@ngommans/codefocus 0.1.0 → 0.1.4

package/dist/{query-PS6QVPXP.js.map → query-64CFCXTD.js.map}

@@ -1 +1 @@
-{"version":3,"sources":["../src/commands/query.ts","../src/config.ts"],"sourcesContent":["import { createRequire } from \"node:module\";\nimport { resolve } from \"node:path\";\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { IndexDatabase, type SymbolRow } from \"../db.js\";\nimport { resolveRoot } from \"../root.js\";\nimport {\n  loadScoringConfig,\n  DEFAULT_SCORING_CONFIG,\n  type ScoringConfig,\n} from \"../config.js\";\n\nconst require = createRequire(import.meta.url);\nconst { DirectedGraph } = require(\"graphology\");\nconst pagerank = require(\"graphology-metrics/centrality/pagerank\");\nconst { getEncoding } = require(\"js-tiktoken\");\n\n// ── types ───────────────────────────────────────────────────────────────\n\ninterface ScoredSymbol {\n  symbol: SymbolRow;\n  score: number;\n  matchType: \"exact\" | \"contains\" | \"graph\";\n  depth: number;\n}\n\ninterface FileSection {\n  filePath: string;\n  symbols: ScoredSymbol[];\n  score: number;\n  startLine: number;\n  endLine: number;\n}\n\n// ── helpers ─────────────────────────────────────────────────────────────\n\n/**\n * Compute PageRank scores for all files in the index.\n */\nfunction computeFilePagerank(db: IndexDatabase): Map<string, number> {\n  const graph = new DirectedGraph();\n\n  for (const file of db.getAllFiles()) {\n    graph.addNode(file.path);\n  }\n\n  for (const edge of db.getFileImportEdges()) {\n    const key = `${edge.source_file}->${edge.target_file}`;\n    if (!graph.hasEdge(key)) {\n      graph.addEdgeWithKey(key, edge.source_file, edge.target_file);\n    }\n  }\n\n  const ranks: Record<string, number> =\n    graph.order > 0 ? pagerank(graph, { getEdgeWeight: null }) : {};\n\n  return new Map(Object.entries(ranks));\n}\n\n/**\n * Use FTS5 to find symbols whose containing file matches the search term.\n * Scores FTS5 hits by proximity to symbol boundaries: a match inside a\n * function body promotes that function, not the entire file.\n *\n * Spike 8 A1: Weighted term frequency — files where the term appears more\n * often (relative to file length) get a log-scaled boost.\n * Spike 8 A2: Symbol-name proximity — files containing a symbol whose name\n * includes the search term get a 1.5x boost.\n */\nfunction ftsSeededSymbols(\n  db: IndexDatabase,\n  term: string,\n  rootDir: string,\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): ScoredSymbol[] {\n  const ftsResults = db.searchContent(term);\n  if (ftsResults.length === 0) return [];\n\n  const results: ScoredSymbol[] = [];\n  const maxRank = Math.max(...ftsResults.map((r) => r.rank));\n\n  for (const fts of ftsResults) {\n    // Normalize FTS5 BM25 score to 0-0.4 range (below exact match, above graph)\n    let normalizedScore = maxRank > 0 ? (fts.rank / maxRank) * 0.4 : 0.2;\n\n    // Get file content to find which symbols contain the search term\n    const absPath = resolve(rootDir, fts.file_path);\n    let content: string;\n    try {\n      content = readFileSync(absPath, \"utf-8\");\n    } catch {\n      continue;\n    }\n\n    const lines = content.split(\"\\n\");\n    const termLower = term.toLowerCase();\n\n    // Find line numbers where the term appears\n    const matchingLines: number[] = [];\n    for (let i = 0; i < lines.length; i++) {\n      if (lines[i].toLowerCase().includes(termLower)) {\n        matchingLines.push(i + 1); // 1-indexed\n      }\n    }\n\n    if (matchingLines.length === 0) continue;\n\n    // A1: Weighted term frequency — boost files where the term is\n    // structurally important (many mentions) vs. incidental (1-2 mentions).\n    // Uses absolute count: log2(1 + count). Large files with many mentions\n    // score higher than small files with few, unlike density-based metrics\n    // which penalise important large files.\n    const tfBoost = Math.log2(1 + matchingLines.length);\n    normalizedScore *= tfBoost;\n\n    // A2: Symbol-name proximity boost — if any symbol in this file has a\n    // name or signature that includes the search term, the file is more\n    // relevant than one where the term only appears in code comments.\n    const fileSymbols = db.getSymbolsByFile(fts.file_path);\n    const hasSymbolNameMatch = fileSymbols.some(\n      (s) =>\n        s.name.toLowerCase().includes(termLower) ||\n        (s.signature?.toLowerCase().includes(termLower) ?? false),\n    );\n    if (hasSymbolNameMatch) {\n      normalizedScore *= config.symbolProximityBoost;\n    }\n\n    // Get symbols in this file and score by proximity\n    for (const sym of fileSymbols) {\n      if (!sym.id) continue;\n\n      // Check if any match is within this symbol's line range\n      const containsMatch = matchingLines.some(\n        (line) => line >= sym.start_line && line <= sym.end_line,\n      );\n\n      if (containsMatch) {\n        // Match is inside this symbol's body — high relevance\n        results.push({\n          symbol: sym,\n          score: normalizedScore,\n          matchType: \"contains\" as const,\n          depth: 0,\n        });\n      }\n    }\n  }\n\n  return results;\n}\n\n/**\n * Search for symbols matching the term, then expand via graph traversal\n * up to `maxDepth` hops.\n */\nfunction searchAndExpand(\n  db: IndexDatabase,\n  term: string,\n  maxDepth: number,\n  rootDir: string,\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): ScoredSymbol[] {\n  const scored = new Map<number, ScoredSymbol>();\n\n  // Phase 1: Direct symbol name matches\n  const directMatches = db.findSymbols(term);\n\n  for (const sym of directMatches) {\n    if (!sym.id) continue;\n    const isExact = sym.name.toLowerCase() === term.toLowerCase();\n    scored.set(sym.id, {\n      symbol: sym,\n      score: isExact ? 1.0 : 0.5,\n      matchType: isExact ? \"exact\" : \"contains\",\n      depth: 0,\n    });\n  }\n\n  // Phase 1b: FTS5 full-text content search (secondary seed)\n  // Use only when symbol-name matching returns no results\n  if (scored.size === 0) {\n    const ftsSymbols = ftsSeededSymbols(db, term, rootDir, config);\n    for (const ss of ftsSymbols) {\n      if (ss.symbol.id && !scored.has(ss.symbol.id)) {\n        scored.set(ss.symbol.id, ss);\n      }\n    }\n  }\n\n  // Phase 2: Graph expansion (BFS) with edge-weight scoring\n  // Weight by reference type: import (0.4) > type_ref (0.2)\n  // Dampen high-degree hub nodes: multiply score by 1/sqrt(fileDegree)\n  // Uses total degree (in + out) to catch both importers (cli.ts) and\n  // importees (db.ts) that act as hubs\n  if (maxDepth > 0) {\n    // Precompute file-level total degree (in + out) from import graph\n    const fileDegree = new Map<string, number>();\n    for (const edge of db.getFileImportEdges()) {\n      fileDegree.set(\n        edge.source_file,\n        (fileDegree.get(edge.source_file) ?? 0) + 1,\n      );\n      fileDegree.set(\n        edge.target_file,\n        (fileDegree.get(edge.target_file) ?? 0) + 1,\n      );\n    }\n\n    let frontier = new Set(scored.keys());\n\n    for (let hop = 1; hop <= maxDepth && frontier.size > 0; hop++) {\n      const nextFrontier = new Set<number>();\n\n      for (const symbolId of frontier) {\n        // Walk outgoing references (what this symbol depends on)\n        const outRefs = db.getOutgoingReferences(symbolId);\n        for (const ref of outRefs) {\n          if (!scored.has(ref.target_id)) {\n            const sym = db.getSymbolById(ref.target_id);\n            if (sym) {\n              const baseWeight =\n                ref.ref_type === \"import\" ? config.importEdgeWeight : config.typeRefWeight;\n              const deg = fileDegree.get(ref.target_file) ?? 0;\n              const hubDampening =\n                deg > 1 ? 1 / Math.sqrt(deg) : 1;\n              const graphScore = (baseWeight / hop) * hubDampening;\n\n              scored.set(ref.target_id, {\n                symbol: sym,\n                score: graphScore,\n                matchType: \"graph\",\n                depth: hop,\n              });\n              nextFrontier.add(ref.target_id);\n            }\n          }\n        }\n\n        // Walk incoming references (what depends on this symbol)\n        const inRefs = db.getIncomingReferences(symbolId);\n        for (const ref of inRefs) {\n          if (!scored.has(ref.source_id)) {\n            const sym = db.getSymbolById(ref.source_id);\n            if (sym) {\n              const baseWeight =\n                ref.ref_type === \"import\" ? config.importEdgeWeight : config.typeRefWeight;\n              const deg = fileDegree.get(ref.source_file) ?? 0;\n              const hubDampening =\n                deg > 1 ? 1 / Math.sqrt(deg) : 1;\n              const graphScore = (baseWeight / hop) * hubDampening;\n\n              scored.set(ref.source_id, {\n                symbol: sym,\n                score: graphScore,\n                matchType: \"graph\",\n                depth: hop,\n              });\n              nextFrontier.add(ref.source_id);\n            }\n          }\n        }\n      }\n\n      frontier = nextFrontier;\n    }\n  }\n\n  return Array.from(scored.values());\n}\n\n/**\n * Group scored symbols by file and compute file-level sections.\n */\nfunction groupByFile(\n  scoredSymbols: ScoredSymbol[],\n  pagerankScores: Map<string, number>,\n): FileSection[] {\n  const fileMap = new Map<string, ScoredSymbol[]>();\n\n  for (const ss of scoredSymbols) {\n    const fp = ss.symbol.file_path;\n    if (!fileMap.has(fp)) fileMap.set(fp, []);\n    fileMap.get(fp)!.push(ss);\n  }\n\n  const sections: FileSection[] = [];\n\n  for (const [filePath, symbols] of fileMap) {\n    symbols.sort((a, b) => a.symbol.start_line - b.symbol.start_line);\n\n    // File score: max symbol score, with pagerank boost only for direct matches\n    // Graph-expanded files should not get pagerank boost (it undoes hub dampening)\n    const maxSymScore = Math.max(...symbols.map((s) => s.score));\n    const hasDirectMatch = symbols.some((s) => s.matchType !== \"graph\");\n    const prScore = hasDirectMatch ? (pagerankScores.get(filePath) ?? 