diff --git a/gns3server/agent/gns3_copilot/agent/gns3_copilot.py b/gns3server/agent/gns3_copilot/agent/gns3_copilot.py
index c5839b8f2..f85ea3dfd 100644
--- a/gns3server/agent/gns3_copilot/agent/gns3_copilot.py
+++ b/gns3server/agent/gns3_copilot/agent/gns3_copilot.py
@@ -214,12 +214,10 @@ def llm_call(state: dict, config: RunnableConfig | None = None):
         llm_config=llm_config
     )
 
-    # Store jwt_token in state for Tools to use when calling GNS3 API
     return {
         "messages": [model_with_tools.invoke(full_messages)],
         "llm_calls": state.get("llm_calls", 0) + 1,
         "topology_info": topology_info,
-        "jwt_token": jwt_token,
     }
 
 
@@ -305,9 +303,18 @@ def generate_title(state: MessagesState, config: RunnableConfig | None = None) -
 
 
 # Define tool node
-def tool_node(state: dict):
+def tool_node(state: dict, config: RunnableConfig | None = None):
     """Performs the tool call"""
 
+    # Extract jwt_token from config for tools to use
+    configurable = config.get("configurable", {}) if config else {}
+    jwt_token = configurable.get("jwt_token")
+
+    # Set jwt_token for connector_factory to access
+    if jwt_token:
+        from gns3server.agent.gns3_copilot.gns3_client import set_current_jwt_token
+        set_current_jwt_token(jwt_token)
+
     result = []
     for tool_call in state["messages"][-1].tool_calls:
         tool = tools_by_name[tool_call["name"]]
diff --git a/gns3server/agent/gns3_copilot/agent_service.py b/gns3server/agent/gns3_copilot/agent_service.py
index a3a9cda56..1a409931a 100644
--- a/gns3server/agent/gns3_copilot/agent_service.py
+++ b/gns3server/agent/gns3_copilot/agent_service.py
@@ -46,7 +46,7 @@ class AgentService:
 
     def _get_checkpoint_dir(self) -> str:
         """Get or create the checkpoint directory for this project."""
-        checkpoint_dir = os.path.join(self.project_path, ".gns3-copilot")
+        checkpoint_dir = os.path.join(self.project_path, "gns3-copilot")
         os.makedirs(checkpoint_dir, exist_ok=True)
         return checkpoint_dir
 
@@ -103,6 +103,7 @@ class AgentService:
         message: str,
         session_id: str,
         project_id: Optional[str] = None,
+        user_id: Optional[str] = None,
         jwt_token: Optional[str] = None,
         mode: str = "text",
         llm_config: Optional[Dict[str, Any]] = None
@@ -114,6 +115,7 @@ class AgentService:
             message: User message
             session_id: Session/thread ID for conversation continuity
             project_id: GNS3 project ID (optional, for context)
+            user_id: User ID for metadata tracking
             jwt_token: JWT token for API authentication (optional)
             mode: Interaction mode (default: "text")
             llm_config: LLM configuration dict (provider, model, api_key, etc.)
@@ -121,12 +123,16 @@ class AgentService:
         Yields:
             Dict containing SSE-compatible response chunks
         """
-        # Build config with LLM configuration
+        # Build config with LLM configuration and metadata
         config = {
             "configurable": {
                 "thread_id": session_id,
                 "jwt_token": jwt_token,
                 "llm_config": llm_config,
+            },
+            "metadata": {
+                "user_id": user_id,
+                "project_id": project_id,
             }
         }
 
diff --git a/gns3server/agent/gns3_copilot/gns3_client/__init__.py b/gns3server/agent/gns3_copilot/gns3_client/__init__.py
index 309dd47ef..2bc89f76b 100644
--- a/gns3server/agent/gns3_copilot/gns3_client/__init__.py
+++ b/gns3server/agent/gns3_copilot/gns3_client/__init__.py
@@ -25,6 +25,8 @@ from .connector_factory import (
     get_gns3_connector_with_llm_config,
     get_gns3_server_host,
     get_llm_config,
+    set_current_jwt_token,
+    get_current_jwt_token,
 )
 from .custom_gns3fy import (
     CONSOLE_TYPES,
@@ -62,4 +64,6 @@ __all__ = [
     "get_gns3_connector_with_llm_config",
     "get_gns3_server_host",
     "get_llm_config",
+    "set_current_jwt_token",
+    "get_current_jwt_token",
 ]
diff --git a/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py b/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py
index 70b809c1b..0ad8b0d03 100644
--- a/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py
+++ b/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py
@@ -28,6 +28,21 @@ Authentication:
 
 import logging
 from typing import Optional
+from contextvars import ContextVar
+
+# Context variable for request-scoped jwt_token
+# Automatically cleaned up when request context ends
+_jwt_token_context: ContextVar[Optional[str]] = ContextVar("_jwt_token_context", default=None)
+
+
+def set_current_jwt_token(token: str) -> None:
+    """Set the JWT token for the current request context."""
+    _jwt_token_context.set(token)
+
+
+def get_current_jwt_token() -> Optional[str]:
+    """Get the JWT token for the current request context."""
+    return _jwt_token_context.get()
 from uuid import UUID
 
 from gns3server.agent.gns3_copilot.gns3_client.custom_gns3fy import Gns3Connector
@@ -136,9 +151,12 @@ def get_gns3_connector(jwt_token: str, url: Optional[str] = None) -> Optional[Gn
     """
     try:
         # Validate JWT token
+        # If not provided, try to get from current request context
         if not jwt_token:
-            logger.error("JWT token parameter is required")
-            return None
+            jwt_token = get_current_jwt_token()
+            if not jwt_token:
+                logger.error("JWT token is required")
+                return None
 
         # Resolve URL with fallback strategy
         if url is None:
diff --git a/gns3server/api/routes/controller/chat.py b/gns3server/api/routes/controller/chat.py
index 56a329f0e..1e8030aa5 100644
--- a/gns3server/api/routes/controller/chat.py
+++ b/gns3server/api/routes/controller/chat.py
@@ -117,6 +117,7 @@ async def stream_chat(
                 message=request.message,
                 session_id=session_id,
                 project_id=str(project.id),
+                user_id=user_id,
                 jwt_token=jwt_token,
                 mode=request.mode,
                 llm_config=llm_config