✨ feat: Add MCP Reinitialization to MCPPanel (#8418)

* ✨ 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.

* 🔃 refactor: Simplify Plugin Deduplication and Clear Cache Post-MCP Initialization

- Replaced manual deduplication of tools with the dedicated `filterUniquePlugins` function for improved readability.
- Added back cache clearing for tools after MCP initialization to ensure fresh data is used.
- Removed unused exports from `PluginController.js` to clean up the codebase.

api/app/clients/tools/util/handleTools.js

@@ -230,7 +230,7 @@ const loadTools = async ({
 
   /** @type {Record<string, string>} */
   const toolContextMap = {};
-  const appTools = (await getCachedTools({ includeGlobal: true })) ?? {};
+  const cachedTools = (await getCachedTools({ userId: user, includeGlobal: true })) ?? {};
 
   for (const tool of tools) {
     if (tool === Tools.execute_code) {
@@ -298,7 +298,7 @@ Current Date & Time: ${replaceSpecialVars({ text: '{{iso_datetime}}' })}
         });
       };
       continue;
-    } else if (tool && appTools[tool] && mcpToolPattern.test(tool)) {
+    } else if (tool && cachedTools && mcpToolPattern.test(tool)) {
       requestedTools[tool] = async () =>
         createMCPTool({
           req: options.req,