Fix HTTP/Stdio Transport UX and Test Bug

MCPForUnity/Editor/Clients/McpClientConfiguratorBase.cs

@@ -467,8 +467,8 @@ private void Register()
             else
             {
                 var (uvxPath, gitUrl, packageName) = AssetPathUtility.GetUvxCommandParts();
-                bool devForceRefresh = GetDevModeForceRefresh();
-                string devFlags = devForceRefresh ? "--no-cache --refresh " : string.Empty;
+                // Use central helper that checks both DevModeForceServerRefresh AND local path detection.
+                string devFlags = AssetPathUtility.ShouldForceUvxRefresh() ? "--no-cache --refresh " : string.Empty;
                 args = $"mcp add --transport stdio UnityMCP -- \"{uvxPath}\" {devFlags}--from \"{gitUrl}\" {packageName}";
             }
 
@@ -586,8 +586,8 @@ public override string GetManualSnippet()
             }
 
             string gitUrl = AssetPathUtility.GetMcpServerGitUrl();
-            bool devForceRefresh = GetDevModeForceRefresh();
-            string devFlags = devForceRefresh ? "--no-cache --refresh " : string.Empty;
+            // Use central helper that checks both DevModeForceServerRefresh AND local path detection.
+            string devFlags = AssetPathUtility.ShouldForceUvxRefresh() ? "--no-cache --refresh " : string.Empty;
 
             return "# Register the MCP server with Claude Code:\n" +
                    $"claude mcp add --transport stdio UnityMCP -- \"{uvxPath}\" {devFlags}--from \"{gitUrl}\" mcp-for-unity\n\n" +
@@ -597,12 +597,6 @@ public override string GetManualSnippet()
                    "claude mcp list # Only works when claude is run in the project's directory";
         }
 
-        private static bool GetDevModeForceRefresh()
-        {
-            try { return EditorPrefs.GetBool(EditorPrefKeys.DevModeForceServerRefresh, false); }
-            catch { return false; }
-        }
-
         public override IList<string> GetInstallationSteps() => new List<string>
         {
             "Ensure Claude CLI is installed",

MCPForUnity/Editor/Helpers/AssetPathUtility.cs

@@ -186,6 +186,88 @@ public static (string uvxPath, string fromUrl, string packageName) GetUvxCommand
             return (uvxPath, fromUrl, packageName);
         }
 
+        /// <summary>
+        /// Determines whether uvx should use --no-cache --refresh flags.
+        /// Returns true if DevModeForceServerRefresh is enabled OR if the server URL is a local path.
+        /// Local paths (file:// or absolute) always need fresh builds to avoid stale uvx cache.
+        /// </summary>
+        public static bool ShouldForceUvxRefresh()
+        {
+            bool devForceRefresh = false;
+            try { devForceRefresh = EditorPrefs.GetBool(EditorPrefKeys.DevModeForceServerRefresh, false); } catch { }
+
+            if (devForceRefresh)
+                return true;
+
+            // Auto-enable force refresh when using a local path override.
+            return IsLocalServerPath();
+        }
+
+        /// <summary>
+        /// Returns true if the server URL is a local path (file:// or absolute path).
+        /// </summary>
+        public static bool IsLocalServerPath()
+        {
+            string fromUrl = GetMcpServerGitUrl();
+            if (string.IsNullOrEmpty(fromUrl))
+                return false;
+
+            // Check for file:// protocol or absolute local path
+            return fromUrl.StartsWith("file://", StringComparison.OrdinalIgnoreCase) ||
+                   System.IO.Path.IsPathRooted(fromUrl);
+        }
+
+        /// <summary>
+        /// Gets the local server path if GitUrlOverride points to a local directory.
+        /// Returns null if not using a local path.
+        /// </summary>
+        public static string GetLocalServerPath()
+        {
+            if (!IsLocalServerPath())
+                return null;
+
+            string fromUrl = GetMcpServerGitUrl();
+            if (fromUrl.StartsWith("file://", StringComparison.OrdinalIgnoreCase))
+            {
+                // Strip file:// prefix
+                fromUrl = fromUrl.Substring(7);
+            }
+
+            return fromUrl;
+        }
+
+        /// <summary>
+        /// Cleans stale Python build artifacts from the local server path.
+        /// This is necessary because Python's build system doesn't remove deleted files from build/,
+        /// and the auto-discovery mechanism will pick up old .py files causing ghost resources/tools.
+        /// </summary>
+        /// <returns>True if cleaning was performed, false if not applicable or failed.</returns>
+        public static bool CleanLocalServerBuildArtifacts()
+        {
+            string localPath = GetLocalServerPath();
+            if (string.IsNullOrEmpty(localPath))
+                return false;
+
+            // Clean the build/ directory which can contain stale .py files
+            string buildPath = System.IO.Path.Combine(localPath, "build");
+            if (System.IO.Directory.Exists(buildPath))
+            {
+                try
+                {
+                    System.IO.Directory.Delete(buildPath, recursive: true);
+                    McpLog.Info($"Cleaned stale build artifacts from: {buildPath}");
+                    return true;
+                }
+                catch (Exception ex)
+                {
+                    McpLog.Warn($"Failed to clean build artifacts: {ex.Message}");
+                    return false;
+                }
+            }
+
+            return false;
+        }
+
         /// <summary>
         /// Gets the package version from package.json
         /// </summary>

