Fix: #709 - Preserve tool enabled/disabled state and filter tools in client listings

MCPForUnity/Editor/Services/ToolDiscoveryService.cs

@@ -226,16 +226,6 @@ private void EnsurePreferenceInitialized(ToolMetadata metadata)
             {
                 bool defaultValue = metadata.AutoRegister || metadata.IsBuiltIn;
                 EditorPrefs.SetBool(key, defaultValue);
-                return;
-            }
-
-            if (metadata.IsBuiltIn && !metadata.AutoRegister)
-            {
-                bool currentValue = EditorPrefs.GetBool(key, metadata.AutoRegister);
-                if (currentValue == metadata.AutoRegister)
-                {
-                    EditorPrefs.SetBool(key, true);
-                }
             }
         }
 

MCPForUnity/Editor/Services/Transport/IMcpTransportClient.cs

@@ -14,5 +14,6 @@ public interface IMcpTransportClient
         Task<bool> StartAsync();
         Task StopAsync();
         Task<bool> VerifyAsync();
+        Task ReregisterToolsAsync();
     }
 }

MCPForUnity/Editor/Services/Transport/TransportManager.cs

@@ -42,16 +42,6 @@ private IMcpTransportClient GetOrCreateClient(TransportMode mode)
             };
         }
 
-        private IMcpTransportClient GetClient(TransportMode mode)
-        {
-            return mode switch
-            {
-                TransportMode.Http => _httpClient,
-                TransportMode.Stdio => _stdioClient,
-                _ => throw new ArgumentOutOfRangeException(nameof(mode), mode, "Unsupported transport mode"),
-            };
-        }
-
         public async Task<bool> StartAsync(TransportMode mode)
         {
             IMcpTransportClient client = GetOrCreateClient(mode);
@@ -128,6 +118,20 @@ public TransportState GetState(TransportMode mode)
 
         public bool IsRunning(TransportMode mode) => GetState(mode).IsConnected;
 
+        /// <summary>
+        /// Gets the active transport client for the specified mode.
+        /// Returns null if the client hasn't been created yet.
+        /// </summary>
+        public IMcpTransportClient GetClient(TransportMode mode)
+        {
+            return mode switch
+            {
+                TransportMode.Http => _httpClient,
+                TransportMode.Stdio => _stdioClient,
+                _ => throw new ArgumentOutOfRangeException(nameof(mode), mode, "Unsupported transport mode"),
+            };
+        }
+
         private void UpdateState(TransportMode mode, TransportState state)
         {
             switch (mode)

MCPForUnity/Editor/Services/Transport/Transports/StdioTransportClient.cs

@@ -46,5 +46,12 @@ public Task<bool> VerifyAsync()
             return Task.FromResult(running);
         }
 
+        public Task ReregisterToolsAsync()
+        {
+            // Stdio transport doesn't support dynamic tool reregistration
+            // Tools are registered at server startup
+            return Task.CompletedTask;
+        }
+
     }
 }

MCPForUnity/Editor/Services/Transport/Transports/WebSocketTransportClient.cs

@@ -506,6 +506,29 @@ private async Task SendRegisterToolsAsync(CancellationToken token)
             McpLog.Info($"[WebSocket] Sent {tools.Count} tools registration", false);
         }
 
+        public async Task ReregisterToolsAsync()
+        {
+            if (!IsConnected || _lifecycleCts == null)
+            {
+                McpLog.Warn("[WebSocket] Cannot reregister tools: not connected");
+                return;
+            }
+
+            try
+            {
+                await SendRegisterToolsAsync(_lifecycleCts.Token).ConfigureAwait(false);
+                McpLog.Info("[WebSocket] Tool reregistration completed", false);
+            }
+            catch (System.OperationCanceledException)
+            {
+                McpLog.Warn("[WebSocket] Tool reregistration cancelled");
+            }
+            catch (System.Exception ex)
+            {
+                McpLog.Error($"[WebSocket] Tool reregistration failed: {ex.Message}");
+            }
+        }
+
         private async Task HandleExecuteAsync(JObject payload, CancellationToken token)
         {
             string commandId = payload.Value<string>("id");

MCPForUnity/Editor/Windows/Components/Tools/McpToolsSection.cs

@@ -1,11 +1,14 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using System.Threading.Tasks;
 using MCPForUnity.Editor.Constants;
 using MCPForUnity.Editor.Helpers;
 using MCPForUnity.Editor.Services;
+using MCPForUnity.Editor.Services.Transport;
 using MCPForUnity.Editor.Tools;
 using UnityEditor;
+using UnityEditor.UIElements;
 using UnityEngine.UIElements;
 
 namespace MCPForUnity.Editor.Windows.Components.Tools
@@ -223,23 +226,63 @@ private VisualElement CreateToolRow(ToolMetadata tool)
             return row;
         }
 
