@juspay/neurolink 6.1.0 → 6.2.0

package/dist/cli/commands/mcp.js

@@ -1,1272 +0,0 @@
-#!/usr/bin/env node
-/**
- * MCP Server Management Commands
- * Real MCP server connectivity and management
- */
-import ora from "ora";
-import chalk from "chalk";
-import fs from "fs";
-import { spawn } from "child_process";
-import path from "path";
-import { discoverMCPServers } from "../../lib/mcp/auto-discovery.js";
-import { unifiedRegistry } from "../../lib/mcp/unified-registry.js";
-import { ContextManager } from "../../lib/mcp/context-manager.js";
-import { MCPOrchestrator } from "../../lib/mcp/orchestrator.js";
-import { initializeNeuroLinkMCP } from "../../lib/mcp/initialize.js";
-import { mcpLogger, setGlobalMCPLogLevel } from "../../lib/mcp/logging.js";
-// import type { LogLevel } from "../../lib/mcp/logging.js"; // Commented out as unused
-import { defaultTimeoutManager } from "../../lib/utils/timeout-manager.js";
-// Default MCP config file location
-const MCP_CONFIG_FILE = path.join(process.cwd(), ".mcp-config.json");
-// Load MCP configuration
-function loadMCPConfig() {
-    if (!fs.existsSync(MCP_CONFIG_FILE)) {
-        return { mcpServers: {} };
-    }
-    try {
-        const content = fs.readFileSync(MCP_CONFIG_FILE, "utf-8");
-        return JSON.parse(content);
-    }
-    catch (error) {
-        throw new Error(`Invalid MCP config file: ${error.message}`);
-    }
-}
-// Save MCP configuration
-function saveMCPConfig(config) {
-    fs.writeFileSync(MCP_CONFIG_FILE, JSON.stringify(config, null, 2));
-}
-// Check if MCP server process is running
-async function checkMCPServerStatus(serverConfig) {
-    try {
-        if (serverConfig.transport === "stdio") {
-            // For stdio servers, use timeout manager for proper cleanup
-            const result = await defaultTimeoutManager.wrapMCPOperation(async () => {
-                const child = spawn(serverConfig.command, serverConfig.args || [], {
-                    stdio: ["pipe", "pipe", "pipe"],
-                    env: { ...process.env, ...serverConfig.env },
-                    cwd: serverConfig.cwd,
-                });
-                return new Promise((resolve, reject) => {
-                    child.on("spawn", () => {
-                        child.kill();
-                        resolve(true);
-                    });
-                    child.on("error", (error) => {
-                        reject(error);
-                    });
-                    child.on("exit", (code) => {
-                        if (code === null) {
-                            // Process was terminated (expected for quick check)
-                            resolve(true);
-                        }
-                        else {
-                            resolve(false);
-                        }
-                    });
-                });
-            }, "server-status-check", 10000);
-            return result.success && result.data === true;
-        }
-        else if (serverConfig.transport === "sse" && serverConfig.url) {
-            // For SSE servers, check if URL is accessible with timeout
-            const result = await defaultTimeoutManager.wrapMCPOperation(async () => {
-                if (!serverConfig.url) {
-                    throw new Error("SSE URL not configured");
-                }
-                const response = await fetch(serverConfig.url, { method: "HEAD" });
-                return response.ok;
-            }, "sse-status-check", 10000);
-            return result.success && result.data === true;
-        }
-        return false;
-    }
-    catch {
-        return false;
-    }
-}
-// Connect to MCP server and get capabilities
-async function getMCPServerCapabilities(serverConfig) {
-    if (serverConfig.transport === "stdio") {
-        // Use timeout manager for proper cleanup and longer timeout
-        const result = await defaultTimeoutManager.wrapMCPOperation(async () => {
-            const child = spawn(serverConfig.command, serverConfig.args || [], {
-                stdio: ["pipe", "pipe", "pipe"],
-                env: { ...process.env, ...serverConfig.env },
-                cwd: serverConfig.cwd,
-            });
-            return new Promise((resolve, reject) => {
-                let responseData = "";
-                child.stdout?.on("data", (data) => {
-                    responseData += data.toString();
-                    // Look for JSON-RPC response
-                    try {
-                        const lines = responseData.split("\n");
-                        for (const line of lines) {
-                            if (line.trim() && line.includes('"result"')) {
-                                const response = JSON.parse(line.trim());
-                                if (response.result && response.result.capabilities) {
-                                    child.kill();
-                                    resolve(response.result);
-                                    return;
-                                }
-                            }
-                        }
-                    }
-                    catch {
-                        // Continue parsing
-                    }
-                });
-                child.on("spawn", () => {
-                    // Send initialize request
-                    const initRequest = {
-                        jsonrpc: "2.0",
-                        id: 1,
-                        method: "initialize",
-                        params: {
-                            protocolVersion: "2024-11-05",
-                            capabilities: {},
-                            clientInfo: {
-                                name: "neurolink-cli",
-                                version: "1.0.0",
-                            },
-                        },
-                    };
-                    child.stdin?.write(JSON.stringify(initRequest) + "\n");
-                });
-                child.on("error", (error) => {
-                    reject(error);
-                });
-            });
-        }, "server-capabilities-check", 15000);
-        if (result.success) {
-            return result.data;
-        }
-        else {
-            throw result.error || new Error("Failed to get MCP server capabilities");
-        }
-    }
-    throw new Error("SSE transport not yet implemented for capabilities");
-}
-// List available tools from MCP server
-async function listMCPServerTools(serverConfig) {
-    if (serverConfig.transport === "stdio") {
-        // Use timeout manager for proper cleanup and longer timeout
-        const result = await defaultTimeoutManager.wrapMCPOperation(async () => {
-            const child = spawn(serverConfig.command, serverConfig.args || [], {
-                stdio: ["pipe", "pipe", "pipe"],
-                env: { ...process.env, ...serverConfig.env },
-                cwd: serverConfig.cwd,
-            });
-            return new Promise((resolve, reject) => {
-                let responseData = "";
-                // let initialized = false; // Commented out as unused
-                child.stdout?.on("data", (data) => {
-                    responseData += data.toString();
-                    try {
-                        const lines = responseData.split("\n");
-                        for (const line of lines) {