0) : 0;\n    const fileScore = maxSymScore + prScore;\n\n    // Combined line range (union of all symbol ranges)\n    const startLine = Math.min(...symbols.map((s) => s.symbol.start_line));\n    const endLine = Math.max(...symbols.map((s) => s.symbol.end_line));\n\n    sections.push({\n      filePath,\n      symbols,\n      score: fileScore,\n      startLine,\n      endLine,\n    });\n  }\n\n  // Sort by score descending, then alphabetically\n  sections.sort(\n    (a, b) => b.score - a.score || a.filePath.localeCompare(b.filePath),\n  );\n\n  return sections;\n}\n\n/**\n * B1: Apply relevance threshold cutoff.\n * Drop sections whose score falls below scoreFloorRatio * maxScore.\n */\nfunction applyScoreFloor(\n  sections: FileSection[],\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): FileSection[] {\n  if (sections.length === 0) return sections;\n  const maxScore = sections[0].score;\n  const floor = config.scoreFloorRatio * maxScore;\n  return sections.filter((s) => s.score >= floor);\n}\n\n/**\n * B3: Detect the \"elbow\" in the score distribution.\n * Returns the index of the last section to keep (inclusive), or null\n * if no significant elbow is found.\n *\n * Looks for the first gap where the relative drop between consecutive\n * sorted scores exceeds elbowDropRatio. Only triggers when the score\n * below the gap is less than 30% of the max score, preventing cuts\n * between clustered high-relevance results.\n */\nfunction findElbow(\n  scores: number[],\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): number | null {\n  if (scores.length <= 1) return null;\n  const maxScore = scores[0];\n  for (let i = 0; i < scores.length - 1; i++) {\n    const drop = (scores[i] - scores[i + 1]) / scores[i];\n    if (drop > config.elbowDropRatio && scores[i + 1] < 0.3 * maxScore) {\n      return i;\n    }\n  }\n  return null;\n}\n\n/**\n * B3: Apply elbow detection to trim sections.\n * Only applies when there are 3+ sections to avoid over-trimming small\n * result sets where graph expansion may be genuinely useful.\n */\nfunction applyElbow(\n  sections: FileSection[],\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): FileSection[] {\n  if (sections.length < 3) return sections;\n  const scores = sections.map((s) => s.score);\n  const elbowIdx = findElbow(scores, config);\n  if (elbowIdx !== null) {\n    return sections.slice(0, elbowIdx + 1);\n  }\n  return sections;\n}\n\n/**\n * Read source lines from a file, returning the specified range.\n */\nfunction readSourceLines(\n  rootDir: string,\n  filePath: string,\n  startLine: number,\n  endLine: number,\n): string | null {\n  const absPath = resolve(rootDir, filePath);\n  try {\n    const content = readFileSync(absPath, \"utf-8\");\n    const lines = content.split(\"\\n\");\n    // Lines are 1-indexed in the database\n    const start = Math.max(0, startLine - 1);\n    const end = Math.min(lines.length, endLine);\n    return lines.slice(start, end).join(\"\\n\");\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Render a file section with header and source code.\n */\nfunction renderSection(rootDir: string, section: FileSection): string {\n  const symbolNames = section.symbols\n    .map((s) => s.symbol.name)\n    .filter((name, i, arr) => arr.indexOf(name) === i)\n    .slice(0, 5);\n\n  const nameList = symbolNames.join(\", \");\n  const header = `── ${section.filePath}:${section.startLine}-${section.endLine} (${nameList}) ──`;\n\n  const source = readSourceLines(\n    rootDir,\n    section.filePath,\n    section.startLine,\n    section.endLine,\n  );\n\n  if (source === null) {\n    return `${header}\\n[file not readable]`;\n  }\n\n  return `${header}\\n${source}`;\n}\n\n// ── core query logic (shared by CLI and MCP server) ───────────────────\n\nexport function runQueryCore(\n  root: string,\n  term: string,\n  budget: number,\n  depth: number,\n  options?: { stats?: boolean; config?: ScoringConfig },\n): string {\n  const dbPath = resolve(root, \".codefocus\", \"index.db\");\n\n  if (!existsSync(dbPath)) {\n    throw new Error(\n      `no index found at ${dbPath}\\nRun 'codefocus index --root ${root}' first.`,\n    );\n  }\n\n  const config = options?.config ?? loadScoringConfig(root);\n\n  const db = new IndexDatabase(dbPath);\n  try {\n    // 1. Search + graph expansion\n    const scoredSymbols = searchAndExpand(db, term, depth, root, config);\n\n    if (scoredSymbols.length === 0) {\n      return `No results found for \"${term}\"`;\n    }\n\n    // 2. Compute file PageRank\n    const pagerankScores = computeFilePagerank(db);\n\n    // 3. Group by file and rank\n    const allSections = groupByFile(scoredSymbols, pagerankScores);\n\n    // 4. Phase B: Apply relevance thresholds\n    // B1: Score floor — drop sections below scoreFloorRatio * maxScore\n    const afterFloor = applyScoreFloor(allSections, config);\n    // B3: Elbow detection — find natural gap in score distribution\n    const sections = applyElbow(afterFloor, config);\n\n    // 5. Render with token budget enforcement + B2 marginal value\n    const enc = getEncoding(\"cl100k_base\");\n    const blocks: string[] = [];\n    let tokenCount = 0;\n    let totalSymbols = 0;\n    let truncated = false;\n\n    for (const section of sections) {\n      const block = renderSection(root, section);\n      const blockTokens = enc.encode(block).length;\n\n      // B2: Marginal value per token — stop when value density is too low.\n      // Only apply after the first block (always include the top result).\n      if (blocks.length > 0 && blockTokens > 0) {\n        const marginalValue = section.score / blockTokens;\n        if (marginalValue < config.minMarginalValue) {\n          break;\n        }\n      }\n\n      if (tokenCount + blockTokens <= budget) {\n        blocks.push(block);\n        tokenCount += blockTokens;\n        totalSymbols += section.symbols.length;\n        continue;\n      }\n\n      // Try partial fit — include header + as many source lines as budget allows\n      const lines = block.split(\"\\n\");\n      let partial = lines[0];\n      let partialTokens = enc.encode(partial).length;\n\n      if (tokenCount + partialTokens > budget) {\n        truncated = true;\n        break;\n      }\n\n      for (let i = 1; i < lines.length; i++) {\n        const candidate = partial + \"\\n\" + lines[i];\n        const candidateTokens = enc.encode(candidate).length;\n        if (tokenCount + candidateTokens > budget) break;\n        partial = candidate;\n        partialTokens = candidateTokens;\n      }\n\n      blocks.push(partial);\n      tokenCount += partialTokens;\n      totalSymbols += section.symbols.length;\n      truncated = true;\n      break;\n    }\n\n    // Compute confidence from score distribution (B3 enhancement)\n    // Use the post-threshold sections for confidence calculation\n    const allScores = sections.map((s) => s.score).sort((a, b) => b - a);\n    const topScore = allScores[0] ?? 0;\n    const medianScore =\n      allScores.length > 0\n        ? allScores[Math.floor(allScores.length / 2)]\n        : 0;\n    const hasExact = sections.some((s) =>\n      s.symbols.some((ss) => ss.matchType === \"exact\"),\n    );\n    // B3: Enhanced confidence — factor in score concentration\n    // High: exact match and scores are tightly clustered (elbow removed noise)\n    // Low: no exact matches or scores are very spread out\n    const scoreRange = allScores.length > 1\n      ? (allScores[0] - allScores[allScores.length - 1]) / allScores[0]\n      : 0;\n    const confidence: \"high\" | \"medium\" | \"low\" =\n      hasExact && (medianScore >= 0.3 || sections.length <= 2)\n        ? \"high\"\n        : !hasExact || medianScore < 0.1\n          ? scoreRange < 0.3 ? \"medium\" : \"low\"\n          : \"medium\";\n\n    // Build output string\n    const output: string[] = [];\n\n    // YAML front matter\n    const shown = blocks.length;\n    const frontMatter = [\n      \"---\",\n      `query: ${term}`,\n      `tokens: ${tokenCount}`,\n      `files: ${shown}`,\n      `symbols: ${totalSymbols}`,\n      `truncated: ${truncated}`,\n      `confidence: ${confidence}`,\n      `top_score: ${topScore.toFixed(2)}`,\n      `median_score: ${medianScore.toFixed(2)}`,\n      \"---\",\n    ].join(\"\\n\");\n\n    output.push(frontMatter);\n    output.push(\"\");\n    output.push(blocks.join(\"\\n\\n\"));\n\n    // --stats: verbose scoring detail\n    if (options?.stats) {\n      output.push(\"\");\n      const totalCandidates = allSections.length;\n      const afterFloorCount = afterFloor.length;\n      const afterElbowCount = sections.length;\n      if (totalCandidates > afterElbowCount) {\n        output.push(\n          `[stats] filtering: ${totalCandidates} candidates → ${afterFloorCount} after B1 floor → ${afterElbowCount} after B3 elbow`,\n        );\n      }\n      for (const section of sections.slice(0, shown)) {\n        const topSym = section.symbols.reduce(\n          (best, s) => (s.score > best.score ? s : best),\n          section.symbols[0],\n        );\n        const block = renderSection(root, section);\n        const blockTokens = enc.encode(block).length;\n        const marginal = blockTokens > 0\n          ? (section.score / blockTokens).toFixed(6)\n          : \"N/A\";\n        output.push(\n          `[stats] ${section.filePath.padEnd(40)} score=${section.score.toFixed(2)}  match=${topSym.matchType.padEnd(8)} depth=${topSym.depth}  value/tok=${marginal}`,\n        );\n      }\n      const p25 =\n        allScores.length > 0\n          ? allScores[Math.floor(allScores.length * 0.75)]\n          : 0;\n      const minScore = allScores[allScores.length - 1] ?? 