@ngommans/codefocus 0.1.0

package/README.md

@@ -0,0 +1,124 @@
+# codefocus
+
+Smart code context aggregator — AST-powered search that returns structured,
+ranked code context for LLM agents.
+
+Tree-sitter parses your codebase into a SQLite graph database. Queries combine
+full-text search, symbol-aware graph traversal, and PageRank scoring to return
+the most relevant code sections within a token budget. One call replaces
+multiple grep/read round-trips.
+
+## Install
+
+```bash
+npm install -g codefocus
+# or use directly
+npx codefocus
+```
+
+Requires Node 18+.
+
+## Quick start
+
+```bash
+# Index your project (creates .codefocus/index.db)
+npx codefocus index --root .
+
+# Search for relevant code context
+npx codefocus query "handleSync" --budget 8000
+
+# Get a high-level codebase overview
+npx codefocus map --budget 2000
+```
+
+## Commands
+
+| Command | Description |
+|---------|-------------|
+| `index` | Parse the codebase with tree-sitter and store symbols in SQLite |
+| `query` | Search and return ranked, budget-constrained code context |
+| `find` | Quick symbol lookup by name and optional kind filter |
+| `graph` | Show dependency graph for a file or symbol |
+| `map` | High-level codebase overview (Aider-style repo map) |
+| `serve` | Start MCP server (stdio transport, keeps DB warm) |
+| `benchmark` | Benchmark codefocus vs. Explore agent pattern |
+
+## Claude Code integration
+
+### MCP server (recommended)
+
+Add a `.mcp.json` file to your project root:
+
+```json
+{
+  "mcpServers": {
+    "codefocus": {
+      "command": "npx",
+      "args": ["codefocus", "serve", "--root", "."]
+    }
+  }
+}
+```
+
+Claude Code auto-discovers the MCP server and gains `query`, `find`, `graph`,
+and `map` as tools. The server stays warm with sub-10ms response times after
+the first call.
+
+### Auto-indexing via SessionStart hook
+
+Add `.claude/hooks.json` to keep the index fresh on every session:
+
+```json
+{
+  "hooks": {
+    "SessionStart": [{
+      "command": "npx codefocus index --root .",
+      "timeout": 30000
+    }]
+  }
+}
+```
+
+## How it works
+
+1. **Index** — tree-sitter parses TypeScript/JavaScript files, extracting
+   symbols (functions, classes, interfaces, types), imports, and cross-file
+   references. Everything is stored in a SQLite database with FTS5 full-text
+   search.
+
+2. **Query** — searches combine direct symbol-name matching, FTS5 content
+   search, and graph expansion (BFS along import/reference edges). Results
+   are ranked by match strength, term frequency, symbol proximity, hub
+   dampening, and PageRank. Relevance thresholds (score floor, elbow
+   detection, marginal value) prune noise.
+
+3. **Output** — ranked code sections with YAML front matter (confidence,
+   score distribution), constrained to a token budget. One query replaces
+   3-7 grep/read round-trips with 50x fewer tokens.
+
+## Scoring configuration
+
+Tuning parameters can be customized per-project via `.codefocus/config.json`:
+
+```json
+{
+  "scoring": {
+    "scoreFloorRatio": 0.20,
+    "elbowDropRatio": 0.60,
+    "minMarginalValue": 0.00003,
+    "symbolProximityBoost": 1.5,
+    "importEdgeWeight": 0.4,
+    "typeRefWeight": 0.2,
+    "defaultBudget": 8000,
+    "defaultDepth": 2
+  }
+}
+```
+
+Use `codefocus benchmark --emit-config` to print the active configuration.
+Use `codefocus benchmark --extended` to validate parameters against dependency
+codebases.
+
+## License
+
+MIT

package/dist/benchmark-43DOYNYR.js

@@ -0,0 +1,465 @@
+#!/usr/bin/env node
+
+// src/benchmark.ts
+import { createRequire } from "module";
+import { execFileSync } from "child_process";
+import { readFileSync } from "fs";
+import { resolve, relative } from "path";
+var require2 = createRequire(import.meta.url);
+var { getEncoding } = require2("js-tiktoken");
+var TASKS = [
+  {
+    id: "cli-routing",
+    question: "How does the CLI route commands to their handlers?",
+    searchTerms: ["parseArgs", "handlers", "command"],
+    queryTerm: "parseArgs",
+    expectedFiles: ["src/cli.ts"],
+    essentialFiles: ["src/cli.ts"],
+    bonusFiles: [],
+    expectedSymbols: ["parseArgs", "main", "ParsedArgs"]
+  },
+  {
+    id: "callers-of-runIndex",
+    question: "Find all callers of runIndex and understand the indexing entry point",
+    searchTerms: ["runIndex"],
+    queryTerm: "runIndex",
+    // B1: Added src/watcher.ts — legitimate caller added in Spike 7 Phase C
+    expectedFiles: ["src/cli.ts", "src/commands/index.ts", "src/indexer.ts", "src/watcher.ts"],
+    essentialFiles: ["src/commands/index.ts", "src/indexer.ts"],
+    bonusFiles: ["src/cli.ts", "src/watcher.ts"],
+    expectedSymbols: ["runIndex", "indexProject"]
+  },
+  {
+    id: "token-budget",
+    question: "How does the token budget system work in the query command?",
+    searchTerms: ["budget", "tokenCount", "getEncoding"],
+    queryTerm: "budget",
+    // B1: src/mcp.ts re-exports query logic with budget param — valid but not essential
+    expectedFiles: ["src/commands/query.ts", "src/mcp.ts"],
+    essentialFiles: ["src/commands/query.ts"],
+    bonusFiles: ["src/mcp.ts"],
+    expectedSymbols: ["runQuery", "ScoredSymbol", "FileSection"]
+  },
+  {
+    id: "db-schema",
+    question: "What is the database schema and what operations does it support?",
+    searchTerms: ["IndexDatabase", "CREATE TABLE"],
+    queryTerm: "IndexDatabase",
+    expectedFiles: ["src/db.ts"],
