agentic-qe 2.5.10 → 2.6.1

package/dist/cli/init/claude-config.js

@@ -45,6 +45,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.generateClaudeSettings = generateClaudeSettings;
+exports.generateMcpJson = generateMcpJson;
 exports.setupMCPServer = setupMCPServer;
 const chalk_1 = __importDefault(require("chalk"));
 const fs = __importStar(require("fs-extra"));
@@ -244,10 +245,69 @@ function mergeHooks(existing, aqeHooks) {
     }
     return merged;
 }
+/**
+ * Generate MCP server definitions file
+ *
+ * Creates the .claude/mcp.json file that defines available MCP servers.
+ * This is REQUIRED for enabledMcpjsonServers in settings.json to work.
+ *
+ * @param config - Fleet configuration
+ */
+async function generateMcpJson(_fleetConfig) {
+    const mcpJsonPath = path.join(process.cwd(), '.claude', 'mcp.json');
+    // Check if mcp.json already exists
+    const mcpJsonExists = await fs.pathExists(mcpJsonPath);
+    let existingConfig = { mcpServers: {} };
+    if (mcpJsonExists) {
+        console.log(chalk_1.default.yellow('  ⓘ  .claude/mcp.json already exists - merging AQE server'));
+        try {
+            existingConfig = await fs.readJson(mcpJsonPath);
+            if (!existingConfig.mcpServers) {
+                existingConfig.mcpServers = {};
+            }
+        }
+        catch (error) {
+            console.log(chalk_1.default.red('  ⚠️  Could not parse existing mcp.json - creating backup'));
+            await fs.copy(mcpJsonPath, `${mcpJsonPath}.backup`);
+            console.log(chalk_1.default.gray(`    Backup saved to: ${mcpJsonPath}.backup`));
+        }
+    }
+    // Define agentic-qe MCP server
+    const aqeMcpServer = {
+        command: "npx",
+        args: ["aqe-mcp"],
+        env: {
+            AQE_MEMORY_PATH: ".agentic-qe/memory.db",
+            AQE_LEARNING_ENABLED: "true",
+            NODE_NO_WARNINGS: "1"
+        }
+    };
+    // Merge with existing config
+    const mcpConfig = {
+        mcpServers: {
+            ...existingConfig.mcpServers,
+            "agentic-qe": aqeMcpServer
+        }
+    };
+    await fs.ensureDir(path.dirname(mcpJsonPath));
+    await fs.writeJson(mcpJsonPath, mcpConfig, { spaces: 2 });
+    if (mcpJsonExists) {
+        console.log(chalk_1.default.green('  ✓ Merged agentic-qe server into existing .claude/mcp.json'));
+    }
+    else {
+        console.log(chalk_1.default.green('  ✓ Created .claude/mcp.json with agentic-qe server'));
+    }
+    console.log(chalk_1.default.gray('    • Server: agentic-qe'));
+    console.log(chalk_1.default.gray('    • Command: npx aqe-mcp'));
+    console.log(chalk_1.default.gray('    • Tools: 102 MCP tools for learning, memory, analysis'));
+}
 /**
  * Setup MCP server configuration
  *
- * Configures the Model Context Protocol server for agent coordination
+ * Configures the Model Context Protocol server for agent coordination.
+ * This function handles both:
+ * 1. Project-level config (.claude/mcp.json) - via generateMcpJson()
+ * 2. Global config (claude mcp add) - for users who prefer global setup
  */
 async function setupMCPServer() {
     console.log(chalk_1.default.cyan('\n  🔌 Setting up MCP server integration...\n'));
@@ -259,16 +319,17 @@ async function setupMCPServer() {
         }
         catch {
             console.log(chalk_1.default.yellow('  ⚠️  Claude Code CLI not found'));
-            console.log(chalk_1.default.gray('  ℹ️  Please add MCP server manually after installing Claude Code:'));
+            console.log(chalk_1.default.gray('  ℹ️  MCP server defined in .claude/mcp.json (project-level)'));
+            console.log(chalk_1.default.gray('  ℹ️  For global setup after installing Claude Code:'));
             console.log(chalk_1.default.cyan('     claude mcp add agentic-qe npx aqe-mcp'));
             console.log(chalk_1.default.gray('\n  Download Claude Code: https://claude.com/claude-code'));
             return;
         }
-        // Check if MCP server is already added
+        // Check if MCP server is already added globally
         try {
             const mcpList = execSync('claude mcp list', { encoding: 'utf-8' });
             if (mcpList.includes('agentic-qe')) {
-                console.log(chalk_1.default.green('  ✓ MCP server already configured'));
+                console.log(chalk_1.default.green('  ✓ MCP server already configured globally'));
                 console.log(chalk_1.default.gray('    • Server: agentic-qe'));
                 console.log(chalk_1.default.gray('    • Command: npx aqe-mcp'));
                 return;
@@ -277,8 +338,8 @@ async function setupMCPServer() {
         catch {
             // Ignore errors, proceed with adding
         }
-        // Add MCP server
-        console.log(chalk_1.default.gray('  • Adding MCP server to Claude Code...'));
+        // Add MCP server globally
+        console.log(chalk_1.default.gray('  • Adding MCP server to Claude Code globally...'));
         execSync('claude mcp add agentic-qe npx aqe-mcp', { stdio: 'inherit' });
         console.log(chalk_1.default.green('\n  ✓ MCP server added successfully'));
         console.log(chalk_1.default.gray('    • Server: agentic-qe'));
@@ -286,9 +347,10 @@ async function setupMCPServer() {
         console.log(chalk_1.default.gray('    • Memory: Shared memory coordination enabled'));
     }
     catch (error) {
-        console.log(chalk_1.default.yellow('  ⚠️  Could not auto-configure MCP server'));
+        console.log(chalk_1.default.yellow('  ⚠️  Could not auto-configure MCP server globally'));
         console.log(chalk_1.default.gray(`  Error: ${error.message}`));
-        console.log(chalk_1.default.gray('\n  Please add manually:'));
+        console.log(chalk_1.default.gray('  ℹ️  Project-level config in .claude/mcp.json will still work'));
+        console.log(chalk_1.default.gray('\n  For global setup, run manually:'));
         console.log(chalk_1.default.cyan('     claude mcp add agentic-qe npx aqe-mcp'));
     }
 }