-                            if (line.trim() && line.includes('"result"')) {
-                                const response = JSON.parse(line.trim());
-                                if (response.id === 1 && response.result.capabilities) {
-                                    // Initialize successful, now list tools
-                                    // initialized = true; // Commented out as unused
-                                    const listToolsRequest = {
-                                        jsonrpc: "2.0",
-                                        id: 2,
-                                        method: "tools/list",
-                                        params: {},
-                                    };
-                                    child.stdin?.write(JSON.stringify(listToolsRequest) + "\n");
-                                }
-                                else if (response.id === 2 && response.result.tools) {
-                                    child.kill();
-                                    resolve(response.result.tools);
-                                    return;
-                                }
-                            }
-                        }
-                    }
-                    catch {
-                        // Continue parsing
-                    }
-                });
-                child.on("spawn", () => {
-                    // Send initialize request first
-                    const initRequest = {
-                        jsonrpc: "2.0",
-                        id: 1,
-                        method: "initialize",
-                        params: {
-                            protocolVersion: "2024-11-05",
-                            capabilities: {},
-                            clientInfo: {
-                                name: "neurolink-cli",
-                                version: "1.0.0",
-                            },
-                        },
-                    };
-                    child.stdin?.write(JSON.stringify(initRequest) + "\n");
-                });
-                child.on("error", (error) => {
-                    reject(error);
-                });
-            });
-        }, "server-tools-list", 15000);
-        if (result.success) {
-            return result.data || [];
-        }
-        else {
-            throw result.error || new Error("Failed to list MCP server tools");
-        }
-    }
-    throw new Error("SSE transport not yet implemented for tool listing");
-}
-// Execute tool on MCP server
-export async function executeMCPTool(serverConfig, toolName, toolParams) {
-    if (serverConfig.transport === "stdio") {
-        // Use timeout manager for proper cleanup and configurable timeout
-        const result = await defaultTimeoutManager.wrapMCPOperation(async () => {
-            const child = spawn(serverConfig.command, serverConfig.args || [], {
-                stdio: ["pipe", "pipe", "pipe"],
-                env: { ...process.env, ...serverConfig.env },
-                cwd: serverConfig.cwd,
-            });
-            return new Promise((resolve, reject) => {
-                let responseData = "";
-                // let initialized = false; // Commented out as unused
-                child.stdout?.on("data", (data) => {
-                    responseData += data.toString();
-                    try {
-                        const lines = responseData.split("\n");
-                        for (const line of lines) {
-                            if (line.trim() && line.includes('"result"')) {
-                                const response = JSON.parse(line.trim());
-                                if (response.id === 1 && response.result.capabilities) {
-                                    // Initialize successful, now execute tool
-                                    // initialized = true; // Commented out as unused
-                                    const toolCallRequest = {
-                                        jsonrpc: "2.0",
-                                        id: 2,
-                                        method: "tools/call",
-                                        params: {
-                                            name: toolName,
-                                            arguments: toolParams,
-                                        },
-                                    };
-                                    child.stdin?.write(JSON.stringify(toolCallRequest) + "\n");
-                                }
-                                else if (response.id === 2) {
-                                    child.kill();
-                                    if (response.result) {
-                                        resolve(response.result);
-                                    }
-                                    else if (response.error) {
-                                        reject(new Error(`MCP Error: ${response.error.message || "Unknown error"}`));
-                                    }
-                                    else {
-                                        reject(new Error("Unknown MCP response format"));
-                                    }
-                                    return;
-                                }
-                            }
-                            else if (line.trim() && line.includes('"error"')) {
-                                const response = JSON.parse(line.trim());
-                                if (response.error) {
-                                    child.kill();
-                                    reject(new Error(`MCP Error: ${response.error.message || "Unknown error"}`));
-                                    return;
-                                }
-                            }
-                        }
-                    }
-                    catch {
-                        // Continue parsing
-                    }
-                });
-                child.stderr?.on("data", (data) => {
-                    console.error(chalk.red(`MCP Server Error: ${data.toString()}`));
-                });
-                child.on("spawn", () => {
-                    // Send initialize request first
-                    const initRequest = {
-                        jsonrpc: "2.0",
-                        id: 1,
-                        method: "initialize",
-                        params: {
-                            protocolVersion: "2024-11-05",
-                            capabilities: {},
-                            clientInfo: {
-                                name: "neurolink-cli",
-                                version: "1.0.0",
-                            },
-                        },
-                    };
-                    child.stdin?.write(JSON.stringify(initRequest) + "\n");
-                });
-                child.on("error", (error) => {
-                    reject(error);
-                });
-            });
-        }, "tool-execution", 30000);
-        if (result.success) {
-            return result.data || null;
-        }
-        else {
-            throw result.error || new Error("Failed to execute MCP tool");
-        }
-    }
-    throw new Error("SSE transport not yet implemented for tool execution");
-}
-/**
- * Display discovery results in table format
- */
-function _displayTable(discoveryResult) {
