codecortex-ai 0.1.1 → 0.2.1

package/README.md

@@ -2,6 +2,8 @@
 
 > Persistent codebase knowledge layer for AI agents. Your AI shouldn't re-learn your codebase every session.
 
+[Website](https://codecortex-ai.vercel.app) · [npm](https://www.npmjs.com/package/codecortex-ai) · [GitHub](https://github.com/rushikeshmore/CodeCortex)
+
 ## The Problem
 
 Every AI coding session starts from scratch. When context compacts or a new session begins, the AI re-scans the entire codebase. Same files, same tokens, same wasted time. It's like hiring a new developer every session who has to re-learn everything before writing a single line.
@@ -15,7 +17,7 @@ Every AI coding session starts from scratch. When context compacts or a new sess
 
 CodeCortex pre-digests codebases into layered knowledge files and serves them to any AI agent via MCP. Instead of re-understanding your codebase every session, the AI starts with knowledge.
 
-**Hybrid extraction:** tree-sitter native N-API for structure (symbols, imports, calls across 27 languages) + host LLM for semantics (what modules do, why they're built that way). Zero extra API keys.
+**Hybrid extraction:** tree-sitter native N-API for structure (symbols, imports, calls across 28 languages) + host LLM for semantics (what modules do, why they're built that way). Zero extra API keys.
 
 ## Quick Start
 
@@ -136,11 +138,11 @@ vs. raw scan of entire codebase:    ~37,800 tokens
 
 85-90% token reduction. 7-10x efficiency gain.
 
-## Supported Languages (27)
+## Supported Languages (28)
 
 | Category | Languages |
 |----------|-----------|
-| Web | TypeScript, TSX, JavaScript |
+| Web | TypeScript, TSX, JavaScript, Liquid |
 | Systems | C, C++, Objective-C, Rust, Zig, Go |
 | JVM | Java, Kotlin, Scala |
 | .NET | C# |
@@ -152,7 +154,7 @@ vs. raw scan of entire codebase:    ~37,800 tokens
 ## Tech Stack
 
 - TypeScript ESM, Node.js 20+
-- `tree-sitter` (native N-API) + 27 language grammar packages
+- `tree-sitter` (native N-API) + 28 language grammar packages
 - `@modelcontextprotocol/sdk` - MCP server
 - `commander` - CLI
 - `simple-git` - git integration

package/dist/{chunk-F4WTE7R3.js → chunk-DWUIP3WA.js}

@@ -947,16 +947,21 @@ export {
   writeManifest,
   createManifest,
   updateManifest,
+  readGraph,
   writeGraph,
   buildGraph,
+  getModuleDependencies,
   enrichCouplingWithImports,
+  readModuleDoc,
+  writeModuleDoc,
   listModuleDocs,
   listDecisions,
   writeSession,
   listSessions,
   getLatestSession,
   createSession,
+  searchKnowledge,
   createServer,
   startServer
 };
-//# sourceMappingURL=chunk-F4WTE7R3.js.map
+//# sourceMappingURL=chunk-DWUIP3WA.js.map

package/dist/cli/index.js

@@ -7,21 +7,27 @@ import {
   enrichCouplingWithImports,
   ensureDir,
   getLatestSession,
+  getModuleDependencies,
   listDecisions,
   listModuleDocs,
   listSessions,
   readFile,
+  readGraph,
   readManifest,
+  readModuleDoc,
+  searchKnowledge,
   startServer,
   updateManifest,
   writeFile,
   writeGraph,
   writeJsonStream,
   writeManifest,
+  writeModuleDoc,
   writeSession
-} from "../chunk-F4WTE7R3.js";
+} from "../chunk-DWUIP3WA.js";
 
 // src/cli/index.ts
+import { createRequire as createRequire2 } from "module";
 import { Command } from "commander";
 
 // src/cli/commands/init.ts
@@ -74,9 +80,11 @@ var LANGUAGE_LOADERS = {
   ocaml: () => require2("tree-sitter-ocaml").ocaml,
   elm: () => require2("tree-sitter-elm"),
   elisp: () => require2("tree-sitter-elisp"),
+  // Web / Templating
+  vue: () => require2("tree-sitter-vue"),
+  liquid: () => require2("tree-sitter-liquid"),
   // Web3 / Other
   solidity: () => require2("tree-sitter-solidity"),
-  vue: () => require2("tree-sitter-vue"),
   ql: () => require2("tree-sitter-ql")
 };
 var EXTENSION_MAP = {
@@ -147,6 +155,8 @@ var EXTENSION_MAP = {
   ".sol": "solidity",
   // Vue
   ".vue": "vue",
+  // Liquid
+  ".liquid": "liquid",
   // CodeQL
   ".ql": "ql"
 };
@@ -1492,6 +1502,75 @@ function extractGenericCalls(tree, file) {
 