MCPForUnity/Editor/Helpers/CodexConfigHelper.cs

@@ -17,22 +17,11 @@ namespace MCPForUnity.Editor.Helpers
     /// </summary>
     public static class CodexConfigHelper
     {
-        private static bool GetDevModeForceRefresh()
-        {
-            try
-            {
-                return EditorPrefs.GetBool(EditorPrefKeys.DevModeForceServerRefresh, false);
-            }
-            catch
-            {
-                return false;
-            }
-        }
-
-        private static void AddDevModeArgs(TomlArray args, bool devForceRefresh)
+        private static void AddDevModeArgs(TomlArray args)
         {
             if (args == null) return;
-            if (!devForceRefresh) return;
+            // Use central helper that checks both DevModeForceServerRefresh AND local path detection.
+            if (!AssetPathUtility.ShouldForceUvxRefresh()) return;
             args.Add(new TomlString { Value = "--no-cache" });
             args.Add(new TomlString { Value = "--refresh" });
         }
@@ -59,12 +48,11 @@ public static string BuildCodexServerBlock(string uvPath)
             {
                 // Stdio mode: Use command and args
                 var (uvxPath, fromUrl, packageName) = AssetPathUtility.GetUvxCommandParts();
-                bool devForceRefresh = GetDevModeForceRefresh();
 
                 unityMCP["command"] = uvxPath;
 
                 var args = new TomlArray();
-                AddDevModeArgs(args, devForceRefresh);
+                AddDevModeArgs(args);
                 if (!string.IsNullOrEmpty(fromUrl))
                 {
                     args.Add(new TomlString { Value = "--from" });
@@ -209,12 +197,11 @@ private static TomlTable CreateUnityMcpTable(string uvPath)
             {
                 // Stdio mode: Use command and args
                 var (uvxPath, fromUrl, packageName) = AssetPathUtility.GetUvxCommandParts();
-                bool devForceRefresh = GetDevModeForceRefresh();
 
                 unityMCP["command"] = new TomlString { Value = uvxPath };
 
                 var argsArray = new TomlArray();
-                AddDevModeArgs(argsArray, devForceRefresh);
+                AddDevModeArgs(argsArray);
                 if (!string.IsNullOrEmpty(fromUrl))
                 {
                     argsArray.Add(new TomlString { Value = "--from" });