+    essentialFiles: ["src/db.ts"],
+    bonusFiles: [],
+    expectedSymbols: [
+      "IndexDatabase",
+      "SymbolRow",
+      "FileRow",
+      "ImportRow",
+      "ReferenceRow"
+    ]
+  },
+  {
+    id: "incremental-indexing",
+    question: "How does incremental indexing work? How are unchanged files skipped?",
+    searchTerms: ["hashContent", "existingHash", "filesSkipped"],
+    queryTerm: "hashContent",
+    expectedFiles: ["src/indexer.ts"],
+    essentialFiles: ["src/indexer.ts"],
+    bonusFiles: [],
+    expectedSymbols: ["hashContent", "indexProject"]
+  },
+  {
+    id: "cross-file-refs",
+    question: "How are cross-file symbol references created during indexing?",
+    searchTerms: ["insertReference", "referencesCreated"],
+    queryTerm: "insertReference",
+    expectedFiles: ["src/indexer.ts", "src/db.ts"],
+    essentialFiles: ["src/indexer.ts", "src/db.ts"],
+    bonusFiles: [],
+    expectedSymbols: ["insertReference", "indexProject"]
+  },
+  {
+    id: "parser-node-types",
+    question: "What tree-sitter node types does the parser handle?",
+    searchTerms: ["parseSource", "extractDeclaration", "node_type"],
+    queryTerm: "parseSource",
+    expectedFiles: ["src/parser.ts"],
+    essentialFiles: ["src/parser.ts"],
+    bonusFiles: [],
+    expectedSymbols: ["parseSource", "extractDeclaration"]
+  },
+  {
+    id: "graph-rendering",
+    question: "How does the graph command render dependency trees?",
+    searchTerms: ["runGraph", "renderTree"],
+    queryTerm: "runGraph",
+    expectedFiles: ["src/commands/graph.ts"],
+    essentialFiles: ["src/commands/graph.ts"],
+    bonusFiles: [],
+    expectedSymbols: ["runGraph"]
+  }
+];
+function simulateExplore(rootDir, task) {
+  const enc = getEncoding("cl100k_base");
+  const matchedFiles = /* @__PURE__ */ new Set();
+  let roundTrips = 0;
+  for (const term of task.searchTerms) {
+    roundTrips++;
+    try {
+      const grepResult = execFileSync(
+        "grep",
+        ["-rl", "--include=*.ts", term, resolve(rootDir, "src")],
+        { encoding: "utf-8", timeout: 1e4 }
+      );
+      for (const line of grepResult.trim().split("\n")) {
+        if (line) {
+          matchedFiles.add(relative(rootDir, line));
+        }
+      }
+    } catch {
+    }
+  }
+  let totalTokens = 0;
+  let totalBytes = 0;
+  const filesRead = [];
+  for (const filePath of matchedFiles) {
+    roundTrips++;
+    try {
+      const content = readFileSync(resolve(rootDir, filePath), "utf-8");
+      totalBytes += Buffer.byteLength(content, "utf-8");
+      totalTokens += enc.encode(content).length;
+      filesRead.push(filePath);
+    } catch {
+    }
+  }
+  return {
+    tokensConsumed: totalTokens,
+    roundTrips,
+    filesRead,
+    bytesRead: totalBytes
+  };
+}
+function runCodefocusQuery(rootDir, cliPath, task) {
+  let stdout;
+  try {
+    stdout = execFileSync(
+      "node",
+      [cliPath, "query", task.queryTerm, "--root", rootDir, "--budget", "8000"],
+      { encoding: "utf-8", timeout: 3e4 }
+    );
+  } catch (err) {
+    stdout = (err.stdout || "") + (err.stderr || "");
+  }
+  const tokenMatch = stdout.match(/~(\d+) tokens/);
+  const tokensOutput = tokenMatch ? parseInt(tokenMatch[1], 10) : 0;
+  const fileMatches = stdout.matchAll(/── ([\w/.]+\.ts):\d+-\d+/g);
+  const filesReturned = [...fileMatches].map((m) => m[1]);
+  return {
+    tokensOutput,
+    roundTrips: 1,
+    filesReturned,
+    stdout
+  };
+}
+function computeCompleteness(returnedFiles, expectedFiles) {
+  if (expectedFiles.length === 0) return 1;
+  const returned = new Set(returnedFiles);
+  const found = expectedFiles.filter((f) => returned.has(f)).length;
+  return found / expectedFiles.length;
+}
+function computePrecision(returnedFiles, expectedFiles) {
+  if (returnedFiles.length === 0) return 0;
+  const expected = new Set(expectedFiles);
+  const relevant = returnedFiles.filter((f) => expected.has(f)).length;
+  return relevant / returnedFiles.length;
+}
+function runBenchmark(rootDir, cliPath, exploreAgentTokens) {
+  const results = [];
+  for (const task of TASKS) {
+    const explore = simulateExplore(rootDir, task);
+    const codefocus = runCodefocusQuery(rootDir, cliPath, task);
+    const exploreCompleteness = computeCompleteness(
+      explore.filesRead,
+      task.expectedFiles
+    );
+    const codefocusCompleteness = computeCompleteness(
+      codefocus.filesReturned,
+      task.expectedFiles
+    );
+    const exploreEssentialCompleteness = computeCompleteness(
+      explore.filesRead,
+      task.essentialFiles
+    );
+    const codefocusEssentialCompleteness = computeCompleteness(
+      codefocus.filesReturned,
+      task.essentialFiles
+    );
+    const explorePrecision = computePrecision(
+      explore.filesRead,
+      task.expectedFiles
+    );
+    const codefocusPrecision = computePrecision(
+      codefocus.filesReturned,
+      task.expectedFiles
+    );
+    const tokenSavingsRatio = codefocus.tokensOutput > 0 ? explore.tokensConsumed / codefocus.tokensOutput : 0;
+    results.push({
+      task,
+      explore,
+      codefocus,
+      exploreCompleteness,
+      codefocusCompleteness,
+      exploreEssentialCompleteness,
+      codefocusEssentialCompleteness,
+      explorePrecision,
+      codefocusPrecision,
+      tokenSavingsRatio
+    });
+  }
+  const avg = (arr) => arr.length > 0 ? arr.reduce((a, b) => a + b, 0) / arr.length : 0;
