@optave/codegraph 2.3.0 → 2.4.0

package/README.md

@@ -55,7 +55,7 @@ cd your-project
 codegraph build
 ```
 
-That's it. No config files, no Docker, no JVM, no API keys, no accounts. The graph is ready to query. Add `codegraph mcp` to your AI agent's config and it has full access to your dependency graph through 17 MCP tools.
+That's it. No config files, no Docker, no JVM, no API keys, no accounts. The graph is ready to query. Add `codegraph mcp` to your AI agent's config and it has full access to your dependency graph through 19 MCP tools.
 
 ### Why it matters
 
@@ -78,7 +78,9 @@ That's it. No config files, no Docker, no JVM, no API keys, no accounts. The gra
 | Semantic search | **Yes** | — | **Yes** | **Yes** | — | **Yes** | — | — |
 | MCP / AI agent support | **Yes** | — | **Yes** | **Yes** | **Yes** | **Yes** | **Yes** | — |
 | Git diff impact | **Yes** | — | — | — | — | **Yes** | — | **Yes** |
+| Git co-change analysis | **Yes** | — | — | — | — | — | **Yes** | **Yes** |
 | Watch mode | **Yes** | — | **Yes** | — | — | — | — | — |
+| Dead code / role classification | **Yes** | — | **Yes** | — | — | — | — | **Yes** |
 | Cycle detection | **Yes** | — | **Yes** | — | — | — | — | **Yes** |
 | Incremental rebuilds | **O(changed)** | — | O(n) Merkle | — | — | — | — | — |
 | Zero config | **Yes** | — | **Yes** | — | — | — | — | — |
@@ -94,9 +96,10 @@ That's it. No config files, no Docker, no JVM, no API keys, no accounts. The gra
 | **⚡** | **Always-fresh graph** | Three-tier change detection: journal (O(changed)) → mtime+size (O(n) stats) → hash (O(changed) reads). Sub-second rebuilds even on large codebases |
 | **🔓** | **Zero-cost core, LLM-enhanced when you want** | Full graph analysis with no API keys, no accounts, no cost. Optionally bring your own LLM provider — your code only goes where you choose |
 | **🔬** | **Function-level, not just files** | Traces `handleAuth()` → `validateToken()` → `decryptJWT()` and shows 14 callers across 9 files break if `decryptJWT` changes |
-| **🤖** | **Built for AI agents** | 17-tool [MCP server](https://modelcontextprotocol.io/) — AI assistants query your graph directly. Single-repo by default |
+| **🏷️** | **Role classification** | Every symbol auto-tagged as `entry`/`core`/`utility`/`adapter`/`dead`/`leaf` — agents instantly know what they're looking at |
+| **🤖** | **Built for AI agents** | 19-tool [MCP server](https://modelcontextprotocol.io/) — AI assistants query your graph directly. Single-repo by default |
 | **🌐** | **Multi-language, one CLI** | JS/TS + Python + Go + Rust + Java + C# + PHP + Ruby + HCL in a single graph |
-| **💥** | **Git diff impact** | `codegraph diff-impact` shows changed functions, their callers, and full blast radius — ships with a GitHub Actions workflow |
+| **💥** | **Git diff impact** | `codegraph diff-impact` shows changed functions, their callers, and full blast radius — enriched with historically coupled files from git co-change analysis. Ships with a GitHub Actions workflow |
 | **🧠** | **Semantic search** | Local embeddings by default, LLM-powered when opted in — multi-query with RRF ranking via `"auth; token; JWT"` |
 
 ---
@@ -141,10 +144,10 @@ After modifying code:
 Or connect directly via MCP:
 