package/dist/cli/init/claude-config.js.map

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package/dist/cli/init/code-intelligence-init.d.ts

@@ -0,0 +1,52 @@
+/**
+ * Code Intelligence initialization module
+ *
+ * Sets up Code Intelligence System for semantic code search and knowledge graph.
+ * Requires: Ollama (nomic-embed-text) + RuVector PostgreSQL
+ *
+ * @module cli/init/code-intelligence-init
+ */
+import { FleetConfig } from '../../types';
+/**
+ * Code Intelligence configuration stored in .agentic-qe/config
+ */
+export interface CodeIntelligenceConfig {
+    enabled: boolean;
+    ollamaUrl: string;
+    embeddingModel: string;
+    database: {
+        host: string;
+        port: number;
+        database: string;
+        user: string;
+        password: string;
+    };
+    indexPaths: string[];
+    autoIndex: boolean;
+    watchEnabled: boolean;
+}
+/**
+ * Check if Code Intelligence prerequisites are available
+ */
+export declare function checkCodeIntelligencePrerequisites(): Promise<{
+    ollama: boolean;
+    ollamaModel: boolean;
+    postgres: boolean;
+    allReady: boolean;
+    messages: string[];
+}>;
+/**
+ * Initialize Code Intelligence System
+ *
+ * Optionally sets up Code Intelligence if prerequisites are available.
+ * Creates configuration file and optionally triggers initial indexing.
+ *
+ * @param config - Fleet configuration
+ * @param interactive - Whether to prompt user for options
+ */
+export declare function initializeCodeIntelligence(config: FleetConfig, interactive?: boolean): Promise<void>;
+/**
+ * Load Code Intelligence configuration
+ */
+export declare function loadCodeIntelligenceConfig(): Promise<CodeIntelligenceConfig | null>;
+//# sourceMappingURL=code-intelligence-init.d.ts.map