+  return {
+    tasks: results,
+    summary: {
+      avgExploreTokens: avg(results.map((r) => r.explore.tokensConsumed)),
+      avgCodefocusTokens: avg(results.map((r) => r.codefocus.tokensOutput)),
+      avgTokenSavingsRatio: avg(results.map((r) => r.tokenSavingsRatio)),
+      avgExploreRoundTrips: avg(results.map((r) => r.explore.roundTrips)),
+      avgCodefocusRoundTrips: avg(
+        results.map((r) => r.codefocus.roundTrips)
+      ),
+      avgExploreCompleteness: avg(results.map((r) => r.exploreCompleteness)),
+      avgCodefocusCompleteness: avg(
+        results.map((r) => r.codefocusCompleteness)
+      ),
+      avgExploreEssentialCompleteness: avg(
+        results.map((r) => r.exploreEssentialCompleteness)
+      ),
+      avgCodefocusEssentialCompleteness: avg(
+        results.map((r) => r.codefocusEssentialCompleteness)
+      ),
+      avgExplorePrecision: avg(results.map((r) => r.explorePrecision)),
+      avgCodefocusPrecision: avg(results.map((r) => r.codefocusPrecision))
+    },
+    exploreAgentTokens: exploreAgentTokens ?? {}
+  };
+}
+function formatResults(results) {
+  const lines = [];
+  lines.push("# codefocus Benchmark \u2014 Spike 8");
+  lines.push("");
+  lines.push(
+    "Comparison of codefocus query vs. Explore agent pattern (grep/glob/read)"
+  );
+  lines.push(`for ${results.tasks.length} representative code comprehension tasks.`);
+  lines.push("");
+  lines.push(`Benchmark run: ${(/* @__PURE__ */ new Date()).toISOString()}`);
+  lines.push("");
+  lines.push("## Per-task results");
+  lines.push("");
+  lines.push(
+    "| Task | Explore tokens | CF tokens | Savings | CF compl. | CF essential | CF prec. |"
+  );
+  lines.push(
+    "|------|---------------:|----------:|--------:|----------:|-------------:|---------:|"
+  );
+  for (const r of results.tasks) {
+    const savings = r.tokenSavingsRatio.toFixed(1) + "x";
+    lines.push(
+      `| ${r.task.id} | ${r.explore.tokensConsumed} | ${r.codefocus.tokensOutput} | ${savings} | ${pct(r.codefocusCompleteness)} | ${pct(r.codefocusEssentialCompleteness)} | ${pct(r.codefocusPrecision)} |`
+    );
+  }
+  lines.push("");
+  lines.push("## Summary");
+  lines.push("");
+  const s = results.summary;
+  lines.push(
+    "| Metric | Explore (grep/glob/read) | codefocus query |"
+  );
+  lines.push("|--------|------------------------:|----------------:|");
+  lines.push(
+    `| Avg tokens consumed | ${Math.round(s.avgExploreTokens)} | ${Math.round(s.avgCodefocusTokens)} |`
+  );
+  lines.push(
+    `| Avg token savings | \u2014 | ${s.avgTokenSavingsRatio.toFixed(1)}x less |`
+  );
+  lines.push(
+    `| Avg round-trips | ${s.avgExploreRoundTrips.toFixed(1)} | ${s.avgCodefocusRoundTrips.toFixed(1)} |`
+  );
+  lines.push(
+    `| Avg completeness (total) | ${pct(s.avgExploreCompleteness)} | ${pct(s.avgCodefocusCompleteness)} |`
+  );
+  lines.push(
+    `| Avg completeness (essential) | ${pct(s.avgExploreEssentialCompleteness)} | ${pct(s.avgCodefocusEssentialCompleteness)} |`
+  );
+  lines.push(
+    `| Avg precision | ${pct(s.avgExplorePrecision)} | ${pct(s.avgCodefocusPrecision)} |`
+  );
+  lines.push("");
+  if (Object.keys(results.exploreAgentTokens).length > 0) {
+    lines.push("## Real Explore agent token counts");
+    lines.push("");
+    lines.push(
+      "These are actual token counts from running the Explore subagent"
+    );
+    lines.push("(Claude Code Task tool, subagent_type=Explore).");
+    lines.push("");
+    lines.push("| Task | Explore agent tokens | codefocus tokens | Savings |");
+    lines.push("|------|---------------------:|-----------------:|--------:|");
+    for (const r of results.tasks) {
+      const agentTokens = results.exploreAgentTokens[r.task.id];
+      if (agentTokens !== void 0) {
+        const cfTokens = r.codefocus.tokensOutput;
+        const ratio = cfTokens > 0 ? (agentTokens / cfTokens).toFixed(1) + "x" : "\u2014";
+        lines.push(
+          `| ${r.task.id} | ${agentTokens} | ${cfTokens} | ${ratio} |`
+        );
+      }
+    }
+    lines.push("");
+  }
+  lines.push("## Per-task detail");
+  lines.push("");
+  for (const r of results.tasks) {
+    lines.push(`### ${r.task.id}`);
+    lines.push("");
+    lines.push(`**Question:** ${r.task.question}`);
+    lines.push("");
+    lines.push(
+      `**Search terms:** ${r.task.searchTerms.map((t) => `\`${t}\``).join(", ")}`
+    );
+    lines.push(`**Query term:** \`${r.task.queryTerm}\``);
+    lines.push("");
+    lines.push("**Explore pattern:**");
+    lines.push(`- Files read: ${r.explore.filesRead.join(", ") || "(none)"}`);
+    lines.push(`- Tokens consumed: ${r.explore.tokensConsumed}`);
+    lines.push(`- Round-trips: ${r.explore.roundTrips}`);
+    lines.push("");
+    lines.push("**codefocus query:**");
+    lines.push(
+      `- Files returned: ${r.codefocus.filesReturned.join(", ") || "(none)"}`
+    );
+    lines.push(`- Tokens output: ${r.codefocus.tokensOutput}`);
+    lines.push(`- Round-trips: ${r.codefocus.roundTrips}`);
+    lines.push("");
+    lines.push(
+      `**Essential files:** ${r.task.essentialFiles.join(", ")}`
+    );
+    if (r.task.bonusFiles.length > 0) {
+      lines.push(
+        `**Bonus files:** ${r.task.bonusFiles.join(", ")}`
+      );
+    }
+    lines.push(
+      `**Expected symbols:** ${r.task.expectedSymbols.map((s2) => `\`${s2}\``).join(", ")}`
+    );
+    lines.push("");
+  }
+  lines.push("## Methodology");