-    console.log(chalk.green(`\n📋 Found ${discoveryResult.discovered.length} MCP servers:`));
-    console.log(chalk.gray("─".repeat(80)));
-    discoveryResult.discovered.forEach((server, index) => {
-        const source = server.source;
-        const sourceIcon = getSourceIcon(source?.tool);
-        const typeColor = source?.type === "global"
-            ? chalk.blue
-            : source?.type === "workspace"
-                ? chalk.green
-                : chalk.gray;
-        console.log(`${chalk.white(`${index + 1}.`)} ${sourceIcon} ${chalk.cyan(server.id)}`);
-        console.log(`   ${chalk.gray("Title:")} ${server.title}`);
-        console.log(`   ${chalk.gray("Source:")} ${source?.tool} ${typeColor(`(${source?.type})`)}`);
-        console.log(`   ${chalk.gray("Command:")} ${server.command} ${server.args?.join(" ") || ""}`);
-        console.log(`   ${chalk.gray("Config:")} ${server.configPath}`);
-        if (server.env && Object.keys(server.env).length > 0) {
-            console.log(`   ${chalk.gray("Environment:")} ${Object.keys(server.env).length} variable(s)`);
-        }
-        console.log();
-    });
-    // Display statistics
-    console.log(chalk.blue("📊 Discovery Statistics:"));
-    console.log(`   ${chalk.gray("Execution time:")} ${discoveryResult.stats.executionTime}ms`);
-    console.log(`   ${chalk.gray("Config files found:")} ${discoveryResult.stats.configFilesFound}`);
-    console.log(`   ${chalk.gray("Servers discovered:")} ${discoveryResult.stats.serversDiscovered}`);
-    console.log(`   ${chalk.gray("Duplicates removed:")} ${discoveryResult.stats.duplicatesRemoved}`);
-    // Display sources
-    if (discoveryResult.sources.length > 0) {
-        console.log(chalk.blue("\n🎯 Search Sources:"));
-        const sourcesByTool = discoveryResult.sources.reduce((acc, source) => {
-            const tool = String(source.tool || "unknown");
-            acc[tool] = (Number(acc[tool]) || 0) + 1;
-            return acc;
-        }, {});
-        Object.entries(sourcesByTool).forEach(([tool, count]) => {
-            const icon = getSourceIcon(tool);
-            console.log(`   ${icon} ${tool}: ${count} location(s)`);
-        });
-    }
-}
-/**
- * Display discovery results in summary format
- */
-function _displaySummary(discoveryResult) {
-    console.log(chalk.green(`\n📊 Discovery Summary`));
-    console.log(chalk.gray("==================="));
-    console.log(`${chalk.cyan("Total servers found:")} ${discoveryResult.discovered.length}`);
-    console.log(`${chalk.cyan("Execution time:")} ${discoveryResult.stats.executionTime}ms`);
-    console.log(`${chalk.cyan("Config files found:")} ${discoveryResult.stats.configFilesFound}`);
-    console.log(`${chalk.cyan("Duplicates removed:")} ${discoveryResult.stats.duplicatesRemoved}`);
-    // Group by source tool
-    const serversByTool = discoveryResult.discovered.reduce((acc, server) => {
-        const tool = String(server.source?.tool || "unknown");
-        acc[tool] = (Number(acc[tool]) || 0) + 1;
-        return acc;
-    }, {});
-    if (Object.keys(serversByTool).length > 0) {
-        console.log(chalk.blue("\n🔧 Servers by Tool:"));
-        Object.entries(serversByTool).forEach(([tool, count]) => {
-            const icon = getSourceIcon(tool);
-            console.log(`   ${icon} ${tool}: ${count} server(s)`);
-        });
-    }
-    // Group by type
-    const serversByType = discoveryResult.discovered.reduce((acc, server) => {
-        const type = String(server.source?.type || "unknown");
-        acc[type] = (Number(acc[type]) || 0) + 1;
-        return acc;
-    }, {});
-    if (Object.keys(serversByType).length > 0) {
-        console.log(chalk.blue("\n📍 Servers by Type:"));
-        Object.entries(serversByType).forEach(([type, count]) => {
-            const typeColor = type === "global"
-                ? chalk.blue
-                : type === "workspace"
-                    ? chalk.green
-                    : chalk.gray;
-            console.log(`   ${typeColor(`${type}:`)} ${count} server(s)`);
-        });
-    }
-}
-/**
- * Get icon for source tool
- */
-function getSourceIcon(tool) {
-    const icons = {
-        "Claude Desktop": "🤖",
-        "VS Code": "📝",
-        Cursor: "🖱️",
-        Windsurf: "🏄",
-        "Roo Code": "🦘",
-        Generic: "⚙️",
-        "Cline AI Coder": "🔧",
-        "Continue Dev": "🔄",
-        Aider: "🛠️",
-    };
-    return icons[tool] || "🔧";
-}
-/**
- * Get icon for source type
- */
-function getSourceTypeIcon(sourceType) {
-    const icons = {
-        manual: "📝",
-        auto: "🔍",
-        default: "⚙️",
-    };
-    return icons[sourceType] || "❓";
-}
-/**
- * Get icon for server status
- */
-function _getStatusIcon(status) {
-    const icons = {
-        available: "✅",
-        unavailable: "❌",
-        unknown: "❓",
-    };
-    return icons[status] || "❓";
-}
-// Export the tool execution function for use in other parts of the CLI
-export async function mcpExecuteTool(serverName, toolName, toolParams) {
-    // First try unified registry (includes built-in NeuroLink servers)
-    try {
-        await unifiedRegistry.initialize();
-        const orchestrator = new MCPOrchestrator(unifiedRegistry);
-        const result = await orchestrator.executeTool(toolName, toolParams, {
-            sessionId: `cli-${Date.now()}`,
-            userId: "cli-user",
-            aiProvider: "unified-mcp",
-        }, {
-            preferredSource: "default", // Try built-in servers first
-            fallbackEnabled: true,
-            validateBeforeExecution: true,
-            timeoutMs: 30000,
-        });
-        if (result.success) {
-            return result.data;
-        }
-    }
-    catch (error) {
-        mcpLogger.debug("[mcpExecuteTool] Unified registry failed, trying manual config:", {
-            error: error instanceof Error ? error.message : String(error),
-            serverName,
-            toolName: toolName,
-        });
-    }
-    // Fallback to manual configuration (legacy behavior)
-    const config = loadMCPConfig();
-    const serverConfig = config.mcpServers[serverName];
-    if (!serverConfig) {
-        throw new Error(`MCP server '${serverName}' not found`);
-    }
-    const result = await executeMCPTool(serverConfig, toolName, toolParams);
-    mcpLogger.debug("[mcpExecuteTool] Tool executed via manual config:", {
-        serverName,
-        toolName,
-        hasResult: !!result,
-        resultType: typeof result,
-    });
-    // Extract the text content from MCP result format
-    if (result &&
-        result.content &&
-        Array.isArray(result.content)) {
-        const textContent = result.content.find((item) => item.type === "text");
-        if (textContent) {
-            return JSON.parse(textContent.text);
-        }
-    }
-    return result;
-}
-// MCP Commands for yargs
-export function addMCPCommands(yargs) {
-    return yargs.command("mcp <subcommand>", "Manage MCP (Model Context Protocol) servers", (yargsBuilder) => {
-        yargsBuilder
-            .usage("Usage: $0 mcp <subcommand> [options]")
-            // List MCP servers
-            .command("list", "List configured MCP servers", (y) => y
-            .usage("Usage: $0 mcp list [options]")
-            .option("status", {
-            type: "boolean",
-            description: "Check server status",
-        })
-            .example("$0 mcp list", "List all MCP servers")
-            .example("$0 mcp list --status", "List servers with status check"), async (argv) => {
-            const config = loadMCPConfig();
-            const servers = Object.entries(config.mcpServers);
-            if (servers.length === 0) {
-                console.log(chalk.yellow("📭 No MCP servers configured"));
-                console.log(chalk.blue("💡 Add a server with: neurolink mcp add <name> <command>"));
-                return;
-            }
-            console.log(chalk.blue(`📋 Configured MCP servers (${servers.length}):\n`));
-            for (const [name, serverConfig] of servers) {
-                console.log(chalk.bold(`🔧 ${name}`));
-                console.log(`   Command: ${serverConfig.command} ${(serverConfig.args || []).join(" ")}`);
-                console.log(`   Transport: ${serverConfig.transport}`);
-                if (argv.status) {
-                    const spinner = ora(`Checking ${name}...`).start();
-                    try {
-                        const isRunning = await checkMCPServerStatus(serverConfig);
-                        if (isRunning) {
-                            spinner.succeed(`${name}: ${chalk.green("✅ Available")}`);
-                        }
-                        else {
-                            spinner.fail(`${name}: ${chalk.red("❌ Not available")}`);
-                        }
-                    }
-                    catch (error) {
-                        spinner.fail(`${name}: ${chalk.red("❌ Error")} - ${error.message}`);
-                    }
-                }
-                console.log(); // Empty line
-            }
-        })
-            // Add MCP server
-            .command("add <name> <command>", "Add a new MCP server", (y) => y
-            .usage("Usage: $0 mcp add <name> <command> [options]")
-            .positional("name", {
-            type: "string",
-            description: "Server name",
-            demandOption: true,
-        })
-            .positional("command", {
-            type: "string",
-            description: "Command to run server",
-            demandOption: true,
-        })
-            .option("args", {
-            type: "array",
-            description: "Command arguments",
-        })
-            .option("transport", {
-            choices: ["stdio", "sse"],
-            default: "stdio",
-            description: "Transport type",
-        })
-            .option("url", {
-            type: "string",
-            description: "URL for SSE transport",
-        })
-            .option("env", {
-            type: "string",
-            description: "Environment variables (JSON)",
-        })
-            .option("cwd", {
-            type: "string",
-            description: "Working directory",
-        })
-            .example('$0 mcp add filesystem "npx @modelcontextprotocol/server-filesystem"', "Add filesystem server")
-            .example('$0 mcp add github "npx @modelcontextprotocol/server-github"', "Add GitHub server"), async (argv) => {
-            const config = loadMCPConfig();
-            const serverConfig = {
-                name: argv.name,
-                command: argv.command,
-                args: argv.args || [],
-                transport: argv.transport,
-                url: argv.url,
-                cwd: argv.cwd,
-            };
-            if (argv.env) {
-                try {
-                    serverConfig.env = JSON.parse(argv.env);
-                }
-                catch (error) {
-                    console.error(chalk.red("❌ Invalid JSON for environment variables"));
-                    process.exit(1);
-                }
-            }
-            config.mcpServers[argv.name] = serverConfig;
-            saveMCPConfig(config);
-            console.log(chalk.green(`✅ Added MCP server: ${argv.name}`));
-            console.log(chalk.blue(`💡 Test it with: neurolink mcp test ${argv.name}`));
-        })
-            // Remove MCP server
-            .command("remove <name>", "Remove an MCP server", (y) => y
-            .usage("Usage: $0 mcp remove <name>")
-            .positional("name", {
-            type: "string",
-            description: "Server name to remove",
-            demandOption: true,
-        })
-            .example("$0 mcp remove filesystem", "Remove filesystem server"), async (argv) => {
-            const config = loadMCPConfig();
-            if (!config.mcpServers[argv.name]) {
-                console.error(chalk.red(`❌ MCP server '${argv.name}' not found`));
-                process.exit(1);
-            }
-            delete config.mcpServers[argv.name];
-            saveMCPConfig(config);
-            console.log(chalk.green(`✅ Removed MCP server: ${argv.name}`));
-        })
-            // Test MCP server
-            .command("test <name>", "Test connection to an MCP server", (y) => y
-            .usage("Usage: $0 mcp test <name>")
-            .positional("name", {
-            type: "string",
-            description: "Server name to test",
-            demandOption: true,
-        })
-            .example("$0 mcp test filesystem", "Test filesystem server"), async (argv) => {
-            const config = loadMCPConfig();
-            const serverConfig = config.mcpServers[argv.name];
-            if (!serverConfig) {
-                console.error(chalk.red(`❌ MCP server '${argv.name}' not found`));
-                process.exit(1);
-            }
-            console.log(chalk.blue(`🔍 Testing MCP server: ${argv.name}\n`));
-            const spinner = ora("Connecting...").start();
-            try {
-                // Test basic connectivity
-                const isRunning = await checkMCPServerStatus(serverConfig);
-                if (!isRunning) {
-                    spinner.fail(chalk.red("❌ Server not available"));
-                    return;
-                }
-                spinner.text = "Getting capabilities...";
-                const capabilities = await getMCPServerCapabilities(serverConfig);
-                spinner.text = "Listing tools...";
-                const tools = await listMCPServerTools(serverConfig);
-                spinner.succeed(chalk.green("✅ Connection successful!"));
-                console.log(chalk.blue("\n📋 Server Capabilities:"));
-                console.log(`   Protocol Version: ${capabilities.protocolVersion || "Unknown"}`);
-                if (capabilities.tools) {
-                    console.log(`   Tools: ✅ Supported`);
-                }
-                if (capabilities.resources) {
-                    console.log(`   Resources: ✅ Supported`);
-                }
-                console.log(chalk.blue("\n🛠️  Available Tools:"));
-                if (tools.length === 0) {
-                    console.log("   No tools available");
-                }
-                else {
-                    tools.forEach((tool) => {
-                        const toolObj = tool;
-                        console.log(`   • ${String(toolObj.name)}: ${String(toolObj.description) || "No description"}`);
-                    });
-                }
-            }
-            catch (error) {
-                spinner.fail(chalk.red("❌ Connection failed"));
-                console.error(chalk.red(`Error: ${error.message}`));
-            }