package/dist/cli/init/code-intelligence-init.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"code-intelligence-init.d.ts","sourceRoot":"","sources":["../../../src/cli/init/code-intelligence-init.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAMH,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAE1C;;GAEG;AACH,MAAM,WAAW,sBAAsB;IACrC,OAAO,EAAE,OAAO,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;IACvB,QAAQ,EAAE;QACR,IAAI,EAAE,MAAM,CAAC;QACb,IAAI,EAAE,MAAM,CAAC;QACb,QAAQ,EAAE,MAAM,CAAC;QACjB,IAAI,EAAE,MAAM,CAAC;QACb,QAAQ,EAAE,MAAM,CAAC;KAClB,CAAC;IACF,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,SAAS,EAAE,OAAO,CAAC;IACnB,YAAY,EAAE,OAAO,CAAC;CACvB;AAED;;GAEG;AACH,wBAAsB,kCAAkC,IAAI,OAAO,CAAC;IAClE,MAAM,EAAE,OAAO,CAAC;IAChB,WAAW,EAAE,OAAO,CAAC;IACrB,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB,CAAC,CAuDD;AAED;;;;;;;;GAQG;AACH,wBAAsB,0BAA0B,CAC9C,MAAM,EAAE,WAAW,EACnB,WAAW,GAAE,OAAc,GAC1B,OAAO,CAAC,IAAI,CAAC,CAsGf;AAWD;;GAEG;AACH,wBAAsB,0BAA0B,IAAI,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC,CAOzF"}