+  lines.push("");
+  lines.push("### Explore agent simulation");
+  lines.push("");
+  lines.push("The Explore agent simulation models a **conservative lower bound**");
+  lines.push("of what a real grep/glob/read agent would consume:");
+  lines.push("");
+  lines.push("1. For each search term, run `grep -rl` in `src/` (1 round-trip per grep)");
+  lines.push("2. Read each matching file in full (1 round-trip per file)");
+  lines.push("3. Count total tokens of all file content with cl100k_base");
+  lines.push("");
+  lines.push("Real agents typically consume **2-5x more** tokens because they:");
+  lines.push("- Read files speculatively that turn out to be irrelevant");
+  lines.push("- Re-read files across multiple turns");
+  lines.push("- Read test files, configs, and docs for context");
+  lines.push("- Include directory listing and file search overhead");
+  lines.push("- Receive tool-call framing tokens (prompts, system messages)");
+  lines.push("");
+  lines.push("### codefocus query");
+  lines.push("");
+  lines.push("A single `codefocus query <term> --budget 8000` call.");
+  lines.push("The output is pre-ranked, budget-constrained, and includes only");
+  lines.push("the relevant symbol ranges (not entire files).");
+  lines.push("");
+  lines.push("### Metrics");
+  lines.push("");
+  lines.push("- **Tokens:** cl100k_base token count of content consumed/output");
+  lines.push("- **Round-trips:** Number of tool calls (grep/read for explore, 1 for codefocus)");
+  lines.push("- **Completeness:** Fraction of expected files present in results");
+  lines.push("- **Precision:** Fraction of returned files that are in the expected set");
+  lines.push("- **Token savings:** Explore tokens / codefocus tokens");
+  return lines.join("\n");
+}
+function pct(n) {
+  return `${Math.round(n * 100)}%`;
+}
+async function runBenchmarkCommand(positional, flags) {
+  if (flags.help) {
+    console.log(`codefocus benchmark \u2014 Compare codefocus query vs. Explore agent pattern
+
+Usage: codefocus benchmark [options]
+
+Options:
+  --root <path>     Root directory of indexed project (default: auto-detect)
+  --json            Output raw JSON instead of markdown
+  --extended        Run extended cross-codebase benchmarks against dependencies
+  --emit-config     Print the active scoring config as JSON and exit
+  --help            Show this help message`);
+    return;
+  }
+  const { resolveRoot } = await import("./root-ODTOXM2J.js");
+  const root = resolveRoot(flags.root);
+  const cliPath = resolve(
+    new URL(".", import.meta.url).pathname,
+    "../dist/cli.js"
+  );
+  if (flags["emit-config"]) {
+    const { loadScoringConfig, serializeConfig } = await import("./config-OCBWYENF.js");
+    const config = loadScoringConfig(root);
+    console.log(serializeConfig(config));
+    return;
+  }
+  if (flags.extended) {
+    const {
+      discoverSuites,
+      runExtendedBenchmark,
+      formatExtendedResults
+    } = await import("./extended-benchmark-5RUXDG3D.js");
+    const suites = discoverSuites(root);
+    if (suites.length === 0) {
+      console.error(
+        "[benchmark] No dependency libraries found for extended benchmarks."
+      );
+      console.error(
+        "[benchmark] Run 'npm install' first to install dependencies."
+      );
+      process.exitCode = 1;
+      return;
+    }
+    console.log(
+      `[benchmark] Running extended benchmarks against ${suites.length} libraries ...`
+    );
+    for (const s of suites) {
+      console.log(`[benchmark]   ${s.name} (${s.rootDir})`);
+    }
+    console.log(`[benchmark] CLI: ${cliPath}`);
+    console.log("");
+    const results2 = runExtendedBenchmark(root, cliPath, suites);
+    if (flags.json) {
+      console.log(JSON.stringify(results2, null, 2));
+    } else {
+      console.log(formatExtendedResults(results2));
+    }
+    return;
+  }
+  console.log(`[benchmark] Running ${TASKS.length} tasks against ${root} ...`);
+  console.log(`[benchmark] CLI: ${cliPath}`);
+  console.log("");
+  const results = runBenchmark(root, cliPath);
+  if (flags.json) {
+    console.log(JSON.stringify(results, null, 2));
+  } else {
+    console.log(formatResults(results));
+  }
+}
+export {
+  formatResults,
+  runBenchmark,
+  runBenchmarkCommand
+};
+//# sourceMappingURL=benchmark-43DOYNYR.js.map

package/dist/benchmark-43DOYNYR.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/benchmark.ts"],"sourcesContent":["import { createRequire } from \"node:module\";\nimport { execFileSync } from \"node:child_process\";\nimport { readFileSync } from \"node:fs\";\nimport { resolve, relative } from \"node:path\";\n\nconst require = createRequire(import.meta.url);\nconst { getEncoding } = require(\"js-tiktoken\");\n\n// ── types ───────────────────────────────────────────────────────────────\n\ninterface BenchmarkTask {\n  /** Short human-readable identifier */\n  id: string;\n  /** Full question an agent would ask */\n  question: string;\n  /** Search terms for grep (explore) and codefocus query */\n  searchTerms: string[];\n  /** codefocus query term (first searchTerm by default) */\n  queryTerm: string;\n  /** Files that contain the \"correct\" answer (for completeness/precision) */\n  expectedFiles: string[];\n  /** B2: Core files that must be present (subset of expectedFiles) */\n  essentialFiles: string[];\n  /** B2: Additional files that provide useful context (nice to