✨ feat: Add MCP Reinitialization to MCPPanel

- Refactored tool caching to include user-specific tools in various service files.
- Refactored MCPManager class for clarity
- Added a new endpoint for reinitializing MCP servers, allowing for dynamic updates of server configurations.
- Enhanced the MCPPanel component to support server reinitialization with user feedback.

api/server/services/initializeMCPs.js

@@ -0,0 +1,68 @@
+const { logger } = require('@librechat/data-schemas');
+const { CacheKeys } = require('librechat-data-provider');
+const { findToken, updateToken, createToken, deleteTokens } = require('~/models');
+const { getMCPManager, getFlowStateManager } = require('~/config');
+const { getCachedTools, setCachedTools } = require('./Config');
+const { getLogStores } = require('~/cache');
+
+/**
+ * Initialize MCP servers
+ * @param {import('express').Application} app - Express app instance
+ */
+async function initializeMCPs(app) {
+  const mcpServers = app.locals.mcpConfig;
+  if (!mcpServers) {
+    return;
+  }
+
+  // Filter out servers with startup: false
+  const filteredServers = {};
+  for (const [name, config] of Object.entries(mcpServers)) {
+    if (config.startup === false) {
+      logger.info(`Skipping MCP server '${name}' due to startup: false`);
+      continue;
+    }
+    filteredServers[name] = config;
+  }
+
+  if (Object.keys(filteredServers).length === 0) {
+    logger.info('[MCP] No MCP servers to initialize (all skipped or none configured)');
+    return;
+  }
+
+  logger.info('Initializing MCP servers...');
+  const mcpManager = getMCPManager();
+  const flowsCache = getLogStores(CacheKeys.FLOWS);
+  const flowManager = flowsCache ? getFlowStateManager(flowsCache) : null;
+
+  try {
+    await mcpManager.initializeMCPs({
+      mcpServers: filteredServers,
+      flowManager,
+      tokenMethods: {
+        findToken,
+        updateToken,
+        createToken,
+        deleteTokens,
+      },
+    });
+
+    delete app.locals.mcpConfig;
+    const availableTools = await getCachedTools();
+
+    if (!availableTools) {
+      logger.warn('No available tools found in cache during MCP initialization');
+      return;
+    }
+
+    const toolsCopy = { ...availableTools };
+    await mcpManager.mapAvailableTools(toolsCopy, flowManager);
+    await setCachedTools(toolsCopy, { isGlobal: true });
+
+    logger.info('MCP servers initialized successfully');
+  } catch (error) {
+    logger.error('Failed to initialize MCP servers:', error);
+  }
+}
+
+module.exports = initializeMCPs;