-        private void HandleToggleChange(ToolMetadata tool, bool enabled, bool updateSummary = true)
+        private void HandleToggleChange(
+            ToolMetadata tool,
+            bool enabled,
+            bool updateSummary = true,
+            bool reregisterTools = true)
         {
             MCPServiceLocator.ToolDiscovery.SetToolEnabled(tool.Name, enabled);
 
             if (updateSummary)
             {
                 UpdateSummary();
             }
+
+            if (reregisterTools)
+            {
+                // Trigger tool reregistration with connected MCP server
+                ReregisterToolsAsync();
+            }
+        }
+
+        private void ReregisterToolsAsync()
+        {
+            // Fire and forget - don't block UI thread
+            var transportManager = MCPServiceLocator.TransportManager;
+            var client = transportManager.GetClient(TransportMode.Http);
+            if (client == null || !client.IsConnected)
+            {
+                return;
+            }
+
+            _ = Task.Run(async () =>
+            {
+                try
+                {
+                    await client.ReregisterToolsAsync().ConfigureAwait(false);
+                }
+                catch (Exception ex)
+                {
+                    McpLog.Warn($"Failed to reregister tools: {ex}");
+                }
+            });
         }
 
         private void SetAllToolsState(bool enabled)
         {
+            bool hasChanges = false;
+
             foreach (var tool in allTools)
             {
                 if (!toolToggleMap.TryGetValue(tool.Name, out var toggle))
                 {
-                    MCPServiceLocator.ToolDiscovery.SetToolEnabled(tool.Name, enabled);
+                    bool currentEnabled = MCPServiceLocator.ToolDiscovery.IsToolEnabled(tool.Name);
+                    if (currentEnabled != enabled)
+                    {
+                        MCPServiceLocator.ToolDiscovery.SetToolEnabled(tool.Name, enabled);
+                        hasChanges = true;
+                    }
                     continue;
                 }
 
@@ -249,10 +292,17 @@ private void SetAllToolsState(bool enabled)
                 }
 
                 toggle.SetValueWithoutNotify(enabled);
-                HandleToggleChange(tool, enabled, updateSummary: false);
+                HandleToggleChange(tool, enabled, updateSummary: false, reregisterTools: false);
+                hasChanges = true;
             }
 
             UpdateSummary();
+
+            if (hasChanges)
+            {
+                // Trigger a single reregistration after bulk change
+                ReregisterToolsAsync();
+            }
         }
 
         private void UpdateSummary()

Server/src/services/custom_tool_service.py

@@ -10,6 +10,7 @@
 from starlette.requests import Request
 from starlette.responses import JSONResponse
 
+from core.config import config
 from models.models import MCPResponse, ToolDefinitionModel, ToolParameterModel
 from core.logging_decorator import log_execution
 from core.telemetry_decorator import telemetry_tool
@@ -28,6 +29,23 @@
 _MAX_POLL_SECONDS = 600
 
 
+def get_user_id_from_context(ctx: Context) -> str | None:
+    """Read user_id from request-scoped context in remote-hosted mode."""
+    if not config.http_remote_hosted:
+        return None
+
+    get_state = getattr(ctx, "get_state", None)
+    if not callable(get_state):
+        return None
+
+    try:
+        user_id = get_state("user_id")
+    except Exception:
+        return None
+
+    return user_id if isinstance(user_id, str) and user_id else None
+
+
 class RegisterToolsPayload(BaseModel):
     project_id: str
     project_hash: str | None = None
@@ -84,30 +102,40 @@ async def register_tools(request: Request) -> JSONResponse:
             return JSONResponse(response.model_dump())
 
     # --- Public API for MCP tools ---------------------------------------
-    async def list_registered_tools(self, project_id: str) -> list[ToolDefinitionModel]:
+    async def list_registered_tools(
+        self,
+        project_id: str,
+        user_id: str | None = None,
+    ) -> list[ToolDefinitionModel]:
         legacy = list(self._project_tools.get(project_id, {}).values())
-        hub_tools = await PluginHub.get_tools_for_project(project_id)
+        hub_tools = await PluginHub.get_tools_for_project(project_id, user_id=user_id)
         return legacy + hub_tools
 