-        })
-            // Install popular MCP servers
-            .command("install <server>", "Install popular MCP servers", (y) => y
-            .usage("Usage: $0 mcp install <server>")
-            .positional("server", {
-            type: "string",
-            choices: [
-                "filesystem",
-                "github",
-                "postgres",
-                "brave-search",
-                "puppeteer",
-            ],
-            description: "Server to install",
-            demandOption: true,
-        })
-            .example("$0 mcp install filesystem", "Install filesystem server")
-            .example("$0 mcp install github", "Install GitHub server"), async (argv) => {
-            const serverName = argv.server;
-            const config = loadMCPConfig();
-            // Pre-configured popular MCP servers
-            const serverConfigs = {
-                filesystem: {
-                    name: "filesystem",
-                    command: "npx",
-                    args: ["-y", "@modelcontextprotocol/server-filesystem", "/"],
-                    transport: "stdio",
-                },
-                github: {
-                    name: "github",
-                    command: "npx",
-                    args: ["-y", "@modelcontextprotocol/server-github"],
-                    transport: "stdio",
-                },
-                postgres: {
-                    name: "postgres",
-                    command: "npx",
-                    args: ["-y", "@modelcontextprotocol/server-postgres"],
-                    transport: "stdio",
-                },
-                "brave-search": {
-                    name: "brave-search",
-                    command: "npx",
-                    args: ["-y", "@modelcontextprotocol/server-brave-search"],
-                    transport: "stdio",
-                },
-                puppeteer: {
-                    name: "puppeteer",
-                    command: "npx",
-                    args: ["-y", "@modelcontextprotocol/server-puppeteer"],
-                    transport: "stdio",
-                },
-            };
-            const serverConfig = serverConfigs[serverName];
-            if (!serverConfig) {
-                console.error(chalk.red(`❌ Unknown server: ${serverName}`));
-                process.exit(1);
-            }
-            console.log(chalk.blue(`📦 Installing MCP server: ${serverName}`));
-            config.mcpServers[serverName] = serverConfig;
-            saveMCPConfig(config);
-            console.log(chalk.green(`✅ Installed MCP server: ${serverName}`));
-            console.log(chalk.blue(`💡 Test it with: neurolink mcp test ${serverName}`));
-        })
-            // Execute tool from MCP server
-            .command("exec <server> <tool>", "Execute a tool from an MCP server", (y) => y
-            .usage("Usage: $0 mcp exec <server> <tool> [options]")
-            .positional("server", {
-            type: "string",
-            description: "Server name",
-            demandOption: true,
-        })
-            .positional("tool", {
-            type: "string",
-            description: "Tool name",
-            demandOption: true,
-        })
-            .option("params", {
-            type: "string",
-            description: "Tool parameters (JSON)",
-        })
-            .example('$0 mcp exec filesystem read_file --params \'{"path": "README.md"}\'', "Read file using filesystem server"), async (argv) => {
-            const config = loadMCPConfig();
-            const serverConfig = config.mcpServers[argv.server];
-            if (!serverConfig) {
-                console.error(chalk.red(`❌ MCP server '${argv.server}' not found`));
-                process.exit(1);
-            }
-            let params = {};
-            if (argv.params) {
-                try {
-                    params = JSON.parse(argv.params);
-                }
-                catch (error) {
-                    console.error(chalk.red("❌ Invalid JSON for parameters"));
-                    process.exit(1);
-                }
-            }
-            console.log(chalk.blue(`🔧 Executing tool: ${argv.tool} on server: ${argv.server}`));
-            const spinner = ora("Executing tool...").start();
-            try {
-                const result = await executeMCPTool(serverConfig, argv.tool, params);
-                spinner.succeed(chalk.green("✅ Tool executed successfully!"));
-                console.log(chalk.blue("\n📋 Result:"));
-                const resultObj = result;
-                if (resultObj.content) {
-                    // Handle different content types
-                    if (Array.isArray(resultObj.content)) {
-                        resultObj.content.forEach((item) => {
-                            if (item.type === "text") {
-                                console.log(String(item.text));
-                            }
-                            else {
-                                console.log(JSON.stringify(item, null, 2));
-                            }
-                        });
-                    }
-                    else {
-                        console.log(JSON.stringify(resultObj.content, null, 2));
-                    }
-                }
-                else {
-                    console.log(JSON.stringify(result, null, 2));
-                }
-            }
-            catch (error) {
-                spinner.fail(chalk.red("❌ Tool execution failed"));
-                console.error(chalk.red(`Error: ${error.message}`));
-                process.exit(1);
-            }
-        })
-            // Enhanced unified list command
-            .command("list-all", "List servers from all sources (manual + auto + default)", (y) => y
-            .usage("Usage: $0 mcp list-all [options]")
-            .option("source", {
-            type: "string",
-            choices: ["manual", "auto", "default", "all"],
-            default: "all",
-            description: "Filter by source type",
-        })
-            .option("format", {
-            type: "string",
-            choices: ["table", "json"],
-            default: "table",
-            description: "Output format",
-        })
-            .option("refresh", {
-            type: "boolean",
-            description: "Force refresh auto-discovery cache",
-        })
-            .example("$0 mcp list-all", "List all servers from all sources")
-            .example("$0 mcp list-all --source auto", "List only auto-discovered servers")
-            .example("$0 mcp list-all --refresh", "Refresh auto-discovery and list all"), async (argv) => {
-            console.log(chalk.blue("🌐 NeuroLink Unified MCP Registry"));
-            console.log(chalk.gray("==================================="));
-            const spinner = ora("Initializing NeuroLink MCP...").start();
-            try {
-                // Initialize built-in NeuroLink servers first - register in unified registry
-                await initializeNeuroLinkMCP(unifiedRegistry);
-                // Initialize unified registry
-                spinner.text = "Initializing unified registry...";
-                await unifiedRegistry.initialize();
-                // Force refresh if requested
-                if (argv.refresh) {
-                    spinner.text = "Refreshing auto-discovery...";
