fix: ensure MCP and skills config changes are immediately reflected

- Use ExtensionsConfig.from_file() instead of cached config to always
  read latest configuration from disk in LangGraph Server
- Add mtime-based cache invalidation for MCP tools to detect config
  file changes made through Gateway API
- Call reload_extensions_config() in Gateway API after updates to
  refresh the global cache
- Remove unnecessary MCP initialization from Gateway startup since
  MCP tools are only used by LangGraph Server

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

backend/src/tools/tools.py

@@ -31,14 +31,21 @@ def get_available_tools(groups: list[str] | None = None, include_mcp: bool = Tru
     loaded_tools = [resolve_variable(tool.use, BaseTool) for tool in config.tools if groups is None or tool.group in groups]
 
     # Get cached MCP tools if enabled
+    # NOTE: We use ExtensionsConfig.from_file() instead of config.extensions
+    # to always read the latest configuration from disk. This ensures that changes
+    # made through the Gateway API (which runs in a separate process) are immediately
+    # reflected when loading MCP tools.
     mcp_tools = []
-    if include_mcp and config.extensions and config.extensions.get_enabled_mcp_servers():
+    if include_mcp:
         try:
+            from src.config.extensions_config import ExtensionsConfig
             from src.mcp.cache import get_cached_mcp_tools
 
-            mcp_tools = get_cached_mcp_tools()
-            if mcp_tools:
-                logger.info(f"Using {len(mcp_tools)} cached MCP tool(s)")
+            extensions_config = ExtensionsConfig.from_file()
+            if extensions_config.get_enabled_mcp_servers():
+                mcp_tools = get_cached_mcp_tools()
+                if mcp_tools:
+                    logger.info(f"Using {len(mcp_tools)} cached MCP tool(s)")
         except ImportError:
             logger.warning("MCP module not available. Install 'langchain-mcp-adapters' package to enable MCP tools.")
         except Exception as e: