feat: multi-repo MCP with global registry (Phase 2.5)

CLAUDE.md

@@ -52,6 +52,7 @@ JS source is plain JavaScript (ES modules) in `src/`. No transpilation step. The
 | `config.js` | `.codegraphrc.json` loading, env overrides, `apiKeyCommand` secret resolution |
 | `constants.js` | `EXTENSIONS` (derived from parser registry) and `IGNORE_DIRS` constants |
 | `native.js` | Native napi-rs addon loader with WASM fallback |
+| `registry.js` | Global repo registry (`~/.codegraph/registry.json`) for multi-repo MCP |
 | `resolve.js` | Import resolution (supports native batch mode) |
 | `logger.js` | Structured logging (`warn`, `debug`, `info`, `error`) |
 

README.md

@@ -128,7 +128,7 @@ codegraph deps src/index.ts  # file-level import/export map
 | 📤 | **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** | Model Context Protocol integration for AI assistants |
+| 🤖 | **MCP server** | 12-tool MCP server with multi-repo support for AI assistants |
 | 🔒 | **Fully local** | No network calls, no data exfiltration, SQLite-backed |
 
 ## 📦 Commands
@@ -213,6 +213,20 @@ A single trailing semicolon is ignored (falls back to single-query mode). The `-
 
 The model used during `embed` is stored in the database, so `search` auto-detects it — no need to pass `--model` when searching.
 
+### Multi-Repo Registry
+
+Manage a global registry of codegraph-enabled projects. AI agents can query any registered repo from a single MCP session using the `repo` parameter.
+
+```bash
+codegraph registry list        # List all registered repos
+codegraph registry list --json # JSON output
+codegraph registry add <dir>   # Register a project directory
+codegraph registry add <dir> -n my-name  # Custom name
+codegraph registry remove <name>  # Unregister
+```
+
+`codegraph build` auto-registers the project — no manual setup needed.
+
 ### AI Integration
 
 ```bash
@@ -310,12 +324,14 @@ Benchmarked on a ~3,200-file TypeScript project:
 
 ### MCP Server
 
-Codegraph includes a built-in [Model Context Protocol](https://modelcontextprotocol.io/) server, so AI assistants can query your dependency graph directly:
+Codegraph includes a built-in [Model Context Protocol](https://modelcontextprotocol.io/) server with 12 tools, so AI assistants can query your dependency graph directly:
 