have) */\n  bonusFiles: string[];\n  /** Key symbols the answer must include */\n  expectedSymbols: string[];\n}\n\ninterface ExploreResult {\n  /** Total tokens of file content consumed */\n  tokensConsumed: number;\n  /** Number of simulated tool calls (grep + read) */\n  roundTrips: number;\n  /** Files that were read */\n  filesRead: string[];\n  /** Total bytes read */\n  bytesRead: number;\n}\n\ninterface CodefocusResult {\n  /** Tokens reported in the query footer */\n  tokensOutput: number;\n  /** Always 1 (single codefocus query call) */\n  roundTrips: number;\n  /** Files included in the output */\n  filesReturned: string[];\n  /** Raw stdout */\n  stdout: string;\n}\n\ninterface TaskResult {\n  task: BenchmarkTask;\n  explore: ExploreResult;\n  codefocus: CodefocusResult;\n  /** What fraction of expectedFiles are in the result? (0-1) */\n  exploreCompleteness: number;\n  codefocusCompleteness: number;\n  /** B2: What fraction of essentialFiles are in the result? (0-1) */\n  exploreEssentialCompleteness: number;\n  codefocusEssentialCompleteness: number;\n  /** What fraction of returned files are in expectedFiles? (0-1) */\n  explorePrecision: number;\n  codefocusPrecision: number;\n  /** Token savings ratio: explore tokens / codefocus tokens */\n  tokenSavingsRatio: number;\n}\n\n// ── task definitions ────────────────────────────────────────────────────\n\nconst TASKS: BenchmarkTask[] = [\n  {\n    id: \"cli-routing\",\n    question:\n      \"How does the CLI route commands to their handlers?\",\n    searchTerms: [\"parseArgs\", \"handlers\", \"command\"],\n    queryTerm: \"parseArgs\",\n    expectedFiles: [\"src/cli.ts\"],\n    essentialFiles: [\"src/cli.ts\"],\n    bonusFiles: [],\n    expectedSymbols: [\"parseArgs\", \"main\", \"ParsedArgs\"],\n  },\n  {\n    id: \"callers-of-runIndex\",\n    question: \"Find all callers of runIndex and understand the indexing entry point\",\n    searchTerms: [\"runIndex\"],\n    queryTerm: \"runIndex\",\n    // B1: Added src/watcher.ts — legitimate caller added in Spike 7 Phase C\n    expectedFiles: [\"src/cli.ts\", \"src/commands/index.ts\", \"src/indexer.ts\", \"src/watcher.ts\"],\n    essentialFiles: [\"src/commands/index.ts\", \"src/indexer.ts\"],\n    bonusFiles: [\"src/cli.ts\", \"src/watcher.ts\"],\n    expectedSymbols: [\"runIndex\", \"indexProject\"],\n  },\n  {\n    id: \"token-budget\",\n    question:\n      \"How does the token budget system work in the query command?\",\n    searchTerms: [\"budget\", \"tokenCount\", \"getEncoding\"],\n    queryTerm: \"budget\",\n    // B1: src/mcp.ts re-exports query logic with budget param — valid but not essential\n    expectedFiles: [\"src/commands/query.ts\", \"src/mcp.ts\"],\n    essentialFiles: [\"src/commands/query.ts\"],\n    bonusFiles: [\"src/mcp.ts\"],\n    expectedSymbols: [\"runQuery\", \"ScoredSymbol\", \"FileSection\"],\n  },\n  {\n    id: \"db-schema\",\n    question: \"What is the database schema and what operations does it support?\",\n    searchTerms: [\"IndexDatabase\", \"CREATE TABLE\"],\n    queryTerm: \"IndexDatabase\",\n    expectedFiles: [\"src/db.ts\"],\n    essentialFiles: [\"src/db.ts\"],\n    bonusFiles: [],\n    expectedSymbols: [\n      \"IndexDatabase\",\n      \"SymbolRow\",\n      \"FileRow\",\n      \"ImportRow\",\n      \"ReferenceRow\",\n    ],\n  },\n  {\n    id: \"incremental-indexing\",\n    question:\n      \"How does incremental indexing work? How are unchanged files skipped?\",\n    searchTerms: [\"hashContent\", \"existingHash\", \"filesSkipped\"],\n    queryTerm: \"hashContent\",\n    expectedFiles: [\"src/indexer.ts\"],\n    essentialFiles: [\"src/indexer.ts\"],\n    bonusFiles: [],\n    expectedSymbols: [\"hashContent\", \"indexProject\"],\n  },\n  {\n    id: \"cross-file-refs\",\n    question:\n      \"How are cross-file symbol references created during indexing?\",\n    searchTerms: [\"insertReference\", \"referencesCreated\"],\n    queryTerm: \"insertReference\",\n    expectedFiles: [\"src/indexer.ts\", \"src/db.ts\"],\n    essentialFiles: [\"src/indexer.ts\", \"src/db.ts\"],\n    bonusFiles: [],\n    expectedSymbols: [\"insertReference\", \"indexProject\"],\n  },\n  {\n    id: \"parser-node-types\",\n    question:\n      \"What tree-sitter node types does the parser handle?\",\n    searchTerms: [\"parseSource\", \"extractDeclaration\", \"node_type\"],\n    queryTerm: \"parseSource\",\n    expectedFiles: [\"src/parser.ts\"],\n    essentialFiles: [\"src/parser.ts\"],\n    bonusFiles: [],\n    expectedSymbols: [\"parseSource\", \"extractDeclaration\"],\n  },\n  {\n    id: \"graph-rendering\",\n    question:\n      \"How does the graph command render dependency trees?