MCPForUnity/Editor/Helpers/ConfigJsonBuilder.cs

@@ -51,7 +51,9 @@ public static JObject ApplyUnityServerToExistingConfig(JObject root, string uvPa
         private static void PopulateUnityNode(JObject unity, string uvPath, McpClient client, bool isVSCode)
         {
             // Get transport preference (default to HTTP)
-            bool useHttpTransport = client?.SupportsHttpTransport != false && EditorPrefs.GetBool(EditorPrefKeys.UseHttpTransport, true);
+            bool prefValue = EditorPrefs.GetBool(EditorPrefKeys.UseHttpTransport, true);
+            bool clientSupportsHttp = client?.SupportsHttpTransport != false;
+            bool useHttpTransport = clientSupportsHttp && prefValue;
             string httpProperty = string.IsNullOrEmpty(client?.HttpUrlProperty) ? "url" : client.HttpUrlProperty;
             var urlPropsToRemove = new HashSet<string>(StringComparer.OrdinalIgnoreCase) { "url", "serverUrl" };
             urlPropsToRemove.Remove(httpProperty);
@@ -81,10 +83,7 @@ private static void PopulateUnityNode(JObject unity, string uvPath, McpClient cl
                 // Stdio mode: Use uvx command
                 var (uvxPath, fromUrl, packageName) = AssetPathUtility.GetUvxCommandParts();
 
-                bool devForceRefresh = false;
-                try { devForceRefresh = EditorPrefs.GetBool(EditorPrefKeys.DevModeForceServerRefresh, false); } catch { }
-
-                var toolArgs = BuildUvxArgs(fromUrl, packageName, devForceRefresh);
+                var toolArgs = BuildUvxArgs(fromUrl, packageName);
 
                 if (ShouldUseWindowsCmdShim(client))
                 {
@@ -152,13 +151,15 @@ private static JObject EnsureObject(JObject parent, string name)
             return created;
         }
 
-        private static IList<string> BuildUvxArgs(string fromUrl, string packageName, bool devForceRefresh)
+        private static IList<string> BuildUvxArgs(string fromUrl, string packageName)
         {
             // Dev mode: force a fresh install/resolution (avoids stale cached builds while iterating).
             // `--no-cache` is the key flag; `--refresh` ensures metadata is revalidated.
             // Keep ordering consistent with other uvx builders: dev flags first, then --from <url>, then package name.
             var args = new List<string>();
-            if (devForceRefresh)
+
+            // Use central helper that checks both DevModeForceServerRefresh AND local path detection.
+            if (AssetPathUtility.ShouldForceUvxRefresh())
             {
                 args.Add("--no-cache");
                 args.Add("--refresh");

MCPForUnity/Editor/Services/ClientConfigurationService.cs

@@ -2,6 +2,7 @@
 using System.Collections.Generic;
 using System.Linq;
 using MCPForUnity.Editor.Clients;
+using MCPForUnity.Editor.Helpers;
 using MCPForUnity.Editor.Models;
 
 namespace MCPForUnity.Editor.Services
@@ -22,11 +23,24 @@ public ClientConfigurationService()
 
         public void ConfigureClient(IMcpClientConfigurator configurator)
         {
+            // When using a local server path, clean stale build artifacts first.
+            // This prevents old deleted .py files from being picked up by Python's auto-discovery.
+            if (AssetPathUtility.IsLocalServerPath())
+            {
+                AssetPathUtility.CleanLocalServerBuildArtifacts();
+            }
+
             configurator.Configure();
         }
 
         public ClientConfigurationSummary ConfigureAllDetectedClients()
         {
+            // When using a local server path, clean stale build artifacts once before configuring all clients.
+            if (AssetPathUtility.IsLocalServerPath())
+            {
+                AssetPathUtility.CleanLocalServerBuildArtifacts();
+            }
+
             var summary = new ClientConfigurationSummary();
             foreach (var configurator in configurators)
             {

