges it — a malformed extractor must fail loudly, never silently\n * corrupt the graph.\n */\nexport const ConfidenceSchema = z.enum(['EXTRACTED', 'INFERRED', 'AMBIGUOUS']);\n\nexport const RelationSchema = z.enum([\n  'calls',\n  'imports',\n  'imports_from',\n  'inherits',\n  'implements',\n  'mixes_in',\n  'embeds',\n  'references',\n  'contains',\n  'method',\n  're_exports',\n]);\n\nexport const GraphNodeSchema = z.object({\n  id: z.string().min(1, 'node id must be non-empty'),\n  label: z.string(),\n  sourceFile: z.string(),\n  sourceLocation: z.string(),\n});\n\nexport const GraphEdgeSchema = z.object({\n  source: z.string().min(1, 'edge source must be non-empty'),\n  target: z.string().min(1, 'edge target must be non-empty'),\n  relation: RelationSchema,\n  confidence: ConfidenceSchema,\n});\n\nexport const ExtractionResultSchema = z.object({\n  nodes: z.array(GraphNodeSchema),\n  edges: z.array(GraphEdgeSchema),\n});\n\nexport interface ExtractionValidationIssue {\n  path: Array<string | number>;\n  message: string;\n}\n\n/** Thrown by validateExtraction() on schema mismatch. Carries the raw zod issues. */\nexport class ExtractionValidationError extends Error {\n  readonly issues: ExtractionValidationIssue[];\n\n  constructor(message: string, issues: ExtractionValidationIssue[]) {\n    super(message);\n    this.name = 'ExtractionValidationError';\n    this.issues = issues;\n  }\n}\n\n/**\n * Validate an unknown value (typically an extractor's return value) against\n * the ExtractionResult schema. Throws ExtractionValidationError with a clear,\n * human-readable message on mismatch instead of letting malformed data reach\n * buildGraph().\n */\nexport function validateExtraction(value: unknown, context?: string): ExtractionResult {\n  const result = ExtractionResultSchema.safeParse(value);\n  if (!result.success) {\n    const label = context ? ` (${context})` : '';\n    const issues: ExtractionValidationIssue[] = result.error.issues.map((issue) => ({\n      path: issue.path as Array<string | number>,\n      message: issue.message,\n    }));\n    const details = issues\n      .map((issue) => `${issue.path.join('.') || '<root>'}: ${issue.message}`)\n      .join('; ');\n    throw new ExtractionValidationError(`Invalid ExtractionResult${label}: ${details}`, issues);\n  }\n  return result.data;\n}\n","import * as fs from 'node:fs';\nimport * as path from 'node:path';\nimport type { FileCategory, FileManifest } from './types.js';\n\n/** Directories that are never worth walking into. */\nconst SKIP_DIRS = new Set([\n  'node_modules',\n  '.git',\n  'dist',\n  'build',\n  'out',\n  'graphify-out',\n  '.next',\n  '.venv',\n  'venv',\n  '__pycache__',\n  '.cache',\n  'coverage',\n  '.turbo',\n]);\n\nconst CODE_EXTENSIONS = new Set([\n  '.ts',\n  '.tsx',\n  '.js',\n  '.jsx',\n  '.mjs',\n  '.cjs',\n  '.mts',\n  '.cts',\n  '.py',\n  '.go',\n  '.rs',\n  '.java',\n  '.cs',\n  '.rb',\n  '.c',\n  '.h',\n  '.cpp',\n  '.hpp',\n  '.cc',\n  '.php',\n  '.kt',\n  '.swift',\n  '.scala',\n  '.lua',\n  '.sh',\n  '.sql',\n]);\n\nconst DOCUMENT_EXTENSIONS = new Set(['.md', '.mdx', '.txt', '.rst', '.adoc', '.org', '.json', '.yaml', '.yml', '.toml']);\n\nconst PAPER_EXTENSIONS = new Set(['.pdf', '.tex', '.bib']);\n\nconst IMAGE_EXTENSIONS = new Set(['.png', '.jpg', '.jpeg', '.gif', '.svg', '.webp', '.bmp', '.ico']);\n\nconst VIDEO_EXTENSIONS = new Set(['.mp4', '.mov', '.avi', '.mkv', '.webm']);\n\n/**\n * Filenames or name fragments that must never be read into the graph or an\n * LLM prompt — credentials, secrets, key material. Skipped into\n * `skippedSensitive` rather than silently ignored, so a run's manifest is\n * auditable.\n */\nconst SENSITIVE_NAME_PATTERNS: RegExp[] = [\n  /^\\.env(\\..*)?$/i,\n  /^\\.npmrc$/i,\n  /^\\.pypirc$/i,\n  /credentials/i,\n  /secret/i,\n  /^id_rsa$/i,\n  /^id_ed25519$/i,\n  /\\.pem$/i,\n  /\\.key$/i,\n  /\\.pfx$/i,\n  /\\.p12$/i,\n  /^\\.aws\\//i,\n  /service[-_]?account.*\\.json$/i,\n];\n\nfunction isSensitiveName(name: string): boolean {\n  return SENSITIVE_NAME_PATTERNS.some((pattern) => pattern.test(name));\n}\n\nfunction categorize(ext: string): FileCategory | null {\n  const lower = ext.toLowerCase();\n  if (CODE_EXTENSIONS.has(lower)) return 'code';\n  if (DOCUMENT_EXTENSIONS.has(lower)) return 'document';\n  if (PAPER_EXTENSIONS.has(lower)) return 'paper';\n  if (IMAGE_EXTENSIONS.has(lower)) return 'image';\n  if (VIDEO_EXTENSIONS.has(lower)) return 'video';\n  return null;\n}\n\nfunction countWords(content: string): number {\n  const trimmed = content.trim();\n  if (trimmed.length === 0) return 0;\n  return trimmed.split(/\\s+/).length;\n}\n\n/** Decode a file's bytes as UTF-8 with a replacement strategy — never throw on invalid bytes. */\nfunction readTextSafely(filePath: string): string {\n  const buf = fs.readFileSync(filePath);\n  return buf.toString('utf-8');\n}\n\n/**\n * Walk `root` and categorize files into code/document/paper/image/video\n * buckets. Does not follow symlinks (security.ts §5 — symlink traversal).\n * Sensitive-looking files (.env, credentials, key material) are recorded in\n * `skippedSensitive` and excluded from every other bucket/count.\n */\nexport function collectFiles(root: string): FileManifest {\n  const scanRoot = path.resolve(root);\n  const stat = fs.statSync(scanRoot);\n  if (!stat.isDirectory()) {\n    throw new Error(`collectFiles: not a directory: ${scanRoot}`);\n  }\n\n  const files: Record<FileCategory, string[]> = {\n    code: [],\n    document: [],\n    paper: [],\n    image: [],\n    video: [],\n  };\n  const skippedSensitive: string[] = [];\n  let totalWords = 0;\n\n  const stack: string[] = [scanRoot];\n  const textCategories: Set<FileCategory> = new Set(['code', 'document', 'paper']);\n\n  while (stack.length > 0) {\n    const dir = stack.pop() as string;\n    let entries: fs.Dirent[];\n    try {\n      entries = fs.readdirSync(dir, { withFileTypes: true });\n    } catch {\n      continue; // unreadable directory (permissions) — skip, don't crash the run\n    }\n\n    // Sort for deterministic traversal order.\n    entries.sort((a, b) => a.name.localeCompare(b.name));\n\n    for (const entry of entries) {\n      if (entry.isSymbolicLink()) continue; // never follow symlinks\n\n      const fullPath = path.join(dir, entry.name);\n      const relPath = path.relative(scanRoot, fullPath);\n\n      if (entry.isDirectory()) {\n        if (SKIP_DIRS.has(entry.name) || entry.name.startsWith('.')) continue;\n        stack.push(fullPath);\n        continue;\n      }\n\n      if (!entry.isFile()) continue; // sockets, devices, fifos, etc.\n\n      if (isSensitiveName(entry.name)) {\n        skippedSensitive.push(relPath);\n        continue;\n      }\n\n      const ext = path.extname(entry.name);\n      const category = categorize(ext);\n      if (category === null) continue; // unrecognized extension — not tracked\n\n      files[category].push(relPath);\n\n      if (textCategories.has(category)) {\n        try {\n          const content = readTextSafely(fullPath);\n          totalWords += countWords(content);\n        } catch {\n          // Unreadable/binary-under-a-text-extension — degrade gracefully.\n        }\n      }\n    }\n  }\n\n  for (const category of Object.keys(files) as FileCategory[]) {\n    files[category].sort();\n  }\n  skippedSensitive.sort();\n\n  const totalFiles = Object.values(files).reduce((sum, list) => sum + list.length, 0);\n\n  return {\n    scanRoot,\n    files,\n    totalFiles,\n    totalWords,\n    skippedSensitive,\n  };\n}\n","import * as path from 'node:path';\nimport { extractCSharp } from './extractors/csharp.js';\nimport { extractGo } from './extractors/go.js';\nimport { extractJava } from './extractors/java.js';\nimport { extractPython } from './extractors/python.js';\nimport { extractRuby } from './extractors/ruby.js';\nimport { extractRust } from './extractors/rust.js';\nimport { extractTypeScript } from './extractors/typescript.js';\nimport type { ExtractionResult } from './types.js';\n\nexport type Extractor = (path: string) => Promise<ExtractionResult>;\n\n/** File extension -> extractor module. Register new languages here. */\nexport const EXTRACTOR_REGISTRY: Record<string, Extractor> = {\n  '.ts': extractTypeScript,\n  '.tsx': extractTypeScript,\n  '.js': extractTypeScript,\n  '.jsx': extractTypeScript,\n  '.mjs': extractTypeScript,\n  '.cjs': extractTypeScript,\n  '.mts': extractTypeScript,\n  '.cts': extractTypeScript,\n  '.py': extractPython,\n  '.go': extractGo,\n  '.rs': extractRust,\n  '.java': extractJava,\n  '.cs': extractCSharp,\n  '.rb': extractRuby,\n};\n\n/**\n * Dispatch a single file to its language extractor. Returns an empty\n * extraction (not a thrown error) for unregistered extensions so detect's\n * file list and extract's coverage can diverge without crashing a run.\n */\nexport async function extract(filePath: string): Promise<ExtractionResult> {\n  const ext = path.extname(filePath);\n  const extractor = EXTRACTOR_REGISTRY[ext];\n  if (!extractor) {\n    return { nodes: [], edges: [] };\n  }\n  return extractor(filePath);\n}\n","import * as fs from 'node:fs/promises';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\n/**\n * Structural extraction for .cs via web-tree-sitter (WASM, no native\n * compilation, no eval/exec of source content).\n *\n * Like Java, C# has no free top-level functions — methods live inside a\n * class or interface — but unlike Java, top-level types are usually\n * nested one level deeper inside a `namespace Foo { ... }` block, so pass\n * 1 flattens namespace bodies (recursively, for nested namespaces) before\n * walking classes/interfaces/methods, exactly as if their members were\n * declared at the top level.\n *\n * C#'s base-type list (`class Calculator : Base, IGreeter`) doesn't\n * distinguish a base class from an implemented interface syntactically —\n * that's only knowable from the *referenced* declaration. The one\n * compiler-enforced rule this grammar does guarantee is ordering: a base\n * class, if present, must be listed first. So the first entry becomes an\n * `inherits` edge and every subsequent entry becomes `implements` — a\n * deliberate best-effort heuristic, not a guarantee.\n *\n * Every `invocation_expression` is resolved (pass 2): a same-file\n * method/`this.Method()` call resolved against the enclosing class is\n * EXTRACTED; a call qualified by a `using Alias = Namespace.Type;`\n * binding (or an unqualified call resolved only through one) is\n * INFERRED — the \"cross-file second pass\" placeholder described in the\n * master prompt §3. It intentionally does not open and parse the\n * referenced type to confirm the target. An unresolvable callee produces\n * no edge at all.\n */\nexport async function extractCSharp(filePath: string): Promise<ExtractionResult> {\n  const parser = await createParser('c_sharp');\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractCSharp: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (class/interface) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every method entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** tree-sitter class/interface declaration node id -> method name -> our graph id. */\n  const classMethods = new Map<number, Map<string, string>>();\n  /** tree-sitter method_declaration node id -> its enclosing type's node id. */\n  const enclosingClassOf = new Map<number, number>();\n  /** local binding name (`using Alias = ...`) -> the module it came from. */\n  const importIndex = new Map<string, ReturnType<typeof resolveModuleRef>>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  function resolveHeritageTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  function handleUsingDirective(node: TSNode): void {\n    const children = namedChildren(node);\n    const first = children[0];\n    if (!first) return;\n\n    let aliasName: string | undefined;\n    let targetNode: TSNode | undefined;\n    if (first.type === 'name_equals') {\n      aliasName = namedChildren(first)[0]?.text;\n      targetNode = children[1];\n    } else {\n      targetNode = first;\n    }\n    if (!targetNode) return;\n\n    const ref = resolveModuleRef(sourceFile, targetNode.text);\n    addModuleNode(ref);\n    if (aliasName) importIndex.set(aliasName, ref);\n    builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n  }\n\n  function handleMethodDeclaration(typeNode: TSNode, typeId: string, typeName: string, member: TSNode): void {\n    const methodName = member.childForFieldName('name')?.text ?? '(anonymous)';\n    const methodId = entityId(sourceFile, `${typeName}.