 // src/cli/commands/init.ts
 import { readFile as readFile2 } from "fs/promises";
+
+// src/core/module-gen.ts
+import { existsSync as existsSync3 } from "fs";
+async function generateStructuralModuleDocs(projectRoot, data) {
+  let generated = 0;
+  for (const mod of data.graph.modules) {
+    const docPath = cortexPath(projectRoot, "modules", `${mod.name}.md`);
+    if (existsSync3(docPath)) continue;
+    const moduleFiles = new Set(mod.files);
+    const exported = data.symbols.filter((s) => moduleFiles.has(s.file) && s.exported).map((s) => {
+      const loc = s.endLine > s.startLine ? `${s.file}:${s.startLine}-${s.endLine}` : `${s.file}:${s.startLine}`;
+      return `${s.name} (${s.kind}, ${loc})`;
+    });
+    const deps = getModuleDependencies(data.graph, mod.name);
+    const importsFromModules = /* @__PURE__ */ new Set();
+    const importedByModules = /* @__PURE__ */ new Set();
+    for (const edge of deps.imports) {
+      for (const other of data.graph.modules) {
+        if (other.name !== mod.name && other.files.includes(edge.target)) {
+          importsFromModules.add(other.name);
+        }
+      }
+    }
+    for (const edge of deps.importedBy) {
+      for (const other of data.graph.modules) {
+        if (other.name !== mod.name && other.files.includes(edge.source)) {
+          importedByModules.add(other.name);
+        }
+      }
+    }
+    const depLines = [];
+    if (importsFromModules.size > 0) depLines.push(`Imports from: ${[...importsFromModules].join(", ")}`);
+    if (importedByModules.size > 0) depLines.push(`Imported by: ${[...importedByModules].join(", ")}`);
+    let temporalSignals;
+    if (data.temporal) {
+      const hotspots = data.temporal.hotspots.filter((h) => moduleFiles.has(h.file));
+      const topHotspot = hotspots[0];
+      const couplings = data.temporal.coupling.filter(
+        (c) => moduleFiles.has(c.fileA) || moduleFiles.has(c.fileB)
+      );
+      const coupledWith = couplings.map((c) => {
+        const other = moduleFiles.has(c.fileA) ? c.fileB : c.fileA;
+        return `${other} (${c.cochanges} co-changes, ${Math.round(c.strength * 100)}%)`;
+      });
+      const bugs = data.temporal.bugHistory.filter((b) => moduleFiles.has(b.file));
+      temporalSignals = {
+        churn: topHotspot ? `${topHotspot.changes} changes (${topHotspot.stability})` : "no hotspot data",
+        coupledWith,
+        stability: topHotspot?.stability ?? "unknown",
+        bugHistory: bugs.flatMap((b) => b.lessons),
+        lastChanged: topHotspot?.lastChanged ?? "unknown"
+      };
+    }
+    const analysis = {
+      name: mod.name,
+      purpose: `${mod.files.length} files, ${mod.lines} lines (${mod.language}). Auto-generated from code structure \u2014 use \`analyze_module\` MCP tool for semantic analysis.`,
+      dataFlow: `Files: ${mod.files.join(", ")}`,
+      publicApi: exported,
+      gotchas: [],
+      dependencies: depLines,
+      temporalSignals
+    };
+    await writeModuleDoc(projectRoot, analysis);
+    generated++;
+  }
+  return generated;
+}
+
+// src/cli/commands/init.ts
 async function initCommand(opts) {
   const root = resolve(opts.root);
   const days = parseInt(opts.days, 10);
@@ -1619,7 +1698,12 @@ async function initCommand(opts) {
   });
   await writeManifest(root, manifest);
   await writeFile(cortexPath(root, "patterns.md"), "# Coding Patterns\n\nNo patterns recorded yet. Use `update_patterns` to add patterns.\n");
-  console.log("  Written: cortex.yaml, symbols.json, graph.json, temporal.json, overview.md, patterns.md");
+  const moduleDocsGenerated = await generateStructuralModuleDocs(root, {
+    graph,
+    symbols: allSymbols,
+    temporal: temporalData
+  });
+  console.log(`  Written: cortex.yaml, symbols.json, graph.json, temporal.json, overview.md, patterns.md, ${moduleDocsGenerated} module docs`);
   console.log("");
   console.log("Step 6/6: Generating constitution...");
   await generateConstitution(root, {
@@ -1689,10 +1773,10 @@ function generateOverview(project) {
 