package/dist/cli/init/code-intelligence-init.js

@@ -0,0 +1,250 @@
+"use strict";
+/**
+ * Code Intelligence initialization module
+ *
+ * Sets up Code Intelligence System for semantic code search and knowledge graph.
+ * Requires: Ollama (nomic-embed-text) + RuVector PostgreSQL
+ *
+ * @module cli/init/code-intelligence-init
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.checkCodeIntelligencePrerequisites = checkCodeIntelligencePrerequisites;
+exports.initializeCodeIntelligence = initializeCodeIntelligence;
+exports.loadCodeIntelligenceConfig = loadCodeIntelligenceConfig;
+const chalk_1 = __importDefault(require("chalk"));
+const inquirer_1 = __importDefault(require("inquirer"));
+const fs = __importStar(require("fs-extra"));
+const path = __importStar(require("path"));
+/**
+ * Check if Code Intelligence prerequisites are available
+ */
+async function checkCodeIntelligencePrerequisites() {
+    const messages = [];
+    let ollama = false;
+    let ollamaModel = false;
+    let postgres = false;
+    // Check Ollama
+    try {
+        const ollamaUrl = process.env.OLLAMA_URL || 'http://localhost:11434';
+        const controller = new AbortController();
+        const timeoutId = setTimeout(() => controller.abort(), 3000);
+        const response = await fetch(`${ollamaUrl}/api/tags`, {
+            signal: controller.signal,
+        });
+        clearTimeout(timeoutId);
+        if (response.ok) {
+            ollama = true;
+            const data = await response.json();
+            const models = data.models || [];
+            ollamaModel = models.some((m) => m.name.includes('nomic-embed-text'));
+            if (!ollamaModel) {
+                messages.push('nomic-embed-text model not found. Run: ollama pull nomic-embed-text');
+            }
+        }
+    }
+    catch {
+        messages.push('Ollama not available at http://localhost:11434. Start with: ollama serve');
+    }
+    // Check PostgreSQL/RuVector
+    try {
+        const { Pool } = await Promise.resolve().then(() => __importStar(require('pg')));
+        const pool = new Pool({
+            host: process.env.RUVECTOR_HOST || 'localhost',
+            port: parseInt(process.env.RUVECTOR_PORT || '5432'),
+            database: process.env.RUVECTOR_DATABASE || 'ruvector_db',
+            user: process.env.RUVECTOR_USER || 'ruvector',
+            password: process.env.RUVECTOR_PASSWORD || 'ruvector',
+            connectionTimeoutMillis: 3000,
+        });
+        await pool.query('SELECT 1');
+        await pool.end();
+        postgres = true;
+    }
+    catch {
+        messages.push('RuVector PostgreSQL not available. Start with: docker-compose up -d ruvector');
+    }
+    return {
+        ollama,
+        ollamaModel,
+        postgres,
+        allReady: ollama && ollamaModel && postgres,
+        messages,
+    };
+}
+/**
+ * Initialize Code Intelligence System
+ *
+ * Optionally sets up Code Intelligence if prerequisites are available.
+ * Creates configuration file and optionally triggers initial indexing.
+ *
+ * @param config - Fleet configuration
+ * @param interactive - Whether to prompt user for options
+ */
+async function initializeCodeIntelligence(config, interactive = true) {
+    console.log(chalk_1.default.cyan('\n🧠 Code Intelligence System Setup\n'));
+    // Check prerequisites
+    const prereqs = await checkCodeIntelligencePrerequisites();
+    if (!prereqs.allReady) {
+        console.log(chalk_1.default.yellow('  ⚠️  Code Intelligence prerequisites not available:'));
+        prereqs.messages.forEach(msg => {
+            console.log(chalk_1.default.gray(`     • ${msg}`));
+        });
+        console.log(chalk_1.default.gray('\n  Skipping Code Intelligence setup. You can enable it later with:'));
+        console.log(chalk_1.default.cyan('     aqe code-intel setup\n'));
+        // Create disabled config
+        await saveCodeIntelligenceConfig({
+            enabled: false,
+            ollamaUrl: 'http://localhost:11434',
+            embeddingModel: 'nomic-embed-text',
+            database: {
+                host: 'localhost',
+                port: 5432,
+                database: 'ruvector_db',
+                user: 'ruvector',
+                password: 'ruvector',
+            },
+            indexPaths: ['src'],
+            autoIndex: false,
+            watchEnabled: false,
+        });
+        return;
+    }