\",\n    searchTerms: [\"runGraph\", \"renderTree\"],\n    queryTerm: \"runGraph\",\n    expectedFiles: [\"src/commands/graph.ts\"],\n    essentialFiles: [\"src/commands/graph.ts\"],\n    bonusFiles: [],\n    expectedSymbols: [\"runGraph\"],\n  },\n];\n\n// ── explore simulation ──────────────────────────────────────────────────\n\n/**\n * Simulate what an Explore agent (grep/glob/read pattern) would do\n * to answer a question. This models a realistic lower-bound:\n *\n * 1. For each search term, grep the src/ directory for matching files\n * 2. Read each matching file in full\n * 3. Count total tokens consumed\n *\n * Real agents typically consume MORE tokens because they:\n * - Read files speculatively that turn out to be irrelevant\n * - Re-read files across multiple turns\n * - Read test files, configs, and docs for context\n * - Include file listing / directory exploration overhead\n */\nfunction simulateExplore(\n  rootDir: string,\n  task: BenchmarkTask,\n): ExploreResult {\n  const enc = getEncoding(\"cl100k_base\");\n  const matchedFiles = new Set<string>();\n  let roundTrips = 0;\n\n  // Step 1: Grep for each search term (each grep = 1 round-trip)\n  for (const term of task.searchTerms) {\n    roundTrips++;\n    try {\n      const grepResult = execFileSync(\n        \"grep\",\n        [\"-rl\", \"--include=*.ts\", term, resolve(rootDir, \"src\")],\n        { encoding: \"utf-8\", timeout: 10_000 },\n      );\n      for (const line of grepResult.trim().split(\"\\n\")) {\n        if (line) {\n          matchedFiles.add(relative(rootDir, line));\n        }\n      }\n    } catch {\n      // grep returns exit 1 when no matches — that's fine\n    }\n  }\n\n  // Step 2: Read each matched file (each read = 1 round-trip)\n  let totalTokens = 0;\n  let totalBytes = 0;\n  const filesRead: string[] = [];\n\n  for (const filePath of matchedFiles) {\n    roundTrips++;\n    try {\n      const content = readFileSync(resolve(rootDir, filePath), \"utf-8\");\n      totalBytes += Buffer.byteLength(content, \"utf-8\");\n      totalTokens += enc.encode(content).length;\n      filesRead.push(filePath);\n    } catch {\n      // skip unreadable\n    }\n  }\n\n  return {\n    tokensConsumed: totalTokens,\n    roundTrips,\n    filesRead,\n    bytesRead: totalBytes,\n  };\n}\n\n// ── codefocus query ─────────────────────────────────────────────────────\n\nfunction runCodefocusQuery(\n  rootDir: string,\n  cliPath: string,\n  task: BenchmarkTask,\n): CodefocusResult {\n  let stdout: string;\n  try {\n    stdout = execFileSync(\n      \"node\",\n      [cliPath, \"query\", task.queryTerm, \"--root\", rootDir, \"--budget\", \"8000\"],\n      { encoding: \"utf-8\", timeout: 30_000 },\n    );\n  } catch (err: any) {\n    stdout = (err.stdout || \"\") + (err.stderr || \"\");\n  }\n\n  // Parse token count from footer: ~N tokens\n  const tokenMatch = stdout.match(/~(\\d+) tokens/);\n  const tokensOutput = tokenMatch ? parseInt(tokenMatch[1], 10) : 0;\n\n  // Parse files from section headers: ── file:line-line (...) ──\n  const fileMatches = stdout.matchAll(/── ([\\w/.]+\\.ts):\\d+-\\d+/g);\n  const filesReturned = [...fileMatches].map((m) => m[1]);\n\n  return {\n    tokensOutput,\n    roundTrips: 1,\n    filesReturned,\n    stdout,\n  };\n}\n\n// ── scoring ─────────────────────────────────────────────────────────────\n\nfunction computeCompleteness(\n  returnedFiles: string[],\n  expectedFiles: string[],\n): number {\n  if (expectedFiles.length === 0) return 1;\n  const returned = new Set(returnedFiles);\n  const found = expectedFiles.filter((f) => returned.has(f)).length;\n  return found / expectedFiles.length;\n}\n\nfunction computePrecision(\n  returnedFiles: string[],\n  expectedFiles: string[],\n): number {\n  if (returnedFiles.length === 0) return 0;\n  const expected = new Set(expectedFiles);\n  const relevant = returnedFiles.filter((f) => expected.has(f)).length;\n  return relevant / returnedFiles.length;\n}\n\n// ── main ────────────────────────────────────────────────────────────────\n\nexport interface BenchmarkResults {\n  tasks: TaskResult[];\n  summary: {\n    avgExploreTokens: number;\n    avgCodefocusTokens: number;\n    avgTokenSavingsRatio: number;\n    avgExploreRoundTrips: number;\n    avgCodefocusRoundTrips: number;\n    avgExploreCompleteness: number;\n    avgCodefocusCompleteness: number;\n    /** B2: Essential completeness — must-have files only */\n    avgExploreEssentialCompleteness: number;\n    avgCodefocusEssentialCompleteness: number;\n    avgExplorePrecision: number;\n    avgCodefocusPrecision: number;\n  };\n  /** Optional: real Explore agent token counts recorded during benchmark */\n  exploreAgentTokens: Record<string, number>;\n}\n\nexport function runBenchmark(\n  rootDir: string,\n  cliPath: string,\n  exploreAgentTokens?: Record<string, number>,\n): BenchmarkResults {\n  const results: TaskResult[] = [];\n\n  for (const task of TASKS) {\n    const explore = simulateExplore(rootDir, task);\n    const codefocus = runCodefocusQuery(rootDir, cliPath, task);\n\n    const exploreCompleteness = computeCompleteness(\n      explore.filesRead,\n      task.expectedFiles,\n    );\n    const codefocusCompleteness = computeCompleteness(\n      codefocus.filesReturned,\n      task.expectedFiles,\n    );\n\n    // B2: Essential completeness — only essential files\n    const exploreEssentialCompleteness = computeCompleteness(\n      explore.filesRead,\n      task.essentialFiles,\n    );\n    const codefocusEssentialCompleteness = computeCompleteness(\n      codefocus.filesReturned,\n      task.essentialFiles,\n    );\n\n    const explorePrecision = computePrecision(\n      explore.filesRead,\n      task.expectedFiles,\n    );\n    const codefocusPrecision = computePrecision(\n      codefocus.filesReturned,\n      task.expectedFiles,\n    );\n\n    const tokenSavingsRatio =\n      codefocus.tokensOutput > 0\n        ? explore.tokensConsumed / codefocus.tokensOutput\n        : 0;\n\n    results.push({\n      task,\n      explore,\n      codefocus,\n      exploreCompleteness,\n      codefocusCompleteness,\n      exploreEssentialCompleteness,\n      codefocusEssentialCompleteness,\n      