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

@@ -1,9 +1,11 @@
 using System;
 using System.Collections.Generic;
 using System.Linq;
+using System.Threading;
 using MCPForUnity.Editor.Constants;
 using MCPForUnity.Editor.Helpers;
 using MCPForUnity.Editor.Services;
+using MCPForUnity.Editor.Services.Transport;
 using MCPForUnity.Editor.Tools;
 using UnityEditor;
 using UnityEngine.UIElements;
@@ -223,23 +225,61 @@ 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
+            ThreadPool.QueueUserWorkItem(_ =>
+            {
+                try
+                {
+                    var transportManager = MCPServiceLocator.TransportManager;
+                    var client = transportManager.GetClient(TransportMode.Http);
+                    if (client != null && client.IsConnected)
+                    {
+                        client.ReregisterToolsAsync().Wait();
+                    }
+                }
+                catch (Exception ex)
+                {
+                    McpLog.Warn($"Failed to reregister tools: {ex.Message}");
+                }
+            });
         }
 
         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 +289,17 @@ 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/transport/unity_instance_middleware.py

@@ -55,6 +55,43 @@ def __init__(self):
         super().__init__()
         self._active_by_key: dict[str, str] = {}
         self._lock = RLock()
+        self._unity_managed_tool_names = {
+            "batch_execute",
+            "execute_menu_item",
+            "find_gameobjects",
+            "get_test_job",
+            "manage_asset",
+            "manage_components",
+            "manage_editor",
+            "manage_gameobject",
+            "manage_material",
+            "manage_prefabs",
+            "manage_scene",
+            "manage_script",
+            "manage_scriptable_object",
+            "manage_shader",
+            "manage_texture",
+            "manage_vfx",
+            "read_console",
+            "refresh_unity",
+            "run_tests",
+        }
+        self._tool_alias_to_unity_target = {
+            # Server-side script helpers route to Unity's manage_script command.
+            "apply_text_edits": "manage_script",
+            "create_script": "manage_script",
+            "delete_script": "manage_script",
+            "find_in_file": "manage_script",
+            "get_sha": "manage_script",
+            "script_apply_edits": "manage_script",
+            "validate_script": "manage_script",
+        }
+        self._server_only_tool_names = {
+            "debug_request_context",
+            "execute_custom_tool",
+            "manage_script_capabilities",
+            "set_active_instance",
+        }
 
     def get_session_key(self, ctx) -> str:
         """
@@ -260,3 +297,108 @@ async def on_read_resource(self, context: MiddlewareContext, call_next):
         """Inject active Unity instance into resource context if available."""
         await self._inject_unity_instance(context)
         return await call_next(context)
+
+    async def on_list_tools(self, context: MiddlewareContext, call_next):
+        """Filter MCP tool listing to the Unity-enabled set when session data is available."""
+        await self._inject_unity_instance(context)
+        tools = await call_next(context)
+
+        if not self._should_filter_tool_listing():
+            return tools
+
+        enabled_tool_names = await self._resolve_enabled_tool_names_for_context(context)
+        if not enabled_tool_names:
+            return tools
+
+        filtered = []
+        for tool in tools:
+            tool_name = getattr(tool, "name", None)
+            if self._is_tool_visible(tool_name, enabled_tool_names):
+                filtered.append(tool)
+
+        return filtered
+
+    def _should_filter_tool_listing(self) -> bool:
+        transport = (config.transport_mode or "stdio").lower()
+        return transport == "http" and PluginHub.is_configured()
+
+    async def _resolve_enabled_tool_names_for_context(
+        self,
+        context: MiddlewareContext,
+    ) -> set[str] | None:
+        ctx = context.fastmcp_context
+        user_id = ctx.get_state("user_id") if config.http_remote_hosted else None
+        active_instance = ctx.get_state("unity_instance")
+
+        project_hashes = self._resolve_candidate_project_hashes(active_instance)
+        if not project_hashes:
+            try:
+                sessions_data = await PluginHub.get_sessions(user_id=user_id)
+                sessions = sessions_data.sessions if sessions_data else {}
+            except Exception:
+                return None
+
+            if not sessions:
+                return None
+
+            if len(sessions) == 1:
+                only_session = next(iter(sessions.values()))
+                only_hash = getattr(only_session, "hash", None)
+                if only_hash:
+                    project_hashes = [only_hash]
+            else:
+                # Multiple sessions without explicit selection: use a union so we don't
+                # hide tools that are valid in at least one visible Unity instance.
+                project_hashes = [
+                    session.hash
+                    for session in sessions.values()
+                    if getattr(session, "hash", None)
+                ]
+
+        if not project_hashes:
+            return None
+
+        enabled_tool_names: set[str] = set()
+        for project_hash in project_hashes:
+            try:
+                registered_tools = await PluginHub.get_tools_for_project(project_hash)
+            except Exception:
+                continue
+
+            for tool in registered_tools:
+                tool_name = getattr(tool, "name", None)
+                if isinstance(tool_name, str) and tool_name:
+                    enabled_tool_names.add(tool_name)
+
+        return enabled_tool_names or None
+
+    @staticmethod
+    def _resolve_candidate_project_hashes(active_instance: str | None) -> list[str]:
+        if not active_instance:
+            return []
+
+        if "@" in active_instance:
+            _, _, suffix = active_instance.rpartition("@")
+            return [suffix] if suffix else []
+
+        return [active_instance]
+
+    def _is_tool_visible(self, tool_name: str | None, enabled_tool_names: set[str]) -> bool:
+        if not isinstance(tool_name, str) or not tool_name:
+            return True
+
+        if tool_name in self._server_only_tool_names:
+            return True
+
+        if tool_name in enabled_tool_names:
+            return True
+
+        unity_target = self._tool_alias_to_unity_target.get(tool_name)
+        if unity_target:
+            return unity_target in enabled_tool_names
+
+        # Keep unknown tools visible for forward compatibility.
+        if tool_name not in self._unity_managed_tool_names:
+            return True
+
+        return False