${methodName}`);\n    builder.addNode({\n      id: methodId,\n      label: `method ${typeName}.${methodName}`,\n      sourceFile,\n      sourceLocation: lineOf(member),\n    });\n    builder.addEdge({ source: typeId, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n\n    let methods = classMethods.get(typeNode.id);\n    if (!methods) {\n      methods = new Map();\n      classMethods.set(typeNode.id, methods);\n    }\n    methods.set(methodName, methodId);\n    functionNodeMap.set(member.id, methodId);\n    enclosingClassOf.set(member.id, typeNode.id);\n  }\n\n  function handleBaseList(typeId: string, node: TSNode): void {\n    const baseList = node.childForFieldName('bases');\n    if (!baseList) return;\n    const entries = namedChildren(baseList);\n    entries.forEach((entry, index) => {\n      builder.addEdge({\n        source: typeId,\n        target: resolveHeritageTarget(entry.text),\n        relation: index === 0 ? 'inherits' : 'implements',\n        confidence: 'EXTRACTED',\n      });\n    });\n  }\n\n  function handleClassDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const classId = entityId(sourceFile, name);\n    builder.addNode({ id: classId, label: `class ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: classId, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, classId);\n    functionNodeMap.set(node.id, classId);\n    classMethods.set(node.id, new Map());\n\n    handleBaseList(classId, node);\n\n    const body = node.childForFieldName('body');\n    if (body) {\n      for (const member of namedChildren(body)) {\n        if (member.type !== 'method_declaration') continue; // constructors intentionally not tracked\n        handleMethodDeclaration(node, classId, name, member);\n      }\n    }\n  }\n\n  function handleInterfaceDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `interface ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    handleBaseList(id, node); // interface-extends-interface(s) — same shape as a class base list\n  }\n\n  // Pass 1: top-level declarations (usings, classes, interfaces),\n  // flattening `namespace Foo { ... }` wrappers (recursively).\n  function walkTopLevel(node: TSNode): void {\n    for (const child of namedChildren(node)) {\n      switch (child.type) {\n        case 'using_directive':\n          handleUsingDirective(child);\n          break;\n        case 'class_declaration':\n          handleClassDeclaration(child);\n          break;\n        case 'interface_declaration':\n          handleInterfaceDeclaration(child);\n          break;\n        case 'namespace_declaration': {\n          const nsBody = child.childForFieldName('body');\n          if (nsBody) walkTopLevel(nsBody);\n          break;\n        }\n        case 'file_scoped_namespace_declaration':\n          // `namespace Foo;` (C# 10+) — declarations are direct named\n          // children of this node itself (no separate `body` field).\n          walkTopLevel(child);\n          break;\n        default:\n          break;\n      }\n    }\n  }\n  walkTopLevel(root);\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingClassMethods(node: TSNode): Map<string, string> | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'method_declaration') {\n        const typeNodeId = enclosingClassOf.get(current.id);\n        if (typeNodeId !== undefined) return classMethods.get(typeNodeId);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  // Pass 2: calls (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of descendantsOfType(root, ['invocation_expression'])) {\n    const fn = call.childForFieldName('function');\n    if (!fn) continue;\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (fn.type === 'identifier') {\n      const name = fn.text;\n      const methodId = closestEnclosingClassMethods(call)?.get(name);\n      if (methodId) {\n        targetId = methodId;\n      } else {\n        const viaImport = importIndex.get(name);\n        if (viaImport) {\n          targetId = viaImport.id;\n          confidence = 'INFERRED';\n        }\n      }\n    } else if (fn.type === 'member_access_expression') {\n      const expression = fn.childForFieldName('expression');\n      const name = fn.childForFieldName('name')?.text;\n      if (expression && name) {\n        if (expression.type === 'this_expression') {\n          const methodId = closestEnclosingClassMethods(call)?.get(name);\n          if (methodId) targetId = methodId;\n        } else if (expression.type === 'identifier') {\n          const viaImport = importIndex.get(expression.text);\n          if (viaImport) {\n            targetId = viaImport.id;\n            confidence = 'INFERRED';\n          }\n        }\n      }\n    }\n\n    if (!targetId) continue; // unresolved callee (builtin, external value, ...) — no noisy guess\n    const callerId = closestTrackedCaller(call);\n    builder.addEdge({ source: callerId, target: targetId, relation: 'calls', confidence });\n  }\n\n  return builder.build();\n}\n","import * as path from 'node:path';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult, GraphEdge, GraphNode } from '../types.js';\n\n/**\n * web-tree-sitter types `namedChildren`/`descendantsOfType` as\n * `(Node | null)[]` (a node slot can be null for a missing/erroneous\n * child). These two helpers give every extractor a non-null array to\n * iterate without repeating the same `.filter()` everywhere.\n */\nexport function namedChildren(node: TSNode): TSNode[] {\n  return node.namedChildren.filter((c): c is TSNode => c !== null);\n}\n\nexport function descendantsOfType(node: TSNode, types: string | string[]): TSNode[] {\n  return node.descendantsOfType(types).filter((c): c is TSNode => c !== null);\n}\n\n/** Normalize a path to forward slashes so ids/labels are stable across platforms. */\nexport function toPosix(p: string): string {\n  return p.split(path.sep).join('/');\n}\n\n/** `tree-sitter` node shape narrowed to what id/location helpers need. */\nexport interface PositionedNode {\n  startPosition: { row: number };\n}\n\n/** 1-based \"L<line>\" source location string, matching the schema example (`\"L42\"`). */\nexport function lineOf(node: PositionedNode): string {\n  return `L${node.startPosition.row + 1}`;\n}\n\n/** Build a stable, file-scoped node id: unique across the whole graph once merged. */\nexport function entityId(sourceFile: string, qualifiedName: string): string {\n  return `${toPosix(sourceFile)}::${qualifiedName}`;\n}\n\n/** Id for a reference we could not resolve to any declaration we saw (best-effort target). */\nexport function externalId(name: string): string {\n  return `external:${name}`;\n}\n\nexport interface ModuleRef {\n  id: string;\n  label: string;\n  /** true when the specifier is a bare package (not resolvable to an in-repo file). */\n  external: boolean;\n}\n\n/**\n * Resolve an import/require specifier to a best-effort module id relative\n * to the importing file. This is intentionally lightweight (string/path\n * math only, no filesystem probing, no extension resolution) — it exists\n * so same-repo relative imports get a deterministic, file-shaped id that a\n * later cross-file pass (or a second extraction of the target file) can\n * line up against, not to fully replicate a module resolver.\n */\nexport function resolveModuleRef(sourceFile: string, specifier: string): ModuleRef {\n  if (specifier.startsWith('.') || specifier.startsWith('/')) {\n    const dir = path.posix.dirname(toPosix(sourceFile));\n    const joined = specifier.startsWith('/') ? specifier : path.posix.join(dir, specifier);\n    const normalized = path.posix.normalize(joined);\n    return { id: normalized, label: specifier, external: false };\n  }\n  return { id: `module:${specifier}`, label: specifier, external: true };\n}\n\n/**\n * Accumulates nodes/edges for one file's ExtractionResult with node-id\n * dedup (a file can otherwise easily emit the same module/external\n * placeholder node twice — once per import, once per call resolution).\n */\nexport class ExtractionBuilder {\n  private readonly nodeIds = new Set<string>();\n  readonly nodes: GraphNode[] = [];\n  readonly edges: GraphEdge[] = [];\n\n  addNode(node: GraphNode): void {\n    if (this.nodeIds.has(node.id)) return;\n    this.nodeIds.add(node.id);\n    this.nodes.push(node);\n  }\n\n  hasNode(id: string): boolean {\n    return this.nodeIds.has(id);\n  }\n\n  addEdge(edge: GraphEdge): void {\n    this.edges.push(edge);\n  }\n\n  build(): ExtractionResult {\n    return { nodes: this.nodes, edges: this.edges };\n  }\n}\n","import { createRequire } from 'node:module';\nimport { Language, Parser } from 'web-tree-sitter';\n\n/**\n * Shared web-tree-sitter bootstrapping for every language extractor.\n *\n * Pinned to web-tree-sitter@^0.25.x deliberately (not the newer 0.26.x\n * major that ships with the rest of the dependency set): 0.26 requires\n * every language grammar to carry a \"dylink.0\" WASM custom section (the\n * newer wasm dynamic-linking convention), but `tree-sitter-wasms`'s\n * prebuilt grammars still use the legacy \"dylink\" section — loading any\n * grammar under 0.26 throws `need dylink section` before a single file can\n * be parsed. 0.25.x accepts the legacy section and loads every grammar\n * `tree-sitter-wasms` ships. Revisit this pin once `tree-sitter-wasms`\n * republishes grammars built against a dylink.0-era tree-sitter-cli.\n */\n\nconst require = createRequire(import.meta.url);\n\nlet initPromise: Promise<void> | null = null;\n\nfunction ensureInitialized(): Promise<void> {\n  if (!initPromise) {\n    initPromise = Parser.init();\n  }\n  return initPromise;\n}\n\nconst languageCache = new Map<string, Promise<Language>>();\n\n/** Load (and cache) a tree-sitter-wasms grammar by its `tree-sitter-<name>.wasm` basename. */\nexport async function loadLanguage(grammarName: string): Promise<Language> {\n  await ensureInitialized();\n  let cached = languageCache.get(grammarName);\n  if (!cached) {\n    const wasmPath = require.resolve(`tree-sitter-wasms/out/tree-sitter-${grammarName}.wasm`);\n    cached = Language.load(wasmPath);\n    languageCache.set(grammarName, cached);\n  }\n  return cached;\n}\n\n/** Create a fresh Parser bound to the given grammar. Parsers are cheap and not thread-shared. */\nexport async function createParser(grammarName: string): Promise<Parser> {\n  const language = await loadLanguage(grammarName);\n  const parser = new Parser();\n  parser.setLanguage(language);\n  return parser;\n}\n","import * as fs from 'node:fs/promises';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\n/** Strip the surrounding quotes tree-sitter keeps on an interpreted/raw string literal's text. */\nfunction stripQuotes(text: string): string {\n  if (text.length >= 2) {\n    const first = text[0];\n    const last = text[text.length - 1];\n    if ((first === '\"' || first === '`') && first === last) {\n      return text.slice(1, -1);\n    }\n  }\n  return text;\n}\n\n/** Default package qualifier Go infers from an import path when no explicit alias is given. */\nfunction defaultPackageQualifier(importPath: string): string {\n  const segments = importPath.split('/');\n  return segments[segments.length - 1] ?? importPath;\n}\n\n/**\n * Structural extraction for .go via web-tree-sitter (WASM, no native\n * compilation, no eval/exec of source content).\n *\n * Pattern mirrors typescript.ts, adapted to Go's shape: top-level named\n * types (struct/interface/defined types), functions, methods (declared\n * separately from their receiver type via `func (recv T) Name(...)