+    console.log(chalk_1.default.green('  ✓ All prerequisites available'));
+    console.log(chalk_1.default.gray(`     • Ollama: running with nomic-embed-text`));
+    console.log(chalk_1.default.gray(`     • RuVector PostgreSQL: connected`));
+    // Ask user if they want to enable Code Intelligence
+    let enableCodeIntel = true;
+    let autoIndex = false;
+    if (interactive) {
+        const answers = await inquirer_1.default.prompt([
+            {
+                type: 'confirm',
+                name: 'enable',
+                message: 'Enable Code Intelligence for semantic code search?',
+                default: true,
+            },
+            {
+                type: 'confirm',
+                name: 'autoIndex',
+                message: 'Index the codebase now? (can be done later with: aqe code-intel index)',
+                default: false,
+                when: (ans) => ans.enable,
+            },
+        ]);
+        enableCodeIntel = answers.enable;
+        autoIndex = answers.autoIndex ?? false;
+    }
+    // Save configuration
+    const codeIntelConfig = {
+        enabled: enableCodeIntel,
+        ollamaUrl: process.env.OLLAMA_URL || 'http://localhost:11434',
+        embeddingModel: 'nomic-embed-text',
+        database: {
+            host: process.env.RUVECTOR_HOST || 'localhost',
+            port: parseInt(process.env.RUVECTOR_PORT || '5432'),
+            database: process.env.RUVECTOR_DATABASE || 'ruvector_db',
+            user: process.env.RUVECTOR_USER || 'ruvector',
+            password: process.env.RUVECTOR_PASSWORD || 'ruvector',
+        },
+        indexPaths: ['src'],
+        autoIndex: false,
+        watchEnabled: false,
+    };
+    await saveCodeIntelligenceConfig(codeIntelConfig);
+    if (!enableCodeIntel) {
+        console.log(chalk_1.default.gray('  Code Intelligence disabled. Enable later with: aqe code-intel enable'));
+        return;
+    }
+    console.log(chalk_1.default.green('  ✓ Code Intelligence enabled'));
+    // Perform initial indexing if requested
+    if (autoIndex) {
+        console.log(chalk_1.default.cyan('\n  📊 Indexing codebase (this may take a few minutes)...\n'));
+        try {
+            await indexCodebase();
+            console.log(chalk_1.default.green('  ✓ Codebase indexed successfully'));
+        }
+        catch (error) {
+            console.log(chalk_1.default.yellow(`  ⚠️  Indexing failed: ${error.message}`));
+            console.log(chalk_1.default.gray('     Run manually with: aqe code-intel index'));
+        }
+    }
+    else {
+        console.log(chalk_1.default.gray('\n  To index your codebase, run:'));
+        console.log(chalk_1.default.cyan('     aqe code-intel index'));
+    }
+}
+/**
+ * Save Code Intelligence configuration
+ */
+async function saveCodeIntelligenceConfig(config) {
+    const configDir = path.join(process.cwd(), '.agentic-qe', 'config');
+    await fs.ensureDir(configDir);
+    await fs.writeJson(path.join(configDir, 'code-intelligence.json'), config, { spaces: 2 });
+}
+/**
+ * Load Code Intelligence configuration
+ */
+async function loadCodeIntelligenceConfig() {
+    const configPath = path.join(process.cwd(), '.agentic-qe', 'config', 'code-intelligence.json');
+    try {
+        return await fs.readJson(configPath);
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Index the codebase using Code Intelligence System
+ */
+async function indexCodebase() {
+    const { initializeCodeIntelligence } = await Promise.resolve().then(() => __importStar(require('../../code-intelligence/service/CodeIntelligenceService.js')));
+    const service = await initializeCodeIntelligence();
+    const result = await service.indexDirectory('src', (progress) => {
+        const pct = progress.totalFiles > 0
+            ? Math.round((progress.processedFiles / progress.totalFiles) * 100)
+            : 0;
+        process.stdout.write(`\r  Processing: ${progress.processedFiles}/${progress.totalFiles} files (${pct}%) - ${progress.chunksCreated} chunks`);
+    });
+    process.stdout.write('\n');
+    console.log(chalk_1.default.gray(`     • Files indexed: ${result.filesIndexed}`));
+    console.log(chalk_1.default.gray(`     • Chunks created: ${result.chunksCreated}`));
+    console.log(chalk_1.default.gray(`     • Graph nodes: ${result.nodesCreated}`));
+    console.log(chalk_1.default.gray(`     • Graph edges: ${result.edgesCreated}`));
+}
+//# sourceMappingURL=code-intelligence-init.js.map