 ```bash
-codegraph mcp          # 17-tool MCP server — AI queries the graph directly
+codegraph mcp          # 19-tool MCP server — AI queries the graph directly
 ```
 
-Full agent setup: [AI Agent Guide](docs/ai-agent-guide.md) · [CLAUDE.md template](docs/ai-agent-guide.md#claudemd-template)
+Full agent setup: [AI Agent Guide](docs/guides/ai-agent-guide.md) · [CLAUDE.md template](docs/guides/ai-agent-guide.md#claudemd-template)
 
 ---
 
@@ -159,15 +162,19 @@ Full agent setup: [AI Agent Guide](docs/ai-agent-guide.md) · [CLAUDE.md t
 | 🎯 | **Deep context** | `context` gives AI agents source, deps, callers, signature, and tests for a function in one call; `explain` gives structural summaries of files or functions |
 | 📍 | **Fast lookup** | `where` shows exactly where a symbol is defined and used — minimal, fast |
 | 📊 | **Diff impact** | Parse `git diff`, find overlapping functions, trace their callers |
+| 🔗 | **Co-change analysis** | Analyze git history for files that always change together — surfaces hidden coupling the static graph can't see; enriches `diff-impact` with historically coupled files |
 | 🗺️ | **Module map** | Bird's-eye view of your most-connected files |
 | 🏗️ | **Structure & hotspots** | Directory cohesion scores, fan-in/fan-out hotspot detection, module boundaries |
+| 🏷️ | **Node role classification** | Every symbol auto-tagged as `entry`/`core`/`utility`/`adapter`/`dead`/`leaf` based on connectivity patterns — agents instantly know architectural role |
 | 🔄 | **Cycle detection** | Find circular dependencies at file or function level |
 | 📤 | **Export** | DOT (Graphviz), Mermaid, and JSON graph export |
 | 🧠 | **Semantic search** | Embeddings-powered natural language search with multi-query RRF ranking |
 | 👀 | **Watch mode** | Incrementally update the graph as files change |
-| 🤖 | **MCP server** | 17-tool MCP server for AI assistants; single-repo by default, opt-in multi-repo |
+| 🤖 | **MCP server** | 19-tool MCP server for AI assistants; single-repo by default, opt-in multi-repo |
 | ⚡ | **Always fresh** | Three-tier incremental detection — sub-second rebuilds even on large codebases |
 
+See [docs/examples](docs/examples) for real-world CLI and MCP usage examples.
+
 ## 📦 Commands
 
 ### Build & Watch
@@ -189,6 +196,9 @@ codegraph map -n 50 --no-tests # Top 50, excluding test files
 codegraph where <name>         # Where is a symbol defined and used?
 codegraph where --file src/db.js  # List symbols, imports, exports for a file
 codegraph stats                # Graph health: nodes, edges, languages, quality score
+codegraph roles                # Node role classification (entry, core, utility, adapter, dead, leaf)
+codegraph roles --role dead -T # Find dead code (unreferenced, non-exported symbols)
+codegraph roles --role core --file src/  # Core symbols in src/
 ```
 
 ### Deep Context (AI-Optimized)
@@ -213,6 +223,22 @@ codegraph diff-impact HEAD~3   # Impact vs a specific ref
 codegraph diff-impact main --format mermaid -T  # Mermaid flowchart of blast radius
 ```
 
+### Co-Change Analysis
+
+Analyze git history to find files that always change together — surfaces hidden coupling the static graph can't see. Requires a git repository.
+
+```bash
+codegraph co-change --analyze          # Scan git history and populate co-change data
+codegraph co-change src/queries.js     # Show co-change partners for a file
+codegraph co-change                    # Show top co-changing file pairs globally
+codegraph co-change --since 6m         # Limit to last 6 months of history
+codegraph co-change --min-jaccard 0.5  # Only show strong coupling (Jaccard >= 0.5)
+codegraph co-change --min-support 5    # Minimum co-commit count
+codegraph co-change --full             # Include all details
+```
+
+Co-change data also enriches `diff-impact` — historically coupled files appear in a `historicallyCoupled` section alongside the static dependency analysis.
+
 ### Structure & Hotspots
 