`), and\n * imports (pass 1) -> every `call_expression` resolved against what pass 1\n * saw (pass 2). A same-file callee, or a call through the receiver\n * variable of the enclosing method onto a method of the same struct, is\n * EXTRACTED; a call through an imported package qualifier (e.g.\n * `m.Add(x, x)` where `m` is an import alias) is INFERRED — the\n * \"cross-file second pass\" placeholder described in the master prompt §3.\n * An unresolvable callee produces no edge at all.\n *\n * Go has no `extends`/`implements` clauses; struct embedding\n * (`type Calculator struct { Base }`) is the one heritage-like construct\n * Go's grammar exposes directly, so it becomes an `embeds` edge.\n */\nexport async function extractGo(filePath: string): Promise<ExtractionResult> {\n  const parser = await createParser('go');\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractGo: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (function or named type) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every function/method entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** graph id of a named type -> method name -> our graph id. */\n  const typeMethods = new Map<string, Map<string, string>>();\n  /** tree-sitter method_declaration node id -> { receiver variable name, owning type's graph id }. */\n  const receiverInfo = new Map<number, { varName: string; typeId: string }>();\n  /** local package qualifier (import alias or inferred name) -> the module it came from. */\n  const importIndex = new Map<string, ReturnType<typeof resolveModuleRef>>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  function resolveTypeTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  function handleImportSpec(spec: TSNode): void {\n    const pathNode = spec.childForFieldName('path');\n    if (!pathNode) return;\n    const specifier = stripQuotes(pathNode.text);\n    const ref = resolveModuleRef(sourceFile, specifier);\n    addModuleNode(ref);\n    builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n\n    const aliasNode = spec.childForFieldName('name');\n    const alias = aliasNode?.text;\n    if (alias && alias !== '_' && alias !== '.') {\n      importIndex.set(alias, ref);\n    } else if (!alias) {\n      importIndex.set(defaultPackageQualifier(specifier), ref);\n    }\n  }\n\n  function handleImportDeclaration(node: TSNode): void {\n    for (const child of namedChildren(node)) {\n      if (child.type === 'import_spec') {\n        handleImportSpec(child);\n      } else if (child.type === 'import_spec_list') {\n        for (const spec of namedChildren(child)) {\n          if (spec.type === 'import_spec') handleImportSpec(spec);\n        }\n      }\n    }\n  }\n\n  function handleFunctionDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `function ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    functionNodeMap.set(node.id, id);\n  }\n\n  function handleTypeDeclaration(node: TSNode): void {\n    for (const spec of namedChildren(node)) {\n      if (spec.type !== 'type_spec') continue; // skip `type X = Y` aliases\n      const name = spec.childForFieldName('name')?.text;\n      if (!name) continue;\n      const underlying = spec.childForFieldName('type');\n      const kind = underlying?.type === 'struct_type' ? 'struct' : underlying?.type === 'interface_type' ? 'interface' : 'type';\n      const id = entityId(sourceFile, name);\n      builder.addNode({ id, label: `${kind} ${name}`, sourceFile, sourceLocation: lineOf(spec) });\n      builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n      nameIndex.set(name, id);\n      typeMethods.set(id, new Map());\n\n      if (underlying?.type === 'struct_type') {\n        const fieldList = namedChildren(underlying).find((c) => c.type === 'field_declaration_list');\n        if (fieldList) {\n          for (const field of namedChildren(fieldList)) {\n            if (field.type !== 'field_declaration') continue;\n            if (field.childForFieldName('name')) continue; // named field, not embedding\n            const embeddedType = namedChildren(field)[0];\n            if (!embeddedType) continue;\n            const base = embeddedType.type === 'pointer_type' ? namedChildren(embeddedType)[0] : embeddedType;\n            if (!base) continue;\n            builder.addEdge({\n              source: id,\n              target: resolveTypeTarget(base.text),\n              relation: 'embeds',\n              confidence: 'EXTRACTED',\n            });\n          }\n        }\n      }\n    }\n  }\n\n  /** Receiver's declared type name, unwrapping a pointer receiver (`*T`). */\n  function receiverTypeName(receiver: TSNode): string | null {\n    const paramDecl = namedChildren(receiver)[0];\n    if (!paramDecl) return null;\n    let typeNode = paramDecl.childForFieldName('type');\n    if (typeNode?.type === 'pointer_type') {\n      typeNode = namedChildren(typeNode)[0] ?? null;\n    }\n    return typeNode?.type === 'type_identifier' ? typeNode.text : null;\n  }\n\n  function receiverVarName(receiver: TSNode): string | null {\n    const paramDecl = namedChildren(receiver)[0];\n    return paramDecl?.childForFieldName('name')?.text ?? null;\n  }\n\n  function handleMethodDeclaration(node: TSNode): void {\n    const receiver = node.childForFieldName('receiver');\n    const methodName = node.childForFieldName('name')?.text ?? '(anonymous)';\n    if (!receiver) return;\n    const typeName = receiverTypeName(receiver);\n    if (!typeName) return;\n    const typeId = resolveTypeTarget(typeName);\n\n    const methodId = entityId(sourceFile, `${typeName}.${methodName}`);\n    builder.addNode({ id: methodId, label: `method ${typeName}.${methodName}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: typeId, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n\n    let methods = typeMethods.get(typeId);\n    if (!methods) {\n      methods = new Map();\n      typeMethods.set(typeId, methods);\n    }\n    methods.set(methodName, methodId);\n\n    functionNodeMap.set(node.id, methodId);\n    const varName = receiverVarName(receiver);\n    if (varName) receiverInfo.set(node.id, { varName, typeId });\n  }\n\n  // Pass 1: top-level declarations (imports, named types, functions, methods).\n  for (const child of namedChildren(root)) {\n    switch (child.type) {\n      case 'import_declaration':\n        handleImportDeclaration(child);\n        break;\n      case 'type_declaration':\n        handleTypeDeclaration(child);\n        break;\n      case 'function_declaration':\n        handleFunctionDeclaration(child);\n        break;\n      case 'method_declaration':\n        handleMethodDeclaration(child);\n        break;\n      default:\n        break;\n    }\n  }\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingReceiver(node: TSNode): { varName: string; typeId: string } | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'method_declaration') {\n        return receiverInfo.get(current.id);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  // Pass 2: calls (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of descendantsOfType(root, ['call_expression'])) {\n    const fn = call.childForFieldName('function');\n    if (!fn) continue;\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (fn.type === 'identifier') {\n      const sameFile = nameIndex.get(fn.text);\n      if (sameFile) targetId = sameFile;\n    } else if (fn.type === 'selector_expression') {\n      const operand = fn.childForFieldName('operand');\n      const property = fn.childForFieldName('field')?.text;\n      if (operand && property && operand.type === 'identifier') {\n        const receiver = closestEnclosingReceiver(call);\n        if (receiver && receiver.varName === operand.text) {\n          const methodId = typeMethods.get(receiver.typeId)?.get(property);\n          if (methodId) targetId = methodId;\n        } else {\n          const viaImport = importIndex.get(operand.text);\n          if (viaImport) {\n            targetId = viaImport.id;\n            confidence = 'INFERRED';\n          }\n        }\n      }\n    }\n\n    if (!targetId) continue; // unresolved callee (builtin, external value, ...) — no noisy guess\n    const callerId = closestTrackedCaller(call);\n    builder.addEdge({ source: callerId, target: targetId, relation: 'calls', confidence });\n  }\n\n  return builder.build();\n}\n","import * as fs from 'node:fs/promises';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\n/**\n * Structural extraction for .java via web-tree-sitter (WASM, no native\n * compilation, no eval/exec of source content).\n *\n * Java has no free top-level functions — every method lives inside a\n * class or interface — so pass 1 walks top-level class/interface\n * declarations and, for classes, their methods (an interface's methods\n * are abstract signatures with no body, so only the interface itself\n * becomes a node, mirroring typescript.ts's interface handling).\n * Constructors (`constructor_declaration`, distinct from\n * `method_declaration` in this grammar) are intentionally not tracked as\n * separate entities — same \"structural, not exhaustive\" scope as the\n * other extractors in this file.\n *\n * Every `method_invocation` is then resolved (pass 2): a same-file\n * method/`this.method()` call resolved against the enclosing class is\n * EXTRACTED; a call qualified by an imported class name (or bound via a\n * static import) is INFERRED — the \"cross-file second pass\" placeholder\n * described in the master prompt §3. It intentionally does not open and\n * parse the imported class to confirm the target. An unresolvable callee\n * produces no edge at all.\n *\n * Fully-qualified import paths (`com.example.math.MathUtils`) have no\n * clean mapping to a same-repo relative file without real classpath/\n * package-root information, so every import resolves to an external\n * module placeholder via resolveModuleRef — consistent with how the Go\n * extractor treats its (also always-absolute) import paths.\n */\nexport async function extractJava(filePath: string): Promise<ExtractionResult> {\n  const parser = await createParser('java');\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractJava: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (class/interface) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every method entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** tree-sitter class_declaration node id -> method name -> our graph id. */\n  const classMethods = new Map<number, Map<string, string>>();\n  /** tree-sitter method_declaration node id -> its enclosing class's node id. */\n  const enclosingClassOf = new Map<number, number>();\n  /** local binding name (imported class or statically-imported member) -> the module it came from. */\n  const importIndex = new Map<string, ReturnType<typeof resolveModuleRef>>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  function resolveHeritageTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  function handleImportDeclaration(node: TSNode): void {\n    // Java's grammar keeps `static`/`*` as bare tokens (no field name), so\n    // we detect them structurally rather than via childForFieldName.\n    const hasWildcard = namedChildren(node).some((c) => c.type === 'asterisk');\n    const scoped = namedChildren(node).find((c) => c.type === 'scoped_identifier' || c.type === 'identifier');\n    if (!scoped) return;\n    const fullPath = scoped.text;\n    const ref = resolveModuleRef(sourceFile, fullPath);\n    addModuleNode(ref);\n\n    if (hasWildcard) {\n      // `import com.example.util.*;` — whole package, no single local binding to record.\n      builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n      return;\n    }\n\n    // Plain class import (`import a.b.Foo;`) and static-member import\n    // (`import static a.b.Foo.bar;`) both bind their last dotted segment\n    // as the local name callers use unqualified.\n    const segments = fullPath.split('.');\n    const localName = segments[segments.length - 1];\n    if (localName) importIndex.set(localName, ref);\n    builder.addEdge({ source: fileId, target: ref.id, relation: 'imports_from', confidence: 'EXTRACTED' });\n  }\n\n  function handleMethodDeclaration(classNode: TSNode, classId: string, className: string, member: TSNode): void {\n    const methodName = member.childForFieldName('name')?.text ?? '(anonymous)';\n    const methodId = entityId(sourceFile, `${className}.