 // src/cli/commands/serve.ts
 import { resolve as resolve2 } from "path";
-import { existsSync as existsSync3 } from "fs";
+import { existsSync as existsSync4 } from "fs";
 async function serveCommand(opts) {
   const root = resolve2(opts.root);
-  if (!existsSync3(cortexPath(root, "cortex.yaml"))) {
+  if (!existsSync4(cortexPath(root, "cortex.yaml"))) {
     console.error("Error: No CodeCortex knowledge found.");
     console.error(`Run 'codecortex init' first to analyze the codebase.`);
     console.error(`Expected: ${cortexPath(root, "cortex.yaml")}`);
@@ -1703,7 +1787,7 @@ async function serveCommand(opts) {
 
 // src/cli/commands/update.ts
 import { resolve as resolve3 } from "path";
-import { existsSync as existsSync4 } from "fs";
+import { existsSync as existsSync5 } from "fs";
 
 // src/git/diff.ts
 import simpleGit2 from "simple-git";
@@ -1739,7 +1823,7 @@ import { readFile as fsRead3 } from "fs/promises";
 async function updateCommand(opts) {
   const root = resolve3(opts.root);
   const days = parseInt(opts.days, 10);
-  if (!existsSync4(cortexPath(root, "cortex.yaml"))) {
+  if (!existsSync5(cortexPath(root, "cortex.yaml"))) {
     console.error("Error: No CodeCortex knowledge found. Run `codecortex init` first.");
     process.exit(1);
   }
@@ -1821,6 +1905,11 @@ async function updateCommand(opts) {
   if (temporalData) {
     await writeFile(cortexPath(root, "temporal.json"), JSON.stringify(temporalData, null, 2));
   }
+  await generateStructuralModuleDocs(root, {
+    graph,
+    symbols: allSymbols,
+    temporal: temporalData
+  });
   await updateManifest(root, {
     totalFiles: project.files.length,
     totalSymbols: allSymbols.length,
@@ -1856,10 +1945,10 @@ async function updateCommand(opts) {
 
 // src/cli/commands/status.ts
 import { resolve as resolve4 } from "path";
-import { existsSync as existsSync5 } from "fs";
+import { existsSync as existsSync6 } from "fs";
 async function statusCommand(opts) {
   const root = resolve4(opts.root);
-  if (!existsSync5(cortexPath(root, "cortex.yaml"))) {
+  if (!existsSync6(cortexPath(root, "cortex.yaml"))) {
     console.log("No CodeCortex knowledge found.");
     console.log(`Run 'codecortex init' to analyze this codebase.`);
     return;
@@ -1946,12 +2035,300 @@ async function statusCommand(opts) {
   }
 }
 
