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/gateway/app.py

@@ -23,13 +23,10 @@ async def lifespan(app: FastAPI) -> AsyncGenerator[None, None]:
     config = get_gateway_config()
     logger.info(f"Starting API Gateway on {config.host}:{config.port}")
 
-    # Initialize MCP tools at startup
-    try:
-        from src.mcp import initialize_mcp_tools
-
-        await initialize_mcp_tools()
-    except Exception as e:
-        logger.warning(f"Failed to initialize MCP tools: {e}")
+    # NOTE: MCP tools initialization is NOT done here because:
+    # 1. Gateway doesn't use MCP tools - they are used by Agents in the LangGraph Server
+    # 2. Gateway and LangGraph Server are separate processes with independent caches
+    # MCP tools are lazily initialized in LangGraph Server when first needed
 
     yield
     logger.info("Shutting down API Gateway")

backend/src/gateway/routers/mcp.py

@@ -6,7 +6,6 @@ from fastapi import APIRouter, HTTPException
 from pydantic import BaseModel, Field
 
 from src.config.extensions_config import ExtensionsConfig, get_extensions_config, reload_extensions_config
-from src.mcp.cache import reset_mcp_tools_cache
 
 logger = logging.getLogger(__name__)
 router = APIRouter(prefix="/api", tags=["mcp"])
@@ -139,15 +138,11 @@ async def update_mcp_configuration(request: McpConfigUpdateRequest) -> McpConfig
 
         logger.info(f"MCP configuration updated and saved to: {config_path}")
 
-        # Reload the configuration to update the cache
-        reload_extensions_config()
+        # NOTE: No need to reload/reset cache here - LangGraph Server (separate process)
+        # will detect config file changes via mtime and reinitialize MCP tools automatically
 
-        # Reset MCP tools cache so they will be reinitialized with new config on next use
-        reset_mcp_tools_cache()
-        logger.info("MCP tools cache reset - tools will be reinitialized on next use")
-
-        # Return the updated configuration
-        reloaded_config = get_extensions_config()
+        # Reload the configuration and update the global cache
+        reloaded_config = reload_extensions_config()
         return McpConfigResponse(
             mcp_servers={name: McpServerConfigResponse(**server.model_dump()) for name, server in reloaded_config.mcp_servers.items()}
         )

backend/src/gateway/routers/skills.py

@@ -207,10 +207,10 @@ async def update_skill(skill_name: str, request: SkillUpdateRequest) -> SkillRes
 
         logger.info(f"Skills configuration updated and saved to: {config_path}")
 
-        # Reload the configuration to update the cache
+        # Reload the extensions config to update the global cache
         reload_extensions_config()
 
-        # Reload the skills to get the updated status
+        # Reload the skills to get the updated status (for API response)
         skills = load_skills(enabled_only=False)
         updated_skill = next((s for s in skills if s.name == skill_name), None)