✨ 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/MCP.js

@@ -104,7 +104,7 @@ function createAbortHandler({ userId, serverName, toolName, flowManager }) {
  * @returns { Promise<typeof tool | { _call: (toolInput: Object | string) => unknown}> } An object with `_call` method to execute the tool input.
  */
 async function createMCPTool({ req, res, toolKey, provider: _provider }) {
-  const availableTools = await getCachedTools({ includeGlobal: true });
+  const availableTools = await getCachedTools({ userId: req.user?.id, includeGlobal: true });
   const toolDefinition = availableTools?.[toolKey]?.function;
   if (!toolDefinition) {
     logger.error(`Tool ${toolKey} not found in available tools`);

api/server/services/ToolService.js

@@ -226,7 +226,7 @@ async function processRequiredActions(client, requiredActions) {
     `[required actions] user: ${client.req.user.id} | thread_id: ${requiredActions[0].thread_id} | run_id: ${requiredActions[0].run_id}`,
     requiredActions,
   );
-  const toolDefinitions = await getCachedTools({ includeGlobal: true });
+  const toolDefinitions = await getCachedTools({ userId: client.req.user.id, includeGlobal: true });
   const seenToolkits = new Set();
   const tools = requiredActions
     .map((action) => {

api/server/services/initializeMCPs.js

@@ -9,20 +9,35 @@ const { getLogStores } = require('~/cache');
  * Initialize MCP servers
  * @param {import('express').Application} app - Express app instance
  */
-async function initializeMCP(app) {
+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.initializeMCP({
-      mcpServers,
+    await mcpManager.initializeMCPs({
+      mcpServers: filteredServers,
       flowManager,
       tokenMethods: {
         findToken,
@@ -44,13 +59,10 @@ async function initializeMCP(app) {
     await mcpManager.mapAvailableTools(toolsCopy, flowManager);
     await setCachedTools(toolsCopy, { isGlobal: true });
 
-    const cache = getLogStores(CacheKeys.CONFIG_STORE);
-    await cache.delete(CacheKeys.TOOLS);
-    logger.debug('Cleared tools array cache after MCP initialization');
     logger.info('MCP servers initialized successfully');
   } catch (error) {
     logger.error('Failed to initialize MCP servers:', error);
   }
 }
 
-module.exports = initializeMCP;
+module.exports = initializeMCPs;