0;\n      output.push(\n        `[stats] score distribution: max=${topScore.toFixed(2)} median=${medianScore.toFixed(2)} p25=${p25.toFixed(2)} min=${minScore.toFixed(2)}`,\n      );\n    }\n\n    // Compact footer for backward compatibility with benchmark parsing\n    const total = sections.length;\n    const parts = [\n      `[query] ${shown} files, ${totalSymbols} symbols, ~${tokenCount} tokens`,\n    ];\n    if (truncated) {\n      parts.push(`(budget: ${budget}, truncated)`);\n    }\n    if (total > shown) {\n      parts.push(`(${total - shown} more files not shown)`);\n    }\n    output.push(`\\n${parts.join(\" \")}`);\n\n    return output.join(\"\\n\");\n  } finally {\n    db.close();\n  }\n}\n\n// ── command entry point ────────────────────────────────────────────────\n\nexport async function runQuery(\n  positional: string[],\n  flags: Record<string, string | boolean>,\n): Promise<void> {\n  if (flags.help) {\n    console.log(`codefocus query — Search and return ranked code context\n\nUsage: codefocus query <search-term> [options]\n\nOptions:\n  --budget <tokens>  Token budget for output (default: 8000)\n  --depth <n>        Max graph traversal depth (default: 2)\n  --root <path>      Root directory of indexed project (default: auto-detect)\n  --stats            Show verbose scoring detail per section\n  --help             Show this help message\n\nExamples:\n  codefocus query handleSync\n  codefocus query Calculator --budget 4000\n  codefocus query \"runIndex\" --depth 3`);\n    return;\n  }\n\n  const term = positional[0];\n  if (!term) {\n    console.error(\"Error: query requires a search term\");\n    process.exitCode = 2;\n    return;\n  }\n\n  const root = resolveRoot(flags.root);\n  const config = loadScoringConfig(root);\n\n  const budget = parseInt(String(flags.budget || String(config.defaultBudget)), 10);\n  if (isNaN(budget) || budget <= 0) {\n    console.error(\"Error: --budget must be a positive integer\");\n    process.exitCode = 2;\n    return;\n  }\n\n  const depth = parseInt(String(flags.depth || String(config.defaultDepth)), 10);\n  if (isNaN(depth) || depth < 0) {\n    console.error(\"Error: --depth must be a non-negative integer\");\n    process.exitCode = 2;\n    return;\n  }\n\n  const result = runQueryCore(root, term, budget, depth, {\n    stats: !!flags.stats,\n    config,\n  });\n  console.log(result);\n}\n","import { existsSync, readFileSync } from \"node:fs\";\nimport { resolve } from \"node:path\";\n\n// ── scoring config types ──────────────────────────────────────────────\n\nexport interface ScoringConfig {\n  /** B1: Drop sections scoring below this fraction of the top score (0-1) */\n  scoreFloorRatio: number;\n  /** B3: Relative drop between consecutive scores that signals an elbow (0-1) */\n  elbowDropRatio: number;\n  /** B2: Minimum marginal value (score / tokens) to include a section */\n  minMarginalValue: number;\n  /** A1: TF boost formula — \"log2\" uses log2(1 + count) */\n  tfBoostFormula: \"log2\";\n  /** A2: Multiplier for files containing a symbol whose name matches the term */\n  symbolProximityBoost: number;\n  /** Graph edge weight for import references */\n  importEdgeWeight: number;\n  /** Graph edge weight for type_ref references */\n  typeRefWeight: number;\n  /** Default token budget for query output */\n  defaultBudget: number;\n  /** Default graph traversal depth */\n  defaultDepth: number;\n}\n\n// ── defaults ──────────────────────────────────────────────────────────\n\nexport const DEFAULT_SCORING_CONFIG: Readonly<ScoringConfig> = {\n  scoreFloorRatio: 0.20,\n  elbowDropRatio: 0.60,\n  minMarginalValue: 0.00003,\n  tfBoostFormula: \"log2\",\n  symbolProximityBoost: 1.5,\n  importEdgeWeight: 0.4,\n  typeRefWeight: 0.2,\n  defaultBudget: 8000,\n  defaultDepth: 2,\n};\n\n// ── config file resolution ────────────────────────────────────────────\n\nconst CONFIG_FILENAMES = [\n  \".codefocus/config.json\",\n  \"codefocus.config.json\",\n] as const;\n\n/**\n * Load scoring config for a project. Looks for config files in:\n *   1. `.codefocus/config.json`\n *   2. `codefocus.config.json`\n *\n * Any keys found in the `scoring` object override the defaults.\n * Throws on invalid JSON, unknown keys, wrong types, or out-of-bounds values.\n */\nexport function loadScoringConfig(rootDir: string): ScoringConfig {\n  for (const filename of CONFIG_FILENAMES) {\n    const configPath = resolve(rootDir, filename);\n    if (!existsSync(configPath)) continue;\n\n    let raw: string;\n    try {\n      raw = readFileSync(configPath, \"utf-8\");\n    } catch (err) {\n      throw new Error(\n        `Cannot read config file ${configPath}: ${err instanceof Error ? err.message : String(err)}`,\n      );\n    }\n\n    let parsed: unknown;\n    try {\n      parsed = JSON.parse(raw);\n    } catch {\n      throw new Error(\n        `Invalid JSON in ${configPath}`,\n      );\n    }\n\n    if (parsed && typeof parsed === \"object\" && \"scoring\" in parsed) {\n      const scoring = (parsed as Record<string, unknown>).scoring;\n      if (typeof scoring !== \"object\" || scoring === null) {\n        throw new Error(\n          `\"scoring\" in ${configPath} must be an object`,\n        );\n      }\n      return mergeConfig(scoring as Record<string, unknown>, configPath);\n    }\n\n    // Config file exists but has no \"scoring\" key — use defaults\n    return { ...DEFAULT_SCORING_CONFIG };\n  }\n\n  return { ...DEFAULT_SCORING_CONFIG };\n}\n\n// ── parameter bounds ──────────────────────────────────────────────────\n\ninterface ParamBound {\n  min: number;\n  max: number;\n  integer?: boolean;\n  description: string;\n}\n\nconst PARAM_BOUNDS: Record<string, ParamBound> = {\n  scoreFloorRatio:      { min: 0, max: 1, description: \"B1 score floor ratio (0–1)\" },\n  elbowDropRatio:       { min: 0, max: 1, description: \"B3 elbow drop ratio (0–1)\" },\n  minMarginalValue:     { min: 0, max: 1, description: \"B2 min marginal value (0–1)\" },\n  symbolProximityBoost: { min: 1, max: 10, description: \"A2 symbol proximity multiplier (1–10)\" },\n  importEdgeWeight:     { min: 0, max: 1, description: \"import edge weight (0–1)\" },\n  typeRefWeight:        { min: 0, max: 1, description: \"type_ref edge weight (0–1)\" },\n  defaultBudget:        { min: 1, max: 100_000, integer: true, description: \"default token budget (1–100000)\" },\n  defaultDepth:         { min: 0, max: 10, integer: true, description: \"default graph depth (0–10)\" },\n};\n\n/**\n * Validate a single config value against its bounds.\n * Throws a descriptive error if the value is out of range.\n */\nfunction validateParam(\n  key: string,\n  value: unknown,\n  configPath: string,\n): number {\n  const bound = PARAM_BOUNDS[key];\n  if (!bound) {\n    throw new Error(\n      `Unknown scoring parameter \"${key}\" in ${configPath}`,\n    );\n  }\n\n  if (typeof value !== \"number\" || !isFinite(value)) {\n    throw new Error(\n      `Invalid value for \"${key}\" in ${configPath}: expected a number, got ${typeof value}`,\n    );\n  }\n\n  if (bound.integer && !Number.isInteger(value)) {\n    throw new Error(\n      `Invalid value for \"${key}\" in ${configPath}: expected an integer, got ${value}` +\n        `\\n  ${bound.description}`,\n    );\n  }\n\n  if (value < bound.min || value > bound.max) {\n    throw new Error(\n      `Out-of-bounds value for \"${key}\" in ${configPath}: ${value}` +\n        `\\n  ${bound.description}`,\n    );\n  }\n\n  return value;\n}\n\n/**\n * Merge user-provided scoring overrides with defaults.\n * Throws on unknown keys, wrong types, or out-of-bounds values.\n */\nfunction mergeConfig(\n  overrides: Record<string, unknown>,\n  configPath: string,\n): ScoringConfig {\n  const config = { ...DEFAULT_SCORING_CONFIG };\n  const knownKeys = new Set([...Object.keys(PARAM_BOUNDS), \"tfBoostFormula\"]);\n\n  for (const key of Object.keys(overrides)) {\n    if (!knownKeys.has(key)) {\n      throw new Error(\n        `Unknown scoring parameter \"${key}\" in ${configPath}` +\n          `\\n  Valid parameters: ${[...knownKeys].join(\", \")}`,\n      );\n    }\n  }\n\n  for (const key of Object.keys(PARAM_BOUNDS)) {\n    if (key in overrides) {\n      const validated = validateParam(key, overrides[key], configPath);\n      (config as Record<string, unknown>)[key] = validated;\n    }\n  }\n\n  if (\"tfBoostFormula\" in overrides) {\n    if (overrides.tfBoostFormula !== \"log2\") {\n      throw new Error(\n        `Invalid value for \"tfBoostFormula\" in ${configPath}: \"${String(overrides.tfBoostFormula)}\"` +\n          `\\n  Currently only \"log2\" is supported`,\n      );\n    }\n    config.tfBoostFormula = \"log2\";\n  }\n\n  return config;\n}\n\n/**\n * Serialize current config to JSON (for --emit-config).\n */\nexport function serializeConfig(config: ScoringConfig): string {\n  return JSON.stringify({ scoring: config }, null, 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(fts.rank / maxRank) * 0.4 : 0.2;\n\n    // Get file content to find which symbols contain the search term\n    const absPath = resolve(rootDir, fts.file_path);\n    let content: string;\n    try {\n      content = readFileSync(absPath, \"utf-8\");\n    } catch {\n      continue;\n    }\n\n    const lines = content.split(\"\\n\");\n    const termLower = term.toLowerCase();\n\n    // Find line numbers where the term appears\n    const matchingLines: number[] = [];\n    for (let i = 0; i < lines.length; i++) {\n      if (lines[i].toLowerCase().includes(termLower)) {\n        matchingLines.push(i + 1); // 1-indexed\n      }\n    }\n\n    if (matchingLines.length === 0) continue;\n\n    // A1: Weighted term frequency — boost files where the term is\n    // structurally important (many mentions) vs. incidental (1-2 mentions).\n    // Uses absolute count: log2(1 + count). Large files with many mentions\n    // score higher than small files with few, unlike density-based metrics\n    // which penalise important large files.\n    const tfBoost = Math.log2(1 + matchingLines.length);\n    normalizedScore *= tfBoost;\n\n    // A2: Symbol-name proximity boost — if any symbol in this file has a\n    // name or signature that includes the search term, the file is more\n    // relevant than one where the term only appears in code comments.\n    const fileSymbols = db.getSymbolsByFile(fts.file_path);\n    const hasSymbolNameMatch = fileSymbols.some(\n      (s) =>\n        s.name.toLowerCase().includes(termLower) ||\n        (s.signature?.toLowerCase().includes(termLower) ?? false),\n    );\n    if (hasSymbolNameMatch) {\n      normalizedScore *= config.symbolProximityBoost;\n    }\n\n    // Get symbols in this file and score by proximity\n    for (const sym of fileSymbols) {\n      if (!sym.id) continue;\n\n      // Check if any match is within this symbol's line range\n      const containsMatch = matchingLines.some(\n        (line) => line >= sym.start_line && line <= sym.end_line,\n      );\n\n      if (containsMatch) {\n        // Match is inside this symbol's body — high relevance\n        results.push({\n          symbol: sym,\n          score: normalizedScore,\n          matchType: \"contains\" as const,\n          depth: 0,\n        });\n      }\n    }\n  }\n\n  return results;\n}\n\n/**\n * Search for symbols matching the term, then expand via graph traversal\n * up to `maxDepth` hops.