 ```bash
 codegraph mcp
 ```
 
+All MCP tools accept an optional `repo` parameter to target any registered repository. Use `list_repos` to see available repos. When `repo` is omitted, the local `.codegraph/graph.db` is used (backwards compatible).
+
 ### CLAUDE.md / Agent Instructions
 
 Add this to your project's `CLAUDE.md` to help AI agents use codegraph:
@@ -468,7 +484,7 @@ const { results: fused } = await multiSearchData(
 See **[ROADMAP.md](ROADMAP.md)** for the full development roadmap. 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, 11-tool MCP server, test coverage 62%→75%, `apiKeyCommand` secret resolution
+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
 3. **Intelligent Embeddings** — LLM-generated descriptions, hybrid search
 4. **Natural Language Queries** — `codegraph ask` command, conversational sessions
 5. **Expanded Language Support** — 8 new languages (12 → 20)

ROADMAP.md

@@ -13,7 +13,7 @@ Codegraph is a strong local-first code graph CLI. This roadmap describes planned
 | Phase | Theme | Key Deliverables | Status |
 |-------|-------|-----------------|--------|
 | [**1**](#phase-1--rust-core) | Rust Core | Rust parsing engine via napi-rs, parallel parsing, incremental tree-sitter, JS orchestration layer | **Complete** (v1.3.0) |
-| [**2**](#phase-2--foundation-hardening) | Foundation Hardening | Parser registry, complete MCP, test coverage, enhanced config, multi-repo MCP | **Partial** — core complete (v1.4.0), 2.5 planned |
+| [**2**](#phase-2--foundation-hardening) | Foundation Hardening | Parser registry, complete MCP, test coverage, enhanced config, multi-repo MCP | **Complete** (v1.4.0) |
 | [**3**](#phase-3--intelligent-embeddings) | Intelligent Embeddings | LLM-generated descriptions, hybrid search | Planned |
 | [**4**](#phase-4--natural-language-queries) | Natural Language Queries | `ask` command, conversational sessions | Planned |
 | [**5**](#phase-5--expanded-language-support) | Expanded Language Support | 8 new languages (12 → 20), parser utilities | Planned |
@@ -171,19 +171,19 @@ New configuration options in `.codegraphrc.json`:
 
 **Affected files:** `src/config.js`
 
-### 2.5 — Multi-Repo MCP
+### 2.5 — Multi-Repo MCP ✅
 
 Support querying multiple codebases from a single MCP server instance.
 
-- Registry file at `~/.codegraph/registry.json` mapping repo names to their `.codegraph/graph.db` paths
-- Lazy DB connections — only opened when a repo is first queried
-- Add optional `repo` parameter to all MCP tools to target a specific repository
-- Auto-registration: `codegraph build` adds the current project to the registry
-- New CLI commands: `codegraph registry list|add|remove` for manual management
-- Default behavior: when `repo` is omitted, use the local `.codegraph/graph.db` (backwards compatible)
+- ✅ Registry file at `~/.codegraph/registry.json` mapping repo names to their `.codegraph/graph.db` paths
+- ✅ Add optional `repo` parameter to all 11 MCP tools to target a specific repository
+- ✅ New `list_repos` MCP tool (12th tool) to enumerate registered repositories
+- ✅ Auto-registration: `codegraph build` adds the current project to the registry
+- ✅ New CLI commands: `codegraph registry list|add|remove` for manual management
+- ✅ Default behavior: when `repo` is omitted, use the local `.codegraph/graph.db` (backwards compatible)
 
 **New files:** `src/registry.js`
-**Affected files:** `src/mcp.js`, `src/cli.js`, `src/builder.js`
+**Affected files:** `src/mcp.js`, `src/cli.js`, `src/builder.js`, `src/index.js`
 
 ---
 
@@ -481,6 +481,15 @@ codegraph viz
 
 ---
 
+## Watch List
+
+Technology changes to monitor that may unlock future improvements.
+
+- **`node:sqlite` (Node.js built-in)** — **primary target.** Zero native dependencies, eliminates C++ addon breakage on Node major releases (`better-sqlite3` already broken on Node 24/25). Currently Stability 1.1 (Active Development) as of Node 25.x. Adopt when it reaches Stability 2, or use as a fallback alongside `better-sqlite3` (dual-engine pattern like native/WASM parsing). Backed by the Node.js project — no startup risk.