explorePrecision,\n      codefocusPrecision,\n      tokenSavingsRatio,\n    });\n  }\n\n  const avg = (arr: number[]) =>\n    arr.length > 0 ? arr.reduce((a, b) => a + b, 0) / arr.length : 0;\n\n  return {\n    tasks: results,\n    summary: {\n      avgExploreTokens: avg(results.map((r) => r.explore.tokensConsumed)),\n      avgCodefocusTokens: avg(results.map((r) => r.codefocus.tokensOutput)),\n      avgTokenSavingsRatio: avg(results.map((r) => r.tokenSavingsRatio)),\n      avgExploreRoundTrips: avg(results.map((r) => r.explore.roundTrips)),\n      avgCodefocusRoundTrips: avg(\n        results.map((r) => r.codefocus.roundTrips),\n      ),\n      avgExploreCompleteness: avg(results.map((r) => r.exploreCompleteness)),\n      avgCodefocusCompleteness: avg(\n        results.map((r) => r.codefocusCompleteness),\n      ),\n      avgExploreEssentialCompleteness: avg(\n        results.map((r) => r.exploreEssentialCompleteness),\n      ),\n      avgCodefocusEssentialCompleteness: avg(\n        results.map((r) => r.codefocusEssentialCompleteness),\n      ),\n      avgExplorePrecision: avg(results.map((r) => r.explorePrecision)),\n      avgCodefocusPrecision: avg(results.map((r) => r.codefocusPrecision)),\n    },\n    exploreAgentTokens: exploreAgentTokens ?? {},\n  };\n}\n\n// ── CLI entry point ─────────────────────────────────────────────────────\n\nexport function formatResults(results: BenchmarkResults): string {\n  const lines: string[] = [];\n\n  lines.push(\"# codefocus Benchmark — Spike 8\");\n  lines.push(\"\");\n  lines.push(\n    \"Comparison of codefocus query vs. Explore agent pattern (grep/glob/read)\",\n  );\n  lines.push(`for ${results.tasks.length} representative code comprehension tasks.`);\n  lines.push(\"\");\n  lines.push(`Benchmark run: ${new Date().toISOString()}`);\n  lines.push(\"\");\n\n  // ── per-task table ──────────────────────────────────────────────────\n\n  lines.push(\"## Per-task results\");\n  lines.push(\"\");\n  lines.push(\n    \"| Task | Explore tokens | CF tokens | Savings | CF compl. | CF essential | CF prec. |\",\n  );\n  lines.push(\n    \"|------|---------------:|----------:|--------:|----------:|-------------:|---------:|\",\n  );\n\n  for (const r of results.tasks) {\n    const savings = r.tokenSavingsRatio.toFixed(1) + \"x\";\n    lines.push(\n      `| ${r.task.id} | ${r.explore.tokensConsumed} | ${r.codefocus.tokensOutput} | ${savings} | ${pct(r.codefocusCompleteness)} | ${pct(r.codefocusEssentialCompleteness)} | ${pct(r.codefocusPrecision)} |`,\n    );\n  }\n\n  lines.push(\"\");\n\n  // ── summary ─────────────────────────────────────────────────────────\n\n  lines.push(\"## Summary\");\n  lines.push(\"\");\n\n  const s = results.summary;\n  lines.push(\n    \"| Metric | Explore (grep/glob/read) | codefocus query |\",\n  );\n  lines.push(\"|--------|------------------------:|----------------:|\");\n  lines.push(\n    `| Avg tokens consumed | ${Math.round(s.avgExploreTokens)} | ${Math.round(s.avgCodefocusTokens)} |`,\n  );\n  lines.push(\n    `| Avg token savings | — | ${s.avgTokenSavingsRatio.toFixed(1)}x less |`,\n  );\n  lines.push(\n    `| Avg round-trips | ${s.avgExploreRoundTrips.toFixed(1)} | ${s.avgCodefocusRoundTrips.toFixed(1)} |`,\n  );\n  lines.push(\n    `| Avg completeness (total) | ${pct(s.avgExploreCompleteness)} | ${pct(s.avgCodefocusCompleteness)} |`,\n  );\n  lines.push(\n    `| Avg completeness (essential) | ${pct(s.avgExploreEssentialCompleteness)} | ${pct(s.avgCodefocusEssentialCompleteness)} |`,\n  );\n  lines.push(\n    `| Avg precision | ${pct(s.avgExplorePrecision)} | ${pct(s.avgCodefocusPrecision)} |`,\n  );\n\n  lines.push(\"\");\n\n  // ── real explore agent tokens ───────────────────────────────────────\n\n  if (Object.keys(results.exploreAgentTokens).length > 0) {\n    lines.push(\"## Real Explore agent token counts\");\n    lines.push(\"\");\n    lines.push(\n      \"These are actual token counts from running the Explore subagent\",\n    );\n    lines.push(\"(Claude Code Task tool, subagent_type=Explore).\");\n    lines.push(\"\");\n    lines.push(\"| Task | Explore agent tokens | codefocus tokens | Savings |\");\n    lines.push(\"|------|---------------------:|-----------------:|--------:|\");\n\n    for (const r of results.tasks) {\n      const agentTokens = results.exploreAgentTokens[r.task.id];\n      if (agentTokens !== undefined) {\n        const cfTokens = r.codefocus.tokensOutput;\n        const ratio =\n          cfTokens > 0 ? (agentTokens / cfTokens).toFixed(1) + \"x\" : \"—\";\n        lines.push(\n          `| ${r.task.id} | ${agentTokens} | ${cfTokens} | ${ratio} |`,\n        );\n      }\n    }\n\n    lines.push(\"\");\n  }\n\n  // ── per-task detail ─────────────────────────────────────────────────\n\n  lines.push(\"## Per-task detail\");\n  lines.push(\"\");\n\n  for (const r of results.tasks) {\n    lines.push(`### ${r.task.id}`);\n    lines.push(\"\");\n    lines.push(`**Question:** ${r.task.question}`);\n    lines.push(\"\");\n    lines.push(\n      `**Search terms:** ${r.task.searchTerms.map((t) => `\\`${t}\\``).join(\", \")}`,\n    );\n    lines.push(`**Query term:** \\`${r.task.queryTerm}\\``);\n    lines.push(\"\");\n    lines.push(\"**Explore pattern:**\");\n    lines.push(`- Files read: ${r.explore.filesRead.join(\", \") || \"(none)\"}`);\n    lines.push(`- Tokens consumed: ${r.explore.tokensConsumed}`);\n    lines.push(`- Round-trips: ${r.explore.roundTrips}`);\n    lines.push(\"\");\n    lines.push(\"**codefocus query:**\");\n    lines.push(\n      `- Files returned: ${r.codefocus.filesReturned.join(\", \") || \"(none)\"}`,\n    );\n    lines.push(`- Tokens output: ${r.codefocus.tokensOutput}`);\n    lines.push(`- Round-trips: ${r.codefocus.roundTrips}`);\n    lines.push(\"\");\n    lines.push(\n      `**Essential files:** ${r.task.essentialFiles.join(\", \")}`,\n    );\n    if (r.task.bonusFiles.length > 0) {\n      lines.push(\n        `**Bonus files:** ${r.task.bonusFiles.join(\", \")}`,\n      );\n    }\n    lines.push(\n      `**Expected symbols:** ${r.task.expectedSymbols.map((s) => `\\`${s}\\``).join(\", \")}`,\n    );\n    lines.push(\"\");\n  }\n\n  // ── methodology ─────────────────────────────────────────────────────\n\n  lines.push(\"## Methodology\");\n  lines.push(\"\");\n  lines.push(\"### Explore agent simulation\");\n  lines.push(\"\");\n  lines.push(\"The Explore agent simulation models a **conservative lower bound**\");\n  lines.push(\"of what a real grep/glob/read agent would consume:\");\n  lines.push(\"\");\n  lines.push(\"1. For each search term, run `grep -rl` in `src/` (1 round-trip per grep)\");\n  lines.push(\"2. Read each matching file in full (1 round-trip per file)\");\n  lines.push(\"3. Count total tokens of all file content with cl100k_base\");\n  lines.push(\"\");\n  lines.push(\"Real agents typically consume **2-5x more** tokens because they:\");\n  lines.push(\"- Read files speculatively that turn out to be irrelevant\");\n  lines.push(\"- Re-read files across multiple turns\");\n  lines.push(\"- Read test files, configs, and docs for context\");\n  lines.push(\"- Include directory listing and file search overhead\");\n  lines.push(\"- Receive tool-call framing tokens (prompts, system messages)\");\n  lines.push(\"\");\n  lines.push(\"### codefocus query\");\n  lines.push(\"\");\n  lines.push(\"A single `codefocus query <term> --budget 8000` call.\");\n  lines.push(\"The output is pre-ranked, budget-constrained, and includes only\");\n  lines.push(\"the relevant symbol ranges (not entire files).\");\n  lines.push(\"\");\n  lines.push(\"### Metrics\");\n  lines.push(\"\");\n  lines.push(\"- **Tokens:** cl100k_base token count of content consumed/output\");\n  lines.push(\"- **Round-trips:** Number of tool calls (grep/read for explore, 1 for codefocus)\");\n  lines.push(\"- **Completeness:** Fraction of expected files present in results\");\n  lines.push(\"- **Precision:** Fraction of returned files that are in the expected set\");\n  lines.push(\"- **Token savings:** Explore tokens / codefocus tokens\");\n\n  return lines.join(\"\\n\");\n}\n\nfunction pct(n: number): string {\n  return `${Math.round(n * 100)}%`;\n}\n\nexport async function runBenchmarkCommand(\n  positional: string[],\n  flags: Record<string, string | boolean>,\n): Promise<void> {\n  if (flags.help) {\n    console.log(`codefocus benchmark — Compare codefocus query vs. Explore agent pattern\n\nUsage: codefocus benchmark [options]\n\nOptions:\n  --root <path>     Root directory of indexed project (default: auto-detect)\n  --json            Output raw JSON instead of markdown\n  --extended        Run extended cross-codebase benchmarks against dependencies\n  --emit-config     Print the active scoring config as JSON and exit\n  --help            Show this help message`);\n    return;\n  }\n\n  const { resolveRoot } = await import(\"./root.js\");\n  const root = resolveRoot(flags.root);\n  const cliPath = resolve(\n    new URL(\".\", import.meta.url).pathname,\n    \"../dist/cli.js\",\n  );\n\n  // --emit-config: print active scoring config and exit\n  if (flags[\"emit-config\"]) {\n    const { loadScoringConfig, serializeConfig } = await import(\"./config.js\");\n    const config = loadScoringConfig(root);\n    console.log(serializeConfig(config));\n    return;\n  }\n\n  // --extended: run cross-codebase benchmarks\n  if (flags.extended) {\n    const {\n      discoverSuites,\n      runExtendedBenchmark,\n      formatExtendedResults,\n    } = await import(\"./extended-benchmark.js\");\n\n    const suites = discoverSuites(root);\n    if (suites.length === 0) {\n      console.error(\n        \"[benchmark] No dependency libraries found for extended benchmarks.\",\n      );\n      console.error(\n        \"[benchmark] Run 'npm install' first to install dependencies.\",\n      );\n      process.exitCode = 1;\n      return;\n    }\n\n    console.log(\n      `[benchmark] Running extended benchmarks against ${suites.length} libraries ...`,\n    );\n    for (const s of suites) {\n      console.log(`[benchmark]   ${s.name} (${s.rootDir})`);\n    }\n    console.log(`[benchmark] CLI: ${cliPath}`);\n    console.log(\"\");\n\n    const results = runExtendedBenchmark(root, cliPath, suites);\n\n    if (flags.json) {\n      console.log(JSON.stringify(results, null, 2));\n    } else {\n      console.log(formatExtendedResults(results));\n    }\n    return;\n  }\n\n  // Default: run standard benchmarks against the project itself\n  console.log(`[benchmark] Running ${TASKS.length} tasks against ${root} ...`);\n  console.log(`[benchmark] CLI: ${cliPath}`);\n  console.log(\"\");\n\n  const results = runBenchmark(root, cliPath);\n\n  if (flags.json) {\n    console.log(JSON.stringify(results, null, 2));\n  } else {\n    console.log(formatResults(results));\n  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