\n */\nfunction searchAndExpand(\n  db: IndexDatabase,\n  term: string,\n  maxDepth: number,\n  rootDir: string,\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): ScoredSymbol[] {\n  const scored = new Map<number, ScoredSymbol>();\n\n  // Phase 1: Direct symbol name matches\n  const directMatches = db.findSymbols(term);\n\n  for (const sym of directMatches) {\n    if (!sym.id) continue;\n    const isExact = sym.name.toLowerCase() === term.toLowerCase();\n    scored.set(sym.id, {\n      symbol: sym,\n      score: isExact ? 1.0 : 0.5,\n      matchType: isExact ? \"exact\" : \"contains\",\n      depth: 0,\n    });\n  }\n\n  // Phase 1b: FTS5 full-text content search (secondary seed)\n  // Use only when symbol-name matching returns no results\n  if (scored.size === 0) {\n    const ftsSymbols = ftsSeededSymbols(db, term, rootDir, config);\n    for (const ss of ftsSymbols) {\n      if (ss.symbol.id && !scored.has(ss.symbol.id)) {\n        scored.set(ss.symbol.id, ss);\n      }\n    }\n  }\n\n  // Phase 2: Graph expansion (BFS) with edge-weight scoring\n  // Weight by reference type: import (0.4) > type_ref (0.2)\n  // Dampen high-degree hub nodes: multiply score by 1/sqrt(fileDegree)\n  // Uses total degree (in + out) to catch both importers (cli.ts) and\n  // importees (db.ts) that act as hubs\n  if (maxDepth > 0) {\n    // Precompute file-level total degree (in + out) from import graph\n    const fileDegree = new Map<string, number>();\n    for (const edge of db.getFileImportEdges()) {\n      fileDegree.set(\n        edge.source_file,\n        (fileDegree.get(edge.source_file) ?? 0) + 1,\n      );\n      fileDegree.set(\n        edge.target_file,\n        (fileDegree.get(edge.target_file) ?? 0) + 1,\n      );\n    }\n\n    let frontier = new Set(scored.keys());\n\n    for (let hop = 1; hop <= maxDepth && frontier.size > 0; hop++) {\n      const nextFrontier = new Set<number>();\n\n      for (const symbolId of frontier) {\n        // Walk outgoing references (what this symbol depends on)\n        const outRefs = db.getOutgoingReferences(symbolId);\n        for (const ref of outRefs) {\n          if (!scored.has(ref.target_id)) {\n            const sym = db.getSymbolById(ref.target_id);\n            if (sym) {\n              const baseWeight =\n                ref.ref_type === \"import\" ? config.importEdgeWeight : config.typeRefWeight;\n              const deg = fileDegree.get(ref.target_file) ?? 0;\n              const hubDampening =\n                deg > 1 ? 1 / Math.sqrt(deg) : 1;\n              const graphScore = (baseWeight / hop) * hubDampening;\n\n              scored.set(ref.target_id, {\n                symbol: sym,\n                score: graphScore,\n                matchType: \"graph\",\n                depth: hop,\n              });\n              nextFrontier.add(ref.target_id);\n            }\n          }\n        }\n\n        // Walk incoming references (what depends on this symbol)\n        const inRefs = db.getIncomingReferences(symbolId);\n        for (const ref of inRefs) {\n          if (!scored.has(ref.source_id)) {\n            const sym = db.getSymbolById(ref.source_id);\n            if (sym) {\n              const baseWeight =\n                ref.ref_type === \"import\" ? config.importEdgeWeight : config.typeRefWeight;\n              const deg = fileDegree.get(ref.source_file) ?? 0;\n              const hubDampening =\n                deg > 1 ? 1 / Math.sqrt(deg) : 1;\n              const graphScore = (baseWeight / hop) * hubDampening;\n\n              scored.set(ref.source_id, {\n                symbol: sym,\n                score: graphScore,\n                matchType: \"graph\",\n                depth: hop,\n              });\n              nextFrontier.add(ref.source_id);\n            }\n          }\n        }\n      }\n\n      frontier = nextFrontier;\n    }\n  }\n\n  return Array.from(scored.values());\n}\n\n/**\n * Group scored symbols by file and compute file-level sections.\n */\nfunction groupByFile(\n  scoredSymbols: ScoredSymbol[],\n  pagerankScores: Map<string, number>,\n): FileSection[] {\n  const fileMap = new Map<string, ScoredSymbol[]>();\n\n  for (const ss of scoredSymbols) {\n    const fp = ss.symbol.file_path;\n    if (!fileMap.has(fp)) fileMap.set(fp, []);\n    fileMap.get(fp)!.push(ss);\n  }\n\n  const sections: FileSection[] = [];\n\n  for (const [filePath, symbols] of fileMap) {\n    symbols.sort((a, b) => a.symbol.start_line - b.symbol.start_line);\n\n    // File score: max symbol score, with pagerank boost only for direct matches\n    // Graph-expanded files should not get pagerank boost (it undoes hub dampening)\n    const maxSymScore = Math.max(...symbols.map((s) => s.score));\n    const hasDirectMatch = symbols.some((s) => s.matchType !== \"graph\");\n    const prScore = hasDirectMatch ? (pagerankScores.get(filePath) ?? 0) : 0;\n    const fileScore = maxSymScore + prScore;\n\n    // Combined line range (union of all symbol ranges)\n    const startLine = Math.min(...symbols.map((s) => s.symbol.start_line));\n    const endLine = Math.max(...symbols.map((s) => s.symbol.end_line));\n\n    sections.push({\n      filePath,\n      symbols,\n      score: fileScore,\n      startLine,\n      endLine,\n    });\n  }\n\n  // Sort by score descending, then alphabetically\n  sections.sort(\n    (a, b) => b.score - a.score || a.filePath.localeCompare(b.filePath),\n  );\n\n  return sections;\n}\n\n/**\n * B1: Apply relevance threshold cutoff.\n * Drop sections whose score falls below scoreFloorRatio * maxScore.\n */\nfunction applyScoreFloor(\n  sections: FileSection[],\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): FileSection[] {\n  if (sections.length === 0) return sections;\n  const maxScore = sections[0].score;\n  const floor = config.scoreFloorRatio * maxScore;\n  return sections.filter((s) => s.score >= floor);\n}\n\n/**\n * B3: Detect the \"elbow\" in the score distribution.\n * Returns the index of the last section to keep (inclusive), or null\n * if no significant elbow is found.\n *\n * Looks for the first gap where the relative drop between consecutive\n * sorted scores exceeds elbowDropRatio. Only triggers when the score\n * below the gap is less than 30% of the max score, preventing cuts\n * between clustered high-relevance results.\n */\nfunction findElbow(\n  scores: number[],\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): number | null {\n  if (scores.length <= 1) return null;\n  const maxScore = scores[0];\n  for (let i = 0; i < scores.length - 1; i++) {\n    const drop = (scores[i] - scores[i + 1]) / scores[i];\n    if (drop > config.elbowDropRatio && scores[i + 1] < 0.3 * maxScore) {\n      return i;\n    }\n  }\n  return null;\n}\n\n/**\n * B3: Apply elbow detection to trim sections.\n * Only applies when there are 3+ sections to avoid over-trimming small\n * result sets where graph expansion may be genuinely useful.\n */\nfunction applyElbow(\n  sections: FileSection[],\n  config: ScoringConfig = DEFAULT_SCORING_CONFIG,\n): FileSection[] {\n  if (sections.length < 3) return sections;\n  const scores = sections.map((s) => s.score);\n  const elbowIdx = findElbow(scores, config);\n  if (elbowIdx !== null) {\n    return sections.slice(0, elbowIdx + 1);\n  }\n  return sections;\n}\n\n/**\n * Read source lines from a file, returning the specified range.\n */\nfunction readSourceLines(\n  rootDir: string,\n  filePath: string,\n  startLine: number,\n  endLine: number,\n): string | null {\n  const absPath = resolve(rootDir, filePath);\n  try {\n    const content = readFileSync(absPath, \"utf-8\");\n    const lines = content.split(\"\\n\");\n    // Lines are 1-indexed in the database\n    const start = Math.max(0, startLine - 1);\n    const end = Math.min(lines.length, endLine);\n    return lines.slice(start, end).join(\"\\n\");\n  } catch {\n    return null;\n  }\n}\n\n/**\n * Render a file section with header and source code.\n */\nfunction renderSection(rootDir: string, section: FileSection): string {\n  const symbolNames = section.symbols\n    .map((s) => s.symbol.name)\n    .filter((name, i, arr) => arr.indexOf(name) === i)\n    .slice(0, 5);\n\n  const nameList = symbolNames.join(\", \");\n  const header = `── ${section.filePath}:${section.startLine}-${section.endLine} (${nameList}) ──`;\n\n  const source = readSourceLines(\n    rootDir,\n    section.filePath,\n    section.startLine,\n    section.endLine,\n  );\n\n  if (source === null) {\n    return `${header}\\n[file not readable]`;\n  }\n\n  return `${header}\\n${source}`;\n}\n\n// ── core query logic (shared by CLI and MCP server) ───────────────────\n\nexport function runQueryCore(\n  root: string,\n  term: string,\n  budget: number,\n  depth: number,\n  options?: { stats?: boolean; config?: ScoringConfig },\n): string {\n  const dbPath = resolve(root, \".codefocus\", \"index.db\");\n\n  if (!existsSync(dbPath)) {\n    throw new Error(\n      `no index found at ${dbPath}\\nRun 'codefocus index --root ${root}' first.`,\n    );\n  }\n\n  const config = options?.config ?? loadScoringConfig(root);\n\n  const db = new IndexDatabase(dbPath);\n  try {\n    // 1. Search + graph expansion\n    const scoredSymbols = searchAndExpand(db, term, depth, root, config);\n\n    if (scoredSymbols.length === 0) {\n      return `No results found for \"${term}\"`;\n    }\n\n    // 2. Compute file PageRank\n    const pagerankScores = computeFilePagerank(db);\n\n    // 3. Group by file and rank\n    const allSections = groupByFile(scoredSymbols, pagerankScores);\n\n    // 4. Phase B: Apply relevance thresholds\n    // B1: Score floor — drop sections below scoreFloorRatio * maxScore\n    const afterFloor = applyScoreFloor(allSections, config);\n    // B3: Elbow detection — find natural gap in score distribution\n    const sections = applyElbow(afterFloor, config);\n\n    // 5. Render with token budget enforcement + B2 marginal value\n    const enc = getEncoding(\"cl100k_base\");\n    const blocks: string[] = [];\n    let tokenCount = 0;\n    let totalSymbols = 0;\n    let truncated = false;\n\n    for (const section of sections) {\n      const block = renderSection(root, section);\n      const blockTokens = enc.encode(block).length;\n\n      // B2: Marginal value per token — stop when value density is too low.