diff --git a/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py b/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py
index a2144b2b9..e878ae911 100644
--- a/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py
+++ b/gns3server/agent/gns3_copilot/gns3_client/connector_factory.py
@@ -29,6 +29,10 @@ GNS3 Connector Factory Module
 This module provides factory functions for creating Gns3Connector instances
 with JWT token authentication and context-aware configuration management.
 
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+The get_gns3_connector() function is used by both gns3-copilot and MCP.
+Modifications must be tested with BOTH.
+
 Features:
 - Context variable based request-scoped data management (JWT tokens, LLM
   config)
diff --git a/gns3server/agent/gns3_copilot/gns3_client/custom_gns3fy.py b/gns3server/agent/gns3_copilot/gns3_client/custom_gns3fy.py
index 3f714fd36..6e30af017 100644
--- a/gns3server/agent/gns3_copilot/gns3_client/custom_gns3fy.py
+++ b/gns3server/agent/gns3_copilot/gns3_client/custom_gns3fy.py
@@ -29,6 +29,10 @@ Adapted gns3fy module for GNS3-Copilot
 This module is based on the upstream gns3fy project
 (https://github.com/davidban77/gns3fy).
 
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+The Gns3Connector class is used by MCP handlers to make HTTP calls.
+Modifications to this file must be tested with BOTH gns3-copilot AND MCP.
+
 Modifications made for GNS3-Copilot:
 - Adjusted pydantic usages and dataclass configuration to reduce dependency
   conflicts with langchain (pydantic version/api differences)
diff --git a/gns3server/agent/gns3_copilot/gns3_client/gns3_topology_reader.py b/gns3server/agent/gns3_copilot/gns3_client/gns3_topology_reader.py
index 5ec0f6935..8ecee9409 100644
--- a/gns3server/agent/gns3_copilot/gns3_client/gns3_topology_reader.py
+++ b/gns3server/agent/gns3_copilot/gns3_client/gns3_topology_reader.py
@@ -30,6 +30,10 @@ This module provides a LangChain BaseTool to retrieve the topology of a
 specific GNS3 project by project ID. Returns nodes, links, and project
 metadata.
 
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+GNS3TopologyTool._run() is called by MCP device config handlers.
+The jwt_token/url parameters were added for MCP compatibility.
+Modifications must be tested with BOTH gns3-copilot AND MCP.
 """
 
 import copy
diff --git a/gns3server/agent/gns3_copilot/tools_v2/config_tools_nornir.py b/gns3server/agent/gns3_copilot/tools_v2/config_tools_nornir.py
index 7bce576ee..41ed58f9d 100644
--- a/gns3server/agent/gns3_copilot/tools_v2/config_tools_nornir.py
+++ b/gns3server/agent/gns3_copilot/tools_v2/config_tools_nornir.py
@@ -26,6 +26,11 @@
 
 This module provides a tool to execute configuration commands on multiple
  devices in a GNS3 topology using Nornir.
+
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+ExecuteMultipleDeviceConfigCommands._run() is called by the MCP device_config_send handler.
+The jwt_token/url parameters were added for MCP compatibility.
+Modifications must be tested with BOTH gns3-copilot AND MCP.
 """
 
 import json
diff --git a/gns3server/agent/gns3_copilot/tools_v2/display_tools_nornir.py b/gns3server/agent/gns3_copilot/tools_v2/display_tools_nornir.py
index 7e0061ceb..8fa056650 100644
--- a/gns3server/agent/gns3_copilot/tools_v2/display_tools_nornir.py
+++ b/gns3server/agent/gns3_copilot/tools_v2/display_tools_nornir.py
@@ -26,6 +26,11 @@
 
 This module provides a tool to execute display commands on multiple devices
  in a GNS3 topology using Nornir.
+
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+ExecuteMultipleDeviceCommands._run() is called by the MCP device_command_run handler.
+The jwt_token/url parameters were added for MCP compatibility.
+Modifications must be tested with BOTH gns3-copilot AND MCP.
 """
 
 import json
diff --git a/gns3server/agent/gns3_copilot/tools_v2/vpcs_tools_netmiko.py b/gns3server/agent/gns3_copilot/tools_v2/vpcs_tools_netmiko.py
index b7bb3d661..221bf9bed 100644
--- a/gns3server/agent/gns3_copilot/tools_v2/vpcs_tools_netmiko.py
+++ b/gns3server/agent/gns3_copilot/tools_v2/vpcs_tools_netmiko.py
@@ -26,6 +26,11 @@
 """
 This module provides a tool to execute commands on VPCS devices
 in a GNS3 topology using Nornir with Netmiko.
+
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+VPCSCommands._run() is called by the MCP vpcs_config_set handler.
+The jwt_token/url parameters were added for MCP compatibility.
+Modifications must be tested with BOTH gns3-copilot AND MCP.
 """
 
 import json
diff --git a/gns3server/agent/gns3_copilot/utils/get_gns3_device_port.py b/gns3server/agent/gns3_copilot/utils/get_gns3_device_port.py
index a5c950150..597fd9f64 100644
--- a/gns3server/agent/gns3_copilot/utils/get_gns3_device_port.py
+++ b/gns3server/agent/gns3_copilot/utils/get_gns3_device_port.py
@@ -25,6 +25,11 @@
 """
 
 Public module for getting device port information from GNS3 topology
+
+⚠️ WARNING: This module is shared with the MCP (Model Context Protocol) service.
+get_device_ports_from_topology() is called by MCP device config handlers.
+The jwt_token/url parameters were added for MCP compatibility.
+Modifications must be tested with BOTH gns3-copilot AND MCP.
 """
 
 import logging