 ```bash
@@ -379,7 +405,7 @@ Self-measured on every release via CI ([build benchmarks](generated/BUILD-BENCHM
 |---|---|
 | Build speed (native) | **1.9 ms/file** |
 | Build speed (WASM) | **6.6 ms/file** |
-| Query time | **1ms** |
+| Query time | **2ms** |
 | ~50,000 files (est.) | **~95.0s build** |
 
 Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files.
@@ -402,7 +428,7 @@ Optional: `@huggingface/transformers` (semantic search), `@modelcontextprotocol/
 
 ### MCP Server
 
-Codegraph includes a built-in [Model Context Protocol](https://modelcontextprotocol.io/) server with 17 tools, so AI assistants can query your dependency graph directly:
+Codegraph includes a built-in [Model Context Protocol](https://modelcontextprotocol.io/) server with 19 tools, so AI assistants can query your dependency graph directly:
 
 ```bash
 codegraph mcp                  # Single-repo mode (default) — only local project
@@ -416,7 +442,7 @@ codegraph mcp --repos a,b      # Restrict to specific repos (implies --multi-rep
 
 ### CLAUDE.md / Agent Instructions
 
-Add this to your project's `CLAUDE.md` to help AI agents use codegraph (full template in the [AI Agent Guide](docs/ai-agent-guide.md#claudemd-template)):
+Add this to your project's `CLAUDE.md` to help AI agents use codegraph (full template in the [AI Agent Guide](docs/guides/ai-agent-guide.md#claudemd-template)):
 
 ```markdown
 ## Code Navigation
@@ -474,7 +500,7 @@ Use `--kind function` to cut noise. Use `--file <pattern>` to scope.
 
 ## 📋 Recommended Practices
 
-See **[docs/recommended-practices.md](docs/recommended-practices.md)** for integration guides:
+See **[docs/guides/recommended-practices.md](docs/guides/recommended-practices.md)** for integration guides:
 
 - **Git hooks** — auto-rebuild on commit, impact checks on push, commit message enrichment
 - **CI/CD** — PR impact comments, threshold gates, graph caching
@@ -482,7 +508,7 @@ See **[docs/recommended-practices.md](docs/recommended-practices.md)** for integ
 - **Developer workflow** — watch mode, explore-before-you-edit, semantic search
 - **Secure credentials** — `apiKeyCommand` with 1Password, Bitwarden, Vault, macOS Keychain, `pass`
 
-For AI-specific integration, see the **[AI Agent Guide](docs/ai-agent-guide.md)** — a comprehensive reference covering the 6-step agent workflow, complete command-to-MCP mapping, Claude Code hooks, and token-saving patterns.
+For AI-specific integration, see the **[AI Agent Guide](docs/guides/ai-agent-guide.md)** — a comprehensive reference covering the 6-step agent workflow, complete command-to-MCP mapping, Claude Code hooks, and token-saving patterns.
 
 ## 🔁 CI / GitHub Actions
 
@@ -589,6 +615,8 @@ const { results: fused } = await multiSearchData(
 | Incremental rebuilds | **O(changed)** | — | O(n) Merkle | — | — | — |
 | MCP / AI agent support | **Yes** | — | **Yes** | **Yes** | **Yes** | **Yes** |
 | Git diff impact | **Yes** | — | — | — | — | **Yes** |
+| Git co-change analysis | **Yes** | — | — | — | — | — |
+| Dead code / role classification | **Yes** | — | **Yes** | — | — | — |
 | Semantic search | **Yes** | — | **Yes** | **Yes** | — | **Yes** |
 | Watch mode | **Yes** | — | **Yes** | — | — | — |
 | Zero config, no Docker/JVM | **Yes** | — | **Yes** | — | — | — |
@@ -597,7 +625,7 @@ const { results: fused } = await multiSearchData(
 