${methodName}`);\n    builder.addNode({\n      id: methodId,\n      label: `method ${className}.${methodName}`,\n      sourceFile,\n      sourceLocation: lineOf(member),\n    });\n    builder.addEdge({ source: classId, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n\n    let methods = classMethods.get(classNode.id);\n    if (!methods) {\n      methods = new Map();\n      classMethods.set(classNode.id, methods);\n    }\n    methods.set(methodName, methodId);\n    functionNodeMap.set(member.id, methodId);\n    enclosingClassOf.set(member.id, classNode.id);\n  }\n\n  function handleClassDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const classId = entityId(sourceFile, name);\n    builder.addNode({ id: classId, label: `class ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: classId, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, classId);\n    functionNodeMap.set(node.id, classId);\n    classMethods.set(node.id, new Map());\n\n    const superclass = node.childForFieldName('superclass');\n    if (superclass) {\n      const base = namedChildren(superclass)[0];\n      if (base) {\n        builder.addEdge({\n          source: classId,\n          target: resolveHeritageTarget(base.text),\n          relation: 'inherits',\n          confidence: 'EXTRACTED',\n        });\n      }\n    }\n\n    const interfaces = node.childForFieldName('interfaces');\n    if (interfaces) {\n      const typeList = namedChildren(interfaces).find((c) => c.type === 'type_list');\n      for (const iface of typeList ? namedChildren(typeList) : []) {\n        builder.addEdge({\n          source: classId,\n          target: resolveHeritageTarget(iface.text),\n          relation: 'implements',\n          confidence: 'EXTRACTED',\n        });\n      }\n    }\n\n    const body = node.childForFieldName('body');\n    if (body) {\n      for (const member of namedChildren(body)) {\n        if (member.type !== 'method_declaration') continue; // constructors intentionally not tracked\n        handleMethodDeclaration(node, classId, name, member);\n      }\n    }\n  }\n\n  function handleInterfaceDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `interface ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n\n    const extendsInterfaces = namedChildren(node).find((c) => c.type === 'extends_interfaces');\n    if (extendsInterfaces) {\n      const typeList = namedChildren(extendsInterfaces).find((c) => c.type === 'type_list');\n      for (const parent of typeList ? namedChildren(typeList) : []) {\n        builder.addEdge({\n          source: id,\n          target: resolveHeritageTarget(parent.text),\n          relation: 'inherits',\n          confidence: 'EXTRACTED',\n        });\n      }\n    }\n  }\n\n  // Pass 1: top-level declarations (imports, classes, interfaces).\n  for (const child of namedChildren(root)) {\n    switch (child.type) {\n      case 'import_declaration':\n        handleImportDeclaration(child);\n        break;\n      case 'class_declaration':\n        handleClassDeclaration(child);\n        break;\n      case 'interface_declaration':\n        handleInterfaceDeclaration(child);\n        break;\n      default:\n        break;\n    }\n  }\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingClassMethods(node: TSNode): Map<string, string> | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'method_declaration') {\n        const classNodeId = enclosingClassOf.get(current.id);\n        if (classNodeId !== undefined) return classMethods.get(classNodeId);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  // Pass 2: calls (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of descendantsOfType(root, ['method_invocation'])) {\n    const name = call.childForFieldName('name')?.text;\n    if (!name) continue;\n    const object = call.childForFieldName('object');\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (!object) {\n      // Unqualified call: same-file method (via the tracked caller's own\n      // class) or a statically-imported member.\n      const methodId = closestEnclosingClassMethods(call)?.get(name);\n      if (methodId) {\n        targetId = methodId;\n      } else {\n        const viaImport = importIndex.get(name);\n        if (viaImport) {\n          targetId = viaImport.id;\n          confidence = 'INFERRED';\n        }\n      }\n    } else if (object.type === 'this') {\n      const methodId = closestEnclosingClassMethods(call)?.get(name);\n      if (methodId) targetId = methodId;\n    } else if (object.type === 'identifier') {\n      const viaImport = importIndex.get(object.text);\n      if (viaImport) {\n        targetId = viaImport.id;\n        confidence = 'INFERRED';\n      }\n    }\n\n    if (!targetId) continue; // unresolved callee (builtin, external value, ...) — no noisy guess\n    const callerId = closestTrackedCaller(call);\n    builder.addEdge({ source: callerId, target: targetId, relation: 'calls', confidence });\n  }\n\n  return builder.build();\n}\n","import * as fs from 'node:fs/promises';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\n/**\n * Structural extraction for .py via web-tree-sitter (WASM, no native\n * compilation, no eval/exec of source content).\n *\n * Pattern mirrors typescript.ts: parse -> walk the module body for\n * top-level functions/classes/imports (pass 1) -> walk every `call` node\n * and resolve its callee against what pass 1 saw (pass 2). A same-file\n * callee (or a `self.method()` call resolved against the enclosing class)\n * is EXTRACTED; a callee that only resolves through an imported local\n * binding (a directly-imported name, or a member access on an imported\n * module alias) is emitted as INFERRED — the \"cross-file second pass\"\n * placeholder described in the master prompt §3. It intentionally does not\n * open and parse the imported module to confirm the target. An\n * unresolvable callee (a builtin, a call on some arbitrary local value,\n * etc.) produces no edge at all rather than a noisy guess.\n *\n * Python has no separate interface/heritage-clause concept: every base\n * class listed in `class Foo(Base, Other):` becomes an `inherits` edge.\n */\nexport async function extractPython(filePath: string): Promise<ExtractionResult> {\n  const parser = await createParser('python');\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractPython: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (function/class) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every function-like entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** tree-sitter class_definition node id -> method name -> our graph id. */\n  const classMethods = new Map<number, Map<string, string>>();\n  /** tree-sitter function_definition (method) node id -> its enclosing class's node id. */\n  const enclosingClassOf = new Map<number, number>();\n  /** local binding name (import) -> the module it came from. */\n  const importIndex = new Map<string, ReturnType<typeof resolveModuleRef>>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  function resolveHeritageTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  /** Unwrap a `@decorator` / `decorated_definition` wrapper to the function/class it decorates. */\n  function unwrapDecorated(node: TSNode): TSNode | null {\n    if (node.type !== 'decorated_definition') return node;\n    return (\n      namedChildren(node).find((c) => c.type === 'function_definition' || c.type === 'class_definition') ?? null\n    );\n  }\n\n  /**\n   * Convert a `relative_import` node (e.g. \".\", \".foo\", \"..foo.bar\") into a\n   * relative-path-shaped specifier resolveModuleRef understands (e.g. \".\",\n   * \"./foo\", \"../foo/bar\") — one leading dot means \"this package\" (`.`),\n   * each additional dot means one more directory up.\n   */\n  function relativeSpecifier(relImport: TSNode): string {\n    let dots = 0;\n    for (const ch of relImport.text) {\n      if (ch !== '.') break;\n      dots++;\n    }\n    const dotted = namedChildren(relImport).find((c) => c.type === 'dotted_name');\n    const up = dots - 1;\n    let base = up === 0 ? '.' : Array.from({ length: up }, () => '..').join('/');\n    if (dotted) {\n      base = `${base}/${dotted.text.split('.').join('/')}`;\n    }\n    return base;\n  }\n\n  function moduleSpecifierOf(node: TSNode): string {\n    if (node.type === 'relative_import') return relativeSpecifier(node);\n    return node.text; // dotted_name, e.g. \"pkg.sub\"\n  }\n\n  function handleFunctionDefinition(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `function ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    functionNodeMap.set(node.id, id);\n  }\n\n  function handleClassDefinition(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const classId = entityId(sourceFile, name);\n    builder.addNode({ id: classId, label: `class ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: classId, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, classId);\n    functionNodeMap.set(node.id, classId);\n\n    const superclasses = node.childForFieldName('superclasses');\n    if (superclasses) {\n      for (const base of namedChildren(superclasses)) {\n        if (base.type !== 'identifier' && base.type !== 'attribute') continue; // skip e.g. metaclass=Meta\n        builder.addEdge({\n          source: classId,\n          target: resolveHeritageTarget(base.text),\n          relation: 'inherits',\n          confidence: 'EXTRACTED',\n        });\n      }\n    }\n\n    const methods = new Map<string, string>();\n    classMethods.set(node.id, methods);\n\n    const body = node.childForFieldName('body');\n    if (body) {\n      for (const rawMember of namedChildren(body)) {\n        const member = unwrapDecorated(rawMember);\n        if (!member || member.type !== 'function_definition') continue;\n        const methodName = member.childForFieldName('name')?.text ?? '(anonymous)';\n        const methodId = entityId(sourceFile, `${name}.${methodName}`);\n        builder.addNode({\n          id: methodId,\n          label: `method ${name}.${methodName}`,\n          sourceFile,\n          sourceLocation: lineOf(member),\n        });\n        builder.addEdge({ source: classId, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n        methods.set(methodName, methodId);\n        functionNodeMap.set(member.id, methodId);\n        enclosingClassOf.set(member.id, node.id);\n      }\n    }\n  }\n\n  function handleImportStatement(node: TSNode): void {\n    // `import a, b.c as d` — every item is a top-level named child, either\n    // `dotted_name` (bare module) or `aliased_import` (module `as` alias).\n    for (const item of namedChildren(node)) {\n      if (item.type === 'dotted_name') {\n        const ref = resolveModuleRef(sourceFile, item.text);\n        addModuleNode(ref);\n        const bindingName = namedChildren(item)[0]?.text ?? item.text; // `import pkg.sub` binds `pkg`\n        importIndex.set(bindingName, ref);\n        builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n      } else if (item.type === 'aliased_import') {\n        const dotted = item.childForFieldName('name');\n        const alias = item.childForFieldName('alias')?.text;\n        if (!dotted || !alias) continue;\n        const ref = resolveModuleRef(sourceFile, dotted.text);\n        addModuleNode(ref);\n        importIndex.set(alias, ref);\n        builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n      }\n    }\n  }\n\n  function handleImportFromStatement(node: TSNode): void {\n    const moduleNode = node.childForFieldName('module_name');\n    if (!moduleNode) return;\n    const ref = resolveModuleRef(sourceFile, moduleSpecifierOf(moduleNode));\n    addModuleNode(ref);\n\n    let sawItem = false;\n    for (const child of namedChildren(node)) {\n      if (child.id === moduleNode.id) continue;\n      if (child.type === 'dotted_name') {\n        sawItem = true;\n        importIndex.set(child.text, ref);\n      } else if (child.type === 'aliased_import') {\n        sawItem = true;\n        const alias = child.childForFieldName('alias')?.text;\n        const name = child.childForFieldName('name')?.text;\n        if (alias) importIndex.set(alias, ref);\n        else if (name) importIndex.set(name, ref);\n      } else if (child.type === 'wildcard_import') {\n        sawItem = true;\n      }\n    }\n    if (sawItem) {\n      builder.addEdge({ source: fileId, target: ref.id, relation: 'imports_from', confidence: 'EXTRACTED' });\n    }\n  }\n\n  // Pass 1: top-level declarations (functions, classes, imports),\n  // unwrapping `@decorator` wrappers where present.