graph-indexer 1.2.0 → 2.1.0

package/mcp-server.mjs

@@ -3,9 +3,9 @@
  * @file mcp-server.mjs
  * @description MCP server bootstrap. Resolves configuration, selects the storage
  *              backend (in-memory by default, SQLite when configured), registers
- *              the tool surface (mcp-tools.mjs) and connects over stdio. All
+ *              the tool surface (mcp/tools.mjs) and connects over stdio. All
  *              retrieval logic lives in the store + search-core; all tool logic in
- *              mcp-tools — this file is wiring only.
+ *              mcp/tools.mjs — this file is wiring only.
  * @author MaquinaTech <https://github.com/MaquinaTech>
  * @copyright (c) 2026 MaquinaTech. All rights reserved.
  * @license MIT
@@ -13,18 +13,47 @@
 import { McpServer, ResourceTemplate } from '@modelcontextprotocol/sdk/server/mcp.js';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
 import fs from 'fs';
-import path, { resolve } from 'path';
+import path from 'path';
 import { fileURLToPath } from 'url';
 import { spawn } from 'child_process';
-import { resolveConfig } from './config.mjs';
+import { resolveConfig, describeConfig, configNotices } from './config.mjs';
+import { ensureDataDir, migrateLegacyLayout } from './layout.mjs';
+import { daemonStatus } from './daemon-lock.mjs';
 import { createStore } from './storage.mjs';
-import { registerTools } from './mcp-tools.mjs';
+import { registerTools } from './mcp/tools.mjs';
+import { ensureLanguagesReady } from './parse/languages.mjs';
+import { createEmbedder, readEmbedMeta } from './embeddings.mjs';
+import { loadGitSignals } from './git-signals.mjs';
+import { installEgressGuard } from './seal.mjs';
 
-const config = resolveConfig();
+let config;
+try {
+    config = resolveConfig();
+} catch (err) {
+    if (err && err.name === 'SealViolation') { process.stderr.write(`🔒 ${err.message}\n`); process.exit(2); }
+    throw err;
+}
+// F1: install the deny-by-default egress guard before the store / embedder / providers load.
+if (config.sealed !== 'off') {
+    installEgressGuard({ allow: config.sealed === 'local' ? ['loopback'] : [] });
+}
 const PROJECT_ROOT = config.projectRoot;
-const PID_FILE = resolve(PROJECT_ROOT, '.idx-daemon.pid');
+const PID_FILE = config.pidFile;
 const PACKAGE_DIR = path.dirname(fileURLToPath(import.meta.url));
 
+ensureDataDir(PROJECT_ROOT);
+migrateLegacyLayout(PROJECT_ROOT);
+
+// get_file_skeleton parses on demand at query time — grammars must be resolved
+// (and, outside sealed mode, installed if this server is starting before the
+// first `idx-index` run) before the transport connects and starts serving tools.
+await ensureLanguagesReady({
+    projectRoot: PROJECT_ROOT,
+    enabledLangs: config.languages,
+    autoInstall: config.sealed === 'off',
+    log: (msg) => process.stderr.write(msg + '\n'),
+});
+
 function readPackageVersion() {
     try {
         return JSON.parse(fs.readFileSync(path.join(PACKAGE_DIR, 'package.json'), 'utf-8')).version || '0.0.0';
@@ -38,16 +67,17 @@ function readPackageVersion() {
 // PRAGMA data_version). Either way, a long-running MCP server stays consistent
 // with the working tree without restarts or full re-indexes.
 function ensureDaemonRunning() {
-    if (fs.existsSync(PID_FILE)) {
-        const pid = parseInt(fs.readFileSync(PID_FILE, 'utf-8'), 10);
-        try { process.kill(pid, 0); process.stderr.write(`✅ Daemon already active (PID: ${pid}).\n`); return; }
-        catch { fs.unlinkSync(PID_FILE); }
-    }
+    // The daemon owns the PID lock exclusively (it acquires it atomically on
+    // startup — see daemon-lock.mjs). We only check whether one is already live;
+    // if not, we spawn it detached. Even if two servers race here, the losing
+    // daemon fails to acquire the lock and exits, so never more than one runs.
+    const { running, pid } = daemonStatus(PID_FILE);
+    if (running) { process.stderr.write(`✅ Daemon already active (PID: ${pid}).\n`); return; }
+
     const daemonPath = path.join(PACKAGE_DIR, 'watch-daemon.mjs');
-    const logPath = path.join(PROJECT_ROOT, '.idx-daemon.log');
-    process.stderr.write(`🚀 Starting Watcher Daemon...\n   Log: ${logPath}\n`);
+    process.stderr.write(`🚀 Starting Watcher Daemon...\n   Log: ${config.logFile}\n`);
     let logFd;
-    try { logFd = fs.openSync(logPath, 'a'); } catch { logFd = null; }
+    try { logFd = fs.openSync(config.logFile, 'a'); } catch { logFd = null; }
     const child = spawn(process.execPath, [daemonPath], {
         detached: true,
         stdio: logFd !== null ? ['ignore', logFd, logFd] : 'ignore',
@@ -55,27 +85,29 @@ function ensureDaemonRunning() {
     });
     child.unref();
     if (logFd !== null) fs.closeSync(logFd);
-    fs.writeFileSync(PID_FILE, child.pid.toString());
 }
 