+// src/cli/commands/symbols.ts
+import { resolve as resolve5 } from "path";
+import { existsSync as existsSync7 } from "fs";
+async function symbolsCommand(query, opts) {
+  const root = resolve5(opts.root);
+  if (!existsSync7(cortexPath(root, "cortex.yaml"))) {
+    console.log("No CodeCortex knowledge found.");
+    console.log(`Run 'codecortex init' to analyze this codebase.`);
+    return;
+  }
+  const content = await readFile(cortexPath(root, "symbols.json"));
+  if (!content) {
+    console.log("No symbol index found. Run `codecortex init` first.");
+    return;
+  }
+  const index = JSON.parse(content);
+  if (!query && !opts.kind && !opts.file && !opts.exported) {
+    printSummary(index);
+    return;
+  }
+  let matches = index.symbols;
+  if (query) {
+    const q = query.toLowerCase();
+    matches = matches.filter((s) => s.name.toLowerCase().includes(q));
+  }
+  if (opts.kind) {
+    matches = matches.filter((s) => s.kind === opts.kind);
+  }
+  if (opts.file) {
+    matches = matches.filter((s) => s.file.includes(opts.file));
+  }
+  if (opts.exported) {
+    matches = matches.filter((s) => s.exported);
+  }
+  const limit = parseInt(opts.limit ?? "30", 10);
+  const display = matches.slice(0, limit);
+  if (display.length === 0) {
+    console.log(`No symbols found${query ? ` matching "${query}"` : ""}.`);
+    return;
+  }
+  console.log("");
+  for (const s of display) {
+    const lines = s.endLine > s.startLine ? `${s.startLine}-${s.endLine}` : `${s.startLine}`;
+    const exp = s.exported ? "exported" : "local";
+    console.log(`  ${pad(s.kind, 12)} ${pad(s.name, 30)} ${pad(s.file, 40)} ${pad(lines, 10)} ${exp}`);
+    if (s.signature) {
+      console.log(`${" ".repeat(14)}${s.signature}`);
+    }
+  }
+  console.log("");
+  if (matches.length > limit) {
+    console.log(`Showing ${limit} of ${matches.length} matches. Use -l to show more.`);
+  } else {
+    console.log(`${matches.length} symbol${matches.length === 1 ? "" : "s"} found.`);
+  }
+}
+function printSummary(index) {
+  console.log("");
+  console.log(`Symbol Index: ${index.total} symbols`);
+  console.log("\u2500".repeat(50));
+  const byKind = /* @__PURE__ */ new Map();
+  for (const s of index.symbols) {
+    byKind.set(s.kind, (byKind.get(s.kind) ?? 0) + 1);
+  }
+  console.log("");
+  console.log("By Kind:");
+  for (const [kind, count] of [...byKind.entries()].sort((a, b) => b[1] - a[1])) {
+    console.log(`  ${pad(kind, 14)} ${count}`);
+  }
+  const byFile = /* @__PURE__ */ new Map();
+  for (const s of index.symbols) {
+    byFile.set(s.file, (byFile.get(s.file) ?? 0) + 1);
+  }
+  console.log("");
+  console.log("Top Files:");
+  for (const [file, count] of [...byFile.entries()].sort((a, b) => b[1] - a[1]).slice(0, 10)) {
+    console.log(`  ${pad(file, 45)} ${count} symbols`);
+  }
+  const exported = index.symbols.filter((s) => s.exported).length;
+  console.log("");
+  console.log(`Exported: ${exported}/${index.total}`);
+  console.log("");
+  console.log("Run `codecortex symbols <query>` to search.");
+}
+function pad(str, len) {
+  return str.length >= len ? str : str + " ".repeat(len - str.length);
+}
+
+// src/cli/commands/search.ts
+import { resolve as resolve6 } from "path";
+import { existsSync as existsSync8 } from "fs";
+async function searchCommand(query, opts) {
+  const root = resolve6(opts.root);
+  if (!existsSync8(cortexPath(root, "cortex.yaml"))) {
+    console.log("No CodeCortex knowledge found.");
+    console.log(`Run 'codecortex init' to analyze this codebase.`);
+    return;
+  }
+  const results = await searchKnowledge(root, query);
+  const limit = parseInt(opts.limit ?? "20", 10);
+  const display = results.slice(0, limit);
+  if (display.length === 0) {
+    console.log(`No results for "${query}".`);
+    return;
+  }
+  console.log("");
+  console.log(`Search: "${query}"`);
+  console.log("\u2500".repeat(50));
+  for (let i = 0; i < display.length; i++) {
+    const r = display[i];
+    console.log("");
+    console.log(`  [${i + 1}] ${r.file}:${r.line}`);
+    const ctxLines = r.context.split("\n");
+    for (const line of ctxLines) {
+      const trimmed = line.trim();
+      if (!trimmed) continue;
+      if (trimmed.toLowerCase().includes(query.toLowerCase())) {
+        console.log(`    > ${trimmed}`);
+      } else {
+        console.log(`      ${trimmed}`);
+      }
+    }
+  }
+  console.log("");
+  if (results.length > limit) {
+    console.log(`Showing ${limit} of ${results.length} results. Use -l to show more.`);