\n      // Only apply after the first block (always include the top result).\n      if (blocks.length > 0 && blockTokens > 0) {\n        const marginalValue = section.score / blockTokens;\n        if (marginalValue < config.minMarginalValue) {\n          break;\n        }\n      }\n\n      if (tokenCount + blockTokens <= budget) {\n        blocks.push(block);\n        tokenCount += blockTokens;\n        totalSymbols += section.symbols.length;\n        continue;\n      }\n\n      // Try partial fit — include header + as many source lines as budget allows\n      const lines = block.split(\"\\n\");\n      let partial = lines[0];\n      let partialTokens = enc.encode(partial).length;\n\n      if (tokenCount + partialTokens > budget) {\n        truncated = true;\n        break;\n      }\n\n      for (let i = 1; i < lines.length; i++) {\n        const candidate = partial + \"\\n\" + lines[i];\n        const candidateTokens = enc.encode(candidate).length;\n        if (tokenCount + candidateTokens > budget) break;\n        partial = candidate;\n        partialTokens = candidateTokens;\n      }\n\n      blocks.push(partial);\n      tokenCount += partialTokens;\n      totalSymbols += section.symbols.length;\n      truncated = true;\n      break;\n    }\n\n    // Compute confidence from score distribution (B3 enhancement)\n    // Use the post-threshold sections for confidence calculation\n    const allScores = sections.map((s) => s.score).sort((a, b) => b - a);\n    const topScore = allScores[0] ?? 0;\n    const medianScore =\n      allScores.length > 0\n        ? allScores[Math.floor(allScores.length / 2)]\n        : 0;\n    const hasExact = sections.some((s) =>\n      s.symbols.some((ss) => ss.matchType === \"exact\"),\n    );\n    // B3: Enhanced confidence — factor in score concentration\n    // High: exact match and scores are tightly clustered (elbow removed noise)\n    // Low: no exact matches or scores are very spread out\n    const scoreRange = allScores.length > 1\n      ? (allScores[0] - allScores[allScores.length - 1]) / allScores[0]\n      : 0;\n    const confidence: \"high\" | \"medium\" | \"low\" =\n      hasExact && (medianScore >= 0.3 || sections.length <= 2)\n        ? \"high\"\n        : !hasExact || medianScore < 0.1\n          ? scoreRange < 0.3 ? \"medium\" : \"low\"\n          : \"medium\";\n\n    // Build output string\n    const output: string[] = [];\n\n    // YAML front matter\n    const shown = blocks.length;\n    const frontMatter = [\n      \"---\",\n      `query: ${term}`,\n      `tokens: ${tokenCount}`,\n      `files: ${shown}`,\n      `symbols: ${totalSymbols}`,\n      `truncated: ${truncated}`,\n      `confidence: ${confidence}`,\n      `top_score: ${topScore.toFixed(2)}`,\n      `median_score: ${medianScore.toFixed(2)}`,\n      \"---\",\n    ].join(\"\\n\");\n\n    output.push(frontMatter);\n    output.push(\"\");\n    output.push(blocks.join(\"\\n\\n\"));\n\n    // --stats: verbose scoring detail\n    if (options?.stats) {\n      output.push(\"\");\n      const totalCandidates = allSections.length;\n      const afterFloorCount = afterFloor.length;\n      const afterElbowCount = sections.length;\n      if (totalCandidates > afterElbowCount) {\n        output.push(\n          `[stats] filtering: ${totalCandidates} candidates → ${afterFloorCount} after B1 floor → ${afterElbowCount} after B3 elbow`,\n        );\n      }\n      for (const section of sections.slice(0, shown)) {\n        const topSym = section.symbols.reduce(\n          (best, s) => (s.score > best.score ? s : best),\n          section.symbols[0],\n        );\n        const block = renderSection(root, section);\n        const blockTokens = enc.encode(block).length;\n        const marginal = blockTokens > 0\n          ? (section.score / blockTokens).toFixed(6)\n          : \"N/A\";\n        output.push(\n          `[stats] ${section.filePath.padEnd(40)} score=${section.score.toFixed(2)}  match=${topSym.matchType.padEnd(8)} depth=${topSym.depth}  value/tok=${marginal}`,\n        );\n      }\n      const p25 =\n        allScores.length > 0\n          ? allScores[Math.floor(allScores.length * 0.75)]\n          : 0;\n      const minScore = allScores[allScores.length - 1] ?? 0;\n      output.push(\n        `[stats] score distribution: max=${topScore.toFixed(2)} median=${medianScore.toFixed(2)} p25=${p25.toFixed(2)} min=${minScore.toFixed(2)}`,\n      );\n    }\n\n    // Compact footer for backward compatibility with benchmark parsing\n    const total = sections.length;\n    const parts = [\n      `[query] ${shown} files, ${totalSymbols} symbols, ~${tokenCount} tokens`,\n    ];\n    if (truncated) {\n      parts.push(`(budget: ${budget}, truncated)`);\n    }\n    if (total > shown) {\n      parts.push(`(${total - shown} more files not shown)`);\n    }\n    output.push(`\\n${parts.join(\" \")}`);\n\n    return output.join(\"\\n\");\n  } finally {\n    db.close();\n  }\n}\n\n// ── command entry point ────────────────────────────────────────────────\n\nexport async function runQuery(\n  positional: string[],\n  flags: Record<string, string | boolean>,\n): Promise<void> {\n  if (flags.help) {\n    console.log(`codefocus query — Search and return ranked code context\n\nUsage: codefocus query <search-term> [options]\n\nOptions:\n  --budget <tokens>  Token budget for output (default: 8000)\n  --depth <n>        Max graph traversal depth (default: 2)\n  --root <path>      Root directory of indexed project (default: auto-detect)\n  --stats            Show verbose scoring detail per section\n  --help             Show this help message\n\nExamples:\n  codefocus query handleSync\n  codefocus query Calculator --budget 4000\n  codefocus query \"runIndex\" --depth 3`);\n    return;\n  }\n\n  const term = positional[0];\n  if (!term) {\n    console.error(\"Error: query requires a search term\");\n    process.exitCode = 2;\n    return;\n  }\n\n  const root = resolveRoot(flags.root);\n  const config = loadScoringConfig(root);\n\n  const budget = parseInt(String(flags.budget || String(config.defaultBudget)), 10);\n  if (isNaN(budget) || budget <= 0) {\n    console.error(\"Error: --budget must be a positive integer\");\n    process.exitCode = 2;\n    return;\n  }\n\n  const depth = parseInt(String(flags.depth || String(config.defaultDepth)), 10);\n  if (isNaN(depth) || depth < 0) {\n    console.error(\"Error: --depth must be a non-negative integer\");\n    process.exitCode = 2;\n    return;\n  }\n\n  const result = runQueryCore(root, term, budget, depth, {\n    stats: !!flags.stats,\n    config,\n  });\n  console.log(result);\n}\n","import { existsSync, readFileSync } from \"node:fs\";\nimport { resolve } from \"node:path\";\n\n// ── scoring config types ──────────────────────────────────────────────\n\nexport interface ScoringConfig {\n  /** B1: Drop sections scoring below this fraction of the top score (0-1) */\n  scoreFloorRatio: number;\n  /** B3: Relative drop between consecutive scores that signals an elbow (0-1) */\n  elbowDropRatio: number;\n  /** B2: Minimum marginal value (score / tokens) to include a section */\n  minMarginalValue: number;\n  /** A1: TF boost formula — \"log2\" uses log2(1 + count) */\n  tfBoostFormula: \"log2\";\n  /** A2: Multiplier for files containing a symbol whose name matches the term */\n  symbolProximityBoost: number;\n  /** Graph edge weight for import references */\n  importEdgeWeight: number;\n  /** Graph edge weight for type_ref references */\n  typeRefWeight: number;\n  /** Default token budget for query output */\n  defaultBudget: number;\n  /** Default graph traversal depth */\n  defaultDepth: number;\n}\n\n// ── defaults ──────────────────────────────────────────────────────────\n\nexport const DEFAULT_SCORING_CONFIG: Readonly<ScoringConfig> = {\n  scoreFloorRatio: 0.20,\n  elbowDropRatio: 0.60,\n  minMarginalValue: 0.00003,\n  tfBoostFormula: \"log2\",\n  symbolProximityBoost: 1.5,\n  importEdgeWeight: 0.4,\n  typeRefWeight: 0.2,\n  defaultBudget: 8000,\n  defaultDepth: 2,\n};\n\n// ── config file resolution ────────────────────────────────────────────\n\nconst CONFIG_FILENAMES = [\n  \".codefocus/config.json\",\n  \"codefocus.config.json\",\n] as const;\n\n/**\n * Load scoring config for a project. Looks for config files in:\n *   1. `.codefocus/config.json`\n *   2. `codefocus.config.json`\n *\n * Any keys found in the `scoring` object override the defaults.\n * Throws on invalid JSON, unknown keys, wrong types, or out-of-bounds values.\n */\nexport function loadScoringConfig(rootDir: string): ScoringConfig {\n  for (const filename of CONFIG_FILENAMES) {\n    const configPath = resolve(rootDir, filename);\n    if (!existsSync(configPath)) continue;\n\n    let raw: string;\n    try {\n      raw = readFileSync(configPath, \"utf-8\");\n    } catch (err) {\n      throw new Error(\n        `Cannot read config file ${configPath}: ${err instanceof Error ? err.message : String(err)}`,\n      );\n    }\n\n    let parsed: unknown;\n    try {\n      parsed = JSON.parse(raw);\n    } catch {\n      throw new Error(\n        `Invalid JSON in ${configPath}`,\n      );\n    }\n\n    if (parsed && typeof parsed === \"object\" && \"scoring\" in parsed) {\n      const scoring = (parsed as Record<string, unknown>).scoring;\n      if (typeof scoring !