\n  for (const rawChild of namedChildren(root)) {\n    if (rawChild.type === 'import_statement') {\n      handleImportStatement(rawChild);\n      continue;\n    }\n    if (rawChild.type === 'import_from_statement') {\n      handleImportFromStatement(rawChild);\n      continue;\n    }\n\n    const effective = unwrapDecorated(rawChild);\n    if (!effective) continue;\n\n    switch (effective.type) {\n      case 'function_definition':\n        handleFunctionDefinition(effective);\n        break;\n      case 'class_definition':\n        handleClassDefinition(effective);\n        break;\n      default:\n        break;\n    }\n  }\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingClassMethods(node: TSNode): Map<string, string> | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'function_definition') {\n        const classNodeId = enclosingClassOf.get(current.id);\n        if (classNodeId !== undefined) return classMethods.get(classNodeId);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  // Pass 2: calls (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of descendantsOfType(root, ['call'])) {\n    const fn = call.childForFieldName('function');\n    if (!fn) continue;\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (fn.type === 'identifier') {\n      const name = fn.text;\n      const sameFile = nameIndex.get(name);\n      if (sameFile) {\n        targetId = sameFile;\n      } else {\n        const viaImport = importIndex.get(name);\n        if (viaImport) {\n          targetId = viaImport.id;\n          confidence = 'INFERRED';\n        }\n      }\n    } else if (fn.type === 'attribute') {\n      const object = fn.childForFieldName('object');\n      const property = fn.childForFieldName('attribute')?.text;\n      if (object && property) {\n        if (object.type === 'identifier' && object.text === 'self') {\n          const methodId = closestEnclosingClassMethods(call)?.get(property);\n          if (methodId) targetId = methodId;\n        } else if (object.type === 'identifier') {\n          const viaImport = importIndex.get(object.text);\n          if (viaImport) {\n            targetId = viaImport.id;\n            confidence = 'INFERRED';\n          }\n        }\n      }\n    }\n\n    if (!targetId) continue; // unresolved callee (builtin, external value, ...) — no noisy guess\n    const callerId = closestTrackedCaller(call);\n    builder.addEdge({ source: callerId, target: targetId, relation: 'calls', confidence });\n  }\n\n  return builder.build();\n}\n","import * as fs from 'node:fs/promises';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\n/**\n * Best-effort conversion of a required path's last segment into the\n * CamelCase constant name Ruby convention says it defines (`require_relative\n * './math'` -> `Math`, `require 'active_support/core_ext'` -> `CoreExt`).\n * Ruby's `require`/`require_relative` bind no local alias at all (unlike\n * every other language here), so this is the one available heuristic for\n * giving later `Constant.method(...)` calls something to resolve against —\n * it is a naming-convention guess, not a confirmed binding.\n */\nfunction conventionalConstantName(specifier: string): string {\n  const lastSegment = specifier.split('/').filter(Boolean).pop() ?? specifier;\n  return lastSegment\n    .split('_')\n    .filter(Boolean)\n    .map((word) => word.charAt(0).toUpperCase() + word.slice(1))\n    .join('');\n}\n\n/** Text of a `string` node's `string_content` child (already unquoted), or '' for an empty literal. */\nfunction stringLiteralContent(node: TSNode): string | null {\n  if (node.type !== 'string') return null;\n  const content = namedChildren(node).find((c) => c.type === 'string_content');\n  return content ? content.text : '';\n}\n\n/**\n * Structural extraction for .rb via web-tree-sitter (WASM, no native\n * compilation, no eval/exec of source content).\n *\n * Pattern mirrors typescript.ts, adapted to Ruby's shape: top-level\n * classes/modules and free `method`s (pass 1) -> every `call` node walked\n * once to special-case `require`/`require_relative` into import edges (Ruby\n * has no dedicated import AST node — these are plain method calls, per the\n * master prompt), then a second walk resolves the rest as method calls\n * (pass 2). A same-file callee — including an implicit- or explicit-`self`\n * call resolved against the enclosing class/module — is EXTRACTED; a call\n * through a `Constant.method(...)` receiver that only resolves via the\n * conventional-constant-name heuristic above is INFERRED. An unresolvable\n * callee produces no edge at all.\n *\n * Known, deliberate scope limit: a bare, paren-less, argument-less\n * identifier (`helper_top` with no parens or `()`) is genuinely ambiguous\n * with a local-variable reference at the grammar level — tree-sitter-ruby\n * itself represents it as a plain `identifier`, not a `call` — so this\n * extractor (like a human reading the AST alone) cannot tell them apart\n * and does not attempt to. Only calls that surface as an actual `call`\n * node (parens, and/or arguments, and/or an explicit receiver) are\n * resolved.\n *\n * `include`/`extend`/`prepend` (Ruby's mixin mechanism) become `mixes_in`\n * edges; `class Foo < Bar` becomes `inherits`. Ruby has no `implements`\n * equivalent.\n */\nexport async function extractRuby(filePath: string): Promise<ExtractionResult> {\n  const parser = await createParser('ruby');\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractRuby: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (top-level function/class/module) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every function/method entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** graph id of a class/module -> method name -> our graph id. */\n  const typeMethods = new Map<string, Map<string, string>>();\n  /** tree-sitter method node id -> its enclosing class/module's graph id. */\n  const enclosingTypeOf = new Map<number, string>();\n  /** conventional constant name (derived from a require path) -> the module it came from. */\n  const importIndex = new Map<string, ReturnType<typeof resolveModuleRef>>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  function resolveHeritageTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  function handleTopLevelMethod(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `function ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    functionNodeMap.set(node.id, id);\n  }\n\n  function handleClassOrModule(node: TSNode, kind: 'class' | 'module'): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `${kind} ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    typeMethods.set(id, new Map());\n\n    if (kind === 'class') {\n      const superclass = node.childForFieldName('superclass');\n      const base = superclass ? namedChildren(superclass)[0] : undefined;\n      if (base) {\n        builder.addEdge({\n          source: id,\n          target: resolveHeritageTarget(base.text),\n          relation: 'inherits',\n          confidence: 'EXTRACTED',\n        });\n      }\n    }\n\n    const body = node.childForFieldName('body');\n    if (!body) return;\n    const methods = typeMethods.get(id);\n    for (const member of namedChildren(body)) {\n      if (member.type === 'method') {\n        const methodName = member.childForFieldName('name')?.text ?? '(anonymous)';\n        const methodId = entityId(sourceFile, `${name}.${methodName}`);\n        builder.addNode({\n          id: methodId,\n          label: `method ${name}.${methodName}`,\n          sourceFile,\n          sourceLocation: lineOf(member),\n        });\n        builder.addEdge({ source: id, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n        methods?.set(methodName, methodId);\n        functionNodeMap.set(member.id, methodId);\n        enclosingTypeOf.set(member.id, id);\n      } else if (member.type === 'call') {\n        const methodField = member.childForFieldName('method')?.text;\n        if (methodField !== 'include' && methodField !== 'extend' && methodField !== 'prepend') continue;\n        const args = member.childForFieldName('arguments');\n        for (const arg of args ? namedChildren(args) : []) {\n          if (arg.type !== 'constant' && arg.type !== 'scoped_constant') continue;\n          builder.addEdge({\n            source: id,\n            target: resolveHeritageTarget(arg.text),\n            relation: 'mixes_in',\n            confidence: 'EXTRACTED',\n          });\n        }\n      }\n    }\n  }\n\n  // Pass 1: top-level declarations (free methods, classes, modules).\n  for (const child of namedChildren(root)) {\n    switch (child.type) {\n      case 'method':\n        handleTopLevelMethod(child);\n        break;\n      case 'class':\n        handleClassOrModule(child, 'class');\n        break;\n      case 'module':\n        handleClassOrModule(child, 'module');\n        break;\n      default:\n        break;\n    }\n  }\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingTypeMethods(node: TSNode): Map<string, string> | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'method') {\n        const typeId = enclosingTypeOf.get(current.id);\n        if (typeId !== undefined) return typeMethods.get(typeId);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  const allCalls = descendantsOfType(root, ['call']);\n\n  // Pass 2a: `require`/`require_relative` — plain method calls in Ruby's\n  // grammar, special-cased into import edges instead of `calls` edges.\n  const requireCallIds = new Set<number>();\n  for (const call of allCalls) {\n    const methodName = call.childForFieldName('method')?.text;\n    if (methodName !== 'require' && methodName !== 'require_relative') continue;\n    const args = call.childForFieldName('arguments');\n    const soleArg = args ? namedChildren(args) : [];\n    if (soleArg.length !== 1) continue;\n    const literal = stringLiteralContent(soleArg[0] as TSNode);\n    if (literal === null) continue;\n\n    requireCallIds.add(call.id);\n    const ref = resolveModuleRef(sourceFile, literal);\n    addModuleNode(ref);\n    builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n    importIndex.set(conventionalConstantName(literal), ref);\n  }\n\n  // Pass 2b: every other call (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of allCalls) {\n    if (requireCallIds.has(call.id)) continue;\n    const methodName = call.childForFieldName('method')?.text;\n    if (!methodName) continue;\n    const receiver = call.childForFieldName('receiver');\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (!receiver) {\n      const viaEnclosingType = closestEnclosingTypeMethods(call)?.get(methodName);\n      if (viaEnclosingType) {\n        targetId = viaEnclosingType;\n      } else {\n        const sameFile = nameIndex.get(methodName);\n        if (sameFile) targetId = sameFile;\n      }\n    } else if (receiver.type === 'self') {\n      const methodId = closestEnclosingTypeMethods(call)?.get(methodName);\n      if (methodId) targetId = methodId;\n    } else if (receiver.type === 'constant' || receiver.type === 'scoped_constant') {\n      const sameFileTypeId = nameIndex.get(receiver.text);\n      const methodId = sameFileTypeId ? typeMethods.get(sameFileTypeId)?.get(methodName) : undefined;\n      if (methodId) {\n        targetId = methodId;\n      } else {\n        const viaImport = importIndex.get(receiver.text);\n        if (viaImport) {\n          targetId = viaImport.id;\n          confidence = 'INFERRED';\n        }\n      }\n    }\n\n    if (!targetId) continue; // unresolved callee (builtin, local var, ...) — no noisy guess\n    const callerId = closestTrackedCaller(call);\n    builder.addEdge({ source: callerId, target: targetId, relation: 'calls', confidence });\n  }\n\n  return builder.build();\n}\n","import * as fs from 'node:fs/promises';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\n/**\n * Convert a Rust `use` path's `::`-joined segments into the relative-path\n * shape resolveModuleRef() understands: `crate`/`self` map to \"this\n * directory\" (`.`), each leading `super` walks up one directory, and\n * anything else (an external crate, `std`, ...) is left `::`-joined so\n * resolveModuleRef treats it as an external module specifier.\n */\nfunction convertUsePath(segments: string[]): string {\n  const first = segments[0];\n  if (first === 'crate' || first === 'self') {\n    const rest = segments.slice(1);\n    return rest.length ? `./${rest.join('/')}` : '.';\n  }\n  if (first === 'super') {\n    let i = 0;\n    while (segments[i] === 'super') i++;\n    const ups = Array.from({ length: i }, () => '..').join('/');\n    const rest = segments.slice(i);\n    return rest.length ? `${ups}/${rest.join('/')}` : ups;\n  }\n  return segments.join('::');\n}\n\n/**\n * Structural extraction for .rs via web-tree-sitter (WASM, no native\n * compilation, no eval/exec of source content).\n *\n * Pattern mirrors typescript.ts, adapted to Rust's shape: top-level\n * structs/traits and free functions come from pass 1, but methods are\n * declared separately in `impl` blocks (inherent `impl Type { ... }` or\n * trait `impl Trait for Type { ... }`), so those are walked as their own\n * step and attached to whichever struct/trait `name` they target. Every\n * call_expression is then resolved (pass 2): a same-file callee, or a\n * `self.method()` call resolved against the enclosing impl block's type,\n * is EXTRACTED; a callee that only resolves through a `use`-imported local\n * binding (an imported item, or a module alias via `use ... as`) is\n * INFERRED — the \"cross-file second pass\" placeholder described in the\n * master prompt §3. It intentionally does not open and parse the\n * imported module to confirm the target. An unresolvable callee produces\n * no edge at all.\n *\n * `impl Trait for Type` is Rust's one heritage-like construct exposed\n * directly in the grammar, so it becomes an `implements` edge from `Type`\n * to `Trait`.\n */\nexport async function extractRust(filePath: string): Promise<ExtractionResult> {\n  const parser = await createParser('rust');\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractRust: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (function/struct/trait) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every function/method entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** graph id of a struct/trait -> method name -> our graph id. */\n  const typeMethods = new Map<string, Map<string, string>>();\n  /** tree-sitter function_item (method) node id -> the owning impl block's type graph id. */\n  const enclosingTypeOf = new Map<number, string>();\n  /** local binding name (`use` item/alias) -> the module it came from. */\n  const importIndex = new Map<string, ReturnType<typeof resolveModuleRef>>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  function resolveTypeTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  function processUseArgument(node: TSNode): void {\n    switch (node.type) {\n      case 'identifier': {\n        // `use foo;` — whole-module import, single segment.\n        const ref = resolveModuleRef(sourceFile, convertUsePath([node.text]));\n        addModuleNode(ref);\n        importIndex.set(node.text, ref);\n        builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n        break;\n      }\n      case 'scoped_identifier': {\n        // `use std::fmt;` — single named item `fmt` from module `std`.\n        const pathNode = node.childForFieldName('path');\n        const nameNode = node.childForFieldName('name');\n        if (!pathNode || !nameNode) break;\n        const ref = resolveModuleRef(sourceFile, convertUsePath(pathNode.text.split('::')));\n        addModuleNode(ref);\n        importIndex.set(nameNode.text, ref);\n        builder.addEdge({ source: fileId, target: ref.id, relation: 'imports_from', confidence: 'EXTRACTED' });\n        break;\n      }\n      case 'use_as_clause': {\n        // `use crate::math as m;` — whole module aliased to `m`.\n        const pathNode = node.childForFieldName('path');\n        const aliasNode = node.childForFieldName('alias');\n        if (!pathNode || !aliasNode) break;\n        const ref = resolveModuleRef(sourceFile, convertUsePath(pathNode.text.split('::')));\n        addModuleNode(ref);\n        importIndex.set(aliasNode.text, ref);\n        builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n        break;\n      }\n      case 'scoped_use_list': {\n        // `use crate::math::{add, multiply};` — named items from a module.\n        const pathNode = node.childForFieldName('path');\n        const listNode = node.childForFieldName('list');\n        if (!listNode) break;\n        const prefixSegments = pathNode ? pathNode.text.split('::') : [];\n        const ref = resolveModuleRef(sourceFile, convertUsePath(prefixSegments));\n        addModuleNode(ref);\n        let sawItem = false;\n        for (const item of namedChildren(listNode)) {\n          sawItem = true;\n          if (item.type === 'identifier') {\n            importIndex.set(item.text, ref);\n          } else if (item.type === 'use_as_clause') {\n            const alias = item.childForFieldName('alias')?.text;\n            if (alias) importIndex.set(alias, ref);\n          }\n          // nested scoped_identifier / use_wildcard / `self` items: edge is\n          // still emitted below, just no simple local binding to record.\n        }\n        if (sawItem) {\n          builder.addEdge({ source: fileId, target: ref.id, relation: 'imports_from', confidence: 'EXTRACTED' });\n        }\n        break;\n      }\n      default:\n        break; // `use foo::*;` (use_wildcard) or other rare forms — no clean binding to model\n    }\n  }\n\n  function handleStructItem(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `struct ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    typeMethods.set(id, new Map());\n  }\n\n  function handleTraitItem(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `trait ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n  }\n\n  function handleFunctionItem(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `function ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    functionNodeMap.set(node.id, id);\n  }\n\n  function handleImplItem(node: TSNode): void {\n    const typeName = node.childForFieldName('type')?.text;\n    if (!typeName) return;\n    const typeId = resolveTypeTarget(typeName);\n\n    const traitName = node.childForFieldName('trait')?.text;\n    if (traitName) {\n      builder.addEdge({\n        source: typeId,\n        target: resolveTypeTarget(traitName),\n        relation: 'implements',\n        confidence: 'EXTRACTED',\n      });\n    }\n\n    let methods = typeMethods.get(typeId);\n    if (!methods) {\n      methods = new Map();\n      typeMethods.set(typeId, methods);\n    }\n\n    const body = node.childForFieldName('body');\n    if (!body) return;\n    for (const member of namedChildren(body)) {\n      if (member.type !== 'function_item') continue;\n      const methodName = member.childForFieldName('name')?.text ?? '(anonymous)';\n      const methodId = entityId(sourceFile, `${typeName}.${methodName}`);\n      builder.addNode({\n        id: methodId,\n        label: `method ${typeName}.${methodName}`,\n        sourceFile,\n        sourceLocation: lineOf(member),\n      });\n      builder.addEdge({ source: typeId, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n      methods.set(methodName, methodId);\n      functionNodeMap.set(member.id, methodId);\n      enclosingTypeOf.set(member.id, typeId);\n    }\n  }\n\n  // Pass 1: top-level declarations (imports, structs, traits, free\n  // functions). Impl blocks are handled in their own pass below so every\n  // struct/trait name is already registered before methods attach to it.\n  const implNodes: TSNode[] = [];\n  for (const child of namedChildren(root)) {\n    switch (child.type) {\n      case 'use_declaration': {\n        const arg = child.childForFieldName('argument');\n        if (arg) processUseArgument(arg);\n        break;\n      }\n      case 'struct_item':\n        handleStructItem(child);\n        break;\n      case 'trait_item':\n        handleTraitItem(child);\n        break;\n      case 'function_item':\n        handleFunctionItem(child);\n        break;\n      case 'impl_item':\n        implNodes.push(child);\n        break;\n      default:\n        break;\n    }\n  }\n  for (const impl of implNodes) handleImplItem(impl);\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingTypeMethods(node: TSNode): Map<string, string> | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'function_item') {\n        const typeId = enclosingTypeOf.get(current.id);\n        if (typeId !== undefined) return typeMethods.get(typeId);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  // Pass 2: calls (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of descendantsOfType(root, ['call_expression'])) {\n    const fn = call.childForFieldName('function');\n    if (!fn) continue;\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (fn.type === 'identifier') {\n      const name = fn.text;\n      const sameFile = nameIndex.get(name);\n      if (sameFile) {\n        targetId = sameFile;\n      } else {\n        const viaImport = importIndex.get(name);\n        if (viaImport) {\n          targetId = viaImport.id;\n          confidence = 'INFERRED';\n        }\n      }\n    } else if (fn.type === 'field_expression') {\n      const value = fn.childForFieldName('value');\n      const field = fn.childForFieldName('field')?.text;\n      if (value && field) {\n        if (value.type === 'self') {\n          const methodId = closestEnclosingTypeMethods(call)?.get(field);\n          if (methodId) targetId = methodId;\n        }\n      }\n    } else if (fn.type === 'scoped_identifier') {\n      // `m::add(1, 2)` — call through a `use ... as m` module alias.\n      const path = fn.childForFieldName('path')?.text;\n      const name = fn.childForFieldName('name')?.text;\n      if (path && name) {\n        const viaImport = importIndex.get(path);\n        if (viaImport) {\n          targetId = viaImport.id;\n          confidence = 'INFERRED';\n        }\n      }\n    }\n\n    if (!targetId) continue; // unresolved callee (builtin, external value, ...) — no noisy guess\n    const callerId = closestTrackedCaller(call);\n    builder.addEdge({ source: callerId, target: targetId, relation: 'calls', confidence });\n  }\n\n  return builder.build();\n}\n","import * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport type { Node as TSNode } from 'web-tree-sitter';\nimport type { ExtractionResult } from '../types.js';\nimport {\n  ExtractionBuilder,\n  descendantsOfType,\n  entityId,\n  externalId,\n  lineOf,\n  namedChildren,\n  resolveModuleRef,\n  toPosix,\n} from './common.js';\nimport { createParser } from './wasmLoader.js';\n\nfunction grammarForExtension(ext: string): 'typescript' | 'tsx' | 'javascript' {\n  const lower = ext.toLowerCase();\n  if (lower === '.tsx') return 'tsx';\n  if (lower === '.jsx') return 'javascript';\n  if (lower === '.ts' || lower === '.mts' || lower === '.cts') return 'typescript';\n  return 'javascript'; // .js / .mjs / .cjs\n}\n\n/** Strip the surrounding quotes tree-sitter keeps on a `string` node's text. */\nfunction stripQuotes(text: string): string {\n  if (text.length >= 2) {\n    const first = text[0];\n    const last = text[text.length - 1];\n    if ((first === '\"' || first === \"'\" || first === '`') && first === last) {\n      return text.slice(1, -1);\n    }\n  }\n  return text;\n}\n\n/** The sole string-literal argument of a call, if that's exactly what it has (used for `require('x')` / `import('x')`). */\nfunction firstStringArgument(call: TSNode): string | null {\n  const args = call.childForFieldName('arguments');\n  if (!args) return null;\n  const first = namedChildren(args)[0];\n  if (!first || first.type !