+  } else {
+    console.log(`${results.length} result${results.length === 1 ? "" : "s"} found.`);
+  }
+}
+
+// src/cli/commands/modules.ts
+import { resolve as resolve7 } from "path";
+import { existsSync as existsSync9 } from "fs";
+async function modulesCommand(name, opts) {
+  const root = resolve7(opts.root);
+  if (!existsSync9(cortexPath(root, "cortex.yaml"))) {
+    console.log("No CodeCortex knowledge found.");
+    console.log(`Run 'codecortex init' to analyze this codebase.`);
+    return;
+  }
+  const graph = await readGraph(root);
+  if (!graph) {
+    console.log("No dependency graph found. Run `codecortex init` first.");
+    return;
+  }
+  if (!name) {
+    await printModuleList(root, graph);
+    return;
+  }
+  await printModuleDetail(root, name, graph);
+}
+async function printModuleList(root, graph) {
+  const docsAvailable = new Set(await listModuleDocs(root));
+  console.log("");
+  console.log(`Modules: ${graph.modules.length}`);
+  console.log("\u2500".repeat(70));
+  console.log("");
+  console.log(`  ${pad2("MODULE", 18)} ${pad2("FILES", 6)} ${pad2("LINES", 7)} ${pad2("SYMBOLS", 8)} ${pad2("LANG", 14)} DOC`);
+  for (const mod of [...graph.modules].sort((a, b) => a.name.localeCompare(b.name))) {
+    const hasDoc = docsAvailable.has(mod.name) ? "yes" : "--";
+    console.log(`  ${pad2(mod.name, 18)} ${pad2(String(mod.files.length), 6)} ${pad2(String(mod.lines), 7)} ${pad2(String(mod.symbols), 8)} ${pad2(mod.language, 14)} ${hasDoc}`);
+  }
+  const withDocs = graph.modules.filter((m) => docsAvailable.has(m.name)).length;
+  console.log("");
+  console.log(`${graph.modules.length} modules, ${withDocs} with docs.`);
+  console.log("");
+  console.log("Run `codecortex modules <name>` to deep-dive into a module.");
+}
+async function printModuleDetail(root, name, graph) {
+  const mod = graph.modules.find((m) => m.name === name);
+  if (!mod) {
+    const available = graph.modules.map((m) => m.name).join(", ");
+    console.log(`Module "${name}" not found. Available: ${available}`);
+    return;
+  }
+  console.log("");
+  console.log(`Module: ${name}`);
+  console.log("\u2550".repeat(50));
+  const doc = await readModuleDoc(root, name);
+  if (doc) {
+    console.log("");
+    console.log(doc);
+  } else {
+    console.log("");
+    console.log(`No module doc for "${name}".`);
+    console.log(`Run \`codecortex init\` to generate structural docs.`);
+  }
+  const deps = getModuleDependencies(graph, name);
+  if (deps.imports.length > 0) {
+    console.log("");
+    console.log("Imports:");
+    const seen = /* @__PURE__ */ new Set();
+    for (const edge of deps.imports) {
+      const key = `${edge.source} -> ${edge.target}`;
+      if (seen.has(key)) continue;
+      seen.add(key);
+      const specifiers = edge.specifiers.length > 0 ? ` [${edge.specifiers.join(", ")}]` : "";
+      console.log(`  ${edge.source} -> ${edge.target}${specifiers}`);
+    }
+  }
+  if (deps.importedBy.length > 0) {
+    console.log("");
+    console.log("Imported By:");
+    const seen = /* @__PURE__ */ new Set();
+    for (const edge of deps.importedBy) {
+      const key = `${edge.source} -> ${edge.target}`;
+      if (seen.has(key)) continue;
+      seen.add(key);
+      const specifiers = edge.specifiers.length > 0 ? ` [${edge.specifiers.join(", ")}]` : "";
+      console.log(`  ${edge.source} -> ${edge.target}${specifiers}`);
+    }
+  }
+  console.log("");
+  console.log(`Stats: ${mod.files.length} files, ${mod.lines} lines, ${mod.symbols} symbols (${mod.language})`);
+}
+function pad2(str, len) {
+  return str.length >= len ? str : str + " ".repeat(len - str.length);
+}
+
+// src/cli/commands/hotspots.ts
+import { resolve as resolve8 } from "path";
+import { existsSync as existsSync10 } from "fs";
+async function hotspotsCommand(opts) {
+  const root = resolve8(opts.root);
+  if (!existsSync10(cortexPath(root, "cortex.yaml"))) {
+    console.log("No CodeCortex knowledge found.");
+    console.log(`Run 'codecortex init' to analyze this codebase.`);
+    return;
+  }
+  const content = await readFile(cortexPath(root, "temporal.json"));
+  if (!content) {
+    console.log("No temporal data found. Run `codecortex init` in a git repository.");
+    return;
+  }
+  const temporal = JSON.parse(content);
+  const limit = parseInt(opts.limit ?? "15", 10);
+  const riskMap = /* @__PURE__ */ new Map();
+  for (const h of temporal.hotspots) {