package/dist/cli/init/code-intelligence-init.js.map

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package/dist/cli/init/index.d.ts

@@ -9,7 +9,7 @@
 import { InitOptions } from '../../types';
 import { createDirectoryStructure } from './directory-structure';
 import { initializeDatabases } from './database-init';
-import { generateClaudeSettings, setupMCPServer } from './claude-config';
+import { generateClaudeSettings, generateMcpJson, setupMCPServer } from './claude-config';
 import { copyDocumentation } from './documentation';
 import { createBashWrapper } from './bash-wrapper';
 /**
@@ -28,5 +28,5 @@ export declare function initCommand(options: InitOptions): Promise<void>;
 /**
  * Export individual phase functions for testing and reuse
  */
-export { createDirectoryStructure, initializeDatabases, generateClaudeSettings, setupMCPServer, copyDocumentation, createBashWrapper };
+export { createDirectoryStructure, initializeDatabases, generateClaudeSettings, generateMcpJson, setupMCPServer, copyDocumentation, createBashWrapper };
 //# sourceMappingURL=index.d.ts.map

package/dist/cli/init/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/cli/init/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAAe,WAAW,EAAE,MAAM,aAAa,CAAC;AAIvD,OAAO,EAAE,wBAAwB,EAAE,MAAM,uBAAuB,CAAC;AACjE,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AACtD,OAAO,EAAE,sBAAsB,EAAE,eAAe,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AAyBnD;;;;;;;;;;;GAWG;AACH,wBAAsB,WAAW,CAAC,OAAO,EAAE,WAAW,GAAG,OAAO,CAAC,IAAI,CAAC,CAkMrE;AAmID;;GAEG;AACH,OAAO,EACL,wBAAwB,EACxB,mBAAmB,EACnB,sBAAsB,EACtB,eAAe,EACf,cAAc,EACd,iBAAiB,EACjB,iBAAiB,EAClB,CAAC"}

package/dist/cli/init/index.js

@@ -11,7 +11,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.createBashWrapper = exports.copyDocumentation = exports.setupMCPServer = exports.generateClaudeSettings = exports.initializeDatabases = exports.createDirectoryStructure = void 0;
+exports.createBashWrapper = exports.copyDocumentation = exports.setupMCPServer = exports.generateMcpJson = exports.generateClaudeSettings = exports.initializeDatabases = exports.createDirectoryStructure = void 0;
 exports.initCommand = initCommand;
 const chalk_1 = __importDefault(require("chalk"));
 const ora_1 = __importDefault(require("ora"));
@@ -23,6 +23,7 @@ const database_init_1 = require("./database-init");
 Object.defineProperty(exports, "initializeDatabases", { enumerable: true, get: function () { return database_init_1.initializeDatabases; } });
 const claude_config_1 = require("./claude-config");
 Object.defineProperty(exports, "generateClaudeSettings", { enumerable: true, get: function () { return claude_config_1.generateClaudeSettings; } });
+Object.defineProperty(exports, "generateMcpJson", { enumerable: true, get: function () { return claude_config_1.generateMcpJson; } });
 Object.defineProperty(exports, "setupMCPServer", { enumerable: true, get: function () { return claude_config_1.setupMCPServer; } });
 const documentation_1 = require("./documentation");
 Object.defineProperty(exports, "copyDocumentation", { enumerable: true, get: function () { return documentation_1.copyDocumentation; } });
@@ -35,6 +36,7 @@ const commands_1 = require("./commands");
 const helpers_1 = require("./helpers");
 const learning_init_1 = require("./learning-init");
 const optional_dependencies_1 = require("./optional-dependencies");
+const code_intelligence_init_1 = require("./code-intelligence-init");
 // Import version from package.json
 const packageJson = require('../../../package.json');
 const PACKAGE_VERSION = packageJson.version;
@@ -80,6 +82,7 @@ async function initCommand(options) {
             description: 'Generating Claude Code settings and MCP server',
             execute: async (cfg) => {
                 await (0, claude_config_1.generateClaudeSettings)(cfg);
+                await (0, claude_config_1.generateMcpJson)(cfg); // Creates .claude/mcp.json with server definitions
                 await (0, claude_config_1.setupMCPServer)();
             },
             critical: true // CRITICAL for learning system!
@@ -136,6 +139,12 @@ async function initCommand(options) {
                 enabled: true,
             }),
             critical: false // Non-critical - learning is optional but valuable
+        },
+        {
+            name: 'Code Intelligence',
+            description: 'Setting up Code Intelligence System (semantic search + knowledge graph)',
+            execute: async (cfg, opts) => (0, code_intelligence_init_1.initializeCodeIntelligence)(cfg, !opts.yes && !opts.nonInteractive),
+            critical: false // Non-critical - requires Ollama + PostgreSQL
         }
     ];
     let spinner = null;

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