 // ─── Boot ──────────────────────────────────────────────────────────────────────
 
-if (config.storage === 'sqlite') {
-    process.stderr.write('🗄  Storage backend: SQLite (disk-backed, live daemon updates).\n');
-}
 ensureDaemonRunning();
 
 const version = readPackageVersion();
 const server = new McpServer({ name: 'graph-indexer', version });
 
 const db = await createStore(config, { cacheEmbeddings: false });
+const backend = db.backend;
+
+process.stderr.write('⚙️  Effective configuration:\n');
+for (const line of describeConfig(config, { backend })) process.stderr.write(`     ${line}\n`);
+for (const notice of configNotices(config)) process.stderr.write(`⚠️  ${notice}\n`);
+
 try { db.load(); } catch (err) { process.stderr.write(`⏳ Waiting for initial indexing… (${err.message})\n`); }
 
 // In-memory backend: the daemon is a separate process that rewrites
 // code-index.json — without reloading, this server would answer from a stale
 // snapshot until restart. (The SQLite store refreshes itself per query via
 // PRAGMA data_version, so no watcher is needed there.)
-if (config.storage !== 'sqlite' && typeof db.reload === 'function') {
+if (backend !== 'sqlite' && typeof db.reload === 'function') {
     let reloadTimer = null;
     const scheduleReload = () => {
         if (reloadTimer) clearTimeout(reloadTimer);
@@ -126,17 +158,40 @@ server.resource(
     }
 );
 
+// ─── Query embedder ────────────────────────────────────────────────────────────
+// Query with the SAME provider/model the index was built with (stamped in the
+// embeddings-bin sidecar). No stamp → an index from an older version: keep the
+// legacy behaviour (try Ollama, fall back to lexical). The local pipeline loads
+// lazily on first query, so an unused provider costs nothing at startup.
+const embedMeta = readEmbedMeta(config.embeddingPath);
+const embedder = await createEmbedder(
+    config,
+    embedMeta?.provider
+        ? { provider: embedMeta.provider, model: embedMeta.model }
+        : { provider: config.embeddingsEnabled ? 'ollama' : 'off', model: config.embedModel }
+);
+
+// ─── Git signals (air-gapped sidecar; blast-radius hint + opt-in rank boost) ────
+const gitSignals = config.gitSignals ? loadGitSignals(config.gitSignalsPath) : null;
+
 // ─── Tools ───────────────────────────────────────────────────────────────────
 registerTools(server, db, {
     projectRoot: PROJECT_ROOT,
-    artifactPath: config.storage === 'sqlite' ? config.sqlitePath : config.indexPath,
+    artifactPath: backend === 'sqlite' ? config.sqlitePath : config.indexPath,
     pidFile: PID_FILE,
-    embeddingsEnabled: config.embeddingsEnabled,
-    ollamaHost: config.ollamaHost,
-    embedModel: config.embedModel,
+    embeddingsEnabled: config.embeddingsEnabled && embedder.provider !== 'off',
+    embedder,
     rerank: config.rerank,
+    hyde: config.hyde,
+    ollamaHost: config.ollamaHost,
+    llmProvider: config.llmProvider,
+    mlxLmHost: config.mlxLmHost,
+    gitSignals,
+    gitRankBoost: config.gitRankBoost,
+    sealed: config.sealed,
+    ranker: config.ranker,
 });
 