MCPForUnity/Editor/Services/ServerManagementService.cs

@@ -406,6 +406,9 @@ private string GetPlatformSpecificPathPrepend()
         /// </summary>
         public bool StartLocalHttpServer()
         {
+            /// Clean stale Python build artifacts when using a local dev server path
+            AssetPathUtility.CleanLocalServerBuildArtifacts();
+
             if (!TryGetLocalHttpServerCommandParts(out _, out _, out var displayCommand, out var error))
             {
                 EditorUtility.DisplayDialog(
@@ -1236,10 +1239,8 @@ private bool TryGetLocalHttpServerCommandParts(out string fileName, out string a
                 return false;
             }
 
-            bool devForceRefresh = false;
-            try { devForceRefresh = EditorPrefs.GetBool(EditorPrefKeys.DevModeForceServerRefresh, false); } catch { }
-
-            string devFlags = devForceRefresh ? "--no-cache --refresh " : string.Empty;
+            // Use central helper that checks both DevModeForceServerRefresh AND local path detection.
+            string devFlags = AssetPathUtility.ShouldForceUvxRefresh() ? "--no-cache --refresh " : string.Empty;
             string args = string.IsNullOrEmpty(fromUrl)
                 ? $"{devFlags}{packageName} --transport http --http-url {httpUrl}"
                 : $"{devFlags}--from {fromUrl} {packageName} --transport http --http-url {httpUrl}";

MCPForUnity/Editor/Services/StdioBridgeReloadHandler.cs

@@ -27,8 +27,9 @@ private static void OnBeforeAssemblyReload()
                 bool useHttp = EditorPrefs.GetBool(EditorPrefKeys.UseHttpTransport, true);
                 // Check both TransportManager AND StdioBridgeHost directly, because CI starts via StdioBridgeHost
                 // bypassing TransportManager state.
-                bool isRunning = MCPServiceLocator.TransportManager.IsRunning(TransportMode.Stdio)
-                                 || StdioBridgeHost.IsRunning;
+                bool tmRunning = MCPServiceLocator.TransportManager.IsRunning(TransportMode.Stdio);
+                bool hostRunning = StdioBridgeHost.IsRunning;
+                bool isRunning = tmRunning || hostRunning;
                 bool shouldResume = !useHttp && isRunning;
 
                 if (shouldResume)
@@ -60,10 +61,12 @@ private static void OnAfterAssemblyReload()
             bool resume = false;
             try
             {
-                resume = EditorPrefs.GetBool(EditorPrefKeys.ResumeStdioAfterReload, false);
+                bool resumeFlag = EditorPrefs.GetBool(EditorPrefKeys.ResumeStdioAfterReload, false);
                 bool useHttp = EditorPrefs.GetBool(EditorPrefKeys.UseHttpTransport, true);
-                resume = resume && !useHttp;
-                if (resume)
+                resume = resumeFlag && !useHttp;
+
+                // If we're not going to resume, clear the flag immediately to avoid stuck "Resuming..." state
+                if (!resume)
                 {
                     EditorPrefs.DeleteKey(EditorPrefKeys.ResumeStdioAfterReload);
                 }
@@ -87,6 +90,13 @@ private static void TryStartBridgeImmediate()
             var startTask = MCPServiceLocator.TransportManager.StartAsync(TransportMode.Stdio);
             startTask.ContinueWith(t =>
             {
+                // Clear the flag after attempting to start (success or failure).
+                // This prevents getting stuck in "Resuming..." state.
+                // We do this synchronously on the continuation thread - it's safe because
+                // EditorPrefs operations are thread-safe and any new reload will set the flag
+                // fresh in OnBeforeAssemblyReload before we get here.
+                try { EditorPrefs.DeleteKey(EditorPrefKeys.ResumeStdioAfterReload); } catch { }
+
                 if (t.IsFaulted)
                 {
                     var baseEx = t.Exception?.GetBaseException();