== \"object\" || scoring === null) {\n        throw new Error(\n          `\"scoring\" in ${configPath} must be an object`,\n        );\n      }\n      return mergeConfig(scoring as Record<string, unknown>, configPath);\n    }\n\n    // Config file exists but has no \"scoring\" key — use defaults\n    return { ...DEFAULT_SCORING_CONFIG };\n  }\n\n  return { ...DEFAULT_SCORING_CONFIG };\n}\n\n// ── parameter bounds ──────────────────────────────────────────────────\n\ninterface ParamBound {\n  min: number;\n  max: number;\n  integer?: boolean;\n  description: string;\n}\n\nconst PARAM_BOUNDS: Record<string, ParamBound> = {\n  scoreFloorRatio:      { min: 0, max: 1, description: \"B1 score floor ratio (0–1)\" },\n  elbowDropRatio:       { min: 0, max: 1, description: \"B3 elbow drop ratio (0–1)\" },\n  minMarginalValue:     { min: 0, max: 1, description: \"B2 min marginal value (0–1)\" },\n  symbolProximityBoost: { min: 1, max: 10, description: \"A2 symbol proximity multiplier (1–10)\" },\n  importEdgeWeight:     { min: 0, max: 1, description: \"import edge weight (0–1)\" },\n  typeRefWeight:        { min: 0, max: 1, description: \"type_ref edge weight (0–1)\" },\n  defaultBudget:        { min: 1, max: 100_000, integer: true, description: \"default token budget (1–100000)\" },\n  defaultDepth:         { min: 0, max: 10, integer: true, description: \"default graph depth (0–10)\" },\n};\n\n/**\n * Validate a single config value against its bounds.\n * Throws a descriptive error if the value is out of range.\n */\nfunction validateParam(\n  key: string,\n  value: unknown,\n  configPath: string,\n): number {\n  const bound = PARAM_BOUNDS[key];\n  if (!bound) {\n    throw new Error(\n      `Unknown scoring parameter \"${key}\" in ${configPath}`,\n    );\n  }\n\n  if (typeof value !== \"number\" || !isFinite(value)) {\n    throw new Error(\n      `Invalid value for \"${key}\" in ${configPath}: expected a number, got ${typeof value}`,\n    );\n  }\n\n  if (bound.integer && !Number.isInteger(value)) {\n    throw new Error(\n      `Invalid value for \"${key}\" in ${configPath}: expected an integer, got ${value}` +\n        `\\n  ${bound.description}`,\n    );\n  }\n\n  if (value < bound.min || value > bound.max) {\n    throw new Error(\n      `Out-of-bounds value for \"${key}\" in ${configPath}: ${value}` +\n        `\\n  ${bound.description}`,\n    );\n  }\n\n  return value;\n}\n\n/**\n * Merge user-provided scoring overrides with defaults.\n * Throws on unknown keys, wrong types, or out-of-bounds values.\n */\nfunction mergeConfig(\n  overrides: Record<string, unknown>,\n  configPath: string,\n): ScoringConfig {\n  const config = { ...DEFAULT_SCORING_CONFIG };\n  const knownKeys = new Set([...Object.keys(PARAM_BOUNDS), \"tfBoostFormula\"]);\n\n  for (const key of Object.keys(overrides)) {\n    if (!knownKeys.has(key)) {\n      throw new Error(\n        `Unknown scoring parameter \"${key}\" in ${configPath}` +\n          `\\n  Valid parameters: ${[...knownKeys].join(\", \")}`,\n      );\n    }\n  }\n\n  for (const key of Object.keys(PARAM_BOUNDS)) {\n    if (key in overrides) {\n      const validated = validateParam(key, overrides[key], configPath);\n      (config as Record<string, unknown>)[key] = validated;\n    }\n  }\n\n  if (\"tfBoostFormula\" in overrides) {\n    if (overrides.tfBoostFormula !== \"log2\") {\n      throw new Error(\n        `Invalid value for \"tfBoostFormula\" in ${configPath}: \"${String(overrides.tfBoostFormula)}\"` +\n          `\\n  Currently only \"log2\" is supported`,\n      );\n    }\n    config.tfBoostFormula = \"log2\";\n  }\n\n  return config;\n}\n\n/**\n * Serialize current config to JSON (for --emit-config).\n */\nexport function serializeConfig(config: ScoringConfig): string {\n  return JSON.stringify({ scoring: config }, null, 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package/dist/watcher-6WHIBMPS.js

@@ -0,0 +1,72 @@
+import {
+  indexProject
+} from "./chunk-FQ3L6YEU.js";
+import "./chunk-472RLVFC.js";
+
+// src/watcher.ts
+import { extname } from "path";
+import { execFileSync } from "child_process";
+var TS_EXTENSIONS = /* @__PURE__ */ new Set([".ts", ".tsx", ".js", ".jsx"]);
+var IGNORE_PATTERNS = [
+  "**/node_modules/**",
+  "**/dist/**",
+  "**/.codefocus/**",
+  "**/__tests__/**",
+  "**/*.test.*",
+  "**/*.spec.*",
+  "**/*.d.ts"
+];
+async function startWatcher(options) {
+  const { rootDir, dbPath, onReindex, debounceMs = 300 } = options;
+  const chokidar = await import("chokidar");
+  let debounceTimer = null;
+  let isIndexing = false;
+  const watcher = chokidar.watch("**/*.{ts,tsx,js,jsx}", {
+    cwd: rootDir,
+    ignored: IGNORE_PATTERNS,
+    ignoreInitial: true,
+    persistent: true
+  });
+  function scheduleReindex() {
+    if (debounceTimer) clearTimeout(debounceTimer);
+    debounceTimer = setTimeout(async () => {
+      if (isIndexing) return;
+      isIndexing = true;
+      try {
+        const stats = await indexProject(rootDir, dbPath);
+        onReindex?.(stats);
+      } catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        console.error(`[watch] Re-index error: ${message}`);
+      } finally {
+        isIndexing = false;
+      }
+    }, debounceMs);
+  }
+  watcher.on("add", (_path) => scheduleReindex());
+  watcher.on("change", (_path) => scheduleReindex());
+  watcher.on("unlink", (_path) => scheduleReindex());
+  return {
+    close() {
+      if (debounceTimer) clearTimeout(debounceTimer);
+      watcher.close();
+    }
+  };
+}
+function getGitChangedFiles(rootDir) {
+  try {
+    const result = execFileSync("git", ["diff", "--name-only", "HEAD"], {
+      cwd: rootDir,
+      encoding: "utf-8",
+      timeout: 1e4
+    });
+    return result.trim().split("\n").filter((f) => f && TS_EXTENSIONS.has(extname(f)));
+  } catch {
+    return [];
+  }
+}
+export {
+  getGitChangedFiles,
+  startWatcher
+};
+//# sourceMappingURL=watcher-6WHIBMPS.js.map

package/dist/watcher-6WHIBMPS.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/watcher.ts"],"sourcesContent":["import { resolve, extname } from \"node:path\";\nimport { execFileSync } from \"node:child_process\";\nimport { indexProject, type IndexStats } from \"./indexer.js\";\n\nconst TS_EXTENSIONS = new Set([\".ts\", \".tsx\", \".js\", \".jsx\"]);\nconst IGNORE_PATTERNS = [\n  \"**/node_modules/**\",\n  \"**/dist/**\",\n  \"**/.codefocus/**\",\n  \"**/__tests__/**\",\n  \"**/*.test.*\",\n  \"**/*.spec.*\",\n  \"**/*.d.ts\",\n];\n\nexport interface WatcherOptions {\n  rootDir: string;\n  dbPath: string;\n  /** Callback invoked after each re-index */\n  onReindex?: (stats: IndexStats) => void;\n  /** Debounce delay in ms (default: 300) */\n  debounceMs?: number;\n}\n\nexport interface Watcher {\n  /** Stop watching and clean up */\n  close(): void;\n}\n\n/**\n * Watch for file changes and trigger incremental re-indexing.\n * Uses chokidar for reliable cross-platform file system watching.\n * Changes are debounced to avoid re-indexing on every keystroke.\n */\nexport async function startWatcher(options: WatcherOptions): Promise<Watcher> {\n  const { rootDir, dbPath, onReindex, debounceMs = 300 } = options;\n\n  const chokidar = await import(\"chokidar\");\n\n  let debounceTimer: ReturnType<typeof setTimeout> | null = null;\n  let isIndexing = false;\n\n  const watcher = chokidar.watch(\"**/*.{ts,tsx,js,jsx}\", {\n    cwd: rootDir,\n    ignored: IGNORE_PATTERNS,\n    ignoreInitial: true,\n    persistent: true,\n  });\n\n  function scheduleReindex(): void {\n    if (debounceTimer) clearTimeout(debounceTimer);\n    debounceTimer = setTimeout(async () => {\n      if (isIndexing) return;\n      isIndexing = true;\n      try {\n        const stats = await indexProject(rootDir, dbPath);\n        onReindex?.(stats);\n      } catch (err) {\n        const message = err instanceof Error ? err.message : String(err);\n        console.error(`[watch] Re-index error: ${message}`);\n      } finally {\n        isIndexing = false;\n      }\n    }, debounceMs);\n  }\n\n  watcher.on(\"add\", (_path: string) => scheduleReindex());\n  watcher.on(\"change\", (_path: string) => scheduleReindex());\n  watcher.on(\"unlink\", (_path: string) => scheduleReindex());\n\n  return {\n    close() {\n      if (debounceTimer) clearTimeout(debounceTimer);\n      watcher.close();\n    },\n  };\n}\n\n/**\n * Get list of files changed since last git commit.\n * Useful for git-hook-triggered incremental re-indexing.\n */\nexport function getGitChangedFiles(rootDir: string): string[] {\n  try {\n    const result = execFileSync(\"git\", [\"diff\", \"--name-only\", \"HEAD\"], {\n      cwd: rootDir,\n      encoding: \"utf-8\",\n      timeout: 10_000,\n    });\n\n    return result\n      .trim()\n      .split(\"\\n\")\n      .filter((f) => f && TS_EXTENSIONS.has(extname(f)));\n  } catch {\n    return [];\n  }\n}\n"],"mappings":";;;;;;AAAA,SAAkB,eAAe;AACjC,SAAS,oBAAoB;AAG7B,IAAM,gBAAgB,oBAAI,IAAI,CAAC,OAAO,QAAQ,OAAO,MAAM,CAAC;AAC5D,IAAM,kBAAkB;AAAA,EACtB;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AAAA,EACA;AACF;AAqBA,eAAsB,aAAa,SAA2C;AAC5E,QAAM,EAAE,SAAS,QAAQ,WAAW,aAAa,IAAI,IAAI;AAEzD,QAAM,WAAW,MAAM,OAAO,UAAU;AAExC,MAAI,gBAAsD;AAC1D,MAAI,aAAa;AAEjB,QAAM,UAAU,SAAS,MAAM,wBAAwB;AAAA,IACrD,KAAK;AAAA,IACL,SAAS;AAAA,IACT,eAAe;AAAA,IACf,YAAY;AAAA,EACd,CAAC;AAED,WAAS,kBAAwB;AAC/B,QAAI,cAAe,cAAa,aAAa;AAC7C,oBAAgB,WAAW,YAAY;AACrC,UAAI,WAAY;AAChB,mBAAa;AACb,UAAI;AACF,cAAM,QAAQ,MAAM,aAAa,SAAS,MAAM;AAChD,oBAAY,KAAK;AAAA,MACnB,SAAS,KAAK;AACZ,cAAM,UAAU,eAAe,QAAQ,IAAI,UAAU,OAAO,GAAG;AAC/D,gBAAQ,MAAM,2BAA2B,OAAO,EAAE;AAAA,MACpD,UAAE;AACA,qBAAa;AAAA,MACf;AAAA,IACF,GAAG,UAAU;AAAA,EACf;AAEA,UAAQ,GAAG,OAAO,CAAC,UAAkB,gBAAgB,CAAC;AACtD,UAAQ,GAAG,UAAU,CAAC,UAAkB,gBAAgB,CAAC;AACzD,UAAQ,GAAG,UAAU,CAAC,UAAkB,gBAAgB,CAAC;AAEzD,SAAO;AAAA,IACL,QAAQ;AACN,UAAI,cAAe,cAAa,aAAa;AAC7C,cAAQ,MAAM;AAAA,IAChB;AAAA,EACF;AACF;AAMO,SAAS,mBAAmB,SAA2B;AAC5D,MAAI;AACF,UAAM,SAAS,aAAa,OAAO,CAAC,QAAQ,eAAe,MAAM,GAAG;AAAA,MAClE,KAAK;AAAA,MACL,UAAU;AAAA,MACV,SAAS;AAAA,IACX,CAAC;AAED,WAAO,OACJ,KAAK,EACL,MAAM,IAAI,EACV,OAAO,CAAC,MAAM,KAAK,cAAc,IAAI,QAAQ,CAAC,CAAC,CAAC;AAAA,EACrD,QAAQ;AACN,WAAO,CAAC;AAAA,EACV;AACF;","names":[]}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@ngommans/codefocus",
-  "version": "0.1.0",
+  "version": "0.1.4",
   "description": "Smart code context aggregator — AST-powered search that returns structured, ranked code context for LLM agents",
   "type": "module",
   "bin": {