+- **`libsql` (SQLite fork by Turso)** — monitor only. Drop-in `better-sqlite3` replacement with built-in DiskANN vector search. However, Turso is pivoting engineering focus to Limbo (full Rust SQLite rewrite), leaving libsql as legacy. Pre-1.0 (v0.5.x) with uncertain long-term maintenance. Low switching cost (API-compatible, data is standard SQLite), but not worth adopting until the Turso/Limbo situation clarifies.
+
+---
+
 ## Contributing
 
 Want to help? Contributions to any phase are welcome. See [CONTRIBUTING](README.md#-contributing) for setup instructions.

src/builder.js

@@ -4,7 +4,7 @@ import path from 'node:path';
 import { loadConfig } from './config.js';
 import { EXTENSIONS, IGNORE_DIRS, normalizePath } from './constants.js';
 import { initSchema, openDb } from './db.js';
-import { warn } from './logger.js';
+import { debug, warn } from './logger.js';
 import { getActiveEngine, parseFilesAuto } from './parser.js';
 import { computeConfidence, resolveImportPath, resolveImportsBatch } from './resolve.js';
 
@@ -543,4 +543,11 @@ export async function buildGraph(rootDir, opts = {}) {
   console.log(`Graph built: ${nodeCount} nodes, ${edgeCount} edges`);
   console.log(`Stored in ${dbPath}`);
   db.close();
+
+  try {
+    const { registerRepo } = await import('./registry.js');
+    registerRepo(rootDir);
+  } catch (err) {
+    debug(`Auto-registration failed: ${err.message}`);
+  }
 }

src/cli.js

@@ -19,6 +19,7 @@ import {
   moduleMap,
   queryName,
 } from './queries.js';
+import { listRepos, REGISTRY_PATH, registerRepo, unregisterRepo } from './registry.js';
 import { watchProject } from './watcher.js';
 
 const program = new Command();
@@ -191,6 +192,56 @@ program
     await startMCPServer(opts.db);
   });
 
+// ─── Registry commands ──────────────────────────────────────────────────
+
+const registry = program.command('registry').description('Manage the multi-repo project registry');
+
+registry
+  .command('list')
+  .description('List all registered repositories')
+  .option('-j, --json', 'Output as JSON')
+  .action((opts) => {
+    const repos = listRepos();
+    if (opts.json) {
+      console.log(JSON.stringify(repos, null, 2));
+    } else if (repos.length === 0) {
+      console.log(`No repositories registered.\nRegistry: ${REGISTRY_PATH}`);
+    } else {
+      console.log(`Registered repositories (${REGISTRY_PATH}):\n`);
+      for (const r of repos) {
+        const dbExists = fs.existsSync(r.dbPath);
+        const status = dbExists ? '' : ' [DB missing]';
+        console.log(`  ${r.name}${status}`);
+        console.log(`    Path: ${r.path}`);
+        console.log(`    DB:   ${r.dbPath}`);
+        console.log();
+      }
+    }
+  });
+
+registry
+  .command('add <dir>')
+  .description('Register a project directory')
+  .option('-n, --name <name>', 'Custom name (defaults to directory basename)')
+  .action((dir, opts) => {
+    const absDir = path.resolve(dir);
+    const { name, entry } = registerRepo(absDir, opts.name);
+    console.log(`Registered "${name}" → ${entry.path}`);
+  });
+
+registry
+  .command('remove <name>')
+  .description('Unregister a repository by name')
+  .action((name) => {
+    const removed = unregisterRepo(name);
+    if (removed) {
+      console.log(`Removed "${name}" from registry.`);
+    } else {
+      console.error(`Repository "${name}" not found in registry.`);
+      process.exit(1);
+    }
+  });
+
 // ─── Embedding commands ─────────────────────────────────────────────────
 
 program

src/index.js

@@ -46,5 +46,15 @@ export {
   moduleMapData,
   queryNameData,
 } from './queries.js';
+// Registry (multi-repo)
+export {
+  listRepos,
+  loadRegistry,
+  REGISTRY_PATH,
+  registerRepo,
+  resolveRepoDbPath,
+  saveRegistry,
+  unregisterRepo,
+} from './registry.js';
 // Watch mode
 export { watchProject } from './watcher.js';

src/mcp.js

@@ -9,6 +9,13 @@ import { createRequire } from 'node:module';
 import { findCycles } from './cycles.js';
 import { findDbPath } from './db.js';
 
+const REPO_PROP = {
+  repo: {
+    type: 'string',
+    description: 'Repository name from the registry (omit for local project)',
+  },
+};
+
 const TOOLS = [
   {
     name: 'query_function',
@@ -22,6 +29,7 @@ const TOOLS = [
           description: 'Traversal depth for transitive callers',
           default: 2,
         },
+        ...REPO_PROP,