== 'string') return null;\n  return stripQuotes(first.text);\n}\n\n/**\n * Structural extraction for .ts/.tsx/.js/.jsx via web-tree-sitter (WASM,\n * no native compilation, no eval/exec of source content).\n *\n * Pattern: parse -> walk the AST for top-level functions/classes/\n * interfaces/const-bound functions/imports/re-exports (pass 1) -> walk all\n * `call_expression`s and resolve each callee against what pass 1 saw\n * (pass 2). A same-file callee is EXTRACTED; a callee that resolves only\n * through an imported local binding (e.g. calling a function you imported,\n * or a member on a namespace import) is emitted as INFERRED — this is the\n * \"cross-file second pass\" placeholder described in the master prompt §3.\n * It intentionally does not open and parse the imported file to confirm\n * the target; a real multi-file resolver is future work (see\n * ARCHITECTURE.md). An unresolvable callee (a builtin, a call on some\n * arbitrary local value, etc.) produces no edge at all rather than a noisy\n * guess.\n */\nexport async function extractTypeScript(filePath: string): Promise<ExtractionResult> {\n  const ext = path.extname(filePath);\n  const grammar = grammarForExtension(ext);\n  const parser = await createParser(grammar);\n\n  const raw = await fs.readFile(filePath);\n  const content = raw.toString('utf-8'); // replacement-decoded — never throws on invalid bytes\n\n  const tree = parser.parse(content);\n  if (!tree) {\n    throw new Error(`extractTypeScript: parser produced no tree for ${filePath}`);\n  }\n  const root = tree.rootNode;\n\n  const sourceFile = toPosix(filePath);\n  const builder = new ExtractionBuilder();\n  const fileId = sourceFile;\n  builder.addNode({ id: fileId, label: sourceFile, sourceFile, sourceLocation: 'L1' });\n\n  /** Declared name (function/class/interface/top-level const) -> our graph id. */\n  const nameIndex = new Map<string, string>();\n  /** tree-sitter node id -> our graph id, for every function-like entity we track. */\n  const functionNodeMap = new Map<number, string>();\n  /** tree-sitter class_declaration node id -> method name -> our graph id. */\n  const classMethods = new Map<number, Map<string, string>>();\n  /** tree-sitter method_definition node id -> its enclosing class's node id. */\n  const enclosingClassOf = new Map<number, number>();\n\n  interface ImportBinding {\n    ref: ReturnType<typeof resolveModuleRef>;\n    /** The name as declared in the *source* module — undefined for namespace/default/require-whole\n     *  bindings, where the local name tells us nothing about what the target file actually calls it. */\n    importedName?: string;\n    kind: 'named' | 'namespace' | 'default';\n  }\n  /** local binding name (import, or CommonJS require()) -> where it came from. */\n  const importIndex = new Map<string, ImportBinding>();\n\n  function addModuleNode(ref: ReturnType<typeof resolveModuleRef>): void {\n    if (builder.hasNode(ref.id)) return;\n    builder.addNode({\n      id: ref.id,\n      label: ref.label,\n      sourceFile: ref.external ? '<external>' : ref.id,\n      sourceLocation: 'L1',\n    });\n  }\n\n  /**\n   * Resolve an import/require binding to the most specific target id we can\n   * reasonably guess without opening the target file: a named import of a\n   * same-repo module points at that module's *own* entityId for the name it\n   * was declared under there (not the local alias here) — the same\n   * deterministic id scheme means this will actually line up with the real\n   * node once that file is extracted too. A namespace/require-whole binding\n   * used via member access (`ns.foo()`) does the same with the accessed\n   * property name. Anything else (default import, external package, bare\n   * namespace call) falls back to the module node itself.\n   */\n  function importTargetId(binding: ImportBinding, property?: string): string {\n    if (!binding.ref.external) {\n      if (binding.kind === 'named' && binding.importedName) {\n        return entityId(binding.ref.id, binding.importedName);\n      }\n      if (binding.kind === 'namespace' && property) {\n        return entityId(binding.ref.id, property);\n      }\n    }\n    return binding.ref.id;\n  }\n\n  function resolveHeritageTarget(name: string): string {\n    const resolved = nameIndex.get(name);\n    if (resolved) return resolved;\n    const extId = externalId(name);\n    if (!builder.hasNode(extId)) {\n      builder.addNode({ id: extId, label: name, sourceFile: '<external>', sourceLocation: 'L0' });\n    }\n    return extId;\n  }\n\n  function handleFunctionDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `function ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n    functionNodeMap.set(node.id, id);\n  }\n\n  /** `const foo = require('bar')` / `const { a, b: c } = require('bar')` — register bindings only; pass 2 emits the actual `imports` edge when it walks this same call_expression. */\n  function registerRequireBinding(nameNode: TSNode, ref: ReturnType<typeof resolveModuleRef>): void {\n    if (nameNode.type === 'identifier') {\n      importIndex.set(nameNode.text, { ref, kind: 'namespace' });\n      return;\n    }\n    if (nameNode.type === 'object_pattern') {\n      for (const prop of namedChildren(nameNode)) {\n        if (prop.type === 'shorthand_property_identifier_pattern') {\n          importIndex.set(prop.text, { ref, importedName: prop.text, kind: 'named' });\n        } else if (prop.type === 'pair_pattern') {\n          const key = prop.childForFieldName('key')?.text;\n          const value = prop.childForFieldName('value')?.text;\n          if (key && value) importIndex.set(value, { ref, importedName: key, kind: 'named' });\n        }\n      }\n    }\n  }\n\n  function handleTopLevelVariableFunctions(node: TSNode): void {\n    for (const declarator of namedChildren(node)) {\n      if (declarator.type !== 'variable_declarator') continue;\n      const value = declarator.childForFieldName('value');\n      if (!value) continue;\n\n      if (value.type === 'arrow_function' || value.type === 'function_expression') {\n        const name = declarator.childForFieldName('name')?.text;\n        if (!name) continue;\n        const id = entityId(sourceFile, name);\n        builder.addNode({ id, label: `function ${name}`, sourceFile, sourceLocation: lineOf(declarator) });\n        builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n        nameIndex.set(name, id);\n        functionNodeMap.set(value.id, id);\n        continue;\n      }\n\n      if (value.type === 'call_expression') {\n        const callee = value.childForFieldName('function');\n        const specifier = callee?.type === 'identifier' && callee.text === 'require' ? firstStringArgument(value) : null;\n        if (specifier) {\n          const nameNode = declarator.childForFieldName('name');\n          if (nameNode) {\n            const ref = resolveModuleRef(sourceFile, specifier);\n            addModuleNode(ref);\n            registerRequireBinding(nameNode, ref);\n          }\n        }\n      }\n    }\n  }\n\n  function handleInterfaceDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const id = entityId(sourceFile, name);\n    builder.addNode({ id, label: `interface ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: id, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, id);\n  }\n\n  function handleClassDeclaration(node: TSNode): void {\n    const name = node.childForFieldName('name')?.text ?? '(anonymous)';\n    const classId = entityId(sourceFile, name);\n    builder.addNode({ id: classId, label: `class ${name}`, sourceFile, sourceLocation: lineOf(node) });\n    builder.addEdge({ source: fileId, target: classId, relation: 'contains', confidence: 'EXTRACTED' });\n    nameIndex.set(name, classId);\n    functionNodeMap.set(node.id, classId);\n\n    const heritage = namedChildren(node).find((c) => c.type === 'class_heritage');\n    if (heritage) {\n      for (const clause of namedChildren(heritage)) {\n        if (clause.type === 'extends_clause') {\n          const base = clause.childForFieldName('value')?.text;\n          if (base) {\n            builder.addEdge({\n              source: classId,\n              target: resolveHeritageTarget(base),\n              relation: 'inherits',\n              confidence: 'EXTRACTED',\n            });\n          }\n        } else if (clause.type === 'implements_clause') {\n          for (const iface of namedChildren(clause)) {\n            builder.addEdge({\n              source: classId,\n              target: resolveHeritageTarget(iface.text),\n              relation: 'implements',\n              confidence: 'EXTRACTED',\n            });\n          }\n        }\n      }\n    }\n\n    const methods = new Map<string, string>();\n    classMethods.set(node.id, methods);\n\n    const body = node.childForFieldName('body');\n    if (body) {\n      for (const member of namedChildren(body)) {\n        if (member.type !== 'method_definition') continue;\n        const methodName = member.childForFieldName('name')?.text ?? '(anonymous)';\n        const methodId = entityId(sourceFile, `${name}.${methodName}`);\n        builder.addNode({\n          id: methodId,\n          label: `method ${name}.${methodName}`,\n          sourceFile,\n          sourceLocation: lineOf(member),\n        });\n        builder.addEdge({ source: classId, target: methodId, relation: 'method', confidence: 'EXTRACTED' });\n        methods.set(methodName, methodId);\n        functionNodeMap.set(member.id, methodId);\n        enclosingClassOf.set(member.id, node.id);\n      }\n    }\n  }\n\n  function handleImport(node: TSNode): void {\n    const sourceNode = node.childForFieldName('source');\n    if (!sourceNode) return;\n    const ref = resolveModuleRef(sourceFile, stripQuotes(sourceNode.text));\n    addModuleNode(ref);\n\n    const clause = namedChildren(node).find((c) => c.type === 'import_clause');\n    if (!clause) return; // side-effect-only import, e.g. `import './setup.js'`\n\n    let sawNamed = false;\n    let sawWhole = false;\n\n    for (const child of namedChildren(clause)) {\n      if (child.type === 'named_imports') {\n        sawNamed = true;\n        for (const specifierNode of namedChildren(child)) {\n          const importedName = specifierNode.childForFieldName('name')?.text;\n          const localName = specifierNode.childForFieldName('alias')?.text ?? importedName;\n          if (localName) importIndex.set(localName, { ref, importedName, kind: 'named' });\n        }\n      } else if (child.type === 'namespace_import') {\n        sawWhole = true;\n        const localName = namedChildren(child)[0]?.text;\n        if (localName) importIndex.set(localName, { ref, kind: 'namespace' });\n      } else if (child.type === 'identifier') {\n        sawWhole = true;\n        importIndex.set(child.text, { ref, kind: 'default' });\n      }\n    }\n\n    if (sawNamed) {\n      builder.addEdge({ source: fileId, target: ref.id, relation: 'imports_from', confidence: 'EXTRACTED' });\n    }\n    if (sawWhole) {\n      builder.addEdge({ source: fileId, target: ref.id, relation: 'imports', confidence: 'EXTRACTED' });\n    }\n  }\n\n  function handleReExport(node: TSNode): void {\n    const sourceNode = node.childForFieldName('source');\n    if (!sourceNode) return;\n    const ref = resolveModuleRef(sourceFile, stripQuotes(sourceNode.text));\n    addModuleNode(ref);\n    builder.addEdge({ source: fileId, target: ref.id, relation: 're_exports', confidence: 'EXTRACTED' });\n  }\n\n  function unwrapExport(node: TSNode): TSNode | null {\n    if (node.type !== 'export_statement') return node;\n    return node.childForFieldName('declaration');\n  }\n\n  // Pass 1: top-level declarations (functions, classes, interfaces,\n  // const-bound functions, imports, re-exports).