-                    await unifiedRegistry.refresh();
-                }
-                spinner.succeed(chalk.green("Registry initialized!"));
-                // Get servers based on source filter
-                const servers = unifiedRegistry.list();
-                const filteredServers = argv.source === "all"
-                    ? servers
-                    : servers.filter((s) => s.source === argv.source);
-                if (filteredServers.length === 0) {
-                    console.log(chalk.yellow(`\n📭 No servers found from source: ${argv.source}`));
-                    return;
-                }
-                if (argv.format === "json") {
-                    console.log(JSON.stringify(filteredServers, null, 2));
-                    return;
-                }
-                // Table format
-                console.log(chalk.green(`\n📋 Found ${filteredServers.length} servers:`));
-                console.log(chalk.gray("─".repeat(80)));
-                filteredServers.forEach((server, index) => {
-                    const sourceIcon = getSourceTypeIcon(String(server.source || "unknown"));
-                    console.log(`${chalk.white(`${index + 1}.`)} ${sourceIcon} ${chalk.cyan(server.metadata.name)}`);
-                    console.log(`   ${chalk.gray("Version:")} ${String(server.metadata.version || "unknown")}`);
-                    console.log(`   ${chalk.gray("Source:")} ${server.source}`);
-                    console.log(`   ${chalk.gray("Entry:")} ${server.entryPath}`);
-                    if (server.metadata.description) {
-                        console.log(`   ${chalk.gray("Description:")} ${server.metadata.description}`);
-                    }
-                    // Add spacing between entries
-                    if (index < filteredServers.length - 1) {
-                        console.log();
-                    }
-                });
-                // Display statistics
-                const stats = await unifiedRegistry.getDetailedStats();
-                console.log(chalk.blue("📊 Registry Statistics:"));
-                console.log(`   ${chalk.gray("Total plugins:")} ${stats.total}`);
-                console.log(`   ${chalk.gray("Manual servers:")} ${stats.manual?.servers || 0}`);
-                console.log(`   ${chalk.gray("Auto-discovered:")} ${stats.auto?.servers || 0}`);
-                console.log(`   ${chalk.gray("Total tools:")} ${stats.tools || 0}`);
-            }
-            catch (error) {
-                spinner.fail(chalk.red("Registry initialization failed"));
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            // Enhanced tool execution with unified registry
-            .command("run <tool>", "Execute a tool using unified registry (auto-fallback)", (y) => y
-            .usage("Usage: $0 mcp run <tool> [options]")
-            .positional("tool", {
-            type: "string",
-            description: "Tool name to execute",
-            demandOption: true,
-        })
-            .option("params", {
-            type: "string",
-            description: "Tool parameters (JSON)",
-        })
-            .option("source", {
-            type: "string",
-            choices: ["manual", "auto", "default"],
-            description: "Preferred source (with fallback)",
-        })
-            .option("no-fallback", {
-            type: "boolean",
-            description: "Disable fallback to other sources",
-        })
-            .example('$0 mcp run generate --params \'{"prompt": "Hello world"}\'', "Run tool with fallback")
-            .example('$0 mcp run read_file --params \'{"path": "README.md"}\' --source manual', "Prefer manual config"), async (argv) => {
-            console.log(chalk.blue(`🚀 Executing tool: ${argv.tool}`));
-            const spinner = ora("Initializing NeuroLink MCP...").start();
-            try {
-                // Initialize built-in NeuroLink servers first - register in unified registry
-                await initializeNeuroLinkMCP(unifiedRegistry);
-                // Initialize unified registry
-                spinner.text = "Initializing unified registry...";
-                await unifiedRegistry.initialize();
-                let params = {};
-                if (argv.params) {
-                    try {
-                        params = JSON.parse(argv.params);
-                    }
-                    catch (error) {
-                        spinner.fail(chalk.red("❌ Invalid JSON for parameters"));
-                        process.exit(1);
-                    }
-                }
-                // Create execution context
-                const contextManager = new ContextManager();
-                const context = contextManager.createContext({
-                    sessionId: `cli-${Date.now()}`,
-                    userId: "cli-user",
-                    aiProvider: "unified-mcp",
-                });
-                const executionOptions = {
-                    preferredSource: argv.source,
-                    fallbackEnabled: !argv["no-fallback"],
-                    validateBeforeExecution: true,
-                    timeoutMs: 30000,
-                };
-                spinner.text = "Executing tool...";
-                const orchestrator = new MCPOrchestrator(unifiedRegistry);
-                const result = await orchestrator.executeTool(argv.tool, params, {
-                    sessionId: `cli-${Date.now()}`,
-                    userId: "cli-user",
-                }, executionOptions);
-                if (result.success) {
-                    spinner.succeed(chalk.green("✅ Tool executed successfully!"));
-                    console.log(chalk.blue("\n📋 Result:"));
-                    if (result.data) {
-                        console.log(JSON.stringify(result.data, null, 2));
-                    }
-                    else {
-                        console.log("No data returned");
-                    }
-                    if (result.metadata) {
-                        console.log(chalk.gray("\n🔧 Execution Details:"));
-                        console.log(`   Tool: ${result.metadata.toolName}`);
-                        console.log(`   Server: ${result.metadata.serverId || "unknown"}`);
-                        console.log(`   Execution time: ${result.metadata.executionTime}ms`);
-                        console.log(`   Session: ${result.metadata.sessionId}`);
-                    }
-                }
-                else {
-                    spinner.fail(chalk.red("❌ Tool execution failed"));
-                    console.error(chalk.red(`Error: ${result.error}`));
-                    process.exit(1);
-                }
-            }
-            catch (error) {
-                spinner.fail(chalk.red("❌ Execution failed"));
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            // Configuration management commands
-            .command("config <action>", "Manage unified registry configuration", (y) => y
-            .usage("Usage: $0 mcp config <action> [options]")
-            .command("show", "Show current configuration", {}, async () => {
-            try {
-                await unifiedRegistry.initialize();
-                console.log(chalk.blue("🔧 Unified Registry Configuration"));
-                console.log(chalk.gray("================================"));