       },
       required: ['name'],
     },
@@ -33,6 +41,7 @@ const TOOLS = [
       type: 'object',
       properties: {
         file: { type: 'string', description: 'File path (partial match supported)' },
+        ...REPO_PROP,
       },
       required: ['file'],
     },
@@ -44,6 +53,7 @@ const TOOLS = [
       type: 'object',
       properties: {
         file: { type: 'string', description: 'File path to analyze' },
+        ...REPO_PROP,
       },
       required: ['file'],
     },
@@ -53,7 +63,9 @@ const TOOLS = [
     description: 'Detect circular dependencies in the codebase',
     inputSchema: {
       type: 'object',
-      properties: {},
+      properties: {
+        ...REPO_PROP,
+      },
     },
   },
   {
@@ -63,6 +75,7 @@ const TOOLS = [
       type: 'object',
       properties: {
         limit: { type: 'number', description: 'Number of top files to show', default: 20 },
+        ...REPO_PROP,
       },
     },
   },
@@ -75,6 +88,7 @@ const TOOLS = [
         name: { type: 'string', description: 'Function/method/class name (partial match)' },
         depth: { type: 'number', description: 'Transitive caller depth', default: 3 },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...REPO_PROP,
       },
       required: ['name'],
     },
@@ -89,6 +103,7 @@ const TOOLS = [
         name: { type: 'string', description: 'Function/method/class name (partial match)' },
         depth: { type: 'number', description: 'Max traversal depth', default: 5 },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...REPO_PROP,
       },
       required: ['name'],
     },
@@ -103,6 +118,7 @@ const TOOLS = [
         ref: { type: 'string', description: 'Git ref to diff against (default: HEAD)' },
         depth: { type: 'number', description: 'Transitive caller depth', default: 3 },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...REPO_PROP,
       },
     },
   },
@@ -116,6 +132,7 @@ const TOOLS = [
         query: { type: 'string', description: 'Natural language search query' },
         limit: { type: 'number', description: 'Max results to return', default: 15 },
         min_score: { type: 'number', description: 'Minimum similarity score (0-1)', default: 0.2 },
+        ...REPO_PROP,
       },
       required: ['query'],
     },
@@ -136,6 +153,7 @@ const TOOLS = [
           description: 'File-level graph (true) or function-level (false)',
           default: true,
         },
+        ...REPO_PROP,
       },
       required: ['format'],
     },
@@ -150,9 +168,18 @@ const TOOLS = [
         file: { type: 'string', description: 'Filter by file path (partial match)' },
         pattern: { type: 'string', description: 'Filter by function name (partial match)' },
         no_tests: { type: 'boolean', description: 'Exclude test files', default: false },
+        ...REPO_PROP,
       },
     },
   },
+  {
+    name: 'list_repos',
+    description: 'List all repositories registered in the codegraph registry',
+    inputSchema: {
+      type: 'object',
+      properties: {},
+    },
+  },
 ];
 
 export { TOOLS };
@@ -200,9 +227,19 @@ export async function startMCPServer(customDbPath) {
 
   server.setRequestHandler('tools/call', async (request) => {
     const { name, arguments: args } = request.params;
-    const dbPath = customDbPath || undefined;
 
     try {
+      let dbPath = customDbPath || undefined;
+      if (args.repo) {
+        const { resolveRepoDbPath } = await import('./registry.js');
+        const resolved = resolveRepoDbPath(args.repo);
+        if (!resolved)
+          throw new Error(
+            `Repository "${args.repo}" not found in registry or its database is missing.`,
+          );
+        dbPath = resolved;
+      }
+
       let result;
       switch (name) {
         case 'query_function':
@@ -296,6 +333,11 @@ export async function startMCPServer(customDbPath) {
             noTests: args.no_tests,
           });
           break;
+        case 'list_repos': {
+          const { listRepos } = await import('./registry.js');
+          result = { repos: listRepos() };
+          break;
+        }
         default:
           return { content: [{ type: 'text', text: `Unknown tool: ${name}` }], isError: true };
       }