-    async def get_tool_definition(self, project_id: str, tool_name: str) -> ToolDefinitionModel | None:
+    async def get_tool_definition(
+        self,
+        project_id: str,
+        tool_name: str,
+        user_id: str | None = None,
+    ) -> ToolDefinitionModel | None:
         tool = self._project_tools.get(project_id, {}).get(tool_name)
         if tool:
             return tool
-        return await PluginHub.get_tool_definition(project_id, tool_name)
+        return await PluginHub.get_tool_definition(project_id, tool_name, user_id=user_id)
 
     async def execute_tool(
         self,
         project_id: str,
         tool_name: str,
         unity_instance: str | None,
         params: dict[str, object] | None = None,
+        user_id: str | None = None,
     ) -> MCPResponse:
         params = params or {}
         logger.info(
             f"Executing tool '{tool_name}' for project '{project_id}' (instance={unity_instance}) with params: {params}"
         )
 
-        definition = await self.get_tool_definition(project_id, tool_name)
+        definition = await self.get_tool_definition(project_id, tool_name, user_id=user_id)
         if definition is None:
             return MCPResponse(
                 success=False,
@@ -119,6 +147,7 @@ async def execute_tool(
             unity_instance,
             tool_name,
             params,
+            user_id=user_id,
         )
 
         if not definition.requires_polling:
@@ -132,6 +161,7 @@ async def execute_tool(
             params,
             response,
             definition.poll_action or "status",
+            user_id=user_id,
         )
         logger.info(f"Tool '{tool_name}' polled response: {result}")
         return result
@@ -156,6 +186,7 @@ async def _poll_until_complete(
         initial_params: dict[str, object],
         initial_response,
         poll_action: str,
+        user_id: str | None = None,
     ) -> MCPResponse:
         poll_params = dict(initial_params)
         poll_params["action"] = poll_action or "status"
@@ -180,7 +211,11 @@ async def _poll_until_complete(
 
             try:
                 response = await send_with_unity_instance(
-                    async_send_command_with_retry, unity_instance, tool_name, poll_params
+                    async_send_command_with_retry,
+                    unity_instance,
+                    tool_name,
+                    poll_params,
+                    user_id=user_id,
                 )
             except Exception as exc:  # pragma: no cover - network/domain reload variability
                 logger.debug(f"Polling {tool_name} failed, will retry: {exc}")
@@ -347,8 +382,15 @@ async def _handler(ctx: Context, **kwargs) -> MCPResponse:
                 )
 
             params = {k: v for k, v in kwargs.items() if v is not None}
+            user_id = get_user_id_from_context(ctx)
             service = CustomToolService.get_instance()
-            return await service.execute_tool(project_id, definition.name, unity_instance, params)
+            return await service.execute_tool(
+                project_id,
+                definition.name,
+                unity_instance,
+                params,
+                user_id=user_id,
+            )
 
         _handler.__name__ = f"custom_tool_{definition.name}"
         _handler.__doc__ = definition.description or ""

Server/src/services/registry/tool_registry.py

@@ -10,6 +10,7 @@
 def mcp_for_unity_tool(
     name: str | None = None,
     description: str | None = None,
+    unity_target: str | None = "self",
     **kwargs
 ) -> Callable:
     """
@@ -20,6 +21,10 @@ def mcp_for_unity_tool(
     Args:
         name: Tool name (defaults to function name)
         description: Tool description
+        unity_target: Visibility target used by middleware filtering.
+            - "self" (default): tool follows its own enabled state.
+            - None: server-only tool, always visible in tool listing.
+            - "<tool_name>": alias tool that follows another Unity tool state.
         **kwargs: Additional arguments passed to @mcp.tool()
 
     Example:
@@ -29,11 +34,29 @@ async def my_custom_tool(ctx: Context, ...):
     """
     def decorator(func: Callable) -> Callable:
         tool_name = name if name is not None else func.__name__
+        # Safety guard: unity_target is internal metadata and must never leak into mcp.tool kwargs.
+        tool_kwargs = dict(kwargs)  # Create a copy to avoid side effects
+        if "unity_target" in tool_kwargs:
+            del tool_kwargs["unity_target"]
+
+        if unity_target is None:
+            normalized_unity_target: str | None = None
+        elif isinstance(unity_target, str) and unity_target.strip():
+            normalized_unity_target = (
+                tool_name if unity_target == "self" else unity_target.strip()
+            )
+        else:
+            raise ValueError(
+                f"Invalid unity_target for tool '{tool_name}': {unity_target!r}. "
+                "Expected None or a non-empty string."
+            )
+
         _tool_registry.append({
             'func': func,
             'name': tool_name,
             'description': description,
-            'kwargs': kwargs
+            'unity_target': normalized_unity_target,
+            'kwargs': tool_kwargs,
         })
 
         return func