-                const stats = await unifiedRegistry.getDetailedStats();
-                console.log(`Total servers: ${stats.total}`);
-                console.log("\nBy Source:");
-                Object.entries(stats.bySource).forEach(([source, count]) => {
-                    console.log(`  ${source}: ${count}`);
-                });
-                console.log("\nBy Type:");
-                Object.entries(stats.byType).forEach(([type, count]) => {
-                    console.log(`  ${type}: ${count}`);
-                });
-            }
-            catch (error) {
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            .command("enable-auto-discovery", "Enable auto-discovery", {}, async () => {
-            try {
-                await unifiedRegistry.initialize();
-                unifiedRegistry.setAutoDiscovery(true);
-                console.log(chalk.green("✅ Auto-discovery enabled"));
-            }
-            catch (error) {
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            .command("disable-auto-discovery", "Disable auto-discovery", {}, async () => {
-            try {
-                await unifiedRegistry.initialize();
-                unifiedRegistry.setAutoDiscovery(false);
-                console.log(chalk.green("✅ Auto-discovery disabled"));
-            }
-            catch (error) {
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            .command("set-sources <sources>", "Set preferred auto-discovery sources", (y) => y.positional("sources", {
-            type: "string",
-            description: "Comma-separated source list",
-            demandOption: true,
-        }), async (argv) => {
-            try {
-                await unifiedRegistry.initialize();
-                const sources = argv.sources
-                    .split(",")
-                    .map((s) => s.trim());
-                // Note: Source preference configuration not yet implemented
-                console.log(chalk.yellow(`⚠️  Source preference configuration not yet implemented`));
-                console.log(chalk.blue(`   Requested sources: ${sources.join(", ")}`));
-            }
-            catch (error) {
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            .command("set-log-level <level>", "Set MCP logging verbosity", (y) => y.positional("level", {
-            type: "string",
-            choices: ["silent", "error", "warn", "info", "debug"],
-            description: "Log level to set",
-            demandOption: true,
-        }), async (argv) => {
-            try {
-                const level = argv.level;
-                // Note: LogLevel is a type, not an enum
-                // 'silent' is not a valid LogLevel, default to 'error' for minimal output
-                const logLevel = level === "silent"
-                    ? "error" // Use 'error' for minimal output
-                    : level === "error"
-                        ? "error"
-                        : level === "warn"
-                            ? "warn"
-                            : level === "info"
-                                ? "info"
-                                : "debug";
-                setGlobalMCPLogLevel(logLevel);
-                console.log(chalk.green(`✅ MCP log level set to: ${level}`));
-                console.log(chalk.gray("This affects auto-discovery, registry operations, and tool execution logging"));
-            }
-            catch (error) {
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            .example("$0 mcp config show", "Show current configuration")
-            .example("$0 mcp config enable-auto-discovery", "Enable auto-discovery")
-            .example('$0 mcp config set-sources "claude,vscode,cursor"', "Set preferred sources")
-            .example("$0 mcp config set-log-level debug", "Enable debug logging for troubleshooting"))
-            // Discover MCP servers from all AI tools
-            .command(["discover [options]", "d [options]"], "Discover MCP servers from all AI development tools", (y) => y
-            .usage("Usage: $0 mcp discover [options]")
-            .option("format", {
-            alias: "f",
-            type: "string",
-            choices: ["table", "json", "yaml", "summary"],
-            default: "table",
-            description: "Output format",
-        })
-            .option("include-inactive", {
-            type: "boolean",
-            default: true,
-            description: "Include servers that may not be currently active",
-        })
-            .option("preferred-tools", {
-            type: "string",
-            description: "Prioritize specific tools (comma-separated)",
-        })
-            .option("workspace-only", {
-            type: "boolean",
-            description: "Search only workspace/project configurations",
-        })
-            .option("global-only", {
-            type: "boolean",
-            description: "Search only global configurations",
-        })
-            .example("$0 mcp discover", "Discover all MCP servers")
-            .example("$0 mcp d --format json", "Export as JSON (using alias)")
-            .example('$0 mcp discover --preferred-tools "claude,cursor"', "Prioritize specific tools"), async (argv) => {
-            console.log(chalk.blue("🔍 NeuroLink MCP Server Discovery"));
-            console.log(chalk.gray("====================================="));
-            const options = {
-                includeDevPlugins: argv["include-inactive"],
-                // Additional search paths if needed
-                searchPaths: [
-                    "./src/lib/mcp/plugins",
-                    "./neurolink-mcp",
-                    "./node_modules",
-                ],
-            };
-            const spinner = ora("Discovering MCP servers...").start();
-            try {
-                mcpLogger.debug("[MCP Discovery] Starting server discovery:", {
-                    includeDevPlugins: options.includeDevPlugins,
-                    searchPaths: options.searchPaths,
-                });
-                const discoveredPlugins = await discoverMCPServers(options);
-                mcpLogger.info("[MCP Discovery] Discovery completed:", {
-                    pluginsFound: discoveredPlugins.length,
-                });
-                spinner.succeed(chalk.green("Discovery completed!"));
-                if (discoveredPlugins.length === 0) {
-                    console.log(chalk.yellow("\n📭 No MCP servers found"));
-                    console.log(chalk.gray("\n💡 Tips for finding MCP servers:"));
-                    console.log(chalk.gray("  • Make sure you have Claude Desktop, VS Code, or Cursor with MCP configurations"));
-                    console.log(chalk.gray("  • Check that MCP configuration files exist in their expected locations"));
-                    console.log(chalk.gray("  • Run with 'neurolink mcp discover' to search all locations"));
-                    return;
-                }
-                // Display results based on format
-                if (argv.format === "json") {
-                    console.log(JSON.stringify(discoveredPlugins, null, 2));
-                    return;
-                }
-                if (argv.format === "yaml") {
-                    // Simple YAML output
-                    console.log("discovered:");
-                    discoveredPlugins.forEach((plugin) => {