package/dist/chunk-ITVAEU6K.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/db.ts","../src/root.ts"],"sourcesContent":["import { createRequire } from \"node:module\";\nimport { mkdirSync, existsSync } from \"node:fs\";\nimport { dirname } from \"node:path\";\n\nconst require = createRequire(import.meta.url);\nconst Database = require(\"better-sqlite3\");\n\nexport interface FileRow {\n  path: string;\n  content_hash: string;\n  language: string;\n  last_indexed: number;\n}\n\nexport interface SymbolRow {\n  id?: number;\n  file_path: string;\n  name: string;\n  kind: string;\n  start_byte: number;\n  end_byte: number;\n  start_line: number;\n  end_line: number;\n  start_column: number;\n  end_column: number;\n  signature: string | null;\n}\n\nexport interface ImportRow {\n  id?: number;\n  file_path: string;\n  specifier: string;\n  source_path: string | null;\n  raw_module: string;\n  is_type_only: number;\n}\n\nexport interface ReferenceRow {\n  id?: number;\n  source_symbol_id: number;\n  target_symbol_id: number;\n  ref_type: string;\n}\n\nexport class IndexDatabase {\n  private db: InstanceType<typeof Database>;\n\n  constructor(dbPath: string) {\n    const dir = dirname(dbPath);\n    if (!existsSync(dir)) {\n      mkdirSync(dir, { recursive: true });\n    }\n    this.db = new Database(dbPath);\n    this.db.pragma(\"journal_mode = WAL\");\n    this.db.pragma(\"foreign_keys = ON\");\n    this.init();\n  }\n\n  private init(): void {\n    this.db.exec(`\n      CREATE TABLE IF NOT EXISTS files (\n        path TEXT PRIMARY KEY,\n        content_hash TEXT NOT NULL,\n        language TEXT,\n        last_indexed INTEGER\n      );\n\n      CREATE TABLE IF NOT EXISTS symbols (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        file_path TEXT NOT NULL,\n        name TEXT NOT NULL,\n        kind TEXT NOT NULL,\n        start_byte INTEGER,\n        end_byte INTEGER,\n        start_line INTEGER,\n        end_line INTEGER,\n        start_column INTEGER,\n        end_column INTEGER,\n        signature TEXT,\n        FOREIGN KEY (file_path) REFERENCES files(path) ON DELETE CASCADE\n      );\n\n      CREATE TABLE IF NOT EXISTS imports (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        file_path TEXT NOT NULL,\n        specifier TEXT NOT NULL,\n        source_path TEXT,\n        raw_module TEXT NOT NULL,\n        is_type_only INTEGER DEFAULT 0,\n        FOREIGN KEY (file_path) REFERENCES files(path) ON DELETE CASCADE\n      );\n\n      CREATE TABLE IF NOT EXISTS \"references\" (\n        id INTEGER PRIMARY KEY AUTOINCREMENT,\n        source_symbol_id INTEGER NOT NULL,\n        target_symbol_id INTEGER NOT NULL,\n        ref_type TEXT NOT NULL DEFAULT 'import',\n        FOREIGN KEY (source_symbol_id) REFERENCES symbols(id) ON DELETE CASCADE,\n        FOREIGN KEY (target_symbol_id) REFERENCES symbols(id) ON DELETE CASCADE\n      );\n\n      CREATE INDEX IF NOT EXISTS idx_symbols_file ON symbols(file_path);\n      CREATE INDEX IF NOT EXISTS idx_symbols_name ON symbols(name);\n      CREATE INDEX IF NOT EXISTS idx_symbols_kind ON symbols(kind);\n      CREATE INDEX IF NOT EXISTS idx_imports_file ON imports(file_path);\n      CREATE INDEX IF NOT EXISTS idx_imports_source ON imports(source_path);\n      CREATE INDEX IF NOT EXISTS idx_refs_source ON \"references\"(source_symbol_id);\n      CREATE INDEX IF NOT EXISTS idx_refs_target ON \"references\"(target_symbol_id);\n\n      CREATE VIRTUAL TABLE IF NOT EXISTS content_fts USING fts5(\n        file_path,\n        content,\n        tokenize='unicode61'\n      );\n    `);\n  }\n\n  clearFile(filePath: string): void {\n    this.db.prepare(\"DELETE FROM symbols WHERE file_path = ?\").run(filePath);\n    this.db.prepare(\"DELETE FROM imports WHERE file_path = ?\").run(filePath);\n    this.db.prepare(\"DELETE FROM files WHERE path = ?\").run(filePath);\n  }\n\n  clearAllImports(): void {\n    this.db.prepare(\"DELETE FROM imports\").run();\n  }\n\n  clearAllReferences(): void {\n    this.db.prepare('DELETE FROM \"references\"').run();\n  }\n\n  upsertFile(file: FileRow): void {\n    this.db\n      .prepare(\n        `INSERT OR REPLACE INTO files (path, content_hash, language, last_indexed)\n         VALUES (@path, @content_hash, @language, @last_indexed)`,\n      )\n      .run(file);\n  }\n\n  insertSymbol(symbol: SymbolRow): number {\n    const result = this.db\n      .prepare(\n        `INSERT INTO symbols (file_path, name, kind, start_byte, end_byte, start_line, end_line, start_column, end_column, signature)\n         VALUES (@file_path, @name, @kind, @start_byte, @end_byte, @start_line, @end_line, @start_column, @end_column, @signature)`,\n      )\n      .run(symbol);\n    return Number(result.lastInsertRowid);\n  }\n\n  insertImport(imp: ImportRow): number {\n    const result = this.db\n      .prepare(\n        `INSERT INTO imports (file_path, specifier, source_path, raw_module, is_type_only)\n         VALUES (@file_path, @specifier, @source_path, @raw_module, @is_type_only)`,\n      )\n      .run(imp);\n    return Number(result.lastInsertRowid);\n  }\n\n  insertReference(ref: ReferenceRow): void {\n    this.db\n      .prepare(\n        `INSERT INTO \"references\" (source_symbol_id, target_symbol_id, ref_type)\n         VALUES (@source_symbol_id, @target_symbol_id, @ref_type)`,\n      )\n      .run(ref);\n  }\n\n  upsertFileContent(filePath: string, content: string): void {\n    // Delete old entry first (FTS5 doesn't support REPLACE)\n    this.db.prepare(\"DELETE FROM content_fts WHERE file_path = ?\").run(filePath);\n    this.db\n      .prepare(\"INSERT INTO content_fts (file_path, content) VALUES (?, ?)\")\n      .run(filePath, content);\n  }\n\n  /**\n   * Search file content using FTS5 full-text search.\n   * Returns files with BM25 relevance scores and matching line ranges.\n   */\n  searchContent(\n    term: string,\n  ): Array<{ file_path: string; rank: number }> {\n    // FTS5 rank is negative (more negative = more relevant), so we negate it\n    return this.db\n      .prepare(\n        `SELECT file_path, -rank AS rank\n         FROM content_fts\n         WHERE content_fts MATCH ?\n         ORDER BY rank DESC`,\n      )\n      .all(term) as Array<{ file_path: string; rank: number }>;\n  }\n\n  getFileHash(filePath: string): string | undefined {\n    const row = this.db\n      .prepare(\"SELECT content_hash FROM files WHERE path = ?\")\n      .get(filePath) as { content_hash: string } | undefined;\n    return row?.content_hash;\n  }\n\n  getSymbolsByFile(filePath: string): SymbolRow[] {\n    return this.db\n      .prepare(\"SELECT * FROM symbols WHERE file_path = ?\")\n      .all(filePath) as SymbolRow[];\n  }\n\n  getSymbolById(id: number): SymbolRow | undefined {\n    return this.db\n      .prepare(\"SELECT * FROM symbols WHERE id = ?\")\n      .get(id) as SymbolRow | undefined;\n  }\n\n  getSymbolByName(name: string): SymbolRow | undefined {\n    return this.db\n      .prepare(\"SELECT * FROM symbols WHERE name = ?\")\n      .get(name) as SymbolRow | undefined;\n  }\n\n  findSymbolsByName(name: string): SymbolRow[] {\n    return this.db\n      .prepare(\"SELECT * FROM symbols WHERE name LIKE ?\")\n      .all(`%${name}%`) as SymbolRow[];\n  }\n\n  findSymbols(name: string, kind?: string): SymbolRow[] {\n    if (kind && kind !== \"all\") {\n      return this.db\n        .prepare(\n          \"SELECT * FROM symbols WHERE name LIKE ? AND kind = ? ORDER BY file_path, start_line\",\n        )\n        .all(`%${name}%`, kind) as SymbolRow[];\n    }\n    return this.db\n      .prepare(\n        \"SELECT * FROM symbols WHERE name LIKE ? ORDER BY file_path, start_line\",\n      )\n      .all(`%${name}%`) as SymbolRow[];\n  }\n\n  /** Get all file-to-file import edges (for file-level graph). */\n  getFileImportEdges(): Array<{\n    source_file: string;\n    target_file: string;\n    specifiers: string;\n    has_type_only: number;\n  }> {\n    return this.db\n      .prepare(\n        `SELECT file_path AS source_file,\n                source_path AS target_file,\n                GROUP_CONCAT(specifier, ', ') AS specifiers,\n                MAX(is_type_only) AS has_type_only\n         FROM imports\n         WHERE source_path IS NOT NULL\n         GROUP BY file_path, source_path\n         ORDER BY file_path, source_path`,\n      )\n      .all() as Array<{\n      source_file: string;\n      target_file: string;\n      specifiers: string;\n      has_type_only: number;\n    }>;\n  }\n\n  /** Get outgoing symbol references (symbols this symbol depends on). */\n  getOutgoingReferences(\n    symbolId: number,\n  ): Array<{\n    target_id: number;\n    target_name: string;\n    target_kind: string;\n    target_file: string;\n    target_line: number;\n    ref_type: string;\n  }> {\n    return this.db\n      .prepare(\n        `SELECT s.id AS target_id, s.name AS target_name, s.kind AS target_kind,\n                s.file_path AS target_file, s.start_line AS target_line, r.ref_type\n         FROM \"references\" r\n         JOIN symbols s ON r.target_symbol_id = s.id\n         WHERE r.source_symbol_id = ?\n         ORDER BY s.file_path, s.start_line`,\n      )\n      .all(symbolId) as Array<{\n      target_id: number;\n      target_name: string;\n      target_kind: string;\n      target_file: string;\n      target_line: number;\n      ref_type: string;\n    }>;\n  }\n\n  /** Get incoming symbol references (symbols that depend on this symbol). */\n  getIncomingReferences(\n    symbolId: number,\n  ): Array<{\n    source_id: number;\n    source_name: string;\n    source_kind: string;\n    source_file: string;\n    source_line: number;\n    ref_type: string;\n  }> {\n    return this.db\n      .prepare(\n        `SELECT s.id AS source_id, s.name AS source_name, s.kind AS source_kind,\n                s.file_path AS source_file, s.start_line AS source_line, r.ref_type\n         FROM \"references\" r\n         JOIN symbols s ON r.source_symbol_id = s.id\n         WHERE r.target_symbol_id = ?