 ## 🗺️ Roadmap
 
-See **[ROADMAP.md](ROADMAP.md)** for the full development roadmap and **[STABILITY.md](STABILITY.md)** for the stability policy and versioning guarantees. Current plan:
+See **[ROADMAP.md](docs/roadmap/ROADMAP.md)** for the full development roadmap and **[STABILITY.md](STABILITY.md)** for the stability policy and versioning guarantees. Current plan:
 
 1. ~~**Rust Core**~~ — **Complete** (v1.3.0) — native tree-sitter parsing via napi-rs, parallel multi-core parsing, incremental re-parsing, import resolution & cycle detection in Rust
 2. ~~**Foundation Hardening**~~ — **Complete** (v1.4.0) — parser registry, 12-tool MCP server with multi-repo support, test coverage 62%→75%, `apiKeyCommand` secret resolution, global repo registry
@@ -606,7 +634,7 @@ See **[ROADMAP.md](ROADMAP.md)** for the full development roadmap and **[STABILI
 5. **Natural Language Queries** — `codegraph ask` command, conversational sessions
 6. **Expanded Language Support** — 8 new languages (12 → 20)
 7. **GitHub Integration & CI** — reusable GitHub Action, PR review, SARIF output
-8. **Visualization & Advanced** — web UI, dead code detection, monorepo support, agentic search
+8. **Visualization & Advanced** — web UI, monorepo support, agentic search
 