 const transport = new StdioServerTransport();
 await server.connect(transport);
-process.stderr.write(`✅ graph-indexer MCP server running (v${version}, ${config.storage} backend).\n`);
+process.stderr.write(`✅ graph-indexer MCP server running (v${version}, ${backend} backend).\n`);

package/package.json

@@ -1,22 +1,33 @@
 {
     "name": "graph-indexer",
-    "version": "1.2.0",
+    "version": "2.1.0",
     "description": "Air-gapped code-retrieval MCP server: AST chunking, hybrid RRF search and cross-language call graph, with an optional zero-dependency SQLite backend for monorepo scale and optional local-LLM semantic enrichment.",
     "type": "module",
-    "main": "core-engine.mjs",
+    "main": "engine/memory.mjs",
     "exports": {
-        ".": "./core-engine.mjs"
+        ".": "./engine/memory.mjs"
     },
     "bin": {
         "graph-indexer": "init.mjs",
         "idx-index": "indexer.mjs",
         "idx-watch": "watch-daemon.mjs",
+        "idx-daemon": "daemon-ctl.mjs",
         "idx-mcp": "mcp-server.mjs"
     },
     "files": [
         "*.mjs",
-        "PROMPT.md",
+        "engine/",
+        "mcp/",
+        "parse/",
+        "embedders/setup-mlx.mjs",
+        "embedders/python/mlx_embed_server.py",
+        "embedders/python/requirements-mlx.txt",
+        "!embedders/python/test_servers.mjs",
+        "prompts/",
         "README.md",
+        "CHANGELOG.md",
+        "SECURITY.md",
+        "TRADEMARK.md",
         "LICENSE"
     ],
     "repository": {
@@ -31,28 +42,70 @@
         "test:enrich": "node test/enrichment.mjs",
         "test:mcp": "node test/mcp.mjs",
         "test:scale": "node test/scale.mjs",
-        "test:all": "node test/unit.mjs && node test/sqlite.mjs && node test/enrichment.mjs && node test/mcp.mjs && node test/scale.mjs",
+        "test:callgraph": "node test/callgraph.mjs",
+        "test:edges": "node test/edges.mjs",
+        "test:references": "node test/references.mjs",
+        "test:routes": "node test/routes.mjs",
+        "test:jsonout": "node test/json-output.mjs",
+        "test:gitsignals": "node test/git-signals.mjs",
+        "test:security": "node test/security.mjs",
+        "test:seal": "node test/seal.mjs",
+        "test:taint": "node test/taint.mjs",
+        "test:scip": "node test/scip.mjs",
+        "test:ranker": "node test/ranker.mjs",
+        "test:sparse": "node test/sparse.mjs",
+        "test:colbert": "node test/colbert.mjs",
+        "test:embed": "node test/embeddings.mjs",
+        "test:languages": "node test/languages.mjs",
+        "test:all": "node test/unit.mjs && node test/sqlite.mjs && node test/enrichment.mjs && node test/mcp.mjs && node test/scale.mjs && node test/callgraph.mjs && node test/edges.mjs && node test/references.mjs && node test/routes.mjs && node test/json-output.mjs && node test/git-signals.mjs && node test/security.mjs && node test/seal.mjs && node test/taint.mjs && node test/scip.mjs && node test/ranker.mjs && node test/sparse.mjs && node test/colbert.mjs && node test/embeddings.mjs && node test/languages.mjs",
         "test:eval": "node test/evaluate.mjs",
-        "test:eval:embeddings": "OLLAMA_HOST=http://localhost:11435 node test/evaluate.mjs --embeddings",