-                        console.log(`  - name: ${plugin.metadata.name}`);
-                        console.log(`    version: ${plugin.metadata.version}`);
-                        console.log(`    source: ${plugin.source}`);
-                        console.log(`    entryPath: ${plugin.entryPath}`);
-                        if (plugin.metadata.description) {
-                            console.log(`    description: ${plugin.metadata.description}`);
-                        }
-                    });
-                    return;
-                }
-                // Default format - show simple list
-                console.log(chalk.green(`\n📋 Found ${discoveredPlugins.length} MCP plugins:`));
-                console.log(chalk.gray("─".repeat(80)));
-                discoveredPlugins.forEach((plugin, index) => {
-                    console.log(`${chalk.white(`${index + 1}.`)} ${chalk.cyan(plugin.metadata.name)} v${plugin.metadata.version}`);
-                    console.log(`   ${chalk.gray("Source:")} ${plugin.source}`);
-                    console.log(`   ${chalk.gray("Entry:")} ${plugin.entryPath}`);
-                    if (plugin.metadata.description) {
-                        console.log(`   ${chalk.gray("Description:")} ${plugin.metadata.description}`);
-                    }
-                    console.log();
-                });
-            }
-            catch (error) {
-                mcpLogger.error("[MCP Discovery] Discovery failed:", {
-                    error: error instanceof Error ? error.message : String(error),
-                    options,
-                });
-                spinner.fail(chalk.red("Discovery failed"));
-                console.error(chalk.red(`Error: ${error instanceof Error ? error.message : String(error)}`));
-                process.exit(1);
-            }
-        })
-            // Add debug command for tool registry diagnostics
-            .command("debug", "Debug MCP tool registry state and diagnose issues", (yargs) => {
-            return yargs.option("verbose", {
-                type: "boolean",
-                default: false,
-                description: "Show detailed debug information",
-            });
-        }, async (argv) => {
-            console.log(chalk.blue("🔍 MCP Tool Registry Debug"));
-            console.log(chalk.gray("=============================\n"));
-            try {
-                // Initialize built-in servers
-                console.log(chalk.cyan("🔧 Initializing Built-in Servers..."));
-                await initializeNeuroLinkMCP(unifiedRegistry);
-                // Initialize unified registry
-                console.log(chalk.cyan("🌐 Initializing Unified Registry..."));
-                await unifiedRegistry.initialize();
-                const registry = unifiedRegistry;
-                // Check built-in tools
-                console.log(chalk.green("\n📦 Built-in Tools:"));
-                const builtInTools = await registry.listTools();
-                if (builtInTools.length === 0) {
-                    console.log(chalk.red("  ❌ No built-in tools found"));
-                }
-                else {
-                    builtInTools.forEach((tool) => {
-                        console.log(`  ✅ ${String(tool.name)} (${String(tool.serverId) || "unknown server"})`);
-                        if (argv.verbose && tool.description) {
-                            console.log(`     └─ ${String(tool.description)}`);
-                        }
-                    });
-                }
-                // Check external servers
-                console.log(chalk.green("\n🌐 External Servers:"));
-                const allTools = await registry.listAllTools();
-                const externalTools = allTools.filter((t) => Boolean(t.isExternal));
-                if (externalTools.length === 0) {
-                    console.log(chalk.yellow("  ⚠️ No external servers connected"));
-                }
-                else {
-                    const serverGroups = externalTools.reduce((acc, tool) => {
-                        const server = String(tool.serverId) || "unknown";
-                        if (!acc[server]) {
-                            acc[server] = [];
-                        }
-                        acc[server].push(tool);
-                        return acc;
-                    }, {});
-                    Object.entries(serverGroups).forEach(([server, tools]) => {
-                        console.log(`  🔧 ${server} (${tools.length} tools)`);
-                        if (argv.verbose) {
-                            tools.forEach((tool) => {
-                                console.log(`     └─ ${String(tool.name)}`);
-                            });
-                        }
-                    });
-                }
-                // Test specific tool execution
-                console.log(chalk.green("\n🧪 Testing 'get-current-time' Tool:"));
-                try {
-                    const result = await registry.executeTool("get-current-time");
-                    console.log(chalk.green("  ✅ Success:"));
-                    if (argv.verbose) {
-                        console.log(JSON.stringify(result, null, 4));
-                    }
-                    else {
-                        console.log(`  └─ Tool executed successfully`);
-                    }
-                }
-                catch (error) {
-                    const errorMessage = error instanceof Error ? error.message : String(error);
-                    console.log(chalk.red("  ❌ Failed:"));
-                    console.log(`  └─ ${errorMessage}`);
-                    if (argv.verbose) {
-                        console.log(chalk.gray("\n📋 Debug Details:"));
-                        console.log(`     Error Type: ${error instanceof Error ? error.constructor.name : typeof error}`);
-                        console.log(`     Stack: ${error instanceof Error && error.stack ? error.stack : "No stack trace available"}`);
-                    }
-                }
-                // Summary
-                console.log(chalk.green(`\n📊 Summary:`));
-                console.log(`  Built-in tools: ${builtInTools.length}`);
-                console.log(`  External tools: ${externalTools.length}`);
-                console.log(`  Total tools: ${allTools.length}`);
-            }
-            catch (error) {
-                const errorMessage = error instanceof Error ? error.message : String(error);
-                console.error(chalk.red("❌ Debug failed:"));
-                console.error(`   ${errorMessage}`);
-                if (argv.verbose) {
-                    console.error(error instanceof Error && error.stack
-                        ? error.stack
-                        : "No stack trace available");
-                }
-                process.exit(1);
-            }
-        })
-            .demandCommand(1, "Please specify an MCP subcommand")
-            .example("$0 mcp list", "List configured MCP servers")
-            .example("$0 mcp discover", "Discover MCP servers from all tools")
-            .example("$0 mcp debug", "Debug tool registry state")
-            .example("$0 mcp install filesystem", "Install filesystem MCP server")
-            .example("$0 mcp test filesystem", "Test filesystem server connection");
-    });
-}