 ## 🤝 Contributing
 
@@ -619,7 +647,7 @@ npm install
 npm test
 ```
 
-Looking to add a new language? Check out **[Adding a New Language](docs/adding-a-language.md)**.
+Looking to add a new language? Check out **[Adding a New Language](docs/guides/adding-a-language.md)**.
 
 ## 📄 License
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@optave/codegraph",
-  "version": "2.3.0",
+  "version": "2.4.0",
   "description": "Local code graph CLI — parse codebases with tree-sitter, build dependency graphs, query them",
   "type": "module",
   "main": "src/index.js",
@@ -62,10 +62,9 @@
   "optionalDependencies": {
     "@huggingface/transformers": "^3.8.1",
     "@modelcontextprotocol/sdk": "^1.0.0",
-    "@optave/codegraph-darwin-arm64": "2.3.0",
-    "@optave/codegraph-darwin-x64": "2.3.0",
-    "@optave/codegraph-linux-x64-gnu": "2.3.0",
-    "@optave/codegraph-win32-x64-msvc": "2.3.0"
+    "@optave/codegraph-darwin-arm64": "2.4.0",
+    "@optave/codegraph-darwin-x64": "2.4.0",
+    "@optave/codegraph-linux-x64-gnu": "2.4.0"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.4",

package/src/builder.js

@@ -827,6 +827,59 @@ export async function buildGraph(rootDir, opts = {}) {
     }
   }
 
+  // For incremental builds, buildStructure needs ALL files (not just changed ones)
+  // because it clears and rebuilds all contains edges and directory metrics.
+  // Load unchanged files from the DB so structure data stays complete.
+  if (!isFullBuild) {
+    const existingFiles = db.prepare("SELECT DISTINCT file FROM nodes WHERE kind = 'file'").all();
+    const defsByFile = db.prepare(
+      "SELECT name, kind, line FROM nodes WHERE file = ? AND kind != 'file' AND kind != 'directory'",
+    );
+    // Count imports per file — buildStructure only uses imports.length for metrics
+    const importCountByFile = db.prepare(
+      `SELECT COUNT(DISTINCT n2.file) AS cnt FROM edges e
+       JOIN nodes n1 ON e.source_id = n1.id
+       JOIN nodes n2 ON e.target_id = n2.id
+       WHERE n1.file = ? AND e.kind = 'imports'`,
+    );
+    const lineCountByFile = db.prepare(
+      `SELECT n.name AS file, m.line_count
+       FROM node_metrics m JOIN nodes n ON m.node_id = n.id
+       WHERE n.kind = 'file'`,
+    );
+    const cachedLineCounts = new Map();
+    for (const row of lineCountByFile.all()) {
+      cachedLineCounts.set(row.file, row.line_count);
+    }
+    let loadedFromDb = 0;
+    for (const { file: relPath } of existingFiles) {
+      if (!fileSymbols.has(relPath)) {
+        const importCount = importCountByFile.get(relPath)?.cnt || 0;
+        fileSymbols.set(relPath, {
+          definitions: defsByFile.all(relPath),
+          imports: new Array(importCount),
+          exports: [],
+        });
+        loadedFromDb++;
+      }
+      if (!lineCountMap.has(relPath)) {
+        const cached = cachedLineCounts.get(relPath);
+        if (cached != null) {
+          lineCountMap.set(relPath, cached);
+        } else {
+          const absPath = path.join(rootDir, relPath);
+          try {
+            const content = fs.readFileSync(absPath, 'utf-8');
+            lineCountMap.set(relPath, content.split('\n').length);
+          } catch {
+            lineCountMap.set(relPath, 0);
+          }
+        }
+      }
+    }
+    debug(`Structure: ${fileSymbols.size} files (${loadedFromDb} loaded from DB)`);
+  }
+
   // Build directory structure, containment edges, and metrics
   const relDirs = new Set();
   for (const absDir of discoveredDirs) {
@@ -839,6 +892,19 @@ export async function buildGraph(rootDir, opts = {}) {
     debug(`Structure analysis failed: ${err.message}`);
   }
 
+  // Classify node roles (entry, core, utility, adapter, dead, leaf)
+  try {
+    const { classifyNodeRoles } = await import('./structure.js');
+    const roleSummary = classifyNodeRoles(db);
+    debug(
+      `Roles: ${Object.entries(roleSummary)
+        .map(([r, c]) => `${r}=${c}`)
+        .join(', ')}`,
+    );
+  } catch (err) {
+    debug(`Role classification failed: ${err.message}`);
+  }
+
   const nodeCount = db.prepare('SELECT COUNT(*) as c FROM nodes').get().c;
   info(`Graph built: ${nodeCount} nodes, ${edgeCount} edges`);
   info(`Stored in ${dbPath}`);

package/src/cli.js

@@ -7,7 +7,13 @@ import { buildGraph } from './builder.js';
 import { loadConfig } from './config.js';
 import { findCycles, formatCycles } from './cycles.js';
 import { openReadonlyOrFail } from './db.js';
-import { buildEmbeddings, EMBEDDING_STRATEGIES, MODELS, search } from './embedder.js';
+import {
+  buildEmbeddings,
+  DEFAULT_MODEL,
+  EMBEDDING_STRATEGIES,
+  MODELS,
+  search,
+} from './embedder.js';
 import { exportDOT, exportJSON, exportMermaid } from './export.js';
 import { setVerbose } from './logger.js';
 import {
@@ -21,7 +27,9 @@ import {
   impactAnalysis,
   moduleMap,
   queryName,
+  roles,
   stats,
+  VALID_ROLES,
   where,
 } from './queries.js';
 import {
@@ -31,6 +39,7 @@ import {
   registerRepo,
   unregisterRepo,
 } from './registry.js';
+import { checkForUpdates, printUpdateNotification } from './update-check.js';
 import { watchProject } from './watcher.js';
 
 const __cliDir = path.dirname(new URL(import.meta.url).pathname.replace(/^\/([A-Z]:)/i, '$1'));
@@ -48,6 +57,17 @@ program
   .hook('preAction', (thisCommand) => {
     const opts = thisCommand.opts();
     if (opts.verbose) setVerbose(true);
+  })
+  .hook('postAction', async (_thisCommand, actionCommand) => {
+    const name = actionCommand.name();
+    if (name === 'mcp' || name === 'watch') return;
+    if (actionCommand.opts().json) return;
+    try {
+      const result = await checkForUpdates(pkg.version);
+      if (result) printUpdateNotification(result.current, result.latest);
+    } catch {
+      /* never break CLI */
+    }
   });
 
 /**
@@ -272,6 +292,7 @@ program
   .option('-T, --no-tests', 'Exclude test/spec files')
   .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
   .option('--min-confidence <score>', 'Minimum edge confidence threshold (default: 0.5)', '0.5')
+  .option('--direction <dir>', 'Flowchart direction for Mermaid: TB, LR, RL, BT', 'LR')
   .option('-o, --output <file>', 'Write to file instead of stdout')
   .action((opts) => {
     const db = openReadonlyOrFail(opts.db);
@@ -279,6 +300,7 @@ program
       fileLevel: !opts.functions,
       noTests: resolveNoTests(opts),
       minConfidence: parseFloat(opts.minConfidence),
+      direction: opts.direction,
     };
 
     let output;
@@ -395,8 +417,15 @@ registry
   .command('prune')
   .description('Remove stale registry entries (missing directories or idle beyond TTL)')
   .option('--ttl <days>', 'Days of inactivity before pruning (default: 30)', '30')
+  .option('--exclude <names>', 'Comma-separated repo names to preserve from pruning')
   .action((opts) => {
-    const pruned = pruneRegistry(undefined, parseInt(opts.ttl, 10));
+    const excludeNames = opts.exclude
+      ? opts.exclude
+          .split(',')
+          .map((s) => s.trim())
+          .filter((s) => s.length > 0)
+      : [];
+    const pruned = pruneRegistry(undefined, parseInt(opts.ttl, 10), excludeNames);
     if (pruned.length === 0) {
       console.log('No stale entries found.');
     } else {
@@ -414,12 +443,13 @@ program
   .command('models')
   .description('List available embedding models')
   .action(() => {
+    const defaultModel = config.embeddings?.model || DEFAULT_MODEL;
     console.log('\nAvailable embedding models:\n');
-    for (const [key, config] of Object.entries(MODELS)) {
-      const def = key === 'minilm' ? ' (default)' : '';
-      const ctx = config.contextWindow ? `${config.contextWindow} ctx` : '';
+    for (const [key, cfg] of Object.entries(MODELS)) {
+      const def = key === defaultModel ? ' (default)' : '';
+      const ctx = cfg.contextWindow ? `${cfg.contextWindow} ctx` : '';
       console.log(
-        `  ${key.padEnd(12)} ${String(config.dim).padStart(4)}d  ${ctx.padEnd(9)} ${config.desc}${def}`,
+        `  ${key.padEnd(12)} ${String(cfg.dim).padStart(4)}d  ${ctx.padEnd(9)} ${cfg.desc}${def}`,
       );
     }
     console.log('\nUsage: codegraph embed --model <name> --strategy <structured|source>');
@@ -433,8 +463,7 @@ program
   )
   .option(
     '-m, --model <name>',
-    'Embedding model: minilm (default), jina-small, jina-base, jina-code, nomic, nomic-v1.5, bge-large. Run `codegraph models` for details',
-    'minilm',
+    'Embedding model (default from config or minilm). Run `codegraph models` for details',
   )
   .option(
     '-s, --strategy <name>',
@@ -449,7 +478,8 @@ program