+    riskMap.set(h.file, { churn: h.changes, couplings: 0, bugs: 0, risk: h.changes });
+  }
+  for (const c of temporal.coupling) {
+    for (const f of [c.fileA, c.fileB]) {
+      const entry = riskMap.get(f) ?? { churn: 0, couplings: 0, bugs: 0, risk: 0 };
+      entry.couplings++;
+      entry.risk += c.strength * 2;
+      riskMap.set(f, entry);
+    }
+  }
+  for (const b of temporal.bugHistory) {
+    const entry = riskMap.get(b.file) ?? { churn: 0, couplings: 0, bugs: 0, risk: 0 };
+    entry.bugs = b.fixCommits;
+    entry.risk += b.fixCommits * 3;
+    riskMap.set(b.file, entry);
+  }
+  const ranked = [...riskMap.entries()].sort((a, b) => b[1].risk - a[1].risk).slice(0, limit).map(([file, data]) => ({ file, ...data, risk: Math.round(data.risk * 100) / 100 }));
+  console.log("");
+  console.log(`Hotspots \u2014 ${temporal.periodDays} days, ${temporal.totalCommits} commits`);
+  console.log("\u2500".repeat(70));
+  console.log("");
+  console.log(`  ${pad3("#", 4)} ${pad3("FILE", 42)} ${pad3("CHURN", 6)} ${pad3("CPLS", 5)} ${pad3("BUGS", 5)} RISK`);
+  for (let i = 0; i < ranked.length; i++) {
+    const r = ranked[i];
+    console.log(`  ${pad3(String(i + 1), 4)} ${pad3(r.file, 42)} ${pad3(String(r.churn), 6)} ${pad3(String(r.couplings), 5)} ${pad3(String(r.bugs), 5)} ${r.risk.toFixed(2)}`);
+  }
+  const hidden = temporal.coupling.filter((c) => !c.hasImport && c.strength >= 0.3);
+  if (hidden.length > 0) {
+    console.log("");
+    console.log("Hidden Dependencies (co-change but no import):");
+    for (const h of hidden.slice(0, 10)) {
+      console.log(`  ${h.fileA} <-> ${h.fileB}  (${h.cochanges} co-changes, ${Math.round(h.strength * 100)}%)`);
+    }
+    if (hidden.length > 10) {
+      console.log(`  ... and ${hidden.length - 10} more`);
+    }
+  }
+  console.log("");
+}
+function pad3(str, len) {
+  return str.length >= len ? str : str + " ".repeat(len - str.length);
+}
+
 // src/cli/index.ts
+var require3 = createRequire2(import.meta.url);
+var { version } = require3("../../package.json");
 var program = new Command();
-program.name("codecortex").description("Persistent, AI-powered codebase knowledge layer").version("0.1.0");
+program.name("codecortex").description("Persistent, AI-powered codebase knowledge layer").version(version);
 program.command("init").description("Initialize codebase knowledge: discover files, extract symbols, analyze git history").option("-r, --root <path>", "Project root directory", process.cwd()).option("-d, --days <number>", "Days of git history to analyze", "90").action(initCommand);
 program.command("serve").description("Start MCP server (stdio transport) for AI agent access").option("-r, --root <path>", "Project root directory", process.cwd()).action(serveCommand);
 program.command("update").description("Update knowledge for changed files since last session").option("-r, --root <path>", "Project root directory", process.cwd()).option("-d, --days <number>", "Days of git history to re-analyze", "90").action(updateCommand);
 program.command("status").description("Show knowledge freshness, stale modules, and symbol counts").option("-r, --root <path>", "Project root directory", process.cwd()).action(statusCommand);
+program.command("symbols [query]").description("Browse and filter the symbol index").option("-r, --root <path>", "Project root directory", process.cwd()).option("-k, --kind <kind>", "Filter by kind: function, class, interface, type, const, enum, method, property, variable").option("-f, --file <path>", "Filter by file path (partial match)").option("-e, --exported", "Show only exported symbols").option("-l, --limit <number>", "Max results", "30").action((query, opts) => symbolsCommand(query, opts));
+program.command("search <query>").description("Search across all CodeCortex knowledge files").option("-r, --root <path>", "Project root directory", process.cwd()).option("-l, --limit <number>", "Max results", "20").action((query, opts) => searchCommand(query, opts));
+program.command("modules [name]").description("List modules or deep-dive into a specific module").option("-r, --root <path>", "Project root directory", process.cwd()).action((name, opts) => modulesCommand(name, opts));
+program.command("hotspots").description("Show files ranked by risk: churn + coupling + bug history").option("-r, --root <path>", "Project root directory", process.cwd()).option("-l, --limit <number>", "Number of files to show", "15").action(hotspotsCommand);
 program.parse();
 //# sourceMappingURL=index.js.map