\n         ORDER BY s.file_path, s.start_line`,\n      )\n      .all(symbolId) as Array<{\n      source_id: number;\n      source_name: string;\n      source_kind: string;\n      source_file: string;\n      source_line: number;\n      ref_type: string;\n    }>;\n  }\n\n  /** Get in-degree (number of incoming references) for a symbol. */\n  getSymbolInDegree(symbolId: number): number {\n    const row = this.db\n      .prepare(\n        'SELECT COUNT(*) as count FROM \"references\" WHERE target_symbol_id = ?',\n      )\n      .get(symbolId) as { count: number };\n    return row.count;\n  }\n\n  /** Get all files in the index. */\n  getAllFiles(): FileRow[] {\n    return this.db\n      .prepare(\"SELECT * FROM files ORDER BY path\")\n      .all() as FileRow[];\n  }\n\n  countFiles(): number {\n    const row = this.db\n      .prepare(\"SELECT COUNT(*) as count FROM files\")\n      .get() as { count: number };\n    return row.count;\n  }\n\n  countSymbols(): number {\n    const row = this.db\n      .prepare(\"SELECT COUNT(*) as count FROM symbols\")\n      .get() as { count: number };\n    return row.count;\n  }\n\n  countImports(): number {\n    const row = this.db\n      .prepare(\"SELECT COUNT(*) as count FROM imports\")\n      .get() as { count: number };\n    return row.count;\n  }\n\n  countReferences(): number {\n    const row = this.db\n      .prepare('SELECT COUNT(*) as count FROM \"references\"')\n      .get() as { count: number };\n    return row.count;\n  }\n\n  transaction<T>(fn: () => T): T {\n    return this.db.transaction(fn)();\n  }\n\n  close(): void {\n    this.db.close();\n  }\n}\n","import { existsSync } from \"node:fs\";\nimport { resolve, dirname } from \"node:path\";\n\nconst ROOT_MARKERS = [\".git\", \"package.json\"] as const;\n\n/**\n * Walk up from `startDir` looking for a directory that contains a root\n * marker (`.git` directory or `package.json`).  Returns the first match,\n * or `null` if the filesystem root is reached without finding one.\n *\n * `.git` is checked first so that in a monorepo the repository root wins\n * over a nested package.json.\n */\nexport function findProjectRoot(startDir: string): string | null {\n  let dir = resolve(startDir);\n  // eslint-disable-next-line no-constant-condition\n  while (true) {\n    for (const marker of ROOT_MARKERS) {\n      if (existsSync(resolve(dir, marker))) return dir;\n    }\n    const parent = dirname(dir);\n    if (parent === dir) return null; // filesystem root\n    dir = parent;\n  }\n}\n\n/**\n * Resolve the effective project root:\n *   1. Explicit `--root` flag (highest priority)\n *   2. Auto-detected via `.git` / `package.json` walk-up\n *   3. 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package/dist/mcp-7WYTXIQS.js.map

@@ -1 +0,0 @@
-{"version":3,"sources":["../src/mcp.ts"],"sourcesContent":["import { createRequire } from \"node:module\";\nimport { resolve } from \"node:path\";\nimport { existsSync, readFileSync } from \"node:fs\";\nimport { McpServer } from \"@modelcontextprotocol/sdk/server/mcp.js\";\nimport { StdioServerTransport } from \"@modelcontextprotocol/sdk/server/stdio.js\";\nimport { z } from \"zod\";\nimport { IndexDatabase } from \"./db.js\";\nimport { resolveRoot } from \"./root.js\";\n\nconst require = createRequire(import.meta.url);\nconst pkg = require(\"../package.json\");\n\n// ── shared state ────────────────────────────────────────────────────────\n// The MCP server keeps the database connection and tiktoken encoder warm\n// so that subsequent tool calls pay ~10ms instead of ~400ms cold start.\n\nlet db: IndexDatabase | null = null;\nlet rootDir: string = \"\";\n\nfunction getDb(root: string): IndexDatabase {\n  if (db && rootDir === root) return db;\n  const dbPath = resolve(root, 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.number()\n        .int()\n        .positive()\n        .default(8000)\n        .describe(\"Token budget for output (default: 8000)\"),\n      depth: z\n        .number()\n        .int()\n        .min(0)\n        .default(2)\n        .describe(\"Max graph traversal depth (default: 2)\"),\n      root: z\n        .string()\n        .optional()\n        .describe(\"Root directory of indexed project\"),\n    },\n    async ({ term, budget, depth, root }) => {\n      const r = root ?? effectiveRoot;\n      // Import runQuery's internal logic so we can capture output\n      const output = await captureQueryOutput(r, term, budget, depth);\n      return { content: [{ type: \"text\" as const, text: output }] };\n    },\n  );\n\n  // ── tool: find ──────────────────────────────────────────────────────\n\n  server.tool(\n    \"find\",\n    \"Quick symbol lookup by name with optional kind filter. \" +\n      \"Returns symbol names, kinds, file paths, and line numbers.\",\n    {\n      symbol: z.string().describe(\"Symbol name to search for\"),\n      kind: z\n        .enum([\n          \"function\",\n          \"class\",\n          \"interface\",\n          \"type\",\n          \"enum\",\n          \"variable\",\n          \"method\",\n          \"all\",\n        ])\n        .default(\"all\")\n        .describe(\"Filter by symbol kind (default: all)\"),\n      root: z\n        .string()\n        .optional()\n        .describe(\"Root directory of indexed project\"),\n    },\n    async ({ symbol, kind, root }) => {\n      const r = root ?? effectiveRoot;\n      const database = getDb(r);\n      const results = database.findSymbols(symbol, kind);\n\n      if (results.length === 0) {\n        return {\n          content: [\n            {\n              type: \"text\" as const,\n              text: `No symbols found matching \"${symbol}\"${kind !== \"all\" ? ` (kind: ${kind})` : \"\"}`,\n            },\n          ],\n        };\n      }\n\n      const lines: string[] = [\n       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   const output = captureMapOutput(r, budget);\n      return { content: [{ type: \"text\" as const, text: output }] };\n    },\n  );\n\n  return server;\n}\n\n// ── output capture helpers ──────────────────────────────────────────────\n// These re-implement the command logic to return strings instead of\n// writing to stdout, keeping the database connection warm.\n\nasync function captureQueryOutput(\n  root: string,\n  term: string,\n  budget: number,\n  depth: number,\n): Promise<string> {\n  const { runQueryCore } = await import(\"./commands/query.js\");\n  return runQueryCore(root, term, budget, depth);\n}\n\nfunction captureGraphOutput(\n  root: string,\n  target: string,\n  direction: \"both\" | \"incoming\" | \"outgoing\",\n): string {\n  const database = getDb(root);\n\n  const isFile =\n    target.includes(\"/\") || target.includes(\"\\\\\") || /\\.\\w+$/.test(target);\n\n  if (isFile) {\n    return renderFileGraphToString(database, target, direction);\n  } else {\n    return renderSymbolGraphToString(database, target, direction);\n  }\n}\n\nfunction renderFileGraphToString(\n  database: IndexDatabase,\n  target: string,\n  direction: \"both\" | \"incoming\" | \"outgoing\",\n): string {\n  const require = createRequire(import.meta.url);\n  const { DirectedGraph } = require(\"graphology\");\n\n  const graph = new DirectedGraph();\n  for (const file of database.getAllFiles()) {\n    graph.addNode(file.path);\n  }\n  for (const edge of database.getFileImportEdges()) {\n    const key = `${edge.source_file}->${edge.target_file}`;\n    if (graph.hasEdge(key)) {\n      const existing = graph.getEdgeAttributes(key);\n      graph.setEdgeAttribute(\n        key,\n        \"specifiers\",\n        `${existing.specifiers}, ${edge.specifiers}`,\n      );\n    } else {\n      graph.addEdgeWithKey(key, edge.source_file, edge.target_file, {\n        specifiers: edge.specifiers,\n      });\n    }\n  }\n\n  if (!graph.hasNode(target)) {\n    return `Error: file \"${target}\" 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sections.push(\n      lines.length > 0\n        ? `Dependencies (outgoing):\\n${lines.join(\"\\n\")}`\n        : \"Dependencies (outgoing): (none)\",\n    );\n  }\n\n  if (direction === \"incoming\" || direction === \"both\") {\n    const refs = database.getIncomingReferences(sym.id);\n    const lines = refs.map(\n      (r) =>\n        `  ${r.source_name} (${r.source_kind}) — ${r.source_file}:${r.source_line}  [${r.ref_type}]`,\n    );\n    sections.push(\n      lines.length > 0\n        ? `Dependents (incoming):\\n${lines.join(\"\\n\")}`\n        : \"Dependents (incoming): (none)\",\n    );\n  }\n\n  return `${heading}\\n\\n${sections.join(\"\\n\\n\")}`;\n}\n\nfunction captureMapOutput(root: string, budget: number): string {\n  const require = createRequire(import.meta.url);\n  const { DirectedGraph } = require(\"graphology\");\n  const pagerank = require(\"graphology-metrics/centrality/pagerank\");\n  const { getEncoding } = require(\"js-tiktoken\");\n\n  const database = 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database.getSymbolsByFile(file.path);\n    symbols.sort((a, b) => a.start_line - b.start_line);\n    const lines: string[] = [file.path];\n    for (const sym of symbols) {\n      if (sym.kind === \"variable\" && !sym.signature) continue;\n      const label = sym.signature ?? `${sym.kind} ${sym.name}`;\n      lines.push(`  ${label}`);\n    }\n    const block = lines.join(\"\\n\");\n    const blockTokens = enc.encode(block).length;\n\n    if (tokenCount + blockTokens <= budget) {\n      blocks.push(block);\n      tokenCount += blockTokens;\n      continue;\n    }\n\n    const blockLines = block.split(\"\\n\");\n    let partial = blockLines[0];\n    let partialTokens = enc.encode(partial).length;\n\n    if (tokenCount + partialTokens > budget) {\n      truncated = true;\n      break;\n    }\n\n    for (let i = 1; i < blockLines.length; i++) {\n      const candidate = partial + \"\\n\" + blockLines[i];\n      const candidateTokens = enc.encode(candidate).length;\n      if (tokenCount + 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tools:\n  query   Search and return ranked code context\n  find    Quick symbol lookup\n  graph   Show dependency graph for a file or symbol\n  map     High-level codebase overview\n\nThe server keeps the database connection and tiktoken encoder warm,\nso subsequent tool calls complete in ~10ms instead of ~400ms.\n\nUsage with Claude Code:\n  Add to .mcp.json:\n  {\n    \"mcpServers\": {\n      \"codefocus\": {\n        \"command\": \"npx\",\n        \"args\": [\"codefocus\", \"serve\", \"--root\", \"/path/to/project\"]\n      }\n    }\n  }`);\n    return;\n  }\n\n  const root = resolveRoot(flags.root);\n  const dbPath = resolve(root, \".codefocus\", \"index.db\");\n\n  if (!existsSync(dbPath)) {\n    console.error(\n      `Error: no index found at ${dbPath}\\nRun 'codefocus index --root ${root}' first.`,\n    );\n    process.exitCode = 1;\n    return;\n  }\n\n  // Pre-warm the database connection\n  getDb(root);\n  console.error(`[codefocus] MCP server starting (root: ${root})`);\n  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