       process.exit(1);
     }
     const root = path.resolve(dir || '.');
-    await buildEmbeddings(root, opts.model, undefined, { strategy: opts.strategy });
+    const model = opts.model || config.embeddings?.model || DEFAULT_MODEL;
+    await buildEmbeddings(root, model, undefined, { strategy: opts.strategy });
   });
 
 program
@@ -464,6 +494,7 @@ program
   .option('-k, --kind <kind>', 'Filter by kind: function, method, class')
   .option('--file <pattern>', 'Filter by file path pattern')
   .option('--rrf-k <number>', 'RRF k parameter for multi-query ranking', '60')
+  .option('-j, --json', 'Output as JSON')
   .action(async (query, opts) => {
     await search(query, opts.db, {
       limit: parseInt(opts.limit, 10),
@@ -473,6 +504,7 @@ program
       kind: opts.kind,
       filePattern: opts.file,
       rrfK: parseInt(opts.rrfK, 10),
+      json: opts.json,
     });
   });
 
@@ -529,6 +561,90 @@ program
     }
   });
 
+program
+  .command('roles')
+  .description('Show node role classification: entry, core, utility, adapter, dead, leaf')
+  .option('-d, --db <path>', 'Path to graph.db')
+  .option('--role <role>', `Filter by role (${VALID_ROLES.join(', ')})`)
+  .option('-f, --file <path>', 'Scope to a specific file (partial match)')
+  .option('-T, --no-tests', 'Exclude test/spec files')
+  .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
+  .option('-j, --json', 'Output as JSON')
+  .action((opts) => {
+    if (opts.role && !VALID_ROLES.includes(opts.role)) {
+      console.error(`Invalid role "${opts.role}". Valid roles: ${VALID_ROLES.join(', ')}`);
+      process.exit(1);
+    }
+    roles(opts.db, {
+      role: opts.role,
+      file: opts.file,
+      noTests: resolveNoTests(opts),
+      json: opts.json,
+    });
+  });
+
+program
+  .command('co-change [file]')
+  .description(
+    'Analyze git history for files that change together. Use --analyze to scan, or query existing data.',
+  )
+  .option('--analyze', 'Scan git history and populate co-change data')
+  .option('--since <date>', 'Git date for history window (default: "1 year ago")')
+  .option('--min-support <n>', 'Minimum co-occurrence count (default: 3)')
+  .option('--min-jaccard <n>', 'Minimum Jaccard similarity 0-1 (default: 0.3)')
+  .option('--full', 'Force full re-scan (ignore incremental state)')
+  .option('-n, --limit <n>', 'Max results', '20')
+  .option('-d, --db <path>', 'Path to graph.db')
+  .option('-T, --no-tests', 'Exclude test/spec files')
+  .option('--include-tests', 'Include test/spec files (overrides excludeTests config)')
+  .option('-j, --json', 'Output as JSON')
+  .action(async (file, opts) => {
+    const { analyzeCoChanges, coChangeData, coChangeTopData, formatCoChange, formatCoChangeTop } =
+      await import('./cochange.js');
+
+    if (opts.analyze) {
+      const result = analyzeCoChanges(opts.db, {
+        since: opts.since || config.coChange?.since,
+        minSupport: opts.minSupport ? parseInt(opts.minSupport, 10) : config.coChange?.minSupport,
+        maxFilesPerCommit: config.coChange?.maxFilesPerCommit,
+        full: opts.full,
+      });
+      if (opts.json) {
+        console.log(JSON.stringify(result, null, 2));
+      } else if (result.error) {
+        console.error(result.error);
+        process.exit(1);
+      } else {
+        console.log(
+          `\nCo-change analysis complete: ${result.pairsFound} pairs from ${result.commitsScanned} commits (since: ${result.since})\n`,
+        );
+      }
+      return;
+    }
+
+    const queryOpts = {
+      limit: parseInt(opts.limit, 10),
+      minJaccard: opts.minJaccard ? parseFloat(opts.minJaccard) : config.coChange?.minJaccard,
+      noTests: resolveNoTests(opts),
+    };
+
+    if (file) {
+      const data = coChangeData(file, opts.db, queryOpts);
+      if (opts.json) {
+        console.log(JSON.stringify(data, null, 2));
+      } else {
+        console.log(formatCoChange(data));
+      }
+    } else {
+      const data = coChangeTopData(opts.db, queryOpts);
+      if (opts.json) {
+        console.log(JSON.stringify(data, null, 2));
+      } else {
+        console.log(formatCoChangeTop(data));
+      }
+    }
+  });
+
 program
   .command('watch [dir]')
   .description('Watch project for file changes and incrementally update the graph')