+        "test:eval:embeddings": "OLLAMA_HOST=http://localhost:11434 node test/evaluate.mjs --embeddings",
         "test:setup": "node test/setup.mjs",
         "test:run": "node test/run.mjs",
-        "test:embeddings": "OLLAMA_HOST=http://localhost:11435 node test/run-embeddings.mjs",
-        "test:embeddings:skip": "OLLAMA_HOST=http://localhost:11435 node test/run-embeddings.mjs --skip-indexing",
+        "test:embeddings": "OLLAMA_HOST=http://localhost:11434 node test/run-embeddings.mjs",
+        "test:embeddings:skip": "OLLAMA_HOST=http://localhost:11434 node test/run-embeddings.mjs --skip-indexing",
         "test:suite": "node test/run.mjs --suite",
         "test:json": "node test/run.mjs --json",
         "test:reset": "rm -rf test/fixtures && node test/setup.mjs",
-        "mcp:index": "node indexer.mjs --repo .",
+        "embed:setup:mlx": "node embedders/setup-mlx.mjs",
+        "embed:setup:local": "npm install @huggingface/transformers",
+        "mcp:index": "idx-index --repo .",
         "mcp:index:sqlite": "node indexer.mjs --repo . --use-sqlite",
-        "mcp:index:enriched": "node indexer.mjs --repo . --llm-enrichment",
+        "mcp:index:enriched": "node indexer.mjs --repo . --enrichment",
         "mcp:watch": "node watch-daemon.mjs",
-        "mcp:start": "node mcp-server.mjs"
+        "mcp:start": "idx-mcp",
+        "mcp:daemon": "node daemon-ctl.mjs status",
+        "mcp:daemon:start": "node daemon-ctl.mjs start",
+        "mcp:daemon:stop": "node daemon-ctl.mjs stop",
+        "mcp:daemon:restart": "node daemon-ctl.mjs restart",
+        "mcp:daemon:status": "node daemon-ctl.mjs status",
+        "mcp:daemon:logs": "node daemon-ctl.mjs logs"
     },
     "dependencies": {
         "@modelcontextprotocol/sdk": "1.29.0",
         "chokidar": "5.0.0",
         "ignore": "5.3.2",
         "tree-sitter": "0.21.1",
-        "zod": "3.23.8"
+        "zod": "^3.25.76"
+    },
+    "devDependencies": {
+        "@huggingface/transformers": "3.8.1",
+        "hnswlib-node": "3.0.0",
+        "tree-sitter-bash": "0.23.3",
+        "tree-sitter-c": "0.21.4",
+        "tree-sitter-c-sharp": "0.21.3",
+        "tree-sitter-css": "0.21.1",
+        "tree-sitter-go": "0.21.0",
+        "tree-sitter-java": "0.21.0",
+        "tree-sitter-javascript": "0.21.4",
+        "tree-sitter-kotlin": "0.3.8",
+        "tree-sitter-php": "0.23.1",
+        "tree-sitter-python": "0.21.0",
+        "tree-sitter-ruby": "0.23.1",
+        "tree-sitter-rust": "0.21.0",
+        "tree-sitter-scss": "1.0.0",
+        "tree-sitter-swift": "0.5.0",
+        "tree-sitter-typescript": "0.21.2"
     },
     "keywords": [
         "mcp",
@@ -85,19 +138,5 @@
     },
     "publishConfig": {
         "access": "public"
-    },
-    "optionalDependencies": {
-        "hnswlib-node": "3.0.0",
-        "tree-sitter-c-sharp": "0.21.3",
-        "tree-sitter-css": "0.21.1",
-        "tree-sitter-go": "0.21.0",
-        "tree-sitter-java": "0.21.0",
-        "tree-sitter-javascript": "0.21.4",
-        "tree-sitter-kotlin": "0.3.8",
-        "tree-sitter-php": "0.23.1",
-        "tree-sitter-python": "0.21.0",
-        "tree-sitter-ruby": "0.23.1",
-        "tree-sitter-rust": "0.21.0",
-        "tree-sitter-typescript": "0.21.2"
     }
-}
+}