\n  for (const child of namedChildren(root)) {\n    if (child.type === 'import_statement') {\n      handleImport(child);\n      continue;\n    }\n    if (child.type === 'export_statement' && child.childForFieldName('source')) {\n      handleReExport(child);\n      continue;\n    }\n\n    const effective = unwrapExport(child);\n    if (!effective) continue;\n\n    switch (effective.type) {\n      case 'function_declaration':\n      case 'generator_function_declaration':\n        handleFunctionDeclaration(effective);\n        break;\n      case 'class_declaration':\n        handleClassDeclaration(effective);\n        break;\n      case 'interface_declaration':\n        handleInterfaceDeclaration(effective);\n        break;\n      case 'lexical_declaration':\n      case 'variable_declaration':\n        handleTopLevelVariableFunctions(effective);\n        break;\n      default:\n        break;\n    }\n  }\n\n  function closestTrackedCaller(node: TSNode): string {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      const tracked = functionNodeMap.get(current.id);\n      if (tracked) return tracked;\n      current = current.parent;\n    }\n    return fileId;\n  }\n\n  function closestEnclosingClassMethods(node: TSNode): Map<string, string> | undefined {\n    let current: TSNode | null = node.parent;\n    while (current) {\n      if (current.type === 'method_definition') {\n        const classNodeId = enclosingClassOf.get(current.id);\n        if (classNodeId !== undefined) return classMethods.get(classNodeId);\n      }\n      current = current.parent;\n    }\n    return undefined;\n  }\n\n  // Pass 2: calls (see the function doc comment above for the\n  // EXTRACTED/INFERRED policy).\n  for (const call of descendantsOfType(root, ['call_expression'])) {\n    const fn = call.childForFieldName('function');\n    if (!fn) continue;\n\n    // CommonJS `require('x')` and dynamic `import('x')` are import\n    // expressions wearing a call's clothing — treat them as `imports`\n    // edges (module-level, EXTRACTED) rather than `calls`, wherever in the\n    // tree they occur (module scope, or lazily inside a function).\n    if ((fn.type === 'identifier' && fn.text === 'require') || fn.type === 'import') {\n      const specifier = firstStringArgument(call);\n      if (specifier) {\n        const ref = resolveModuleRef(sourceFile, specifier);\n        addModuleNode(ref);\n        builder.addEdge({\n          source: closestTrackedCaller(call),\n          target: ref.id,\n          relation: 'imports',\n          confidence: 'EXTRACTED',\n        });\n        continue;\n      }\n    }\n\n    let targetId: string | null = null;\n    let confidence: 'EXTRACTED' | 'INFERRED' = 'EXTRACTED';\n\n    if (fn.type === 'identifier') {\n      const name = fn.text;\n      const sameFile = nameIndex.get(name);\n      if (sameFile) {\n        targetId = sameFile;\n      } else {\n        const binding = importIndex.get(name);\n        if (binding) {\n          targetId = importTargetId(binding);\n          confidence = 'INFERRED';\n        }\n      }\n    } else if (fn.type === 'member_expression') {\n      const object = fn.childForFieldName('object');\n      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string | undefined) ?? id;\n}\n\nfunction bulletList(items: string[]): string {\n  if (items.length === 0) return '_None found._';\n  return items.map((item) => `- ${item}`).join('\\n');\n}\n\ninterface CommunitySummary {\n  label: string;\n  members: string[];\n}\n\nfunction summarizeCommunities(graph: Graph): CommunitySummary[] {\n  const byCommunity = new Map<number, CommunitySummary>();\n  graph.forEachNode((nodeId, attributes) => {\n    const community = attributes.community as number | undefined;\n    if (community === undefined) return;\n    const label = (attributes.communityLabel as string | undefined) ?? `community-${community}`;\n    const existing = byCommunity.get(community);\n    if (existing) {\n      existing.members.push(nodeId);\n    } else {\n      byCommunity.set(community, { label, members: [nodeId] });\n    }\n  });\n\n  const summaries = [...byCommunity.values()];\n  for (const summary of summaries) {\n    summary.members.sort((a, b) => a.localeCompare(b));\n  }\n  summaries.sort((a, b) => b.members.length - a.members.length || a.label.localeCompare(b.label));\n  return summaries;\n}\n\n/**\n * Render the plain-language GRAPH_REPORT.md content: a short summary,\n * community breakdown, god nodes, structural surprises, and open\n * questions — everything a human (or an agent) needs to sanity-check a\n * freshly built graph before trusting it.\n */\nexport function renderReport(graph: Graph, analysis: Analysis, now: Date = new Date()): string {\n  const generatedAt = now.toISOString();\n  const communities = summarizeCommunities(graph);\n\n  const lines: string[] = [];\n  lines.push('# Graph Report');\n  lines.push('');\n  lines.push(`Generated: ${generatedAt}`);\n  lines.push('');\n  lines.push('## Summary');\n  lines.push('');\n  lines.push(`- **Nodes:** ${graph.order}`);\n  lines.push(`- **Edges:** ${graph.size}`);\n  lines.push(`- **Communities:** ${communities.length}`);\n  lines.push(`- **God nodes:** ${analysis.godNodes.length}`);\n  lines.push('');\n\n  lines.push('## Communities');\n  lines.push('');\n  if (communities.length === 0) {\n    lines.push('_No communities detected (graph may be empty, or cluster() has not run yet)._');\n  } else {\n    for (const community of communities) {\n      lines.push(`### ${community.label} (${community.members.length} member(s))`);\n      lines.push('');\n      const shown = community.members.slice(0, 25).map((id) => labelOf(graph, id));\n      lines.push(bulletList(shown));\n      if (community.members.length > 25) {\n        lines.push(`- ...and ${community.members.length - 25} more`);\n      }\n      lines.push('');\n    }\n  }\n\n  lines.push('## God Nodes');\n  lines.push('');\n  lines.push(\n    'Nodes with unusually high fan-in + fan-out relative to the rest of this graph — often a sign of a ' +\n      'shared utility, a bottleneck, or a module that has taken on too many responsibilities.',\n  );\n  lines.push('');\n  lines.push(bulletList(analysis.godNodes.map((id) => labelOf(graph, id))));\n  lines.push('');\n\n  lines.push('## Structural Surprises');\n  lines.push('');\n  lines.push(bulletList(analysis.surprises));\n  lines.push('');\n\n  lines.push('## Open Questions');\n  lines.push('');\n  lines.push(bulletList(analysis.openQuestions));\n  lines.push('');\n\n  return lines.join('\\n');\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { explainNode } from '../../query.js';\n\n/** Plain-language explanation of a single node. */\nexport async function runExplain(nodeName: string): Promise<void> {\n  const graph = await loadGraph();\n  const result = explainNode(graph, nodeName);\n\n  if (!result) {\n    console.log(`No node matched \"${nodeName}\".`);\n    return;\n  }\n\n  const location = result.sourceLocation ? `:${result.sourceLocation}` : '';\n  console.log(result.label);\n  console.log(`  location: ${result.sourceFile}${location}`);\n  if (result.communityLabel) {\n    console.log(`  community: ${result.communityLabel}`);\n  }\n\n  console.log('');\n  console.log(`Calls / references out (${result.outgoing.length}):`);\n  if (result.outgoing.length === 0) {\n    console.log('  (none)');\n  } else {\n    for (const edge of result.outgoing) {\n      console.log(`  --${edge.relation}--> ${edge.target} (${edge.confidence})`);\n    }\n  }\n\n  console.log('');\n  console.log(`Referenced by (${result.incoming.length}):`);\n  if (result.incoming.length === 0) {\n    console.log('  (none)');\n  } else {\n    for (const edge of result.incoming) {\n      console.log(`  ${edge.source} --${edge.relation}--> (${edge.confidence})`);\n    }\n  }\n}\n","import { createRequire } from 'node:module';\nimport * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\n\nconst require = createRequire(import.meta.url);\n\n/**\n * Resolve this package's own root directory, whether we're running from\n * source (tests/dev), the built dist/ bundle, or installed as a real\n * dependency elsewhere. Uses Node's self-reference resolution (walking up\n * from this module's location to the nearest package.json named\n * \"@dreamtree-org/graphify\") rather than a hardcoded relative path, since\n * the number of directories between this file and the package root\n * differs between src/ and the bundled dist/ output.\n */\nfunction packageRoot(): string {\n  const packageJsonPath = require.resolve('@dreamtree-org/graphify/package.json');\n  return path.dirname(packageJsonPath);\n}\n\nexport interface InstallResult {\n  host: string;\n  path: string;\n}\n\n/**\n * Copy SKILL.md into the local agent's skill directory. Claude Code only\n * for v1 (project-local `.claude/skills/graphify/SKILL.md`) — other hosts\n * (Cursor, etc.) are a clearly-flagged follow-up, not faked with an empty\n * or copy-pasted file.\n */\nexport async function runInstall(cwd: string = process.cwd()): Promise<InstallResult[]> {\n  const sourcePath = path.join(packageRoot(), 'src', 'skill', 'SKILL.md');\n  const content = await fs.readFile(sourcePath, 'utf-8');\n\n  const results: InstallResult[] = [];\n\n  const claudeCodeDir = path.join(cwd, '.claude', 'skills', 'graphify');\n  await fs.mkdir(claudeCodeDir, { recursive: true });\n  const claudeCodePath = path.join(claudeCodeDir, 'SKILL.md');\n  await fs.writeFile(claudeCodePath, content, 'utf-8');\n  results.push({ host: 'Claude Code', path: claudeCodePath });\n\n  for (const result of results) {\n    console.log(`Installed graphify skill for ${result.host} -> ${result.path}`);\n  }\n  console.log('');\n  console.log(\n    'Other hosts (Cursor, etc.) are not implemented yet by `graphify install` — see ARCHITECTURE.md.',\n  );\n\n  return results;\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { shortestPath } from '../../query.js';\n\n/** Shortest path between two named nodes. */\nexport async function runPath(fromNode: string, toNode: string): Promise<void> {\n  const graph = await loadGraph();\n  const result = shortestPath(graph, fromNode, toNode);\n\n  if (!result) {\n    console.log(`Could not resolve \"${fromNode}\" and/or \"${toNode}\" to a node in the graph.`);\n    return;\n  }\n\n  if (!result.found) {\n    console.log(\n      `No path found between \"${result.from.label}\" and \"${result.to.label}\" — they may be in ` +\n        'disconnected parts of the graph (see GRAPH_REPORT.md § Open Questions).',\n    );\n    return;\n  }\n\n  console.log(`${result.from.label} -> ${result.to.label} (${result.path.length} node(s)):`);\n  console.log(`  ${result.path.join(' -> ')}`);\n  if (result.edges.length > 0) {\n    console.log('');\n    console.log('Edges along the path:');\n    for (const edge of result.edges) {\n      console.log(`  ${edge.source} --${edge.relation}--> ${edge.target} (${edge.confidence})`);\n    }\n  }\n}\n","import { loadGraph } from '../../graphStore.js';\nimport { queryGraph } from '../../query.js';\n\nexport interface QueryOptions {\n  dfs?: boolean;\n  budget?: number;\n}\n\n/** BFS (default) or DFS traversal answering a natural-language question against the graph. */\nexport async function runQuery(question: string, options: QueryOptions = {}): Promise<void> {\n  const graph = await loadGraph();\n  const result = queryGraph(graph, question, { dfs: options.dfs, budget: options.budget });\n\n  if (result.seeds.length === 0) {\n    console.log(\n      `No nodes matched \"${question}\". Try different keywords, or run \\`graphify explain <node>\\` ` +\n        'if you already know the name.',\n    );\n    return;\n  }\n\n  console.log(`Matched ${result.seeds.length} seed node(s):`);\n  for (const seed of result.seeds) {\n    console.log(`  - ${seed.label} (${seed.id})`);\n  }\n\n  console.log('');\n  console.log(`Context — ${result.visited.length} node(s), ${options.dfs ? 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