MCPForUnity/Editor/Windows/Components/ClientConfig/McpClientConfigSection.cs

@@ -84,6 +84,11 @@ private void InitializeUI()
             }
 
             claudeCliPathRow.style.display = DisplayStyle.None;
+
+            // Initialize the configuration display for the first selected client
+            UpdateClientStatus();
+            UpdateManualConfiguration();
+            UpdateClaudeCliPathVisibility();
         }
 
         private void RegisterCallbacks()

MCPForUnity/Editor/Windows/Components/Connection/McpConnectionSection.cs

@@ -155,6 +155,10 @@ private void RegisterCallbacks()
                 var selected = (TransportProtocol)evt.newValue;
                 bool useHttp = selected != TransportProtocol.Stdio;
                 EditorPrefs.SetBool(EditorPrefKeys.UseHttpTransport, useHttp);
+
+                // Clear any stale resume flags when user manually changes transport
+                try { EditorPrefs.DeleteKey(EditorPrefKeys.ResumeStdioAfterReload); } catch { }
+                try { EditorPrefs.DeleteKey(EditorPrefKeys.ResumeHttpAfterReload); } catch { }
 
                 if (useHttp)
                 {
@@ -274,7 +278,9 @@ public void UpdateConnectionStatus()
             bool isRunning = bridgeService.IsRunning;
             bool showLocalServerControls = IsHttpLocalSelected();
             bool debugMode = EditorPrefs.GetBool(EditorPrefKeys.DebugLogs, false);
-            bool stdioSelected = transportDropdown != null && (TransportProtocol)transportDropdown.value == TransportProtocol.Stdio;
+            // Use EditorPrefs as source of truth for stdio selection - more reliable after domain reload
+            // than checking the dropdown which may not be initialized yet
+            bool stdioSelected = !EditorPrefs.GetBool(EditorPrefKeys.UseHttpTransport, true);
 
             // Keep the Start/Stop Server button label in sync even when the session is not running
             // (e.g., orphaned server after a domain reload).
@@ -327,19 +333,38 @@ public void UpdateConnectionStatus()
                 statusIndicator.RemoveFromClassList("disconnected");
                 statusIndicator.AddToClassList("connected");
                 connectionToggleButton.text = "End Session";
+                connectionToggleButton.SetEnabled(true); // Re-enable in case it was disabled during resumption
 
                 // Force the UI to reflect the actual port being used
                 unityPortField.value = bridgeService.CurrentPort.ToString();
                 unityPortField.SetEnabled(false);
             }
             else
             {
-                connectionStatusLabel.text = "No Session";
-                statusIndicator.RemoveFromClassList("connected");
-                statusIndicator.AddToClassList("disconnected");
-                connectionToggleButton.text = "Start Session";
+                // Check if we're resuming the stdio bridge after a domain reload.
+                // During this brief window, show "Resuming..." instead of "No Session" to avoid UI flicker.
+                bool isStdioResuming = stdioSelected 
+                    && EditorPrefs.GetBool(EditorPrefKeys.ResumeStdioAfterReload, false);
+
+                if (isStdioResuming)
+                {
+                    connectionStatusLabel.text = "Resuming...";
+                    // Keep the indicator in a neutral/transitional state
+                    statusIndicator.RemoveFromClassList("connected");
+                    statusIndicator.RemoveFromClassList("disconnected");
+                    connectionToggleButton.text = "Start Session";
+                    connectionToggleButton.SetEnabled(false);
+                }
+                else
+                {
+                    connectionStatusLabel.text = "No Session";
+                    statusIndicator.RemoveFromClassList("connected");
+                    statusIndicator.AddToClassList("disconnected");
+                    connectionToggleButton.text = "Start Session";
+                    connectionToggleButton.SetEnabled(true);
+                }
 
-                unityPortField.SetEnabled(true);
+                unityPortField.SetEnabled(!isStdioResuming);
 
                 healthStatusLabel.text = HealthStatusUnknown;
                 healthIndicator.RemoveFromClassList("healthy");